Testing an aflatoxin B1 gene signature in rat archival tissues.

PubMed

Merrick, B Alex; Auerbach, Scott S; Stockton, Patricia S; Foley, Julie F; Malarkey, David E; Sills, Robert C; Irwin, Richard D; Tice, Raymond R

2012-05-21

Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 μg of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ≤ 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and β-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced tumors. We conclude that an evaluation of gene signatures in archival tissues can be an important toxicological tool for evaluating critical molecular events associated with chemical exposures.

The NASA Ames Life Sciences Data Archive: Biobanking for the Final Frontier

NASA Technical Reports Server (NTRS)

Rask, Jon; Chakravarty, Kaushik; French, Alison J.; Choi, Sungshin; Stewart, Helen J.

2017-01-01

The NASA Ames Institutional Scientific Collection involves the Ames Life Sciences Data Archive (ALSDA) and a biospecimen repository, which are responsible for archiving information and non-human biospecimens collected from spaceflight and matching ground control experiments. The ALSDA also manages a biospecimen sharing program, performs curation and long-term storage operations, and facilitates distribution of biospecimens for research purposes via a public website (https:lsda.jsc.nasa.gov). As part of our best practices, a tissue viability testing plan has been developed for the repository, which will assess the quality of samples subjected to long-term storage. We expect that the test results will confirm usability of the samples, enable broader science community interest, and verify operational efficiency of the archives. This work will also support NASA open science initiatives and guides development of NASA directives and policy for curation of biological collections.

Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age.

PubMed

Craven, Rachel A; Cairns, David A; Zougman, Alexandre; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

2013-04-01

Protein profiling of formalin-fixed paraffin-embedded (FFPE) tissues has enormous potential for the discovery and validation of disease biomarkers. The aim of this study was to systematically characterize the effect of length of time of storage of such tissue blocks in pathology archives on the quality of data produced using label-free MS. Normal kidney and clear cell renal cell carcinoma tissues routinely collected up to 10 years prior to analysis were profiled using LC-MS/MS and the data analyzed using MaxQuant. Protein identities and quantification data were analyzed to examine differences between tissue blocks of different ages and assess the impact of technical and biological variability. An average of over 2000 proteins was seen in each sample with good reproducibility in terms of proteins identified and quantification for normal kidney tissue, with no significant effect of block age. Greater biological variability was apparent in the renal cell carcinoma tissue, possibly reflecting disease heterogeneity, but again there was good correlation between technical replicates and no significant effect of block age. These results indicate that archival storage time does not have a detrimental effect on protein profiling of FFPE tissues, supporting the use of such tissues in biomarker discovery studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing.

PubMed

Vacca, Davide; Cancila, Valeria; Gulino, Alessandro; Lo Bosco, Giosuè; Belmonte, Beatrice; Di Napoli, Arianna; Florena, Ada Maria; Tripodo, Claudio; Arancio, Walter

2018-02-01

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was successfully detected in the Hairy cell leukemia sample with around 50% of the reads obtained within 2 h of the sequencing start. Notably, the mutational burden of the Hairy cell leukemia sample as derived from nanopore sequencing proved to be comparable to a sensitive method for the detection of point mutations, namely the Digital PCR, using a validated assay. Nanopore sequencing can be adopted for targeted sequencing of genetic lesions on critical DNA samples such as those extracted from archival routine formalin-fixed paraffin-embedded samples. This result let speculating about the possibility that the nanopore sequencing could be trustably adopted for the real-time targeted sequencing of genetic lesions. Our report opens the window for the adoption of nanopore sequencing in molecular pathology for research and diagnostics.

Multiple immunofluorescence labelling of formalin-fixed paraffin-embedded (FFPE) tissue

PubMed Central

Robertson, David; Savage, Kay; Reis-Filho, Jorge S; Isacke, Clare M

2008-01-01

Background Investigating the expression of candidate genes in tissue samples usually involves either immunohistochemical labelling of formalin-fixed paraffin-embedded (FFPE) sections or immunofluorescence labelling of cryosections. Although both of these methods provide essential data, both have important limitations as research tools. Consequently, there is a demand in the research community to be able to perform routine, high quality immunofluorescence labelling of FFPE tissues. Results We present here a robust optimised method for high resolution immunofluorescence labelling of FFPE tissues, which involves the combination of antigen retrieval, indirect immunofluorescence and confocal laser scanning microscopy. We demonstrate the utility of this method with examples of immunofluorescence labelling of human kidney, human breast and a tissue microarray of invasive human breast cancers. Finally, we demonstrate that stained slides can be stored in the short term at 4°C or in the longer term at -20°C prior to images being collected. This approach has the potential to unlock a large in vivo database for immunofluorescence investigations and has the major advantages over immunohistochemistry in that it provides higher resolution imaging of antigen localization and the ability to label multiple antigens simultaneously. Conclusion This method provides a link between the cell biology and pathology communities. For the cell biologist, it will enable them to utilise the vast archive of pathology specimens to advance their in vitro data into in vivo samples, in particular archival material and tissue microarrays. For the pathologist, it will enable them to utilise multiple antibodies on a single section to characterise particular cell populations or to test multiple biomarkers in limited samples and define with greater accuracy cellular heterogeneity in tissue samples. PMID:18366689

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

PubMed Central

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

Direct Formalin Fixation Induces Widespread Genomic Effects in Archival Tissues

EPA Science Inventory

Recent advances in next generation sequencing have dramatically improved transcriptional analysis of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. However, little is known about potential genomic artifacts induced by formalin fixation, which could affect toxi...

An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis

PubMed Central

Karsten, Stanislav L.; Van Deerlin, Vivianna M. D.; Sabatti, Chiara; Gill, Lisa H.; Geschwind, Daniel H.

2002-01-01

Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produce reliable and reproducible microarray expression data. Here we compare the use of RNA isolated from human archival tissues fixed in ethanol and formalin to frozen tissue in cDNA microarray experiments. Since an additional factor that can limit the utility of archival tissue is the often small quantities available, we also evaluate the use of the tyramide signal amplification method (TSA), which allows the use of small amounts of RNA. Detailed analysis indicates that TSA provides a consistent and reproducible signal amplification method for cDNA microarray analysis, across both arrays and the genes tested. Analysis of this method also highlights the importance of performing non-linear channel normalization and dye switching. Furthermore, archived, fixed specimens can perform well, but not surprisingly, produce more variable results than frozen tissues. Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling. PMID:11788730

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens.

PubMed

Loudig, Olivier; Liu, Christina; Rohan, Thomas; Ben-Dov, Iddo Z

2018-05-05

-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas

PubMed Central

DeBoever, Christopher; Reid, Erin G.; Smith, Erin N.; Wang, Xiaoyun; Dumaop, Wilmar; Harismendy, Olivier; Carson, Dennis; Richman, Douglas; Masliah, Eliezer; Frazer, Kelly A.

2013-01-01

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. PMID:24023918

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

PubMed

Dhanapal, Raghu; Ranganathan, K; Kondaiah, Paturu; Devi, R Uma; Joshua, Elizabeth; Saraswathi, T R

2015-01-01

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

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

PubMed

Corces, M Ryan; Trevino, Alexandro E; Hamilton, Emily G; Greenside, Peyton G; Sinnott-Armstrong, Nicholas A; Vesuna, Sam; Satpathy, Ansuman T; Rubin, Adam J; Montine, Kathleen S; Wu, Beijing; Kathiria, Arwa; Cho, Seung Woo; Mumbach, Maxwell R; Carter, Ava C; Kasowski, Maya; Orloff, Lisa A; Risca, Viviana I; Kundaje, Anshul; Khavari, Paul A; Montine, Thomas J; Greenleaf, William J; Chang, Howard Y

2017-10-01

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics.

PubMed

Donczo, Boglarka; Guttman, Andras

2018-06-05

More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field. Copyright © 2018. Published by Elsevier B.V.

Optimization of Single- and Dual-Color Immunofluorescence Protocols for Formalin-Fixed, Paraffin-Embedded Archival Tissues.

PubMed

Kajimura, Junko; Ito, Reiko; Manley, Nancy R; Hale, Laura P

2016-02-01

Performance of immunofluorescence staining on archival formalin-fixed paraffin-embedded human tissues is generally not considered to be feasible, primarily due to problems with tissue quality and autofluorescence. We report the development and application of procedures that allowed for the study of a unique archive of thymus tissues derived from autopsies of individuals exposed to atomic bomb radiation in Hiroshima, Japan in 1945. Multiple independent treatments were used to minimize autofluorescence and maximize fluorescent antibody signals. Treatments with NH3/EtOH and Sudan Black B were particularly useful in decreasing autofluorescent moieties present in the tissue. Deconvolution microscopy was used to further enhance the signal-to-noise ratios. Together, these techniques provide high-quality single- and dual-color fluorescent images with low background and high contrast from paraffin blocks of thymus tissue that were prepared up to 60 years ago. The resulting high-quality images allow the application of a variety of image analyses to thymus tissues that previously were not accessible. Whereas the procedures presented remain to be tested for other tissue types and archival conditions, the approach described may facilitate greater utilization of older paraffin block archives for modern immunofluorescence studies. © 2016 The Histochemical Society.

Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.

PubMed

Vukmirovic, Milica; Herazo-Maya, Jose D; Blackmon, John; Skodric-Trifunovic, Vesna; Jovanovic, Dragana; Pavlovic, Sonja; Stojsic, Jelena; Zeljkovic, Vesna; Yan, Xiting; Homer, Robert; Stefanovic, Branko; Kaminski, Naftali

2017-01-12

Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Our results demonstrate that RNA sequencing of RNA obtained from archived FFPE lung tissues is feasible. The results obtained from FFPE tissue are highly comparable to FF tissues. The ability to perform RNA-Seq on archived FFPE IPF tissues should greatly enhance the availability of tissue biopsies for research in IPF.

Mitigation of formalin-induced RNA damage to advance whole transcriptomic analyses of archival tissues

EPA Science Inventory

Leveraging the use of biorepository samples for genomic analyses holds huge implications for human health, including applications in pathway identification, biomarker discovery, and tumor profiling for precision medicine. However, there is a need for better ways to reduce nucleic...

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

Multiphoton fluorescence lifetime imaging of chemotherapy distribution in solid tumors

NASA Astrophysics Data System (ADS)

Carlson, Marjorie; Watson, Adrienne L.; Anderson, Leah; Largaespada, David A.; Provenzano, Paolo P.

2017-11-01

Doxorubicin is a commonly used chemotherapeutic employed to treat multiple human cancers, including numerous sarcomas and carcinomas. Furthermore, doxorubicin possesses strong fluorescent properties that make it an ideal reagent for modeling drug delivery by examining its distribution in cells and tissues. However, while doxorubicin fluorescence and lifetime have been imaged in live tissue, its behavior in archival samples that frequently result from drug and treatment studies in human and animal patients, and murine models of human cancer, has to date been largely unexplored. Here, we demonstrate imaging of doxorubicin intensity and lifetimes in archival formalin-fixed paraffin-embedded sections from mouse models of human cancer with multiphoton excitation and multiphoton fluorescence lifetime imaging microscopy (FLIM). Multiphoton excitation imaging reveals robust doxorubicin emission in tissue sections and captures spatial heterogeneity in cells and tissues. However, quantifying the amount of doxorubicin signal in distinct cell compartments, particularly the nucleus, often remains challenging due to strong signals in multiple compartments. The addition of FLIM analysis to display the spatial distribution of excited state lifetimes clearly distinguishes between signals in distinct compartments such as the cell nuclei versus cytoplasm and allows for quantification of doxorubicin signal in each compartment. Furthermore, we observed a shift in lifetime values in the nuclei of transformed cells versus nontransformed cells, suggesting a possible diagnostic role for doxorubicin lifetime imaging to distinguish normal versus transformed cells. Thus, data here demonstrate that multiphoton FLIM is a highly sensitive platform for imaging doxorubicin distribution in normal and diseased archival tissues.

Limited yield of diagnoses of intrahepatic infectious causes of canine granulomatous hepatitis from archival liver tissue.

PubMed

Hutchins, Rae G; Breitschwerdt, Edward B; Cullen, John M; Bissett, Sally A; Gookin, Jody L

2012-09-01

Canine granulomatous hepatitis is an uncommon morphologic diagnosis that has been associated with a variety of diseases, including a number of systemic infectious etiologies. Formalin-fixed, paraffin-embedded (FFPE) tissues are typically the only source of liver tissue remaining for additional testing for the presence of infectious disease within granulomas. It is unclear if the more common infectious culprits of granulomatous hepatitis can be identified from such specimens. The aim of the current study was to retrospectively investigate archival FFPE liver tissue from dogs with granulomatous hepatitis for the presence of infectious agents. Semiquantitative analysis of copper accumulation in liver specimens was also performed. Medical records were examined for recorded evidence of systemic infectious disease diagnosis. Formalin-fixed, paraffin-embedded liver was prospectively evaluated for infectious agents via differential staining techniques (n = 13), eubacterial fluorescent in situ hybridization (n = 11), and Bartonella polymerase chain reaction assays (n = 15). An infectious cause of granulomatous hepatitis was not identified within liver tissue from any dog using these diagnostic methodologies. Six out of 25 (24%) dogs were diagnosed with concurrent systemic or localized bacterial infections at the time of presentation. Nine out of 17 (53%) dogs had excessive hepatic copper accumulation when evaluated by a semiquantitative histologic grading scheme or quantitative copper analysis. As definitive infectious causes of granulomatous hepatitis were not identified within archival liver biopsy samples, it was concluded that investigation of infectious etiologies within FFPE liver specimens using these diagnostic approaches may be of low yield.

The NASA Ames Research Center Institutional Scientific Collection: History, Best Practices and Scientific Opportunities

NASA Technical Reports Server (NTRS)

Rask, Jon C.; Chakravarty, Kaushik; French, Alison; Choi, Sungshin; Stewart, Helen

2017-01-01

The NASA Ames Life Sciences Institutional Scientific Collection (ISC), which is composed of the Ames Life Sciences Data Archive (ALSDA) and the Biospecimen Storage Facility (BSF), is managed by the Space Biosciences Division and has been operational since 1993. The ALSDA is responsible for archiving information and animal biospecimens collected from life science spaceflight experiments and matching ground control experiments. Both fixed and frozen spaceflight and ground tissues are stored in the BSF within the ISC. The ALSDA also manages a Biospecimen Sharing Program, performs curation and long-term storage operations, and makes biospecimens available to the scientific community for research purposes via the Life Science Data Archive public website (https:lsda.jsc.nasa.gov). As part of our best practices, a viability testing plan has been developed for the ISC, which will assess the quality of archived samples. We expect that results from the viability testing will catalyze sample use, enable broader science community interest, and improve operational efficiency of the ISC. The current viability test plan focuses on generating disposition recommendations and is based on using ribonucleic acid (RNA) integrity number (RIN) scores as a criteria for measurement of biospecimen viablity for downstream functional analysis. The plan includes (1) sorting and identification of candidate samples, (2) conducting a statiscally-based power analysis to generate representaive cohorts from the population of stored biospecimens, (3) completion of RIN analysis on select samples, and (4) development of disposition recommendations based on the RIN scores. Results of this work will also support NASA open science initiatives and guides development of the NASA Scientific Collections Directive (a policy on best practices for curation of biological collections). Our RIN-based methodology for characterizing the quality of tissues stored in the ISC since the 1980s also creates unique scientific opportunities for temporal assessment across historical missions. Support from the NASA Space Biology Program and the NASA Human Research Program is gratefully acknowledged.

Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks

PubMed Central

Simmons, Alan J.; Scurrah, Cherie’ R.; McKinley, Eliot T.; Herring, Charles A.; Irish, Jonathan M.; Washington, Mary K.; Coffey, Robert J.; Lau, Ken S.

2016-01-01

Cellular heterogeneity poses a significant challenge to understanding tissue level phenotypes and confounds conventional bulk analyses. To facilitate the analysis of signaling at the single-cell level in human tissues, we applied mass cytometry using CyTOF (Cytometry Time-of-Flight) to formalin-fixed paraffin-embedded (FFPE) normal and diseased intestinal specimens. We developed and validated a technique called FFPE-DISSECT (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue), a single-cell approach for characterizing native signaling states from embedded solid tissue samples. We applied FFPE-DISSECT coupled to mass cytometry and found differential signaling by tumor necrosis factor α (TNF-α) in intestinal enterocytes, goblet cells and enteroendocrine cells, implicating the role of the downstream RAS-RAF-MEK-ERK signaling pathway in dictating goblet cell identity. In addition, application of FFPE-DISSECT, mass cytometry, and data-driven computational analyses to human colon specimens confirmed reduced differentiation in colorectal cancer (CRC) compared to normal colon, and revealed quantitative increases in inter- and intra-tissue heterogeneity in CRC with regards to the modular regulation of signaling pathways. Specifically, modular co-regulation of the kinases P38 and ERK, the translation regulator 4EBP1, and the transcription factor CREB in the proliferative compartment of the normal colon was loss in CRC, as evidenced by their impaired coordination over samplings of single cells in tissue. Our data suggest that this single-cell approach, applied in conjunction with genomic annotation, such as microsatellite instability and mutations in KRAS and BRAF, allows rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. FFPE-DISSECT coupled of mass cytometry can be used for deriving cellular landscapes from archived patient samples, beyond CRC, and as a high resolution tool for disease characterization and subtyping. PMID:27729552

Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

PubMed Central

Casadonte, Rita; Caprioli, Richard M

2012-01-01

Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

Lack of concordance in microarray gene expression responses to Phenobarbital in companion aged FFPE and Frozen liver samples

EPA Science Inventory

Despite the immense potential value of public and private biorepositories, direct utilization of archival tissues for molecular profiling has been limited. A major reason for this limited use is the difficulty in obtaining reliable transcriptomic profiles from formalin-fixed par...

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.

PubMed

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker

PubMed Central

Molano, Monica; Tabrizi, Sepehr N.; Garland, Suzanne M.; Roberts, Jennifer M.; Machalek, Dorothy A.; Phillips, Samuel; Chandler, David; Hillman, Richard J.; Grulich, Andrew E.; Jin, Fengyi; Poynten, I. Mary; Templeton, David J.; Cornall, Alyssa M.

2016-01-01

Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC) are associated with human papillomavirus (HPV). Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS) and laser capture microdissected (LCM) tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL. PMID:27529629

CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker.

PubMed

Molano, Monica; Tabrizi, Sepehr N; Garland, Suzanne M; Roberts, Jennifer M; Machalek, Dorothy A; Phillips, Samuel; Chandler, David; Hillman, Richard J; Grulich, Andrew E; Jin, Fengyi; Poynten, I Mary; Templeton, David J; Cornall, Alyssa M

2016-01-01

Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC) are associated with human papillomavirus (HPV). Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS) and laser capture microdissected (LCM) tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL.

Seabird tissue archival and monitoring project: Egg collections and analytical results 1999-2002

USGS Publications Warehouse

Vander Pol, Stacy S.; Christopher, Steven J.; Roseneau, David G.; Becker, Paul R.; Day, Russel D.; Kucklick, John R.; Pugh, Rebecca S.; Simac, Kristin S.; Weston-York, Geoff

2003-01-01

In 1998, the U.S. Geological Survey Biological Resources Division (USGS-BRD), the U.S. Fish and Wildlife Service (USFWS) Alaska Maritime National Wildlife Refuge (AMNWR), and the National Institute of Standards and Technology (NIST) began the Seabird Tissue Archival and Monitoring Project (STAMP) to collect and cryogenically bank tissues from seabirds in Alaska for future retrospective analysis of anthropogenic contaminants. The approach of STAMP was similar to that of the Alaska Marine Mammal Tissue Archival Project (AMMTAP). AMMTAP was started in 1987 by NIST and the National Oceanic and Atmospheric Administration (NOAA) as part of the Outer Continental Shelf Environmental Assessment Program sponsored by the Minerals Management Service. Presently sponsored by the USGS-BRD, AMMTAP continues its work as part of a larger national program, the Marine Mammal Health and Stranding Response Program. AMMTAP developed carefully designed sampling and specimen banking protocols. Since 1987, AMMTAP has collected tissues from marine mammals taken in Alaska Native subsistence hunts and has cryogenically banked these tissues at the NIST National Biomonitoring Specimen Bank (NBSB). Through its own analytical work and working in partnership with other researchers both within and outside Alaska, AMMTAP has helped to develop a substantial database on contaminants in Alaska marine mammals. In contrast, data and information is limited on contaminants in Alaska seabirds, which are similar to marine mammals in that they feed near the top of the food chain and have the potential for accumulating anthropogenic contaminants. During its early planning stages, STAMP managers identified the seabird egg as the first tissue of choice for study by the project. There is a relatively long history of using bird eggs for environmental monitoring and for investigating the health status of bird populations. Since 1998, protocols for collecting and processing eggs, and cryogenically banking egg samples have been developed by STAMP (see York et al. 2001). Eggs are being collected on an annual basis for several species at nesting colonies throughout Alaska. Aliquots of these egg samples are being analyzed on a regular basis for persistent organic pollutants and mercury. Results of this work have been published in scientific journals (Christopher et al. 2002) and in conference proceedings (Kucklick et al. 2002; Vander Pol et al. 2002a, 2002b). The intent of this report is to provide an up-to-date description of STAMP. The report contains the most recent egg collection inventory, analytical data, preliminary interpretations based on these data, and a discussion of possible future directions of the project.

Glucose transporter-1 (GLUT-1) immunoreactivity in benign, premalignant and malignant lesions of the gallbladder.

PubMed

Legan, Mateja; Tevžič, Spela; Tolar, Ana; Luzar, Boštjan; Marolt, Vera Ferlan

2011-03-01

GLUT-1 is a transmembrane glucose transport protein that allows the facilitated transport of glucose into cells, normally expressed in tissues which depend mainly on glucose metabolism. Enhanced expression of GLUT-1 can also be found in a large spectrum of carcinomas. This study aimed to investigate GLUT-1 expression in gallbladder tissue: from normal tissue samples, hyperplasias, low-grade and high-grade dysplasias to gallbladder carcinomas. In all, 115 archived samples of gallbladder tissue from 68 patients, presented after cholecystectomy, were immunohistochemically stained for GLUT-1. According to the intensity of GLUT-1 immunoreactivity, samples were divided into negative (stained 0-10% of cells stained), positive with weak to moderate (10-50%) and positive with strong (>50%) GLUT-1 expression. The GLUT-1 immunoreactivity of the samples showed a characteristic increase from premalignant lesions to carcinomas. Normal gallbladder tissue samples did not express GLUT-1 (100%). Weak expression was shown only focally in hyperplasias, but to a greater extent with low-grade dysplasias (20%), high-grade dysplasias (40%) and carcinomas (51.8%). Normal gallbladder tissue is GLUT-1 negative. GLUT-1 expression in carcinoma tissue is significantly higher than in dysplastic lesions. Strong GLUT-1 expression indicates 100% specificity for detecting gallbladder carcinomas. Therefore, GLUT-1 is a candidate as a diagnostic as well as a tissue prognostic marker in gallbladder carcinoma patients.

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

PubMed

Bendell, L I

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

Targeted Multiplex Imaging Mass Spectrometry with Single Chain Fragment Variable (scfv) Recombinant Antibodies

NASA Astrophysics Data System (ADS)

Thiery, Gwendoline; Mernaugh, Ray L.; Yan, Heping; Spraggins, Jeffrey M.; Yang, Junhai; Parl, Fritz F.; Caprioli, Richard M.

2012-10-01

Recombinant scfv antibodies specific for CYP1A1 and CYP1B1 P450 enzymes were combined with targeted imaging mass spectrometry to simultaneously detect the P450 enzymes present in archived, paraffin-embedded, human breast cancer tissue sections. By using CYP1A1 and CYP1B1 specific scfv, each coupled to a unique reporter molecule (i.e., a mass tag) it was possible to simultaneously detect multiple antigens within a single tissue sample with high sensitivity and specificity using mass spectrometry. The capability of imaging multiple antigens at the same time is a significant advance that overcomes technical barriers encountered when using present day approaches to develop assays that can simultaneously detect more than a single antigen in the same tissue sample.

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

PubMed

Nielsen, E E; Morgan, J A T; Maher, S L; Edson, J; Gauthier, M; Pepperell, J; Holmes, B J; Bennett, M B; Ovenden, J R

2017-05-01

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. © 2016 John Wiley & Sons Ltd.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

PubMed

Bernstein, Matthew N; Doan, AnHai; Dewey, Colin N

2017-09-15

The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. cdewey@biostat.wisc.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Role of Insulin-like growth factors in initiation of follicle growth in normal and polycystic human ovaries.

PubMed

Stubbs, Sharron A; Webber, Lisa J; Stark, Jaroslav; Rice, Suman; Margara, Raul; Lavery, Stuart; Trew, Geoffrey H; Hardy, Kate; Franks, Stephen

2013-08-01

Polycystic ovary syndrome (PCOS), the commonest cause of anovulatory infertility, is characterized by disordered follicle development including increased activation and accelerated growth of preantral follicles. Data from experimental animals and preliminary results from studies of human ovarian tissue suggest that IGFs affect preantral follicle development. Our objectives were to investigate the expression of the type-1 IGF receptor (IGFR-1) in the human ovary and to determine whether IGFs are involved in stimulating the transition of follicles from primordial to primary stage in normal and polycystic ovaries. We used archived ovarian tissue for protein expression studies and small cortical biopsies for follicle isolation and for tissue culture. This was a laboratory-based study, using clinical tissue samples. A total of 54 women, 33 with normal ovaries and 21 with polycystic ovaries, were classified by reference to menstrual cycle history and ultrasonography. We evaluated expression of IGFR-1 mRNA in isolated preantral follicles and of IGFR-1 protein in archived ovarian tissue samples from normal and polycystic ovaries and effects of exogenous IGF-1 on preantral follicle development and survival in cultured fragments of normal and polycystic ovaries. IGFR-1 mRNA and protein was expressed in preantral follicles at all stages of development and enhanced expression was noted in PCOS follicles during early preantral development. IGF-1 stimulated initiation of follicle growth in normal tissue but had little effect on preantral follicle growth in polycystic ovaries in which, characteristically, there was a higher proportion of follicles that had entered the growing phase even before culture. IGFs are plausible candidates in regulation of initiation of human follicle growth, and accelerated preantral follicle growth in PCOS may be due to increased activity of endogenous IGFs.

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

PubMed Central

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE. PMID:24688314

Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing

PubMed Central

Xiao, Yongli; Sheng, Zong-Mei; Taubenberger, Jeffery K.

2015-01-01

The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus at high coverage was determined in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases. PMID:26344216

Histopathological findings in immunohistological staining of the granulomatous tissue reaction associated with tuberculosis.

PubMed

Karimi, Shirin; Shamaei, Masoud; Pourabdollah, Mihan; Sadr, Makan; Karbasi, Mehrdad; Kiani, Arda; Bahadori, Moslem

2014-01-01

Purpose. The histological diagnosis of Mycobacterium tuberculosis (MTB) remains a diagnostic challenge despite different methods. Immunohistochemistry (IHC) not only could confirm granulomatous tissue involvement but also can demonstrate MTB antigen immunolocalization. This study tries to clarify the details of immunohistochemical staining for MTB with pAbBCG. Materials/Methods. Twenty-three confirmed TB granulomatous tissue samples were studied by Ziehl-Neelsen and immunohistochemistry (IHC) staining with pAbBCG. Samples were selected from the archive of the Department of Pathology, National Research Institute of Tuberculosis and Lung Disease, Tehran, Iran. Results. IHC staining was positive in all samples, whereas Ziehl-Neelsen was positive in 9 cases out of 23 (39.1%). Tissue types used were pleural tissue, lymph nodes, and lung tissue. IHC showed positive coarse granular cytoplasmic and round, fragmented bacillary staining. In this study, epithelioid cells clearly showed more positive staining at the periphery of the granuloma rather than the center of granuloma. There is also positive staining in endothelial cells, fibroblasts, plasma cells, lymphocytes, and macrophages outside the granuloma. Conclusion. Considering the criteria of positive immunohistochemical staining of TB granulomatous reactions, this stain not only highlights the presence of mycobacterial antigens for tissue diagnosis, but also could morphologically localize its distribution in different cells.

Histopathological Findings in Immunohistological Staining of the Granulomatous Tissue Reaction Associated with Tuberculosis

PubMed Central

Karimi, Shirin; Pourabdollah, Mihan; Sadr, Makan; Karbasi, Mehrdad; Bahadori, Moslem

2014-01-01

Purpose. The histological diagnosis of Mycobacterium tuberculosis (MTB) remains a diagnostic challenge despite different methods. Immunohistochemistry (IHC) not only could confirm granulomatous tissue involvement but also can demonstrate MTB antigen immunolocalization. This study tries to clarify the details of immunohistochemical staining for MTB with pAbBCG. Materials/Methods. Twenty-three confirmed TB granulomatous tissue samples were studied by Ziehl-Neelsen and immunohistochemistry (IHC) staining with pAbBCG. Samples were selected from the archive of the Department of Pathology, National Research Institute of Tuberculosis and Lung Disease, Tehran, Iran. Results. IHC staining was positive in all samples, whereas Ziehl-Neelsen was positive in 9 cases out of 23 (39.1%). Tissue types used were pleural tissue, lymph nodes, and lung tissue. IHC showed positive coarse granular cytoplasmic and round, fragmented bacillary staining. In this study, epithelioid cells clearly showed more positive staining at the periphery of the granuloma rather than the center of granuloma. There is also positive staining in endothelial cells, fibroblasts, plasma cells, lymphocytes, and macrophages outside the granuloma. Conclusion. Considering the criteria of positive immunohistochemical staining of TB granulomatous reactions, this stain not only highlights the presence of mycobacterial antigens for tissue diagnosis, but also could morphologically localize its distribution in different cells. PMID:24511393

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

PubMed

Munchel, Sarah; Hoang, Yen; Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K; Koestler, Devin; Beyerlein, Peter; Fan, Jian-Bing; Bibikova, Marina; Chien, Jeremy

2015-09-22

Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.

Sensitivity of HER-2/neu antibodies in archival tissue samples: potential source of error in immunohistochemical studies of oncogene expression.

PubMed

Press, M F; Hung, G; Godolphin, W; Slamon, D J

1994-05-15

HER-2/neu oncogene amplification and overexpression of breast cancer tissue has been correlated with poor prognosis in women with both node-positive and node-negative disease. However, several studies have not confirmed this association. Review of these studies reveals the presence of considerable methodological variability including differences in study size, follow-up time, techniques and reagents. The majority of papers with clinical follow-up information are immunohistochemical studies using archival, paraffin-embedded breast cancers, and a variety of HER-2/neu antibodies have been used in these studies. Very little information, however, is available about the ability of the antibodies to detect overexpression following tissue processing for paraffin-embedding. Therefore, a series of antibodies, reported in the literature or commercially available, were evaluated to assess their sensitivity and specificity as immunohistochemical reagents. Paraffin-embedded samples of 187 breast cancers, previously characterized as frozen specimens for HER-2/neu amplification by Southern blot and for overexpression by Northern blot, Western blot, and immunohistochemistry, were used. Two multitumor paraffin-embedded tissue blocks were prepared from the previously analyzed breast cancers as a panel of cases to test a series of previously studied and/or commercially available anti-HER-2/neu antibodies. Immunohistochemical staining results obtained with 7 polyclonal and 21 monoclonal antibodies in sections from paraffin-embedded blocks of these breast cancers were compared. The ability of these antibodies to detect overexpression was extremely variable, providing an important explantation for the variable overexpression rate reported in the literature.

Trends of brominated diphenyl ethers in fresh and archived Great Lakes fish (1979-2005)

USGS Publications Warehouse

Batterman, Stuart; Chernyak, Sergei; Gwynn, Erica; Cantonwine, David; Jia, Chunrong; Begnoche, Linda J.; Hickey, James P.

2007-01-01

While few environmental measurements of brominated diphenyl ethers (BDEs) were completed prior to the mid-1990s, analysis of appropriately archived samples might enable the determination of contaminant trends back to the introduction of these chemicals. In this paper, we first investigate the stability of BDEs in archived frozen and extracted fish samples, and then characterize trends of these chemicals in rainbow smelt (Osmerus mordax) and lake trout (Salvelinus namaycush) in each of the Great Lakes between 1979 and 2005. We focus on the four most common congeners (BDE-47, 100, 99 and 153) and use a change-point analysis to detect shifts in trends. Analyses of archived fish samples yielded precise BDE concentration measurements with only small losses (0.8% per year in frozen fish tissues, 2.2% per year in refrigerated extracts). Trends in fish from all Great Lakes showed large increases in BDE concentrations that started in the early to mid-1980s with fairly consistent doubling times (generally 2–4 years except in Lake Erie smelt where levels increased very slowly), though concentrations and trends show differences by congener, fish species and lake. The most recent data show that accumulation rates are slowing, and concentrations of penta- and hexa-congeners in trout from Lakes Ontario and Michigan and smelt from Lake Ontario started to decrease in the mid-1990s. Trends in smelt and trout are evolving somewhat differently, and trout concentrations in the five lakes are now ranked as Michigan > Superior = Ontario > Huron = Erie, and smelt concentrations as Michigan > Ontario > Huron > Superior > Erie. The analysis of properly archived samples permits the reconstruction of historical trends, congener distributions, biomagnification and other information that can aid the understanding and management of these contaminants.

Molecular evidence of simian virus 40 infections in children

NASA Technical Reports Server (NTRS)

Butel, J. S.; Arrington, A. S.; Wong, C.; Lednicky, J. A.; Finegold, M. J.

1999-01-01

Recent studies have detected simian virus 40 (SV40) DNA in certain human tumors and normal tissues. The significance of human infections by SV40, which was first discovered as a contaminant of poliovirus vaccines used between 1955 and 1963, remains unknown. The occurrence of SV40 infections in unselected hospitalized children was evaluated. Polymerase chain reaction and DNA sequence analyses were done on archival tissue specimens from patients positive for SV40 neutralizing antibody. SV40 DNA was identified in samples from 4 of 20 children (1 Wilms' tumor, 3 transplanted kidney samples). Sequence variation among SV40 regulatory regions ruled out laboratory contamination of specimens. This study shows the presence of SV40 infections in pediatric patients born after 1982.

High-Throughput Sequencing and Copy Number Variation Detection Using Formalin Fixed Embedded Tissue in Metastatic Gastric Cancer

PubMed Central

Hong, Min Eui; Do, In-Gu; Kang, So Young; Ha, Sang Yun; Kim, Seung Tae; Park, Se Hoon; Kang, Won Ki; Choi, Min-Gew; Lee, Jun Ho; Sohn, Tae Sung; Bae, Jae Moon; Kim, Sung; Kim, Duk-Hwan; Kim, Kyoung-Mee

2014-01-01

In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%), APC (10.1%), PIK3CA (5.6%), KRAS (4.5%), SMO (3.4%), STK11 (3.4%), CDKN2A (3.4%) and SMAD4 (3.4%). Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%), 4 (4.5%), 2 (2.2%), 1 (1.1%) and 1 (1.1%) cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes. PMID:25372287

Optimized manual and automated recovery of amplifiable DNA from tissues preserved in buffered formalin and alcohol-based fixative.

PubMed

Duval, Kristin; Aubin, Rémy A; Elliott, James; Gorn-Hondermann, Ivan; Birnboim, H Chaim; Jonker, Derek; Fourney, Ron M; Frégeau, Chantal J

2010-02-01

Archival tissue preserved in fixative constitutes an invaluable resource for histological examination, molecular diagnostic procedures and for DNA typing analysis in forensic investigations. However, available material is often limited in size and quantity. Moreover, recovery of DNA is often severely compromised by the presence of covalent DNA-protein cross-links generated by formalin, the most prevalent fixative. We describe the evaluation of buffer formulations, sample lysis regimens and DNA recovery strategies and define optimized manual and automated procedures for the extraction of high quality DNA suitable for molecular diagnostics and genotyping. Using a 3-step enzymatic digestion protocol carried out in the absence of dithiothreitol, we demonstrate that DNA can be efficiently released from cells or tissues preserved in buffered formalin or the alcohol-based fixative GenoFix. This preparatory procedure can then be integrated to traditional phenol/chloroform extraction, a modified manual DNA IQ or automated DNA IQ/Te-Shake-based extraction in order to recover DNA for downstream applications. Quantitative recovery of high quality DNA was best achieved from specimens archived in GenoFix and extracted using magnetic bead capture.

Feasibility of using the National Marine Mammal Tissue Bank for retrospective exploratory studies of perfluorinated alkyl acids.

PubMed

Lynch, Jennifer M; Ragland, Jared M; Reagen, William K; Wolf, Susan T; Malinsky, Michelle D; Ellisor, Michael B; Moors, Amanda J; Pugh, Rebecca S; Reiner, Jessica L

2018-05-15

Perfluorinated alkyl acids (PFAAs) have been used for 50+ years in materials such as stain-resistant treatments for paper and clothing, lubricants, and foam fire extinguishers. PFAAs are characterized by a fully fluorinated alkyl chain with a terminal acid group. Their long half-lives and ubiquitous environmental distribution create considerable concern for wildlife and human exposure. There is interest in examining temporal trends of PFAAs using the National Marine Mammal Tissue Bank (NMMTB), but NMMTB tissues are frozen and cryohomogenized in polytetrafluoroethylene (PTFE)-based materials. Because PTFE supplies may leach PFAAs into samples, this study mimicked collection, processing and storage steps of NMMTB samples and measured PFAA leaching to determine the feasibility of using this sample archive for PFAA temporal trends. We also explored concentrations in Atlantic white-sided dolphin (Lagenorhynchus acutus, WSDs) and rough-toothed dolphin (Steno bredanensis, RTDs) blubber (n=3 and 0) and liver (n=48 and 12, respectively). The materials used in NMMTB protocols may add up to 0.968ng/g perfluorooctanoic acid (PFOA), 0.090ng/g perfluorononanoic acid (PNFA), and 0.221ng/g perfluorooctane sulfonate (PFOS) to each archived sample. Leaching of PFNA and PFOS from supplies compared to dolphin levels was negligible, but PFOA contributions were substantially higher than levels found in most dolphin liver samples. Therefore, monitoring PFOA temporal trends from the NMMTB would require careful consideration. RTDs had significantly higher levels of PFOS and PFNA than WSDs. Both species have similar life history, trophic status, and foraging behaviors in deep pelagic waters, so differences could be from latitudinal variation in contamination. RTDs stranded in Florida; WSDs stranded farther north mostly in Massachusetts. Juveniles had significantly higher levels of PFOS and PFNA than adults in both species, suggesting growth dilution as they approach maturity. PFOS significantly decreased after 2001 in both species as expected based on changes in production. Published by Elsevier B.V.

RNA sequencing and pathway analysis identify tumor necrosis factor alpha driven small proline-rich protein dysregulation in chronic rhinosinusitis.

PubMed

Ramakrishnan, Vijay R; Gonzalez, Joseph R; Cooper, Sarah E; Barham, Henry P; Anderson, Catherine B; Larson, Eric D; Cool, Carlyne D; Diller, John D; Jones, Kenneth; Kinnamon, Sue C

2017-09-01

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disorder in which many pathways contribute to end-organ disease. Small proline-rich proteins (SPRR) are polypeptides that have recently been shown to contribute to epithelial biomechanical properties relevant in T-helper type 2 inflammation. There is evidence that genetic polymorphism in SPRR genes may predict the development of asthma in children with atopy and, correlatively, that expression of SPRRs is increased under allergic conditions, which leads to epithelial barrier dysfunction in atopic disease. RNAs from uncinate tissue specimens from patients with CRS and control subjects were compared by RNA sequencing by using Ingenuity Pathway Analysis (n = 4 each), and quantitative polymerase chain reaction (PCR) (n = 15). A separate cohort of archived sinus tissue was examined by immunohistochemistry (n = 19). A statistically significant increase of SPRR expression in CRS sinus tissue was identified that was not a result of atopic presence. SPRR1 and SPRR2A expressions were markedly increased in patients with CRS (p < 0.01) on RNA sequencing, with confirmation by using real-time PCR. Immunohistochemistry of archived surgical samples demonstrated staining of SPRR proteins within squamous epithelium of both groups. Pathway analysis indicated tumor necrosis factor (TNF) alpha as a master regulator of the SPRR gene products. Expression of SPRR1 and of SPRR2A is increased in mucosal samples from patients with CRS and appeared as a downstream result of TNF alpha modulation, which possibly resulted in epithelial barrier dysfunction.

Maintaining clinical tissue archives and supporting human research: challenges and solutions.

PubMed

Giannini, Caterina; Oelkers, Michael M; Edwards, William D; Aubry, Marie Christine; Muncil, Maureen M; Mohamud, Koshin H; Sandleback, Sara G; Nowak, John M; Bridgeman, Andrew; Brown, Marie E; Cheville, John C

2011-03-01

The increasing number of requests for use of clinically archived tissue in translational research poses unique challenges. Conflicts may arise between pathologists who are responsible for overseeing and preserving the tissues and investigators who need these materials for research purposes. To evaluate the status of our institution's Tissue Registry Archive and to develop updated written policies and procedures to support a new modern and robust tracking system with features of a library loan system. An observational study was performed. We found the existing process for managing loans of tissue (slides and paraffin blocks) to be insufficient for the complexity and volume of this task. After extensive customization, a new tracking system was implemented in January 2008. Analysis of the first year of the system's use (2008) showed that of the 206,330 slides and 51,416 blocks loaned out in 2008, 92% and 94%, respectively, were returned by the due date. These rates were markedly improved from those before the new system: 61% and 47%, respectively, in 2005. Material permanently "lost" in 2008 represented only 0.02% of slides and 0.05% of blocks, none of which was the only diagnostic material for the case. With expanding needs for archived tissues for clinical care and growing demands for translational research, it is essential that pathology departments at institutions with large tissue-based research endeavors have a tracking and management system in place to meet clinical, educational, and research needs, as well as legal requirements.

Carcinogenesis and Inflammatory Effects of Plutonium-Nitrate Retention in an Exposed Nuclear Worker and Beagle Dogs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielsen, Christopher E.; Wang, Xihai; Robinson, Robert J.

The genetic and inflammatory response pathways elicited following plutonium exposure in archival lung tissue of an occupationally exposed human and experimentally exposed beagle dogs were investigated. These pathways include: tissue injury, apoptosis and gene expression modifications related to carcinogenesis and inflammation. In order to determine which pathways are involved, multiple lung samples from a plutonium exposed worker (Case 0269), a human control (Case 0385), and plutonium exposed beagle dogs were examined using histological staining and immunohistochemistry. Examinations were performed to identify target tissues at risk of radiation-induced fibrosis, inflammation, and carcinogenesis. Case 0269 showed interstitial fibrosis in peripheral and subpleuralmore » regions of the lung, but no pulmonary tumors. In contrast, the dogs with similar and higher doses showed pulmonary tumors primarily in brochiolo-alveolar, peripheral and subpleural alveolar regions. The TUNEL assay showed slight elevation of apoptosis in tracheal mucosa, tumor cells, and nuclear debris was present in the inflammatory regions of alveoli and lymph nodes of both the human and the dogs. The expression of apoptosis and a number of chemokine/cytokine genes was slightly but not significantly elevated in protein or gene levels compared to that of the control samples. In the beagles, mucous production was increased in the airway epithelial goblet cells and glands of trachea, and a number of chemokine/cytokine genes showed positive immunoreactivity. This analysis of archival tissue from an accidentally exposed worker and in a large animal model provides valuable information on the effects of long-term retention of plutonium in the respiratory tract and the histological evaluation study may impact mechanistic studies of radiation carcinogenesis.« less

Three Dimensional Imaging of Paraffin Embedded Human Lung Tissue Samples by Micro-Computed Tomography

PubMed Central

Scott, Anna E.; Vasilescu, Dragos M.; Seal, Katherine A. D.; Keyes, Samuel D.; Mavrogordato, Mark N.; Hogg, James C.; Sinclair, Ian; Warner, Jane A.; Hackett, Tillie-Louise; Lackie, Peter M.

2015-01-01

Background Understanding the three-dimensional (3-D) micro-architecture of lung tissue can provide insights into the pathology of lung disease. Micro computed tomography (µCT) has previously been used to elucidate lung 3D histology and morphometry in fixed samples that have been stained with contrast agents or air inflated and dried. However, non-destructive microstructural 3D imaging of formalin-fixed paraffin embedded (FFPE) tissues would facilitate retrospective analysis of extensive tissue archives of lung FFPE lung samples with linked clinical data. Methods FFPE human lung tissue samples (n = 4) were scanned using a Nikon metrology µCT scanner. Semi-automatic techniques were used to segment the 3D structure of airways and blood vessels. Airspace size (mean linear intercept, Lm) was measured on µCT images and on matched histological sections from the same FFPE samples imaged by light microscopy to validate µCT imaging. Results The µCT imaging protocol provided contrast between tissue and paraffin in FFPE samples (15mm x 7mm). Resolution (voxel size 6.7 µm) in the reconstructed images was sufficient for semi-automatic image segmentation of airways and blood vessels as well as quantitative airspace analysis. The scans were also used to scout for regions of interest, enabling time-efficient preparation of conventional histological sections. The Lm measurements from µCT images were not significantly different to those from matched histological sections. Conclusion We demonstrated how non-destructive imaging of routinely prepared FFPE samples by laboratory µCT can be used to visualize and assess the 3D morphology of the lung including by morphometric analysis. PMID:26030902

Sex Genotyping of Archival Fixed and Immunolabeled Guinea Pig Cochleas.

PubMed

Depreux, Frédéric F; Czech, Lyubov; Whitlon, Donna S

2018-03-26

For decades, outbred guinea pigs (GP) have been used as research models. Various past research studies using guinea pigs used measures that, unknown at the time, may be sex-dependent, but from which today, archival tissues may be all that remain. We aimed to provide a protocol for sex-typing archival guinea pig tissue, whereby past experiments could be re-evaluated for sex effects. No PCR sex-genotyping protocols existed for GP. We found that published sequence of the GP Sry gene differed from that in two separate GP stocks. We used sequences from other species to deduce PCR primers for Sry. After developing a genomic DNA extraction for archival, fixed, decalcified, immunolabeled, guinea pig cochlear half-turns, we used a multiplex assay (Y-specific Sry; X-specific Dystrophin) to assign sex to tissue as old as 3 years. This procedure should allow reevaluation of prior guinea pig studies in various research areas for the effects of sex on experimental outcomes.

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

PubMed

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. Copyright © 2011 Elsevier GmbH. All rights reserved.

Direct-to-PCR tissue preservation for DNA profiling.

PubMed

Sorensen, Amy; Berry, Clare; Bruce, David; Gahan, Michelle Elizabeth; Hughes-Stamm, Sheree; McNevin, Dennis

2016-05-01

Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.

ENDEMIC INFECTION OF STRANDED SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS) WITH NOVEL PARVOVIRUS, POLYOMAVIRUS, AND ADENOVIRUS.

PubMed

Siqueira, Juliana D; Ng, Terry F; Miller, Melissa; Li, Linlin; Deng, Xutao; Dodd, Erin; Batac, Francesca; Delwart, Eric

2017-07-01

Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened subspecies under federal law and a fully protected species under California law, US. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities. Anelloviruses and endogenous retroviral sequences made up over 50% of observed viral sequences. Polyomavirus, parvovirus, and adenovirus sequences made up most of the remaining reads. We characterized and phylogenetically analyzed the full genome of sea otter polyomavirus 1 and the complete coding sequence of sea otter parvovirus 1 and found that the closest known viruses infect primates and domestic pigs ( Sus scrofa domesticus), respectively. We tested archived tissues from 69 stranded SSO necropsied over 14 yr (2000-13) by PCR. Polyomavirus, parvovirus, and adenovirus infections were detected in 51, 61, and 29% of examined animals, respectively, with no significant increase in frequency over time, suggesting endemic infection. We found that 80% of tested SSO were infected with at least one of the three DNA viruses, whose tissue distribution we determined in 261 tissue samples. Parvovirus DNA was most frequently detected in mesenteric lymph node, polyomavirus DNA in spleen, and adenovirus DNA in multiple tissues (spleen, retropharyngeal and mesenteric lymph node, lung, and liver). This study describes the virome in tissues of a threatened species and shows that stranded SSO are frequently infected with multiple viruses, warranting future research to investigate associations between these infections and observed lesions.

Actionable mutations in canine hemangiosarcoma

PubMed Central

Wang, Guannan; Wu, Ming; Maloneyhuss, Martha A.; Wojcik, John; Durham, Amy C.; Mason, Nicola J.

2017-01-01

Background Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma. Methods Splenic hemangiosarcomas are common in dogs, which allowed us to collect a cohort of archived matched tumor and normal tissue samples suitable for whole exome sequencing. Mapping of the reads to the latest canine reference genome (Canfam3) demonstrated that >99% of the targeted exomal regions were covered, with >80% at 20X coverage and >90% at 10X coverage. Results and conclusions Sequence analysis of 20 samples identified somatic mutations in PIK3CA, TP53, PTEN, and PLCG1, all of which correspond to well-known tumor drivers in human cancer, in more than half of the cases. In one case, we identified a mutation in PLCG1 identical to a mutation observed previously in this gene in human visceral AS. Activating PIK3CA mutations present novel therapeutic targets, and clinical trials of targeted inhibitors are underway in human cancers. Our results lay a foundation for similar clinical trials in canine HSA, enabling a precision medicine approach to this disease. PMID:29190660

Actionable mutations in canine hemangiosarcoma.

PubMed

Wang, Guannan; Wu, Ming; Maloneyhuss, Martha A; Wojcik, John; Durham, Amy C; Mason, Nicola J; Roth, David B

2017-01-01

Angiosarcomas (AS) are rare in humans, but they are a deadly subtype of soft tissue sarcoma. Discovery sequencing in AS, especially the visceral form, is hampered by the rarity of cases. Most diagnostic material exists as archival formalin fixed, paraffin embedded tissue which serves as a poor source of high quality DNA for genome-wide sequencing. We approached this problem through comparative genomics. We hypothesized that exome sequencing a histologically similar tumor, hemangiosarcoma (HSA), that occurs in approximately 50,000 dogs per year, may lead to the identification of potential oncogenic drivers and druggable targets that could also occur in angiosarcoma. Splenic hemangiosarcomas are common in dogs, which allowed us to collect a cohort of archived matched tumor and normal tissue samples suitable for whole exome sequencing. Mapping of the reads to the latest canine reference genome (Canfam3) demonstrated that >99% of the targeted exomal regions were covered, with >80% at 20X coverage and >90% at 10X coverage. Sequence analysis of 20 samples identified somatic mutations in PIK3CA, TP53, PTEN, and PLCG1, all of which correspond to well-known tumor drivers in human cancer, in more than half of the cases. In one case, we identified a mutation in PLCG1 identical to a mutation observed previously in this gene in human visceral AS. Activating PIK3CA mutations present novel therapeutic targets, and clinical trials of targeted inhibitors are underway in human cancers. Our results lay a foundation for similar clinical trials in canine HSA, enabling a precision medicine approach to this disease.

Novel Multiplex MethyLight Protocol for Detection of DNA Methylation in Patient Tissues and Bodily Fluids

PubMed Central

Olkhov-Mitsel, Ekaterina; Zdravic, Darko; Kron, Ken; van der Kwast, Theodorus; Fleshner, Neil; Bapat, Bharati

2014-01-01

Aberrant DNA methylation is a hallmark of cancer and is an important potential biomarker. Particularly, combined analysis of a panel of hypermethylated genes shows the most promising clinical performance. Herein, we developed, optimized and standardized a multiplex MethyLight assay to simultaneously detect hypermethylation of APC, HOXD3 and TGFB2 in DNA extracted from prostate cancer (PCa) cell lines, archival tissue specimens, and urine samples. We established that the assay is capable of discriminating between fully methylated and unmethylated alleles with 100% specificity and demonstrated the assay as highly accurate and reproducible as the singleplex approach. For proof of principle, we analyzed the methylation status of these genes in tissue and urine samples of PCa patients as well as PCa-free controls. These data show that the multiplex MethyLight assay offers a significant advantage when working with limited quantities of DNA and has potential applications in research and clinical settings. PMID:24651255

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Emmert-Buck, Michael R

2005-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of pancreatic malignancy and other biological phenomena. This chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed-over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification. High-quality tissue microdissection does not necessarily mean high-quality samples to analyze. The quality of biomaterials obtained for analysis is highly dependent on steps upstream and downstream from tissue microdissection. We provide protocols for each of these steps, and encourage you to improve upon these. It is worth the effort of every laboratory to optimize and document its technique at each stage of the process, and we provide a starting point for those willing to spend the time to optimize. In our view, poor documentation of tissue and cell type of origin and the use of nonoptimized protocols is a source of inefficiency in current life science research. Even incremental improvement in this area will increase productivity significantly.

EZH2 and CD79B mutational status over time in B-cell non-Hodgkin lymphomas detected by high-throughput sequencing using minimal samples

PubMed Central

Saieg, Mauro Ajaj; Geddie, William R; Boerner, Scott L; Bailey, Denis; Crump, Michael; da Cunha Santos, Gilda

2013-01-01

BACKGROUND: Numerous genomic abnormalities in B-cell non-Hodgkin lymphomas (NHLs) have been revealed by novel high-throughput technologies, including recurrent mutations in EZH2 (enhancer of zeste homolog 2) and CD79B (B cell antigen receptor complex-associated protein beta chain) genes. This study sought to determine the evolution of the mutational status of EZH2 and CD79B over time in different samples from the same patient in a cohort of B-cell NHLs, through use of a customized multiplex mutation assay. METHODS: DNA that was extracted from cytological material stored on FTA cards as well as from additional specimens, including archived frozen and formalin-fixed histological specimens, archived stained smears, and cytospin preparations, were submitted to a multiplex mutation assay specifically designed for the detection of point mutations involving EZH2 and CD79B, using MassARRAY spectrometry followed by Sanger sequencing. RESULTS: All 121 samples from 80 B-cell NHL cases were successfully analyzed. Mutations in EZH2 (Y646) and CD79B (Y196) were detected in 13.2% and 8% of the samples, respectively, almost exclusively in follicular lymphomas and diffuse large B-cell lymphomas. In one-third of the positive cases, a wild type was detected in a different sample from the same patient during follow-up. CONCLUSIONS: Testing multiple minimal tissue samples using a high-throughput multiplex platform exponentially increases tissue availability for molecular analysis and might facilitate future studies of tumor progression and the related molecular events. Mutational status of EZH2 and CD79B may vary in B-cell NHL samples over time and support the concept that individualized therapy should be based on molecular findings at the time of treatment, rather than on results obtained from previous specimens. Cancer (Cancer Cytopathol) 2013;121:377–386. © 2013 American Cancer Society. PMID:23361872

GeneLab: Multi-Omics Investigation of Rodent Research-1 Bio-Banked Tissues

NASA Technical Reports Server (NTRS)

Lai, San-Huei; Boyko, Valery; Chakravarty, Kaushik; Chen, Rick; Dueck, Sandra; Berrios, Daniel C.; Fogle, Homer; Marcu, Oana; Timucin, Linda; Reinsch, Sigrid;

Past and Future Work on Radiobiology Mega-Studies: A Case Study At Argonne National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haley, Benjamin; Wang, Qiong; Wanzer, Beau

2011-09-06

Between 1952 and 1992, more than 200 large radiobiology studies were conducted in research institutes throughout Europe, North America, and Japan to determine the effects of external irradiation and internal emitters on the lifespan and tissue toxicity development in animals. At Argonne National Laboratory, 22 external beam studies were conducted on nearly 700 beagle dogs and 50,000 mice between 1969 and 1992. These studies helped to characterize the effects of neutron and gamma irradiation on lifespan, tumorigenesis, and mutagenesis across a range of doses and dosing patterns. The records and tissues collected at Argonne during that time period have beenmore » carefully preserved and redisseminated. Using these archived data, ongoing statistical work has been done and continues to characterize quality of radiation, dose, dose rate, tissue, and gender-specific differences in the radiation responses of exposed animals. The ongoing application of newly-developed molecular biology techniques to the archived tissues has revealed gene-specific mutation rates following exposure to ionizing irradiation. The original and ongoing work with this tissue archive is presented here as a case study of a more general trend in the radiobiology megastudies. These experiments helped form the modern understanding of radiation responses in animals and continue to inform development of new radiation models. Recent archival efforts have facilitated open access to the data and materials produced by these studies, and so a unique opportunity exists to expand this continued research.« less

Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

PubMed

Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

2017-05-01

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

A stable isotope approach to assessing water loss in fruits and vegetables during storage.

PubMed

Greule, Markus; Rossmann, Andreas; Schmidt, Hanns-Ludwig; Mosandl, Armin; Keppler, Frank

2015-02-25

Plant tissue water is the source of oxygen and hydrogen in organic biomatter. Recently, we demonstrated that the stable hydrogen isotope value (δ(2)H) of plant methoxyl groups is a very reliable and easily available archive for the δ(2)H value of this tissue water. Here we show in a model experiment that the δ(2)H values of methoxyl groups remain unchanged after water loss during storage of fruits and vegetables under controlled conditions, while δ(2)H and δ(18)O values of tissue water increase. This enhancement is plant-dependent, and the correlation differs from the meteoric water line. The δ(18)O value is better correlated to the weight decrease of the samples. Therefore, we postulate that the δ(2)H value of methoxyl groups and the δ(18)O value of tissue water are suitable parameters for checking postharvest alterations of tissue water, either addition or loss.

Guidelines for collecting and maintaining archives for genetic monitoring

USGS Publications Warehouse

Jackson, Jennifer A.; Laikre, Linda; Baker, C. Scott; Kendall, Katherine C.; ,

2012-01-01

Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

Calibrating amino acid δ13C and δ15N offsets between polyp and protein skeleton to develop proteinaceous deep-sea corals as paleoceanographic archives

NASA Astrophysics Data System (ADS)

McMahon, Kelton W.; Williams, Branwen; Guilderson, Thomas P.; Glynn, Danielle S.; McCarthy, Matthew D.

2018-01-01

Compound-specific stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3-4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context.

A retrospective survey into the presence of Plasmodium spp. and Toxoplasma gondii in archived tissue samples from New Zealand raptors: New Zealand falcons (Falco novaeseelandiae), Australasian harriers (Circus approximans) and moreporks (Ninox novaeseelandiae).

PubMed

Mirza, V; Burrows, E B; Gils, S; Hunter, S; Gartrell, B D; Howe, L

2017-08-01

Human colonisation of New Zealand has resulted in the introduction of emerging diseases, such as avian malaria and toxoplasmosis, which arrived with their exotic avian and mammalian hosts. Plasmodium spp. and Toxoplasma gondii have a wide host range, and several species of endemic New Zealand birds have developed a fatal disease following infection with either pathogen. However, no reports of either toxoplasmosis or avian malaria in New Zealand raptors, namely, the New Zealand falcons (Falco novaeseelandiae), Australasian harriers (Circus approximans) and moreporks (Ninox novaeseelandiae) exist in the literature. Therefore, this study was designed to determine if these two pathogens are present in these raptors through a retrospective analysis of archived tissue samples. Detection and isolate identification of these pathogens was determined using established histological and molecular techniques. All three species of New Zealand raptors tested positive for the presence of Plasmodium spp. (10/117; 8.5%) and an atypical genotype of T. gondii (9/117; 7.7%). Plasmodium lineages identified include P. elongatum GRW6, P. relictum SGS1, P. relictum PADOM02 and Plasmodium sp. LINN1. Two Australasian harriers and one morepork tested positive for the presence of both Plasmodium spp. and T. gondii. However, the pathogenicity of these organisms to the raptors is unclear as none of the tissues showed histological evidence of clinical disease associated with Plasmodium spp. and T. gondii infections. Thus, these results demonstrate for the first time that these two potential pathogens are present in New Zealand's raptors; however, further research is required to determine the prevalence and pathogenicity of these organisms among the living populations of these birds in the country.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Anthony C. James; Stacey L. McCord

The National Radiobiology Archives (NRA) are an archival program, started in 1989, to collect, organize and maintain data, laboratory notebooks, and animal tissue specimens from government (Department of Energy and its predecessor agencies) sponsored radiobiology life-span animal studies. These unique records, histopathology slides and paraffin embedded tissue blocks are maintained in a central facility and are available for further research study. The materials include electronic and paper records for each of more than 6,000 life-span-observations on dogs as well as details of major studies involving nearly 30,000 mice. Although these studies were performed over many years and at different laboratoriesmore » with differing data management systems, the NRA has translated them into a standardized set of relational database tables. These can be distributed to interested individuals on written request. Specific Aims are: (1) To Maintain the Archive of Written Records from the Animal Experiments - The USTUR continued to maintain the NRA archives which consist of approximately 175 storage boxes containing laboratory notebooks, animal exposure records, animal pathologic records, and radiographs. These were stored in a 6,000 square foot leased facility in Richland, WA. Additionally, through a collaboration with Pacific Northwest National Laboratory's (PNNL) Low Dose Program, many of these records were scanned into digital files. These totaled 34 GB of data, which are saved in 2,407 separate PDF files that are organized by box number and animal identification number. (2) To Maintain the Archive of Animal Tissues at Washington State University - The USTUR continued to house the NRA dog tissue collection in the leased facility. The NRA tissue collection consisted of pathology slides and tissue blocks. Approximately 25% of the laboratory facility was dedicated to the storage of the NRA materials. (3) To Organize the Datasets of These Animals in the Context of Other Datasets so That They Can be Used by the Scientific Community at Large - As was reported in the FY2009 NRA progress report, Dr. Chuck Watson (NRA Database Consultant) completed his service as the US representative on the European Radiobiological Archives (ERA) Advisory Board during FY2009. Unfortunately, due to the lack of financial support during FY2010, the NRA was not able to make further contributions to the ERA's efforts.« less

77 FR 36488 - Marine Mammals; File No. 17350

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-19

... on a variety of health- related analyses such as tissue histology, contaminants analyses, infectious disease research, parasitology studies, and stable isotope work. Additionally, tissues would be collected to augment the National Marine Mammal Tissue Bank or state tissue archives. No animals would be...

Mitochondrial imaging in live or fixed tissues using a luminescent iridium complex.

PubMed

Sorvina, Alexandra; Bader, Christie A; Darby, Jack R T; Lock, Mitchell C; Soo, Jia Yin; Johnson, Ian R D; Caporale, Chiara; Voelcker, Nicolas H; Stagni, Stefano; Massi, Massimiliano; Morrison, Janna L; Plush, Sally E; Brooks, Douglas A

2018-05-29

Mitochondrial morphology is important for the function of this critical organelle and, accordingly, altered mitochondrial structure is exhibited in many pathologies. Imaging of mitochondria can therefore provide important information about disease presence and progression. However, mitochondrial imaging is currently limited by the availability of agents that have the capacity to image mitochondrial morphology in both live and fixed samples. This can be particularly problematic in clinical studies or large, multi-centre cohort studies, where tissue archiving by fixation is often more practical. We previously reported the synthesis of an iridium coordination complex [Ir(ppy) 2 (MeTzPyPhCN)] + ; where ppy is a cyclometalated 2-phenylpyridine and TzPyPhCN is the 5-(5-(4-cyanophen-1-yl)pyrid-2-yl)tetrazolate ligand; and showed that this complex (herein referred to as IraZolve-Mito) has a high specificity for mitochondria in live cells. Here we demonstrate that IraZolve-Mito can also effectively stain mitochondria in both live and fixed tissue samples. The staining protocol proposed is versatile, providing a universal procedure for cell biologists and pathologists to visualise mitochondria.

MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability.

PubMed

Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte; Schultz, Nicolai Aagaard; Jensen, Benny Vittrup; Høgdall, Estrid Vilma Solyom; Johansen, Julia Sidenius

2015-12-29

Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50% reduction over 20 years) but not in CRC. Formalin fixation for 2-6 days decreased miRNA expression 30-65%. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting.

PCB Analysis Plan for Tank Archive Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

NGUYEN, D.M.

2001-03-22

This analysis plan specifies laboratory analysis, quality assurance/quality control (QA/QC), and data reporting requirements for analyzing polychlorinated biphenyls (PCB) concentrations in archive samples. Tank waste archive samples that are planned for PCB analysis are identified in Nguyen 2001. The tanks and samples are summarized in Table 1-1. The analytical data will be used to establish a PCB baseline inventory in Hanford tanks.

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

PubMed Central

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

2014-01-01

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can 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. PMID:24551080

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

PubMed

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

2014-01-01

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

Phenotypic characterisation of cell populations in the brains of horses experimentally infected with West Nile virus.

PubMed

Delcambre, G H; Liu, J; Streit, W J; Shaw, G P J; Vallario, K; Herrington, J; Wenzlow, N; Barr, K L; Long, M T

2017-11-01

West Nile virus (WNV), a mosquito borne member of the Flaviviridae, is one of the most commonly diagnosed agents of viral encephalitis in horses and people worldwide. A cassette of markers for formalin-fixed paraffin-embedded tissue and an archive of tissues from experimental infections in the horse were used to investigate the equine neuroimmune response to WNV meningoencephalomyelitis to phenotype the early response to WNV infection in the horse. Quantitative analysis using archived tissue from experimentally infected horses. The thalamus and hindbrain from 2 groups of 6 horses were compared and consisted of a culture positive tissues from WNV experimentally horses, in the other, normal horses. Formalin-fixed paraffin-embedded tissue from the thalamus and hindbrain were immunolabeled for microglia, astrocytes, B cells, macrophages/neutrophils, CD3 + T cells. Fresh frozen tissues were immunolabeled for CD4 + and CD8 + T lymphocyte cell markers. Cell counts were obtained using a computer software program. Differences, after meeting assumptions of abnormality, were computed using a general linear model with a Tukey test (P<0.05) for pairwise comparisons. In WNV-challenged horses, Iba-1 + microglia, CD3 + T lymphocyte and MAC387 + macrophage staining were significantly increased. The T cell response for the WNV-challenged horses was mixed, composed of CD4 + and CD8 + T lymphocytes. A limited astrocyte response was also observed in WNV-challenged horses, and MAC387 + and B cells were the least abundant cell populations. The results of this study were limited by a single collection time post-infection. Furthermore, a comprehensive analysis of cellular phenotypes is needed for naturally infected horses. Unfortunately, in clinical horses, there is high variability of sampling in terms of days post-infection and tissue handling. The data show that WNV-challenged horses recruit a mixed T cell population at the onset of neurologic disease. © 2017 EVJ Ltd.

Expression of FGFR3 and FGFR4 and clinical risk factors associated with progression-free survival in synovial sarcoma.

PubMed

Charbonneau, Bridget; Vogel, Rachel Isaksson; Manivel, J Carlos; Rizzardi, Anthony; Schmechel, Stephen C; Ognjanovic, Simona; Subramanian, Subbaya; Largaespada, David; Weigel, Brenda

2013-09-01

Although rare, synovial sarcoma (SS) is one of the most common soft tissue sarcomas affecting young adults. To investigate potential tumor markers related to synovial sarcoma prognosis, we carried out a single-institution retrospective analysis of 103 patients diagnosed with SS between 1980 and 2009. Clinical outcome data were obtained from medical records, and archived tissue samples were used to evaluate the relationship between progression-free survival (PFS) and several prognostic factors, including tumor expression of FGFR3 and FGFR4. No associations were found between PFS and gender, body mass index, tumor site, SS18-SSX translocation, or FGFR4 expression. As seen in previous studies, age at diagnosis (<35, 63% versus ≥35 years, 31% 10-year PFS; P = .033), histologic subtype (biphasic, 75% versus monophasic 34% 10-year PFS; P = .034), and tumor size (≤5 cm, 70% versus >5 cm, 22% 10-year PFS; P < .0001) were associated with PFS in SS patients. In addition, in a subset of patients with available archived tumor samples taken prior to chemotherapy or radiation (n = 34), higher FGFR3 expression was associated with improved PFS (P = .030). To the best of our knowledge, this is the largest study of SS to date to suggest a potential clinical role for FGFR3. While small numbers make this investigation somewhat exploratory, the findings merit future investigation on a larger scale. Copyright © 2013 Elsevier Inc. All rights reserved.

Expression of plakophilin 3 in diffuse malignant pleural mesothelioma.

PubMed

Mašić, Silvija; Brčić, Luka; Krušlin, Božo; Šepac, Ana; Pigac, Biserka; Stančić-Rokotov, Dinko; Jakopović, Marko; Seiwerth, Sven

2018-05-03

Diffuse malignant pleural mesothelioma (DMPM) is the most common primary malignant pleural neoplasm still posing major diagnostic, prognostic and therapeutic challenges. Plakophilins are structural proteins considered to be important for cell stability and adhesion in both tumor and normal tissues. Plakophilin 3 is a protein present in desmosomes of stratified and simple epithelia of normal tissues with presence in malignant cells of various tumors where it participates in the process of tumorigenesis. The aim of this study was to investigate the expression of plakophilin 3 protein in DMPM, but also to study its prognostic significance and relation to histologically accessible parameters of aggressive growth. Archival samples of tissue with established diagnosis of DMPM and samples of normal pleural tissue were used. Tumor samples were classified into three histological types of DMPM (epithelioid, sarcomatoid and biphasic). Additional subclassification of epithelioid mesotheliomas into nine patterns based on the prevalent histological component of the tumor was then performed. After immunohistochemical staining, cytoplasmic and membrane immunopositivity of tumor cells was assesed by scoring the intensity of the staining from 0 (no staining) to 4 (very strong staining). Prognostic value and expression of plakophilin 3 with consideration to histologically estimated aggression in tumor growth were then statistically analyzed using non- parametric tests. The results demonstrated higher level of plakophilin 3 expression in tumor samples with histologically more aggressive tumor growth, but no significant prognostic value. According to our study, plakophilin 3 appears to be involved in tumor invasion in malignant mesothelioma.

The use of archived tags in retrospective genetic analysis of fish.

PubMed

Bonanomi, Sara; Therkildsen, Nina Overgaard; Hedeholm, Rasmus Berg; Hemmer-Hansen, Jakob; Nielsen, Einar E

2014-05-01

Collections of historical tissue samples from fish (e.g. scales and otoliths) stored in museums and fisheries institutions are precious sources of DNA for conducting retrospective genetic analysis. However, in some cases, only external tags used for documentation of spatial dynamics of fish populations have been preserved. Here, we test the usefulness of fish tags as a source of DNA for genetic analysis. We extract DNA from historical tags from cod collected in Greenlandic waters between 1950 and 1968. We show that the quantity and quality of DNA recovered from tags is comparable to DNA from archived otoliths from the same individuals. Surprisingly, levels of cross-contamination do not seem to be significantly higher in DNA from external (tag) than internal (otolith) sources. Our study therefore demonstrates that historical tags can be a highly valuable source of DNA for retrospective genetic analysis of fish. © 2013 John Wiley & Sons Ltd.

Evaluation of telomere length in human cardiac tissues using cardiac quantitative FISH.

PubMed

Sharifi-Sanjani, Maryam; Meeker, Alan K; Mourkioti, Foteini

2017-09-01

Telomere length has been correlated with various diseases, including cardiovascular disease and cancer. The use of currently available telomere-length measurement techniques is often restricted by the requirement of a large amount of cells (Southern-based techniques) or the lack of information on individual cells or telomeres (PCR-based methods). Although several methods have been used to measure telomere length in tissues as a whole, the assessment of cell-type-specific telomere length provides valuable information on individual cell types. The development of fluorescence in situ hybridization (FISH) technologies enables the quantification of telomeres in individual chromosomes, but the use of these methods is dependent on the availability of isolated cells, which prevents their use with fixed archival samples. Here we describe an optimized quantitative FISH (Q-FISH) protocol for measuring telomere length that bypasses the previous limitations by avoiding contributions from undesired cell types. We have used this protocol on small paraffin-embedded cardiac-tissue samples. This protocol describes step-by-step procedures for tissue preparation, permeabilization, cardiac-tissue pretreatment and hybridization with a Cy3-labeled telomeric repeat complementing (CCCTAA) 3 peptide nucleic acid (PNA) probe coupled with cardiac-specific antibody staining. We also describe how to quantify telomere length by means of the fluorescence intensity and area of each telomere within individual nuclei. This protocol provides comparative cell-type-specific telomere-length measurements in relatively small human cardiac samples and offers an attractive technique to test hypotheses implicating telomere length in various cardiac pathologies. The current protocol (from tissue collection to image procurement) takes ∼28 h along with three overnight incubations. We anticipate that the protocol could be easily adapted for use on different tissue types.

Dose-Response Analysis of RNA-Seq Profiles in Archival ...

EPA Pesticide Factsheets

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 using RNA-sequencing in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one 20 years old. Experimental treatments included 3 different doses of di(2-ethylhexyl)phthalate or dichloroacetic acid for the recently archived and older studies, respectively. Total RNA was ribo-depleted and sequenced using the Illumina HiSeq platform. In the recently archived study, FFPE samples had 35% lower total counts compared to FROZ samples but high concordance in fold-change values of differentially expressed genes (DEGs) (r2 = 0.99), highly enriched pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (2% difference vs FROZ). In contrast, older FFPE samples had markedly lower total counts (3% of FROZ) and poor concordance in global DEGs and pathways. However, counts from FFPE and FROZ samples still positively correlated (r2 = 0.84 across all transcripts) and showed comparable dose responses for more highly expressed target genes. These findings highlight potential applications and issues in using RNA-sequencing data from FFPE samples. Recently archived FFPE samples were highly similar to FROZ samples in sequencing q

Introducing the PRIDE Archive RESTful web services.

PubMed

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

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

PubMed Central

2013-01-01

Background The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Methods Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. Results An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. Conclusions We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market. PMID:23445834

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability.

PubMed

Welinder, Charlotte; Jönsson, Göran; Ingvar, Christian; Lundgren, Lotta; Olsson, Håkan; Breslin, Thomas; Végvári, Akos; Laurell, Thomas; Rezeli, Melinda; Jansson, Bo; Baldetorp, Bo; Marko-Varga, György

2013-02-27

The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.

RNA analysis of inner ear cells from formalin fixed paraffin embedded (FFPE) archival human temporal bone section using laser microdissection--a technical report.

PubMed

Kimura, Yurika; Kubo, Sachiho; Koda, Hiroko; Shigemoto, Kazuhiro; Sawabe, Motoji; Kitamura, Ken

2013-08-01

Molecular analysis using archival human inner ear specimens is challenging because of the anatomical complexity, long-term fixation, and decalcification. However, this method may provide great benefit for elucidation of otological diseases. Here, we extracted mRNA for RT-PCR from tissues dissected from archival FFPE human inner ears by laser microdissection. Three human temporal bones obtained at autopsy were fixed in formalin, decalcified by EDTA, and embedded in paraffin. The samples were isolated into spiral ligaments, outer hair cells, spiral ganglion cells, and stria vascularis by laser microdissection. RNA was extracted and heat-treated in 10 mM citrate buffer to remove the formalin-derived modification. To identify the sites where COCH and SLC26A5 mRNA were expressed, semi-nested RT-PCR was performed. We also examined how long COCH mRNA could be amplified by semi-nested RT-PCR in archival temporal bone. COCH was expressed in the spiral ligament and stria vascularis. However, SLC26A5 was expressed only in outer hair cells. The maximum base length of COCH mRNA amplified by RT-PCR was 98 bp in 1 case and 123 bp in 2 cases. We detected COCH and SLC26A5 mRNA in specific structures and cells of the inner ear from archival human temporal bone. Our innovative method using laser microdissection and semi-nested RT-PCR should advance future RNA study of human inner ear diseases. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of Newcastle disease virus RNA by reverse transcription-polymerase chain reaction using formalin-fixed, paraffin-embedded tissue and comparison with immunohistochemistry and in situ hybridization.

PubMed

Wakamatsu, Nobuko; King, Daniel J; Seal, Bruce S; Brown, Corrie C

2007-07-01

The usefulness of reverse transcription-polymerase chain reaction (RT-PCR) from formalin-fixed, paraffin-embedded (FFPE) tissues was examined and compared to the immunohistochemistry (IHC) and in situ hybridization (ISH) assays for detection of Newcastle disease virus (NDV). Spleen and lung tissues were collected from chickens experimentally infected with either of 2 NDV isolates: a low virulent virus (LaSota) and a virulent virus (from the 2002-2003 California outbreak). The tissues were harvested immediately postmortem and fixed in 10% neutral buffered formalin for approximately 52 hours. Also, just before euthanasia, oral and cloacal swabs were collected for virus isolation. RNA was obtained from the FFPE tissues by digestion with proteinase K and subsequent extraction with phenol, chloroform, and isoamyl alcohol. By seminested RT-PCR with primers for the NDV matrix gene, a 232-base pair (bp) product was generated and visualized by electrophoresis. The results of PCR were compared to those of IHC for viral nucleoprotein and ISH for matrix gene (850 bp) on 3-microm sections and to those of virus isolation from swabs. All samples from infected chickens were positive by RT-PCR, including samples that were negative by both IHC and ISH. The RT-PCR positives included tissue from chickens that were no longer shedding virus detectable by virus isolation. The RT-PCR was an effective and sensitive method to detect NDV in FFPE tissues. To the authors' knowledge, this is the first report of NDV detection in FFPE tissues as a diagnostic approach possibly suitable for archival materials.

Laying the groundwork for NEON's continental-scale ecological research

NASA Astrophysics Data System (ADS)

Dethloff, G.; Denslow, M.

2013-12-01

The National Ecological Observatory Network (NEON) is designed to examine a suite of ecological issues. Field-collected data from 96 terrestrial and aquatic sites across the U.S. will be combined with remotely sensed data and existing continental-scale data sets. Field collections will include a range of physical and biological types, including soil, sediment, surface water, groundwater, precipitation, plants, animals, insects, and microbes as well as biological sub-samples such as leaf material, blood and tissue samples, and DNA extracts. Initial data analyses and identifications of approximately 175,000 samples per year will occur at numerous external laboratories when all sites are fully staffed in 2017. Additionally, NEON will archive biotic and abiotic specimens at collections facilities where they will be curated and available for additional analyses by the scientific community. The number of archived specimens is currently estimated to exceed 130,000 per year by 2017. We will detail how NEON is addressing the complexities and challenges around this set of analyses and specimens and how the resulting high-quality data can impact ecological understanding. The raw data returned from external laboratories that is quality checked and served by NEON will be the foundation for many NEON data products. For example, sequence-quality nucleic acids extracted from surface waters, benthic biofilms, and soil samples will be building blocks for data products on microbial diversity. The raw sequence data will also be available for uses such as evolutionary investigations, and the extracts will be archived so others can acquire them for additional research. Currently, NEON is establishing contracts for the analysis and archiving of field-collected samples through 2017. During this period, NEON will gather information on the progress and success of this large-scale effort in order to determine the most effective course to pursue with external facilities. Two areas that NEON already knows to evaluate are the need for geographic expertise in taxonomic identifications and the capacity necessary to handle the volume of samples. NEON is also addressing challenges associated with external entities and the logistics of sample movement, data formatting, data ingestion, and reporting. For example, NEON is considering tools, such as web APIs, which could allow efficient transfer of data from external facilities. Having a standard format in place for that data will be critical to transfer success and quality assessment. NEON is also working on the implementation of quality control measures for diverse analytical and taxonomic processes across laboratories, and is developing an external audit process. Additionally, given NEON's open access approach, the Network is focused on selecting a sample identification protocol that aids in tracking samples with more involved analytical needs and also allows maximum utility for the scientific community. Given the complex nature and breadth of the project, NEON will be developing novel sample management systems as well as metadata schemas. These efforts insure integrity and quality from field to external facility to archive for each sample taken, providing high-quality data now and confidence in future research stemming from raw data generated by NEON and its collection specimens.

Image analysis of pubic bone for age estimation in a computed tomography sample.

PubMed

López-Alcaraz, Manuel; González, Pedro Manuel Garamendi; Aguilera, Inmaculada Alemán; López, Miguel Botella

2015-03-01

Radiology has demonstrated great utility for age estimation, but most of the studies are based on metrical and morphological methods in order to perform an identification profile. A simple image analysis-based method is presented, aimed to correlate the bony tissue ultrastructure with several variables obtained from the grey-level histogram (GLH) of computed tomography (CT) sagittal sections of the pubic symphysis surface and the pubic body, and relating them with age. The CT sample consisted of 169 hospital Digital Imaging and Communications in Medicine (DICOM) archives of known sex and age. The calculated multiple regression models showed a maximum R (2) of 0.533 for females and 0.726 for males, with a high intra- and inter-observer agreement. The method suggested is considered not only useful for performing an identification profile during virtopsy, but also for application in further studies in order to attach a quantitative correlation for tissue ultrastructure characteristics, without complex and expensive methods beyond image analysis.

Evidence of SV40 infections in hospitalized children

NASA Technical Reports Server (NTRS)

Butel, J. S.; Jafar, S.; Wong, C.; Arrington, A. S.; Opekun, A. R.; Finegold, M. J.; Adam, E.

1999-01-01

Simian virus 40 (SV40) is known to have contaminated poliovirus vaccines used between 1955 and 1963. Accumulating reports have described the presence of SV40 DNA in human tumors and normal tissues, although the significance of human infections by SV40 is unknown. We investigated whether unselected hospitalized children had evidence of SV40 infections and whether any clinical correlations were apparent. Serum samples were examined for SV40 neutralizing antibody using a specific plaque reduction test; of 337 samples tested, 20 (5.9%) had antibody to SV40. Seropositivity increased with age and was significantly associated with kidney transplants (6 of 15 [40%] positive, P < .001). Many of the antibody-positive patients had impaired immune systems. Molecular assays (polymerase chain reaction and DNA sequence analysis) on archival tissue specimens confirmed the presence of SV40 DNA in 4 of the antibody-positive patients. This study, using 2 independent assays, shows the presence of SV40 infections in children born after 1980. We conclude that SV40 causes natural infections in humans.

TaqMan real-time RT-PCR detection of infectious salmon anaemia virus (ISAV) from formalin-fixed paraffin-embedded Atlantic salmon Salmo salar tissues.

PubMed

Godoy, M G; Kibenge, F S; Kibenge, M J; Olmos, P; Ovalle, L; Yañez, A J; Avendaño-Herrera, R

2010-05-18

The objective of this study was to evaluate the application of a TaqMan real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

Extraction of tamoxifen and its metabolites from formalin-fixed, paraffin-embedded tissues: an innovative quantitation method using liquid chromatography and tandem mass spectrometry.

PubMed

Ng, Ella S M; Kangarloo, S Bill; Konno, Mie; Paterson, Alexander; Magliocco, Anthony M

2014-03-01

Tamoxifen is a key therapeutic option for breast cancer treatment. Understanding its complex metabolism and pharmacokinetics is important for dose optimization. We examined the possibility of utilizing archival formalin-fixed paraffin-embedded (FFPE) tissue as an alternative sample source for quantification since well-annotated retrospective samples were always limited. Six 15 μm sections of FFPE tissues were deparaffinized with xylene and purified using solid-phase extraction. Tamoxifen and its metabolites were separated and detected by liquid chromatography-tandem mass spectrometry using multiple-reaction monitoring. This method was linear between 0.4 and 200 ng/g for 4-hydroxy-tamoxifen and endoxifen, and 4-2,000 ng/g for tamoxifen and N-desmethyl-tamoxifen. Inter- and intra-assay precisions were <9 %, and mean accuracies ranged from 81 to 106 %. Extraction recoveries were between 83 and 88 %. The validated method was applied to FFPE tissues from two groups of patients, who received 20 mg/day of tamoxifen for >6 months, and were classified into breast tumor recurrence and non-recurrence. Our preliminary data show that levels of tamoxifen metabolites were significantly lower in patients with recurrent cancer, suggesting that inter-individual variability in tamoxifen metabolism might partly account for the development of cancer recurrence. Nevertheless, other causes such as non-compliance or stopping therapy of tamoxifen could possibly lead to the concentration differences. The ability to successfully study tamoxifen metabolism in such tissue samples will rapidly increase our knowledge of how tamoxifen's action, metabolism and tissue distribution contribute to breast cancer control. However, larger population studies are required to understand the underlying mechanism of tamoxifen metabolism for optimization of its treatment.

Noninvasive Spatially Offset and Transmission Raman Mapping of Breast Tissue: A Multimodal Approach Towards the In Vivo Assessment of Tissue Pathology

DTIC Science & Technology

2013-06-01

spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased breast tissue. Observed spectral changes are compared to infrared...capabilities and performance. Additionally, we conduct spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased ... disease states, ie hyperplasia, dysplasia, malignant, benign. The instrumentation has been built and characterized using archived tissue that was

Expression of proteins in serum, synovial fluid, synovial membrane, and articular cartilage samples obtained from dogs with stifle joint osteoarthritis secondary to cranial cruciate ligament disease and dogs without stifle joint arthritis.

PubMed

Garner, Bridget C; Kuroki, Keiichi; Stoker, Aaron M; Cook, Cristi R; Cook, James L

2013-03-01

To identify proteins with differential expression between healthy dogs and dogs with stifle joint osteoarthritis secondary to cranial cruciate ligament (CCL) disease. Serum and synovial fluid samples obtained from dogs with stifle joint osteoarthritis before (n = 10) and after (8) surgery and control dogs without osteoarthritis (9) and archived synovial membrane and articular cartilage samples obtained from dogs with stifle joint osteoarthritis (5) and dogs without arthritis (5). Serum and synovial fluid samples were analyzed via liquid chromatography-tandem mass spectrometry; results were compared against a nonredundant protein database. Expression of complement component 3 in archived tissue samples was determined via immunohistochemical methods. No proteins had significantly different expression between serum samples of control dogs versus those of dogs with stifle joint osteoarthritis. Eleven proteins (complement component 3 precursor, complement factor I precursor, apolipoprotein B-100 precursor, serum paraoxonase and arylesterase 1, zinc-alpha-2-glycoprotein precursor, serum amyloid A, transthyretin precursor, retinol-binding protein 4 precursor, alpha-2-macroglobulin precursor, angiotensinogen precursor, and fibronectin 1 isoform 1 preproprotein) had significantly different expression (> 2.0-fold) between synovial fluid samples obtained before surgery from dogs with stifle joint osteoarthritis versus those obtained from control dogs. Complement component 3 was strongly expressed in all (5/5) synovial membrane samples of dogs with stifle joint osteoarthritis and weakly expressed in 3 of 5 synovial membrane samples of dogs without stifle joint arthritis. Findings suggested that the complement system and proteins involved in lipid and cholesterol metabolism may have a role in stifle joint osteoarthritis, CCL disease, or both.

PERFLUORINATED COMPOUNDS IN ARCHIVED HOUSE-DUST SAMPLES

EPA Science Inventory

Archived house-dust samples were analyzed for 13 perfluorinated compounds (PFCs). Results show that PFCs are found in house-dust samples, and the data are log-normally distributed. PFOS/PFOA were present in 94.6% and 96.4% of the samples respectively. Concentrations ranged fro...

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.

PubMed

Amini, Parisa; Ettlin, Julia; Opitz, Lennart; Clementi, Elena; Malbon, Alexandra; Markkanen, Enni

2017-08-23

Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult. We excised matched cancer-associated stroma (CAS) and normal stroma from clinical specimen of FFPE canine mammary tumours using LCM, and compared the commonly used protease-based RNA isolation procedure with an adapted novel technique that additionally incorporates a focused ultrasonication step. We successfully adapted a protocol that uses focused ultrasonication to isolate RNA from small amounts of deparaffinised, stained, clinical LCM samples. Using this approach, we found that total RNA yields could be increased by 8- to 12-fold compared to a commonly used protease-based extraction technique. Surprisingly, RNA extracted using this new approach was qualitatively at least equal if not superior compared to the old approach, as Cq values in RT-qPCR were on average 2.3-fold lower using the new method. Finally, we demonstrate that RNA extracted using the new method performs comparably in NGS as well. We present a successful isolation protocol for extraction of RNA from difficult and limiting FFPE tissue samples that enables successful analysis of small sections of clinically relevant specimen. The possibility to study gene expression signatures in specific small sections of archival FFPE tissue, which often entail large amounts of highly relevant clinical follow-up data, unlocks a new dimension of hitherto difficult-to-analyse samples which now become amenable for investigation.

Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tholouli, Eleni; MacDermott, Sarah; Hoyland, Judith

2012-08-24

Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection inmore » archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.« less

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

PubMed Central

Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J.; Rohan, Thomas; Ben-Dov, Iddo Z.

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens. PMID:28335433

Restoration and PDS Archive of Apollo Lunar Rock Sample Data

NASA Technical Reports Server (NTRS)

Garcia, P. A.; Todd, N. S.; Lofgren, G. E.; Stefanov, W. L.; Runco, S. K.; LaBasse, D.; Gaddis, L. R.

2011-01-01

In 2008, scientists at the Johnson Space Center (JSC) Lunar Sample Laboratory and Image Science & Analysis Laboratory (under the auspices of the Astromaterials Research and Exploration Science Directorate or ARES) began work on a 4-year project to digitize the original film negatives of Apollo Lunar Rock Sample photographs. These rock samples together with lunar regolith and core samples were collected as part of the lander missions for Apollos 11, 12, 14, 15, 16 and 17. The original film negatives are stored at JSC under cryogenic conditions. This effort is data restoration in the truest sense. The images represent the only record available to scientists which allows them to view the rock samples when making a sample request. As the negatives are being scanned, they are also being formatted and documented for permanent archive in the NASA Planetary Data System (PDS) archive. The ARES group is working collaboratively with the Imaging Node of the PDS on the archiving.

Measurement of Gene Expression in Archival Paraffin-Embedded Tissues

PubMed Central

Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C.; Shak, Steven; Kiefer, Michael C.; Esteban, Jose M.; Baker, Joffre B.

2004-01-01

Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10-μm FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests. PMID:14695316

Multiplex KRASG12/G13 mutation testing of unamplified cell-free DNA from the plasma of patients with advanced cancers using droplet digital polymerase chain reaction.

PubMed

Janku, F; Huang, H J; Fujii, T; Shelton, D N; Madwani, K; Fu, S; Tsimberidou, A M; Piha-Paul, S A; Wheler, J J; Zinner, R G; Naing, A; Hong, D S; Karp, D D; Cabrilo, G; Kopetz, E S; Subbiah, V; Luthra, R; Kee, B K; Eng, C; Morris, V K; Karlin-Neumann, G A; Meric-Bernstam, F

2017-03-01

Cell-free DNA (cfDNA) from plasma offers easily obtainable material for KRAS mutation analysis. Novel, multiplex, and accurate diagnostic systems using small amounts of DNA are needed to further the use of plasma cfDNA testing in personalized therapy. Samples of 16 ng of unamplified plasma cfDNA from 121 patients with diverse progressing advanced cancers were tested with a KRASG12/G13 multiplex assay to detect the seven most common mutations in the hotspot of exon 2 using droplet digital polymerase chain reaction (ddPCR). The results were retrospectively compared to mutation analysis of archival primary or metastatic tumor tissue obtained at different points of clinical care. Eighty-eight patients (73%) had KRASG12/G13 mutations in archival tumor specimens collected on average 18.5 months before plasma analysis, and 78 patients (64%) had KRASG12/G13 mutations in plasma cfDNA samples. The two methods had initial overall agreement in 103 (85%) patients (kappa, 0.66; ddPCR sensitivity, 84%; ddPCR specificity, 88%). Of the 18 discordant cases, 12 (67%) were resolved by increasing the amount of cfDNA, using mutation-specific probes, or re-testing the tumor tissue, yielding overall agreement in 115 patients (95%; kappa 0.87; ddPCR sensitivity, 96%; ddPCR specificity, 94%). The presence of ≥ 6.2% of KRASG12/G13 cfDNA in the wild-type background was associated with shorter survival (P = 0.001). Multiplex detection of KRASG12/G13 mutations in a small amount of unamplified plasma cfDNA using ddPCR has good sensitivity and specificity and good concordance with conventional clinical mutation testing of archival specimens. A higher percentage of mutant KRASG12/G13 in cfDNA corresponded with shorter survival. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Archiving Microgravity Flight Data and Samples

NASA Technical Reports Server (NTRS)

1996-01-01

To obtain help in evaluating its current strategy for archiving data and samples obtained in microgravity research, NASA's Microgravity Science and Applications Division (MSAD) asked the Space Studies Board's Committee on Microgravity Research for guidance on the following questions: What data should be archived and where should it be kept? In what form should the data be maintained (electronic files, photographs, hard copy, samples)? What should the general format of the database be? To what extent should it be universally accessible and through what mechanisms? Should there be a period of time for which principal investigators have proprietary access? If so, how long should proprietary data be stored? What provisions should be made for data obtained from ground-based experiments? What should the deadline be for investigators placing their data in the archive? How long should data be saved? How long should data be easily accessible? As a prelude to making recommendations for optimum selection and storage of microgravity data and samples, the committee in this report briefly describes NASA's past archiving practices and outlines MSAD's current archiving strategy. Although the committee found that only a limited number of experiments have thus far been archived, it concluded that the general archiving strategy, characterized by MSAD as minimalist, appears viable. A central focus of attention is the Experiment Data Management Plan (EDMP), MSAD's recently instituted data management and archiving framework for flight experiments. Many of the report's recommendations are aimed at enhancing the effectiveness of the EDMP approach, which the committee regards as an appropriate data management method for MSAD. Other recommendations provide guidance on broader issues related to the questions listed above. This report does not address statutory or regulatory records retention requirements.

Advanced Development of TIES-Enhancing Access to Tissue for Cancer Research | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Archived human tissues are an essential resource for translational research. Formalin-fixed, paraffin embedded (FFPE) tissues from cancer patients are used in a wide range of assays, including RT-PCR, SNP profiling, multiplex biomarkers, imaging biomarkers, targeted exome, whole exome, and whole genome sequencing. Remainder FFPE tissues generated during patient care are ‘retrospective'; use of these tissues under specific conditions does not require consent.

Publications - GMC 407 | Alaska Division of Geological & Geophysical

Science.gov Websites

locations, and archive inventory for 32 near-shore marine sediment Vibracore samples, West Dock Causeway , Drilling procedures, sample descriptions, boring logs, borehole locations, and archive inventory for 32

PDS Archive Release of Apollo 11, Apollo 12, and Apollo 17 Lunar Rock Sample Images

NASA Technical Reports Server (NTRS)

Garcia, P. A.; Stefanov, W. L.; Lofgren, G. E.; Todd, N. S.; Gaddis, L. R.

2013-01-01

Scientists at the Johnson Space Center (JSC) Lunar Sample Laboratory, Information Resources Directorate, and Image Science & Analysis Laboratory have been working to digitize (scan) the original film negatives of Apollo Lunar Rock Sample photographs [1, 2]. The rock samples, and associated regolith and lunar core samples, were obtained during the Apollo 11, 12, 14, 15, 16 and 17 missions. The images allow scientists to view the individual rock samples in their original or subdivided state prior to requesting physical samples for their research. In cases where access to the actual physical samples is not practical, the images provide an alternate mechanism for study of the subject samples. As the negatives are being scanned, they have been formatted and documented for permanent archive in the NASA Planetary Data System (PDS). The Astromaterials Research and Exploration Science Directorate (which includes the Lunar Sample Laboratory and Image Science & Analysis Laboratory) at JSC is working collaboratively with the Imaging Node of the PDS on the archiving of these valuable data. The PDS Imaging Node is now pleased to announce the release of the image archives for Apollo missions 11, 12, and 17.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Su, Gloria H; Emmert-Buck, Michael R

2005-02-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Rodriguez-Canales, Jaime; Hanson, Jeffrey C; Hipp, Jason D; Balis, Ulysses J; Tangrea, Michael A; Emmert-Buck, Michael R; Bova, G Steven

2013-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high-quality, appropriately anatomically tagged scientific results. Improvement in this area will significantly increase life science quality and productivity. The chapter is divided into introduction, materials, protocols, and notes subheadings. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this chapter, readers are advised to read through the entire chapter first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Persistent organic pollutants in Alaskan ringed seal (Phoca hispida) and walrus (Odobenus rosmarus) blubber

USGS Publications Warehouse

Kucklick, John R.; Krahn, Margaret M.; Becker, Paul R.; Porter, Barbara J.; Schantz, Michele M.; York, Geoffrey S.; O'Hara, Todd M.; Wise, Stephen A.

2006-01-01

Since 1987, the Alaska Marine Mammal Tissue Archival Project (AMMTAP) has collected tissues from 18 marine mammal species. Specimens are archived in the National Institute of Standards and Technology's National Biomonitoring Specimen Bank (NIST-NBSB). AMMTAP has collected blubber, liver and/or kidney specimens from a number of ringed seals (Phoca hispida) from the areas near Nome and Barrow, Alaska and walruses (Odobenus rosmarus) from several locations in the Bering Sea. Thirty-three ringed seal and 15 walrus blubber samples from the NIST-NBSB were analyzed for persistent organic pollutants (POPs). The compounds determined included PCBs (28 congeners or congener groups), DDT and related compounds, hexachlorobenzene (HCB), hexachlorocyclohexane isomers (HCHs), chlordanes, dieldrin, and mirex. POP concentrations in ringed seal blubber were significantly higher in Barrow than in Nome when statistically accounting for the interaction of age and gender; HCB, however, was not statistically different between the two locations. Unlike males, POP concentrations and age were not significantly correlated in females probably as a result of lactational loss. POP concentrations in walrus blubber were lower than in ringed seal blubber for ΣPCBs, chlordanes, and HCHs, but higher for dieldrin and mirex. POP concentrations in ringed seals and walrus from Alaska provide further evidence that the western Arctic tends to have lower or similar POP concentrations compared to the eastern Canadian Arctic.

Detection of mycobacterium tuberculosis in paraffin-embedded pleural biopsy specimens by commercial ribosomal RNA and DNA amplification kits.

PubMed

Ruiz-Manzano, J; Manterola, J M; Gamboa, F; Calatrava, A; Monsó, E; Martínez, C; Ausina, V

2000-09-01

To evaluate the utility of two gene amplification systems in historical paraffin-embedded pleural biopsy (PEB) tissues from patients with pleural tuberculosis, and to compare the results to those obtained with conventional histologic and microbiological methods. A retrospective study. Seventy-four formalin-fixed PEB tissues collected and stored over 12 years (1984 through 1995) were retrieved. Gene amplifications were performed in 57 tissues from patients with diagnoses of pleural tuberculosis and in 17 from patients with carcinoma as controls, using the first version of the Amplified Mycobacterium tuberculosis Direct Test (AMTDT; Gen-Probe; San Diego, CA) and the LCx Mycobacterium tuberculosis Assay (LCxMTB; Abbott Laboratories; Abbott Park, IL). The sensitivities of the AMTDT and LCxMTB were 52.6% and 63.2%, respectively (p = not statistically significant). The specificity of both tests was 100%. Twenty tissue samples (35.1%) were positive by both systems, and 10 tissues (17.5%) were positive only by the AMTDT, while 16 tissues (28.1%) were positive only by the LCxMTB. Both tests gave negative results for 11 specimens (19.3%). When both tests were used, a positive diagnosis was achieved in 80.7% of the samples. Diagnosis of 73.7% of patient conditions had previously been made by smear examination of pleural biopsy and sputum, pleural liquid, or biopsy culture. The overall diagnostic yield with both culture and amplification techniques was 96.5% (55 of 57 patients) for pleural tuberculosis, with amplification techniques adding 22.8% of the diagnoses. Amplification techniques are useful in archival PEB tissues, providing additional diagnoses beyond culturing, although the sensitivity should be improved, possibly by standardizing protocols.

Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.

PubMed

Cronin, Maureen; Pho, Mylan; Dutta, Debjani; Stephans, James C; Shak, Steven; Kiefer, Michael C; Esteban, Jose M; Baker, Joffre B

2004-01-01

Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- micro m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests.

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

EPA Science Inventory

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...

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

EPA Science Inventory

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...

Generation of the novel monoclonal antibody against TLS/EWS-CHOP chimeric oncoproteins that is applicable to one of the most sensitive assays for myxoid and round cell liposarcomas.

PubMed

Oikawa, Kosuke; Ishida, Tsuyoshi; Imamura, Tetsuo; Yoshida, Keiichi; Takanashi, Masakatsu; Hattori, Hiroyuki; Ishikawa, Akio; Fujita, Koji; Yamamoto, Kengo; Matsubayashi, Jun; Kuroda, Masahiko; Mukai, Kiyoshi

2006-03-01

The fusion oncoproteins, TLS-CHOP and EWS-CHOP, are characteristic markers for myxoid and round cell liposarcomas (MLS/RCLS). Especially, the peptide sequence of 26 amino acids corresponding to the normally untranslated CHOP exon 2 and parts of exon 3 (5'-UTR) is a unique structure for these chimeric proteins. In this report, we have generated monoclonal antibodies against the unique peptide sequence of TLS/EWS-CHOP oncoproteins. These antibodies reacted with TLS-CHOP fusion protein, but not reacted with normal TLS and CHOP proteins by Western blot analysis. In addition, one of the antibodies also recognized the chimeric oncoprotein in archival paraffin-embedded tissue samples of MLS/RCLS. The oncoprotein was detectable by the antibody even in the paraffin-embedded tissue samples whose mRNAs were too degraded to be detected by a nested reverse transcription-polymerase chain reaction-based assay. Thus, the molecular assay using the novel antibody is expected to be one of the most sensitive diagnostic assays for MLS/RCLS.

Human papillomavirus (HPV) infection in a case-control study of oral squamous cell carcinoma and its increasing trend in northeastern Thailand.

PubMed

Phusingha, Pensiri; Ekalaksananan, Tipaya; Vatanasapt, Patravoot; Loyha, Kulchaya; Promthet, Supannee; Kongyingyoes, Bunkerd; Patarapadungkit, Natcha; Chuerduangphui, Jureeporn; Pientong, Chamsai

2017-06-01

Human papillomavirus (HPV) is an independent risk factor for development of oral squamous cell carcinoma (OSCC). This study aimed to investigate the role of HPV infection and the trend in percentage of HPV-associated OSCC over a 5-year period in northeastern Thailand. In this case-control study, 91 exfoliated oral cell samples and 80 lesion cell samples from OSCC cases and exfoliated oral cells from 100 age/gender-matched controls were collected. HPV infection was investigated by PCR using GP5+/GP6+ primers followed by HPV genotyping using reverse line blot hybridization. Quantitative RT-PCR was used to evaluate HPV oncogene transcription. Temporal trends of HPV infection were evaluated in archived formalin-fixed paraffin-embedded (FFPE) OSCC tissues using in situ hybridization. HPV DNA was found in 17.5% (14/80) of lesion samples from OSCC cases and 29.7% (27/91) of exfoliated oral cell samples from the same cases. These values were significantly higher than in exfoliated oral cell samples from controls (13%, 13/100). HPV-16 was the genotype most frequently found in OSCC cases (92.8%, 13/14 infected cases). Interestingly, HPV oncogene mRNA expression was detected and correlated with OSCC cases (P < 0.005). Of 146 archived FFPE OSCC samples, 82 (56.2%) were positive for high-risk HPV DNA and 64 (43.8%) cases were positive for HPV E6/E7 mRNA expression. There was a trend of increasing percentage of HPV-associated OSCC from 2005 to 2010. This was especially so for females with well-differentiated tumors in specific tongue sub-sites. We suggest that HPV infection plays an important role in oral carcinogenesis in northeastern Thailand. © 2016 Wiley Periodicals, Inc.

Increasing Access to Archival Records in Library Online Public Access Catalogs.

ERIC Educational Resources Information Center

Gilmore, Matthew B.

1988-01-01

Looks at the use of online public access catalogs, the utility of subject and call-number searching, and possible archival applications. The Wallace Archives at the Claremont Colleges is used as an example of the availability of bibliographic descriptions of multiformat archival materials through the library catalog. Sample records and searches…

A biological survey on the Ottoman Archive papers and determination of the D10 value

NASA Astrophysics Data System (ADS)

Kantoğlu, Ömer; Ergun, Ece; Ozmen, Dilan; Halkman, Hilal B. D.

2018-03-01

The Ottoman Archives have one of the richest archive collections in the world. However, not all the archived documents are well preserved and some undergo biodeterioration. Therefore, a rapid and promising treatment method is necessary to preserve the collection for following generations as heritage. Radiation presents as an alternative for the treatment of archival materials for this purpose. In this study, we conducted a survey to determine the contamination species and the D10 values of the samples obtained from the shelves of the Ottoman Archives. The samples also included several insect pests collected at using a pheromone trap placed in the archive storage room. With the exception of few localized problems, no active pest presence was observed. The D10 values of mold contamination and reference mold (A. niger) were found to be 1.0 and 0.68 kGy, respectively. Based on these results, it can be concluded that an absorbed dose of 6 kGy is required to remove the contamination from the materials stored in the Ottoman Archives.

Proteomic Profiling of Paraffin-Embedded Samples Identifies Metaplasia-Specific and Early-Stage Gastric Cancer Biomarkers

PubMed Central

Sousa, Josane F.; Ham, Amy-Joan L.; Whitwell, Corbin; Nam, Ki Taek; Lee, Hyuk-Joon; Yang, Han-Kwang; Kim, Woo Ho; Zhang, Bing; Li, Ming; LaFleur, Bonnie; Liebler, Daniel C.; Goldenring, James R.

2013-01-01

Early diagnosis and curative resection are the predominant factors associated with increased survival in patients with gastric cancer. However, most gastric cancer cases are still diagnosed at later stages. Since most pathologic specimens are archived as FFPE samples, the ability to use them to generate expression profiles can greatly improve cancer biomarker discovery. We sought to uncover new biomarkers for stomach preneoplastic metaplasias and neoplastic lesions by generating proteome profiles using FFPE samples. We combined peptide isoelectric focusing and liquid chromatography–tandem mass spectrometry analysis to generate proteomic profiles from FFPE samples of intestinal-type gastric cancer, metaplasia, and normal mucosa. The expression patterns of selected proteins were analyzed by immunostaining first in single tissue sections from normal stomach, metaplasia, and gastric cancer and later in larger tissue array cohorts. We detected 60 proteins up-regulated and 87 proteins down-regulated during the progression from normal mucosa to metaplasia to gastric cancer. Two of the up-regulated proteins, LTF and DMBT1, were validated as specific markers for spasmolytic polypeptide–expressing metaplasia and intestinal metaplasia, respectively. In cancers, significantly lower levels of DMBT1 or LTF correlated with more advanced disease and worse prognosis. Thus, proteomic profiling using FFPE samples has led to the identification of two novel markers for stomach metaplasias and gastric cancer prognosis. PMID:22944598

Mining the archives: a cross-platform analysis of gene ...

EPA Pesticide Factsheets

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation of nucleic acids. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues using two DNA microarray protocols and two whole transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other three methods by having the highest correlations of differentially expressed genes (DEGs) and best overlap of pathways between FRO and FFPE groups. We next tested the effect of sample time in formalin (18 hours or 3 weeks) on gene expression profiles. Hierarchical clustering of the datasets indicated that test article treatment, and not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18-hour and 3-week FFPE samples compared to FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of age in FFPE block on genomic profiles. RNA-seq analysis of 8-, 19-, and 26-year-old control blocks using the ribo-depletion protocol resulted in comparable quality metrics, inc

Upregulation of angiogenesis in oral lichen planus.

PubMed

Al-Hassiny, A; Friedlander, L T; Parachuru, V P B; Seo, B; Hussaini, H M; Rich, A M

2018-02-01

As angiogenesis is fundamental to the pathogenesis of many chronic inflammatory disorders, this study investigated the expression of various vascular markers in oral lichen planus and non-specific oral mucosal inflammatory tissues. Archival specimens of oral lichen planus (n = 15) and inflamed tissues (n = 13) were stained using immunohistochemistry with antibodies to CD34, vascular endothelial growth factor, vascular endothelial growth factor receptor and vasohibin. Nine representative sites at the epithelial-connective tissue junction and through the fibrous connective tissue were selected, and automated analysis techniques were used to determine the extent of positivity expressed as the percentage of positive cells. Significance was denoted when P < .05. The expression of pro-angiogenic factors was higher in lichen planus samples compared with inflamed controls. A higher level of CD34 was observed in the deeper parts of the connective tissue of Oral lichen planus (OLP) (P = .04), whereas VEGF and VEGFR2 expressions were higher all through the tissues (respectively, P < .02 and P < .01). The expression of the anti-angiogenic VASH1 was higher in inflamed tissue compared with lichen planus in all sites evaluated (P < .01). The findings indicate that angiogenic factors are differentially expressed in oral lichen planus compared with inflamed controls, with increased expression of pro-angiogenic factors and decreased anti-angiogenic expression. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Attitudes of the Japanese public and doctors towards use of archived information and samples without informed consent: preliminary findings based on focus group interviews.

PubMed

Asai, Atsushi; Ohnishi, Motoki; Nishigaki, Etsuyo; Sekimoto, Miho; Fukuhara, Shunichi; Fukui, Tsuguya

2002-01-09

The purpose of this study is to explore laypersons' attitudes toward the use of archived (existing) materials such as medical records and biological samples and to compare them with the attitudes of physicians who are involved in medical research. Three focus group interviews were conducted, in which seven Japanese male members of the general public, seven female members of the general public and seven physicians participated. It was revealed that the lay public expressed diverse attitudes towards the use of archived information and samples without informed consent. Protecting a subject's privacy, maintaining confidentiality, and communicating the outcomes of studies to research subjects were regarded as essential preconditions if researchers were to have access to archived information and samples used for research without the specific informed consent of the subjects who provided the material. Although participating physicians thought that some kind of prior permission from subjects was desirable, they pointed out the difficulties involved in obtaining individual informed consent in each case. The present preliminary study indicates that the lay public and medical professionals may have different attitudes towards the use of archived information and samples without specific informed consent. This hypothesis, however, is derived from our focus groups interviews, and requires validation through research using a larger sample.

Rapid detection of Mannheimia haemolytica in lung tissues of sheep and from bacterial culture.

PubMed

Kumar, Jyoti; Dixit, Shivendra Kumar; Kumar, Rajiv

2015-09-01

This study was aimed to detect Mannheimia haemolytica in lung tissues of sheep and from a bacterial culture. M. haemolytica is one of the most important and well-established etiological agents of pneumonia in sheep and other ruminants throughout the world. Accurate diagnosis of M. haemolytica primarily relies on bacteriological examination, biochemical characteristics and, biotyping and serotyping of the isolates. In an effort to facilitate rapid M. haemolytica detection, polymerase chain reaction assay targeting Pasteurella haemolytica serotype-1 specific antigens (PHSSA), Rpt2 and 12S ribosomal RNA (rRNA) genes were used to detect M. haemolytica directly from lung tissues and from bacterial culture. A total of 12 archived lung tissues from sheep that died of pneumonia on an organized farm were used. A multiplex polymerase chain reaction (mPCR) based on two-amplicons targeted PHSSA and Rpt2 genes of M. haemolytica were used for identification of M. haemolytica isolates in culture from the lung samples. All the 12 lung tissue samples were tested for the presence M. haemolytica by PHSSA and Rpt2 genes based PCR and its confirmation by sequencing of the amplicons. All the 12 lung tissue samples tested for the presence of PHSSA and Rpt2 genes of M. haemolytica by mPCR were found to be positive. Amplification of 12S rRNA gene fragment as internal amplification control was obtained with each mPCR reaction performed from DNA extracted directly from lung tissue samples. All the M. haemolytica were also positive for mPCR. No amplified DNA bands were observed for negative control reactions. All the three nucleotide sequences were deposited in NCBI GenBank (Accession No. KJ534629, KJ534630 and KJ534631). Sequencing of the amplified products revealed the identity of 99-100%, with published sequence of PHSSA and Rpt2 genes of M. haemolytica available in the NCBI database. Sheep specific mitochondrial 12S rRNA gene sequence also revealed the identity of 98% with published sequences in the NCBI database. The present study emphasized the PCR as a valuable tool for rapid detection of M. haemolytica in clinical samples from animals. In addition, it offers the opportunity to perform large-scale epidemiological studies regarding the role of M. haemolytica in clinical cases of pneumonia and other disease manifestations in sheep and other ruminants, thereby providing the basis for effective preventive strategies.

Effect of substrate choice and tissue type on tissue preparation for spectral histopathology by Raman microspectroscopy.

PubMed

Fullwood, Leanne M; Griffiths, Dave; Ashton, Katherine; Dawson, Timothy; Lea, Robert W; Davis, Charles; Bonnier, Franck; Byrne, Hugh J; Baker, Matthew J

2014-01-21

Raman spectroscopy is a non-destructive, non-invasive, rapid and economical technique which has the potential to be an excellent method for the diagnosis of cancer and understanding disease progression through retrospective studies of archived tissue samples. Historically, biobanks are generally comprised of formalin fixed paraffin preserved tissue and as a result these specimens are often used in spectroscopic research. Tissue in this state has to be dewaxed prior to Raman analysis to reduce paraffin contributions in the spectra. However, although the procedures are derived from histopathological clinical practice, the efficacy of the dewaxing procedures that are currently employed is questionable. Ineffective removal of paraffin results in corruption of the spectra and previous experiments have shown that the efficacy can depend on the dewaxing medium and processing time. The aim of this study was to investigate the influence of commonly used spectroscopic substrates (CaF2, Spectrosil quartz and low-E slides) and the influence of different histological tissue types (normal, cancerous and metastatic) on tissue preparation and to assess their use for spectral histopathology. Results show that CaF2 followed by Spectrosil contribute the least to the spectral background. However, both substrates retain paraffin after dewaxing. Low-E substrates, which exhibit the most intense spectral background, do not retain wax and resulting spectra are not affected by paraffin peaks. We also show a disparity in paraffin retention depending upon the histological identity of the tissue with abnormal tissue retaining more paraffin than normal.

FTA Cards for Preservation of Nucleic Acids for Molecular Assays: A Review on the Use of Cytologic/Tissue Samples.

PubMed

da Cunha Santos, Gilda

2018-03-01

- Traditional methods for storing histologic and cytologic specimens for future use in molecular assays have consisted of either snap-freezing with cryopreservation or formalin-fixing, paraffin-embedding the samples. Although snap-freezing with cryopreservation is recommended for better preservation of nucleic acids, the infrastructure and space required for archiving impose challenges for high-volume pathology laboratories. Cost-effective, long-term storage at room temperature; relatively easy shipment; and standardized handling can be achieved with formalin-fixed, paraffin-embedded samples, but formalin fixation induces fragmentation and chemical modification of nucleic acids. Advances in next-generation sequencing platforms, coupled with an increase in diagnostic, prognostic, and predictive molecular biomarkers have created a demand for high-quality nucleic acids. To address issues of the quality of nucleic acid and logistics in sample acquisition, alternatives for specimen preservation and long-term storage have been described and include novel universal tissue fixatives, stabilizers, and technologies. - To collect, retrieve, and review information from studies describing the use of nucleic acids recovered from cytologic/tissue specimens stored on Flinders Technology Associates (FTA, GE Whatman, Maidstone, Kent, United Kingdom) cards for downstream molecular applications. - An electronic literature search in the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database allowed the selection of manuscripts addressing the use of FTA cards for storage of cytologic samples for molecular analysis. Only articles published in English were retrieved. - The use of FTA cards is a versatile method for fostering multicenter, international collaborations and clinical trials that require centralized testing, long-distance shipment, and high-quality nucleic acids for molecular techniques. Studies with controlled temperature are required to test the quality of recovered RNA after long-term storage.

Stability of mercury concentration measurements in archived soil and peat samples

USGS Publications Warehouse

Navrátil, Tomáš; Burns, Douglas; Nováková, Tereza; Kaňa, Jiří; Rohovec, Jan; Roll, Michal; Ettler, Vojtěch

2018-01-01

Archived soil samples can provide important information on the history of environmental contamination and by comparison with recently collected samples, temporal trends can be inferred. Little previous work has addressed whether mercury (Hg) concentrations in soil samples are stable with long-term storage under standard laboratory conditions. In this study, we have re-analyzed using cold vapor atomic adsorption spectroscopy a set of archived soil samples that ranged from relatively pristine mountainous sites to a polluted site near a non-ferrous metal smelter with a wide range of Hg concentrations (6 - 6485 µg kg-1). Samples included organic and mineral soils and peats with a carbon content that ranged from 0.2 to 47.7%. Soil samples were stored in polyethylene bags or bottles and held in laboratory rooms where temperature was not kept to a constant value. Mercury concentrations in four subsets of samples were originally measured in 2000, 2005, 2006 and 2007, and re-analyzed in 2017, i.e. after 17, 12, 11 and 10 years of storage. Statistical analyses of either separated or lumped data yielded no significant differences between the original and current Hg concentrations. Based on these analyses, we show that archived soil and peat samples can be used to evaluate historical soil mercury contamination.

[Evaluation of 3 methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA using PCR].

PubMed

Mesquita, R A; Anzai, E K; Oliveira, R N; Nunes, F D

2001-01-01

There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia) and non-formalin-fixed (normal oral mucosa) samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

Specimen banking of marine organisms in the United States: Current status and long-term prospective

USGS Publications Warehouse

Becker, P.R.; Wise, S.A.; Thorsteinson, L.; Koster, B.J.; Rowles, T.

1997-01-01

A major part of the activities conducted over the last decade by the National Biomonitoring Specimen Bank (NBSB) has involved the archival of marine specimens collected by ongoing environmental monitoring programs. These archived specimens include bivalves, marine sediments, and fish tissues collected by the National Status and Trends and the Exxon Valdez Oil Spill Damage Assessment programs, and marine mammal tissues collected by the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project. In addition to supporting these programs, the specimens have been used to investigate circumpolar patterns of chlorinated hydrocarbon concentrations, genetic separation of marine animal stocks, baseline levels of essential and nonessential elements in marine mammals, and the potential risk to human consumers in the Arctic from anthropogenic contaminants found in local subsistence foods. The NBSB specimens represent a resource that has the potential for addressing future issues of marine environmental quality and ecosystem changes through retrospective analysis; however, an ecosystem-based food web approach would maximize this potential. The current status of the NBSB activities related to the banking of marine organisms is presented and discussed, the long-term prospective of these activities is presented, and the importance of an ecosystem-based food web monitoring approach to the value of specimen banking is discussed.

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--NHEXAS FILTER HANDLING, WEIGHING AND ARCHIVING PROCEDURES FOR AEROSOL SAMPLES (RTI/ACS-AP-209-011)

EPA Science Inventory

This protocol describes the procedures for weighing, handling, and archiving aerosol filters and for managing the associated analytical and quality assurance data. Filter samples were weighed for aerosol mass at RTI laboratory, with only the automated field sampling data transfer...

Decreased expression of 14-3-3 σ, an early event of malignant transformation of respiratory epithelium, also facilitates progression of squamous cell lung cancer

PubMed Central

Sun, Nan; Wu, Yongkai; Huang, Bo; Liu, Qian; Dong, Yinan; Ding, Jianqiao; Liu, Yongyu

2015-01-01

Background It has been shown that 14-3-3 σ serves as a tumor suppressor gene, and is downregulated in various tumor tissues. However, the role of 14-3-3 σ during the initiation and progression of lung squamous cell carcinoma (SqCC) is not well understood. Methods The expression status of 14-3-3 σ in archival tissue samples from 40 lung SqCC patients (36 with normal bronchia, 19 squamous metaplasia, and 17 dysplasia/carcinoma in situ, in their tissue samples) was examined by immunohistochemical analysis. The proliferation rate and tumor formation ability of the H520 cell transfected with 14-3-3 σ was tested with methyl thiazolyl tetrazolium assay and nude mice subcutaneous injection, respectively. Results In the normal bronchial epithelia, 14-3-3 σ was highly expressed, whereas it was significantly decreased in precancerous and cancerous tissues. Compared with matched invasive cancer tissues, the expression level of 14-3-3 σ in squamous metaplasia was significantly higher (P = 0.049), while that in dysplasia/carcinoma in situ showed no significant changes (P = 0.135). Statistical analysis showed that the expression level of 14-3-3 σ in tumor tissue was associated with the differentiation grade of the tumor (P = 0.001) and the prognosis of the patient (P = 0.003). The overexpression of 14-3-3 σ significantly suppressed the proliferation of H520 cells in vitro and in vivo. Conclusion The inactivation of 14-3-3 σ may be a very early event in tumorigenesis and could facilitate the initiation and progression of lung SqCC in a sustainable way. PMID:26557909

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

ERIC Educational Resources Information Center

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…

Erysipelas

MedlinePlus

... Archive JAOCD Information for Authors Information for Reviewers Human & Animal Rights Job ... Share | Erysipelas is a bacterial infection of the skin and subcutaneous tissue, usually involving the face, ears ...

A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics.

PubMed

Chen, Wenjin; Reiss, Michael; Foran, David J

2004-06-01

The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling researchers to reliably determine the protein expression profile for specific types of cancer, it may be possible to elucidate the mechanism by which healthy tissues are transformed into malignancies. Currently, the primary methods used to evaluate arrays involve the interactive review of TMA samples while they are viewed under a microscope, subjectively evaluated, and scored by a technician. This process is extremely slow, tedious, and prone to error. In order to facilitate large-scale, multi-institutional studies, a more automated and reliable means for analyzing TMAs is needed. We report here a web-based prototype which features automated imaging, registration, and distributed archiving of TMAs in multiuser network environments. The system utilizes a principal color decomposition approach to identify and characterize the predominant staining signatures of specimens in color space. This strategy was shown to be reliable for detecting and quantifying the immunohistochemical expression levels for TMAs.

St. Petersburg Coastal and Marine Science Center's Core Archive Portal

USGS Publications Warehouse

Reich, Chris; Streubert, Matt; Dwyer, Brendan; Godbout, Meg; Muslic, Adis; Umberger, Dan

2012-01-01

This Web site contains information on rock cores archived at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center (SPCMSC). Archived cores consist of 3- to 4-inch-diameter coral cores, 1- to 2-inch-diameter rock cores, and a few unlabeled loose coral and rock samples. This document - and specifically the archive Web site portal - is intended to be a 'living' document that will be updated continually as additional cores are collected and archived. This document may also contain future references and links to a catalog of sediment cores. Sediment cores will include vibracores, pushcores, and other loose sediment samples collected for research purposes. This document will: (1) serve as a database for locating core material currently archived at the USGS SPCMSC facility; (2) provide a protocol for entry of new core material into the archive system; and, (3) set the procedures necessary for checking out core material for scientific purposes. Core material may be loaned to other governmental agencies, academia, or non-governmental organizations at the discretion of the USGS SPCMSC curator.

Ames Life Science Data Archive: Translational Rodent Research at Ames

NASA Technical Reports Server (NTRS)

Wood, Alan E.; French, Alison J.; Ngaotheppitak, Ratana; Leung, Dorothy M.; Vargas, Roxana S.; Maese, Chris; Stewart, Helen

2014-01-01

The Life Science Data Archive (LSDA) office at Ames is responsible for collecting, curating, distributing and maintaining information pertaining to animal and plant experiments conducted in low earth orbit aboard various space vehicles from 1965 to present. The LSDA will soon be archiving data and tissues samples collected on the next generation of commercial vehicles; e.g., SpaceX & Cygnus Commercial Cargo Craft. To date over 375 rodent flight experiments with translational application have been archived by the Ames LSDA office. This knowledge base of fundamental research can be used to understand mechanisms that affect higher organisms in microgravity and help define additional research whose results could lead the way to closing gaps identified by the Human Research Program (HRP). This poster will highlight Ames contribution to the existing knowledge base and how the LSDA can be a resource to help answer the questions surrounding human health in long duration space exploration. In addition, it will illustrate how this body of knowledge was utilized to further our understanding of how space flight affects the human system and the ability to develop countermeasures that negate the deleterious effects of space flight. The Ames Life Sciences Data Archive (ALSDA) includes current descriptions of over 700 experiments conducted aboard the Shuttle, International Space Station (ISS), NASA/MIR, Bion/Cosmos, Gemini, Biosatellites, Apollo, Skylab, Russian Foton, and ground bed rest studies. Research areas cover Behavior and Performance, Bone and Calcium Physiology, Cardiovascular Physiology, Cell and Molecular Biology, Chronobiology, Developmental Biology, Endocrinology, Environmental Monitoring, Gastrointestinal Physiology, Hematology, Immunology, Life Support System, Metabolism and Nutrition, Microbiology, Muscle Physiology, Neurophysiology, Pharmacology, Plant Biology, Pulmonary Physiology, Radiation Biology, Renal, Fluid and Electrolyte Physiology, and Toxicology. These experiment descriptions and data can be accessed online via the public LSDA website (http://lsda.jsc.nasa.gov) and information can be requested via the Data Request form at http://lsda.jsc.nasa.gov/common/dataRequest/dataRequest.aspx or by contacting the ALSDA Office at: Alison.J.French@nasa.gov

The preservation of microbial DNA in archived soils of various genetic types.

PubMed

Ivanova, Ekaterina A; Korvigo, Ilia O; Aparin, Boris F; Chirak, Evgenii L; Pershina, Elizaveta V; Romaschenko, Nikolay S; Provorov, Nikolai A; Andronov, Evgeny E

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70-90 years) and modern soils of two different genetic types-chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.

The preservation of microbial DNA in archived soils of various genetic types

PubMed Central

Korvigo, Ilia O.; Aparin, Boris F.; Chirak, Evgenii L.; Pershina, Elizaveta V.; Romaschenko, Nikolay S.; Provorov, Nikolai A.; Andronov, Evgeny E.

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70–90 years) and modern soils of two different genetic types–chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies. PMID:28339464

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

EPA Science Inventory

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...

Tissue-type plasminogen activator-induced fibrinolysis is enhanced in patients with breast, lung, pancreas and colon cancer.

PubMed

Nielsen, Vance G; Matika, Ryan W; Ley, Michele L B; Waer, Amy L; Gharagozloo, Farid; Kim, Samuel; Nfonsam, Valentine N; Ong, Evan S; Jie, Tun; Warneke, James A; Steinbrenner, Evangelina B

2014-04-01

Although cancer-mediated changes in hemostatic proteins unquestionably promote hypercoagulation, the effects of neoplasia on fibrinolysis in the circulation are less well defined. The goals of the present investigation were to determine if plasma obtained from patients with breast, lung, pancreas and colon cancer was less or more susceptible to lysis by tissue-type plasminogen activator (tPA) compared to plasma obtained from normal individuals. Archived plasma obtained from patients with breast (n = 18), colon/pancreas (n = 27) or lung (n = 19) was compared to normal individual plasma (n = 30) using a thrombelastographic assay that assessed fibrinolytic vulnerability to exogenously added tPA. Plasma samples were activated with tissue factor/celite, had tPA added, and had data collected until clot lysis occurred. Additional, similar samples had potato carboxypeptidase inhibitor added to assess the role played by thrombin-activatable fibrinolysis inhibitor in cancer-modulated fibrinolysis. Rather than inflicting a hypofibrinolytic state, the three groups of cancers demonstrated increased vulnerability to tPA (e.g. decreased time to lysis, increased speed of lysis, decreased clot lysis time). However, hypercoagulation manifested as increased speed of clot formation and strength compensated for enhanced fibrinolytic vulnerability, resulting in a clot residence time that was not different from normal individual thrombi. In sum, enhanced hypercoagulability associated with cancer was in part diminished by enhanced fibrinolytic vulnerability to tPA.

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

USGS Publications Warehouse

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.

Atmospheric Fluoroform (CHF3, HFC-23) at Cape Grim, Tasmania (1978-1995)

DOE Data Explorer

Oram, D. E. [University of East Anglia, Norwich, United Kingdom; Sturges, W. T. [University of East Anglia, Norwich, United Kingdom; Penkett, S. A. [University of East Anglia, Norwich, United Kingdom; McCulloch, A. [ICI Chemicals and Polymers, Ltd., Cheshire, United Kingdom; Fraser, P. J. [CRC for Southern Hemisphere Meteorology, Victoria, Australia

2000-10-01

The sampling and analytical methods are described more fully in Oram et al. (1998). In summary, air samples were taken from the archive of Cape Grim, Tasmania (41oS, 145oE) air samples collected from 1978 through 1995. Comparisons of CFC-11, CFC-12, CFC-113, CH3CCl3, and CH4 data between archive samples and corresponding in-situ samples for the same dates confirm that the archive samples are both representative and stable over time. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS), using a KCl-passivated alumina PLOT column. Fluoroform was monitored on mass 69 (CF3+). The analytical precision (one standard deviation of the mean) for two or three replicate analyses was typically ± 1% of the mean measured value. The overall uncertainty of the observed data is ± 10%, taking into account uncertainties in the preparation of the primary standards, the purity of the fluoroform used to make the primary standards, as well as the analytical precision.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the NHEXAS Arizona research project. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and ...

Development of a one-step duplex RT-qPCR for the quantification of phocine distemper virus.

PubMed

Bogomolni, Andrea L; Frasca, Salvatore; Matassa, Keith A; Nielsen, Ole; Rogers, Kara; De Guise, Sylvain

2015-04-01

Worldwide, stranded marine mammals and the network personnel who respond to marine mammal mortality have provided much of the information regarding marine morbillivirus infections. An assay to determine the amount of virus present in tissue samples would be useful to assist in routine surveying of animal health and for monitoring large-scale die-off events. False negatives from poor-quality samples prevent determination of the true extent of infection, while only small amounts of tissue samples or archived RNA may be available at the time of collection for future retrospective analysis. We developed a one-step duplex real-time reverse transcriptase-quantitative-PCR assay (RT-qPCR) based on Taqman probe technology to quantify phocine distemper virus (PDV) isolated from an outbreak in harbor (Phoca vitulina concolor) and gray seals (Halichoerus grypus) along the northeast US coast in 2006. The glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) gene was selected to assess RNA quality. This duplex assay is specific for PDV and sensitive through a range of 10(0) to 10(9) copies ds-plasmid DNA. For the GAPDH target, the reaction in duplex amplified 10(0) to 10(9) copies of ds-plasmid DNA and was detectable in multiple seal species. This assay reduced the likelihood of false negative results due to degradation of tissues and well-to-well variability while providing sensitive and specific detection of PDV, which would be applicable in molecular epidemiologic studies and pathogen detection in field and laboratory investigations involving a variety of seal species.

Outbreaks of Neuroinvasive Astrovirus Associated with Encephalomyelitis, Weakness, and Paralysis among Weaned Pigs, Hungary

PubMed Central

Boros, Ákos; Albert, Mihály; Pankovics, Péter; Bíró, Hunor; Pesavento, Patricia A.; Phan, Tung Gia; Delwart, Eric

2017-01-01

A large, highly prolific swine farm in Hungary had a 2-year history of neurologic disease among newly weaned (25- to 35-day-old) pigs, with clinical signs of posterior paraplegia and a high mortality rate. Affected pigs that were necropsied had encephalomyelitis and neural necrosis. Porcine astrovirus type 3 was identified by reverse transcription PCR and in situ hybridization in brain and spinal cord samples in 6 animals from this farm. Among tissues tested by quantitative RT-PCR, the highest viral loads were detected in brain stem and spinal cord. Similar porcine astrovirus type 3 was also detected in archived brain and spinal cord samples from another 2 geographically distant farms. Viral RNA was predominantly restricted to neurons, particularly in the brain stem, cerebellum (Purkinje cells), and cervical spinal cord. Astrovirus was generally undetectable in feces but present in respiratory samples, indicating a possible respiratory infection. Astrovirus could cause common, neuroinvasive epidemic disease. PMID:29148391

Outbreaks of Neuroinvasive Astrovirus Associated with Encephalomyelitis, Weakness, and Paralysis among Weaned Pigs, Hungary.

PubMed

Boros, Ákos; Albert, Mihály; Pankovics, Péter; Bíró, Hunor; Pesavento, Patricia A; Phan, Tung Gia; Delwart, Eric; Reuter, Gábor

2017-12-01

A large, highly prolific swine farm in Hungary had a 2-year history of neurologic disease among newly weaned (25- to 35-day-old) pigs, with clinical signs of posterior paraplegia and a high mortality rate. Affected pigs that were necropsied had encephalomyelitis and neural necrosis. Porcine astrovirus type 3 was identified by reverse transcription PCR and in situ hybridization in brain and spinal cord samples in 6 animals from this farm. Among tissues tested by quantitative RT-PCR, the highest viral loads were detected in brain stem and spinal cord. Similar porcine astrovirus type 3 was also detected in archived brain and spinal cord samples from another 2 geographically distant farms. Viral RNA was predominantly restricted to neurons, particularly in the brain stem, cerebellum (Purkinje cells), and cervical spinal cord. Astrovirus was generally undetectable in feces but present in respiratory samples, indicating a possible respiratory infection. Astrovirus could cause common, neuroinvasive epidemic disease.

Cambial history of Scots pine trees (Pinus Sylvestris) prior and after the Chernobyl accident as encoded in the xylem.

PubMed

Tulik, M

2001-08-01

Studies were carried out on wood samples collected in October 1997 from breast height of Scots pine trees (Pinus sylvestris) from site located 5 km south from the Chernobyl nuclear power plant. The radioactive contamination at the site was 3.7x10(5) kBq m(-2). These samples of secondary wood were used as an archive of information about the dynamics of a meristematic tissue cambium affected by ionising radiation from the Chernobyl reactor accident. The results show that frequency of the cambial cells events like anticlinal divisions, intrusive growth and cells elimination, was after the Chernobyl accident, about three times higher in comparison to preceding years. The most interesting finding was that after irradiation the length of tracheids increased. This increase is interpreted as an effect of intracambial competition among cells in the initial layer.

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

PubMed Central

Smith, LM; Burgoyne, LA

2004-01-01

Background Methods involving the analysis of nucleic acids have become widespread in the fields of traditional biology and ecology, however the storage and transport of samples collected in the field to the laboratory in such a manner to allow purification of intact nucleic acids can prove problematical. Results FTA® databasing paper is widely used in human forensic analysis for the storage of biological samples and for purification of nucleic acids. The possible uses of FTA® databasing paper in the purification of DNA from samples of wildlife origin were examined, with particular reference to problems expected due to the nature of samples of wildlife origin. The processing of blood and tissue samples, the possibility of excess DNA in blood samples due to nucleated erythrocytes, and the analysis of degraded samples were all examined, as was the question of long term storage of blood samples on FTA® paper. Examples of the end use of the purified DNA are given for all protocols and the rationale behind the processing procedures is also explained to allow the end user to adjust the protocols as required. Conclusions FTA® paper is eminently suitable for collection of, and purification of nucleic acids from, biological samples from a wide range of wildlife species. This technology makes the collection and storage of such samples much simpler. PMID:15072582

Analysis of iron, zinc, selenium and cadmium in paraffin-embedded prostate tissue specimens using inductively coupled plasma mass-spectrometry

USGS Publications Warehouse

Sarafanov, A.G.; Todorov, T.I.; Kajdacsy-Balla, A.; Gray, Michael A.; MacIas, V.; Centeno, J.A.

2008-01-01

Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable and abundant resource of pathologic material for various biomedical studies. In the present study, we report the application of high-resolution inductively coupled mass-spectrometry (ICP-MS) for quantification of Fe, Zn, Se and Cd in FFPE prostate tissue. These elements have a possible role in the development of prostate diseases: while Zn and Se are needed for a healthy prostate, Cd shows multiple toxic and carcinogenic effects. Excessive accumulation of Fe induces the production of highly reactive hydroxyl radical species, which may play a role in cancer etiopathogenesis. To assess whether the levels of these metals in the FFPE prostate tissue represent their original content, we compared their levels with those in the fresh tissue (on dry weight basis) in samples obtained from 15 patients. We found that in FFPE tissue, the recoveries of Se, Fe, Cd and Zn were progressively decreased, 97??11% (r=0.88), 82??22% (r=0.86), 59??23% (r=0.69) and 24??11% (r=0.38), respectively. Thus, the use of correction factors, determined as k=0.16 for Se, k=0.20 for Fe, k=0.27 for Cd and k=0.67 for Zn, is required to estimate the retrospective levels of these elements in the parental non-processed fresh (wet) prostate tissue. The technique used in this study enables the analysis of archival FFPE prostate tissue for the concentrations of Fe, Zn, Se and Cd to study association between the levels of these metals and prostate disease. ?? 2008.

Getting something for nothing: Regeneration of peptide signals from apparently exhausted MALDI samples by “waterboarding"

USDA-ARS?s Scientific Manuscript database

An often cited advantage of MALDI-MS is the ability to archive and reuse sample plates after the initial analysis is complete. However, experience demonstrates that the peptide ion signals decay rapidly as the number of laser shots becomes large. Thus, the signal level obtainable from an archived sa...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR ARCHIVE PROCEDURE FOR STUDY SAMPLES (UA-G-4.0)

EPA Science Inventory

The purpose of this SOP is to outline the archive/custody guidelines used by the Arizona Border Study. This procedure was followed to maintain and locate samples, extracts, tracings and hard copy results after laboratory analysis during the Arizona NHEXAS project and the Border ...

Potential concerns with analytical methods used for the detection of Batrachochytrium salamandrivorans from archived DNA of amphibian swab samples, Oregon, USA

Treesearch

Deborah D. Iwanowicz; William B. Schill; Deanna H. Olson; Michael J. Adams; Christine Densmore; R. Scott Cornman; Cynthia Adams; Jr. Figiel; Chauncey W. Anderson; Andrew R. Blaustein; Tara Chestnut

2017-01-01

We report on the results of surveillance for the salamander chytrid fungus, Batrachochytrium salamandrivorans (Bsal). Two samples from archived DNA used in a previous chytrid study in Oregon were Bsal-positive, alerting us to the first potential finding of this pathogen in North America, infecting American...

Detection and quantification of mast cell, vascular endothelial growth factor, and microvessel density in human inflammatory periapical cysts and granulomas.

PubMed

Fonseca-Silva, T; Santos, C C O; Alves, L R; Dias, L C; Brito, M; De Paula, A M B; Guimarães, A L S

2012-09-01

To identify and quantify mast cell (MC), vascular endothelial growth factor (VEGF) expression and microvessel density (MVD) in human periapical cysts and granulomas. Archived samples of cysts (n = 40) and granulomas (n = 28) were sectioned and stained with toluidine blue. MCs were identified and counted. Immunohistochemical reactions were employed to evaluate the tissue expression of VEGF and vessels. MVD was estimated by determining the areas of tissue labelled with CD31 antibody. The data were analysed using the Mann-Whitney test (P < 0.05). MCs were observed in the peripheral regions of both lesion types, whilst VEGF and MVD were distributed in the stroma. The presence of MCs was higher in cysts than in granulomas (P < 0.05). VEGF and MVD expression were similar in these lesions. The highest number of MCs was observed in cysts. Moreover, the identification of VEGF and MVD was consistent with the immune mechanisms involved in the lesions. © 2012 International Endodontic Journal.

Rapid Intraoperative Molecular Characterization of Glioma

PubMed Central

Shankar, Ganesh M.; Francis, Joshua M.; Rinne, Mikael L.; Ramkissoon, Shakti H.; Huang, Franklin W.; Venteicher, Andrew S.; Akama-Garren, Elliot H.; Kang, Yun Jee; Lelic, Nina; Kim, James C.; Brown, Loreal E.; Charbonneau, Sarah K.; Golby, Alexandra J.; Pedamallu, Chandra Sekhar; Hoang, Mai P.; Sullivan, Ryan J.; Cherniack, Andrew D.; Garraway, Levi A.; Stemmer-Rachamimov, Anat; Reardon, David A.; Wen, Patrick Y.; Brastianos, Priscilla K.; Curry, William T.; Barker, Fred G.; Hahn, William C.; Nahed, Brian V.; Ligon, Keith L.; Louis, David N.; Cahill, Daniel P.; Meyerson, Matthew

2016-01-01

IMPORTANCE Conclusive intraoperative pathologic confirmation of diffuse infiltrative glioma guides the decision to pursue definitive neurosurgical resection. Establishing the intraoperative diagnosis by histologic analysis can be difficult in low-cellularity infiltrative gliomas. Therefore, we developed a rapid and sensitive genotyping assay to detect somatic single-nucleotide variants in the telomerase reverse transcriptase (TERT) promoter and isocitrate dehydrogenase 1 (IDH1). OBSERVATIONS This assay was applied to tissue samples from 190 patients with diffuse gliomas, including archived fixed and frozen specimens and tissue obtained intraoperatively. Results demonstrated 96% sensitivity (95% CI, 90%–99%) and 100% specificity (95% CI, 95%–100%) for World Health Organization grades II and III gliomas. In a series of live cases, glioma-defining mutations could be identified within 60 minutes, which could facilitate the diagnosis in an intraoperative timeframe. CONCLUSIONS AND RELEVANCE The genotyping method described herein can establish the diagnosis of low-cellularity tumors like glioma and could be adapted to the point-of-care diagnosis of other lesions that are similarly defined by highly recurrent somatic mutations. PMID:26181761

Tissues from the irradiated dog/mouse archive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gayle Woloschak

The purpose of this project is to organize the databases/information and organize and move the tissues from the long-term dog (4,000 dogs) and mouse (over 30,000 mice) radiation experiments done at Argonne National Laboratory during the 1970's and 80's to Northwestern University. These studies were done with the intention of understanding the effects of exposure to radiation at a variety of different doses, dose-rates, and radiation qualities on end-points such as life-shortening, carcinogenesis, cause of death, shifts in disease incidence and other biological parameters. Organ and tissue samples from these animals including cancers, metastases and other significant degenerative and inflammatorymore » lesions and those in a regular protocol of normal tissues were preserved in paraffin blocks, tissue impressions and sections and represent a great resource for the radiation biology community. These collections are particularly significant since these experiments are not likely to be repeated because of the extreme cost of monies and time for such large-scale animal studies. The long-term goal is to make these tissues and databases available to the wider scientific community so that questions such as tissue sensitivity, early and late effects, low dose and protracted dose responses of normal and tumor tissues, etc. can be examined and defined. Recent advances in biology particularly at the subcellular and molecular level now permit microarray-based gene expression array analyses from paraffin-embedded tissues (where RNA samples are significantly degraded), synchrotron-based studies of metal and other elemental distribution patterns in tissues, PCR-based analyses for mutation detection, and other similar approaches that were not available when the long¬ term animal studies were designed and initiated. Understanding the basis and progression of radiation damage should also permit rational approaches to prevention and mitigation of those damages. Therefore, as stated earlier, these tissues and their related documentation, represent a significant resource for future studies. For this project, we propose to accomplish the following objectives: (1) inventory and organize the tissues, blood smears, wet-tissues and paper-¬based information that is available in the tissue bank at Argonne National Laboratory; (2) convert the existing Oracle database of the mouse studies to MS Access( the dog data is already in this format which is far more user friendly and widely used in business and research) , (3) move the remaining samples and documentation from dogs that had been transferred from ANL to New Mexico (in Dr. F. Hahn's care) to Northwestern University and add these to the inventory; (4) move the tissues and Access database at Argonne National Laboratory to Northwestern University.« less

Th1 and Th2-like protein balance in human inflammatory radicular cysts and periapical granulomas.

PubMed

de Carvalho Fraga, Carlos Alberto; Alves, Lucas Rodrigues; de Sousa, Adriana Alkmim; de Jesus, Sabrina Ferreira; Vilela, Daniel Nogueira; Pereira, Camila Santos; Batista Domingos, Patrícia Luciana; Viana, Agostinho Gonçalves; Jham, Bruno Correia; Batista de Paula, Alfredo Maurício; Sena Guimarães, André Luiz

2013-04-01

Chronic dental periapical lesions result from chronic inflammation of periapical tissues caused by continuous antigenic stimulation from infected root canals. Recent findings have suggested that T helper (Th) 1 and Th2-like cytokines are important in the pathogenesis of chronic periapical inflammatory diseases. However, the mechanisms regulating these immunoinflammatory pathways have not been fully elucidated. Thus, the aim of this study was to evaluate interleukin (IL)-4, IL-12, and interferon γ (IFN-γ) protein levels in human radicular cysts and periapical granulomas. Archived samples of cysts (n = 52) and granulomas (n = 27) were sectioned and submitted to immunohistochemistry to evaluate the tissue expression of IL-4, IL-12, and IFN-γ. The data were analyzed using the Mann-Whitney U test (P < .05). An increased expression of IFN-γ was observed in radicular cysts. IL-4 expression was stronger in periapical granulomas than in radicular cysts. IL-12 was not detected in any of the samples. Our study showed that IFN-γ protein levels are increased in radicular cysts, whereas IL-4 expression is stronger in samples of periapical granulomas. Further studies are necessary to elucidate the signaling pathways mediated by these cytokines and to facilitate the development of more effective periapical disease management strategies. Copyright © 2013 American Association of Endodontists. All rights reserved.

Sampling and Chemical Analysis of Potable Water for ISS Expeditions 12 and 13

NASA Technical Reports Server (NTRS)

Straub, John E. II; Plumlee, Deborah K.; Schultz, John R.

2007-01-01

The crews of Expeditions 12 and 13 aboard the International Space Station (ISS) continued to rely on potable water from two different sources, regenerated humidity condensate and Russian ground-supplied water. The Space Shuttle launched twice during the 12- months spanning both expeditions and docked with the ISS for delivery of hardware and supplies. However, no Shuttle potable water was transferred to the station during either of these missions. The chemical quality of the ISS onboard potable water supplies was verified by performing ground analyses of archival water samples at the Johnson Space Center (JSC) Water and Food Analytical Laboratory (WAFAL). Since no Shuttle flights launched during Expedition 12 and there was restricted return volume on the Russian Soyuz vehicle, only one chemical archive potable water sample was collected with U.S. hardware and returned during Expedition 12. This sample was collected in March 2006 and returned on Soyuz 11. The number and sensitivity of the chemical analyses performed on this sample were limited due to low sample volume. Shuttle flights STS-121 (ULF1.1) and STS-115 (12A) docked with the ISS in July and September of 2006, respectively. These flights returned to Earth with eight chemical archive potable water samples that were collected with U.S. hardware during Expedition 13. The average collected volume increased for these samples, allowing full chemical characterization to be performed. This paper presents a discussion of the results from chemical analyses performed on Expeditions 12 and 13 archive potable water samples. In addition to the results from the U.S. samples analyzed, results from pre-flight samples of Russian potable water delivered to the ISS on Progress vehicles and in-flight samples collected with Russian hardware during Expeditions 12 and 13 and analyzed at JSC are also discussed.

Antibody against infectious salmon anaemia virus among feral Atlantic salmon (Salmo salar)

USGS Publications Warehouse

Cipriano, R.C.

2009-01-01

Archived sera from Atlantic salmon (Salmo salar) that returned to the Penobscot River (Maine), Merrimack River (Massachusetts), and Connecticut River (in Massachusetts) from 1995 to 2002 were analysed for antibodies against infectious salmon anaemia virus (ISAV) using an enzyme-linked immunosorbent assay (ELISA). Up to 60 samples were archived per river system per year. In a given year, the number of fish sampled by ELISA for ISAV antibodies in the Penobscot River ranged from 2.9 to 11.2, and the range of salmon sampled in the Merrimack River and the Connecticut River was 31.3-100 and 20.0-67.5, respectively. Archived sera were not available for the 1995 and 2002 year classes from the Connecticut River. In all, 1141 samples were processed; 14 serum samples tested positive for antibodies to ISAV. In the Penobscot River, serum from one fish tested positive in each of the 1995 and 1999 year-class returns, and sera from two fish tested positive in the 1998 returns. In the Merrimack River, sera from four fish tested positive in each of the 1996 and 1997 returns, and sera from two fish were positive in the 2002 return. None of the archived sera from Atlantic salmon that returned to the Connecticut River tested positive. ?? 2009 United States Government, Department of the Interior.

Involving citizens in the ethics of biobank research: informing institutional policy through structured public deliberation.

PubMed

O'Doherty, Kieran C; Hawkins, Alice K; Burgess, Michael M

2012-11-01

This paper reports on the design, implementation, and results of a structured public deliberation on human tissue biobanking conducted in Vancouver, Canada, in 2009. This study builds on previous work on the use of deliberative democratic principles and methods to engage publics on the social and ethical implications of human tissue biobanking. In a significant refinement of methods, we focus on providing public input to institutional practice and governance of biobanks using a tailored workbook structure to guide participants' discussion. Our focus is on the local context and practices of a particular institution, the BC BioLibrary. However, elements of both the methodological innovations and the ethical guidance implied by our findings are generalisable for biobanking internationally. Recommendations from the deliberative forum include issues of informed consent, privacy protections, collection of biospecimens, governance of biobanks, and how to manage the process of introduction between biobanks and potential donors. Notable findings include public support for research use of anonymised un-consented tissue samples when these come from archived collections, but lack of support when they are collected prospectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beck, M.A.

1993-07-16

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

The Importance of Measuring Mercury in Wood

NASA Astrophysics Data System (ADS)

Yang, Y.; Yanai, R. D.; Driscoll, C. T.; Montesdeoca, M.

2014-12-01

Forests are important receptors of Hg deposition, and biological Hg hotspots occur mainly in forested regions, but few efforts have been made to determine the Hg content of trees. Mercury concentrations in stem tissue are lower than the foliage and bark, so low that they have often been below detection limits, especially in hardwood species. However, because wood is the largest component of forest biomass, it can be a larger Hg pool than the foliage, and thus quantifying concentrations in wood is important to Hg budgets in forests. The objective of our study was to determine the methods necessary to detect Hg in bole wood of four tree species, including two hardwoods and two conifers. We also evaluated the effect of air-drying and oven-drying samples on Hg recovery, compared to freeze-drying samples prior to analysis, which is the standard procedure. Many archived wood samples that were air-dried or oven-dried could be appropriate for Hg analysis if these methods could be validated; few are freeze-dried. We analyzed samples for total Hg using thermal decomposition, catalytic conversion, amalgamation, and atomic absorption spectrophotometry (Method 7473, USEPA 1998). The result of the method detection limit study was 1.27 ng g-1, based on apple leaf standards (NIST 1515, 44 ± 4 ng/g). Concentrations in the hardwood species were 1.48 ± 0.23 ng g-1 for sugar maple and 1.75 ± 0.14 ng g-1 for American beech. Concentrations were higher in red spruce and balsam fir. Samples that were analyzed fresh, freeze-dried, or oven-dried at 65 ˚C were in close agreement, after correcting for moisture content. However, Hg concentrations were 34 to 45% too high in the air-dry samples, presumably reflecting absorption from the atmosphere, and they were 44 to 66% too low in the samples oven-dried at 103 ˚C, presumably due to volatilization. We recommend that samples be freeze-dried or oven-dried at 65 ˚C for analysis of Hg in wood; archived samples that have been oven-dried at higher temperatures or stored exposed to the air may not be suitable for Hg analysis.

Chorionic Villus Sampling (CVS)

MedlinePlus

... Careers Archives Health Topics Pregnancy Before or between pregnancies Nutrition, weight & fitness Prenatal care Is it safe? Labor & ... Report Cards Careers Archives Pregnancy Before or between pregnancies Nutrition, weight & fitness Prenatal care Is it safe? Labor & ...

Sample Curation in Support of the OSIRIS-REx Asteroid Sample Return Mission

NASA Technical Reports Server (NTRS)

Righter, Kevin; Nakamura-Messenger, Keiko

2017-01-01

The OSIRIS-REx asteroid sample return mission launched to asteroid Bennu Sept. 8, 2016. The spacecraft will arrive at Bennu in late 2019, orbit and map the asteroid, and perform a touch and go (TAG) sampling maneuver in July 2020. After sample is stowed and confirmed the spacecraft will return to Earth, and the sample return capsule (SRC) will land in Utah in September 2023. Samples will be recovered from Utah [2] and then transported and stored in a new sample cleanroom at NASA Johnson Space Center in Houston [3]. The materials curated for the mission are described here. a) Materials Archive and Witness Plate Collection: The SRC and TAGSAM were built between March 2014 and Summer of 2015, and instruments (OTES,OVIRS, OLA, OCAMS, REXIS) were integrated from Summer 2015 until May 2016. A total of 395 items were received for the materials archive at NASA-JSC, with archiving finishing 30 days after launch (with the final archived items being related to launch operations)[4]. The materials fall into several general categories including metals (stainless steel, aluminum, titanium alloys, brass and BeCu alloy), epoxies, paints, polymers, lubricants, non-volatile-residue samples (NVR), sapphire, and various miscellaneous materials. All through the ATLO process (from March 2015 until late August 2016) contamination knowledge witness plates (Si wafer and Al foil) were deployed in the various cleanrooms in Denver and KSC to provide an additional record of particle counts and volatiles that is archived for current and future scientific studies. These plates were deployed in roughly monthly increments with each unit containing 4 Si wafers and 4 Al foils. We archived 128 individual witness plates (64 Si wafers and 64 Al foils); one of each witness plate (Si and Al) was analyzed immediately by the science team after archiving, while the remaining 3 of each are archived indefinitely. Information about each material archived is stored in an extensive database at NASA-JSC, and key summary information for each will be presented in an online catalog. b) Bulk Asteroid sample: The Touch and Go Sampling Mechanism (TAGSAM) head will contain up to 1.5 kg of asteroid material. Upon return to Earth, the TAGSAM head with the sample canister will be subjected to a nitrogen purge and then opened in a nitrogen cabinet in Houston. Once the TAGSAM head is removed from the canister, it will be dis-assembled slowly and carefully under nitrogen until the sample can be removed for processing in a dedicated nitrogen glovebox. Bennu surface samples are expected to be sub-cm sized, based on thermal infrared and radar polarization ratio measurements [1]. The upper limit on material collected by the TAGSAM head is 2 cm. Therefore, we will be prepared to handle, subdivide, and characterize materials of a wide grain size (from 10 ?m to 2 cm), and for both organic (UV fluorescence) and inorganic (SEM, FTIR, optical) properties. Representative portions of the bulk sample will be prepared for JAXA (0.5 %; see also [5]) and Canadian Space Agency (4%), with the remaining divided between the science team (<25%) and archived for future studies (NASA) (>75%). c) Contact Pad samples: The base of the TAGSAM head contains 24 contact pads that are designed to trap the upper surface layer of material and thus offer an opportunity to study asteroid samples that have resided at the very top surface of the regolith. Asteroid material is trapped on the pads in spring steel Velcro hooks, and material will have to be removed from these pads by curation specialists in the lab. d) Hardware: Some canister and SRC hardware items will contain information that will be important to understanding the collected samples, including the canister gas filter, temperature strips, flight witness plates, and the TAGSAM and canister parts that might have adhering dust grains. Some challenges remaining for both bulk sample and contact pad samples include: i) working with intermediate size range (200 to 500 micron) samples - a size range NASA has not previously worked in such detail; ii) techniques for removal of contact pad material from the spring steel hooks, iii) static electrical effects of dust sized particles during sample handling and curation is likely to be significant, and iv) the TAGSAM head and associated canister hardware will undoubtedly be coated with fine adhering dust grains from Bennu. In the case of collection of a large bulk sample mass, the adhering dust grains may be of lower priority. If a small sample mass is returned, the adhering dust may attain a higher priority, so recovery of adhering dust grains is an additional challenge to consider. In the year leading up to sample return we plan a variety of sample handling rehearsals that will enables the curation team to be prepared for many new aspects posed by this sample suite.

Comparison of nucleotide sequences of recent and previous lineages of peste-des-petits-ruminants viruses of sheep and goats in Nigeria.

PubMed

Mantip, Samuel; Quan, Melvyn; Shamaki, David; Van Vuuren, Moritz

2016-08-31

Peste-des-petits-ruminants virus (PPRV) is a highly contagious, fatal and economically important viral disease of small ruminants that is still endemic and militates against the production of sheep and goats in endemic areas of the world. The aim of this study was to describe the viral strains within the country. This was carried out by collecting tissue and swab samples from sheep and goats in various agro-ecological zones of Nigeria. The phylogeny of archived PPRV strains or isolates and those circulating and causing recent outbreaks was determined by sequencing of the nucleoprotein (N)-gene. Twenty tissue and swab samples from apparently healthy and sick sheep and goats were collected randomly from 18 states, namely 3 states in each of the 6 agro-ecological zones visited. A total of 360 samples were collected. A total of 35 samples of 360 (9.7%) tested positive by reverse transcriptase-polymerase chain reaction, of which 25 were from oculo-nasal swabs and 10 were from tissue samples. Neighbour-joining phylogenetic analysis using Phylogenetic Analysis Using Parsimony (PAUP) identified four different lineages, that is, lineages I, II, III and IV. Interestingly, the Nigerian strains described in this study grouped in two separate major lineages, that is, lineages II and IV. Strains from Sokoto, Oyo, Plateau and Ondo states grouped according to the historical distribution of PPRV together with the Nigerian 75/1 strain of lineage II, while other strains from Sokoto, Oyo, Plateau, Akwa-Ibom, Adamawa, Kaduna, Lagos, Bauchi, Niger and Kano states grouped together with the East African and Asian strains of lineage IV. This finding confirms that both lineage II and IV strains of PPRV are circulating in Nigeria. Previously, only strains of lineage II were found to be present in the country.

Prevalence of human papillomavirus genotypes associated with cervical and breast cancers in iran.

PubMed

Hossein, Rassi; Behzad, Salehi; Tahar, Mohammadian; Azadeh, Nahavandi Araghi

2013-12-01

Cancer is a multi-step disease, and infection with a DNA virus could play a role in one or more of the steps in this pathogenic process. High-risk human papillomaviruses (HPV) are the causative agent of several cancers. In this study, we determined the prevalence and genotype distribution of HPV infection among Iranian patients with cervix lesions (CL) and breast cancer (BC). The study group consisted of postoperative tissues from patients diagnosed with cervix lesions and breast cancer. We analyzed 250 formalin-fixed, paraffin-embedded tissue blocks from 100 cervix lesions and 150 breast cancer samples. Verification of each cancer reported in a relative was sought through the pathology reports of the hospital records. Cervix lesions were collected from 100 patients with squamous metaplasia (SM, n=50), cervical intraepithelial neoplasia (CINI, n=18, CINII or III, n=8), and cervical carcinoma (CC, n=24). In this study we evaluated the prevalence of HPV by multiplex PCR in cervix lesions and breast cancer. For paraffin-embedded tissues, DNA extracted by the simple boiling method yielded higher proportions of successful gene amplification (99%) for b-actin gene. Overall prevalence of HPV infection was 6% in the SM group, 34.61% in the CIN group, 75% in the CC group, and 34.66% in the BC group. Furthermore, MY09/11 consensus PCR failed to detect 44 (55.69%) of all HPV infections and interestingly, the predominant genotype detected in all cancers was the oncogenic variant HPV16/18; about 34% of women aged 24 to 54 were infected with at least one type of HPV. Our results demonstrate that DNA derived from archival tissues that archived for less than 8 years could be used successfully for HPV genotyping by multiplex PCR. Infection with HPV was prevalent among Iranian women with CC and BC. The results indicate a likely causal role for high-risk HPV in CC and BC, and also offer the possibility of primary prevention of these cancers by vaccination against HPV in Iran.

Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

PubMed Central

Okello, John B. A.; Rodriguez, Linda; Poinar, Debi; Bos, Kirsten; Okwi, Andrew L.; Bimenya, Gabriel S.; Sewankambo, Nelson K.; Henry, Kenneth R.; Kuch, Melanie; Poinar, Hendrik N.

2010-01-01

Background The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. Methodology/Principal Findings We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. Conclusions/Significance We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation. PMID:21085668

Characterization of an Adhesion-Associated Tumor Suppressor in Breast Cancer

DTIC Science & Technology

2001-08-01

Western blot analysis were invasive and associated with fibrous connective tissue (Fig. 4, B of whole cell lysates resolved by SDS-PAGE was...of breast cancer. Immunohistochemical analyses of archival, formalin-fixed paraffin-embedded specimens of benign and malignant breast tissues confirm...10A cells. In particular, EphA2 destabilizes cell-cell attachments while increasing cell interactions with extracellular matrix (ECM proteins). We have

Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics.

PubMed

Tin, Mandy Man-Ying; Economo, Evan Philip; Mikheyev, Alexander Sergeyevich

2014-01-01

Ancient and archival DNA samples are valuable resources for the study of diverse historical processes. In particular, museum specimens provide access to biotas distant in time and space, and can provide insights into ecological and evolutionary changes over time. However, archival specimens are difficult to handle; they are often fragile and irreplaceable, and typically contain only short segments of denatured DNA. Here we present a set of tools for processing such samples for state-of-the-art genetic analysis. First, we report a protocol for minimally destructive DNA extraction of insect museum specimens, which produced sequenceable DNA from all of the samples assayed. The 11 specimens analyzed had fragmented DNA, rarely exceeding 100 bp in length, and could not be amplified by conventional PCR targeting the mitochondrial cytochrome oxidase I gene. Our approach made these samples amenable to analysis with commonly used next-generation sequencing-based molecular analytic tools, including RAD-tagging and shotgun genome re-sequencing. First, we used museum ant specimens from three species, each with its own reference genome, for RAD-tag mapping. Were able to use the degraded DNA sequences, which were sequenced in full, to identify duplicate reads and filter them prior to base calling. Second, we re-sequenced six Hawaiian Drosophila species, with millions of years of divergence, but with only a single available reference genome. Despite a shallow coverage of 0.37 ± 0.42 per base, we could recover a sufficient number of overlapping SNPs to fully resolve the species tree, which was consistent with earlier karyotypic studies, and previous molecular studies, at least in the regions of the tree that these studies could resolve. Although developed for use with degraded DNA, all of these techniques are readily applicable to more recent tissue, and are suitable for liquid handling automation.

Common Laundry Detergent Ingredient May Help Preserve Muscle Tissue After Severe Injury

MedlinePlus

... this research; and the dissemination of information on research progress in these diseases. Contact Us NIAMS Archive Viewers and Players Social Media Moderation Policy FOIA Privacy Statement Accessibility Disclaimer Digital Strategy ...

Impact of the School Outreach Tour Program of Citizens Archive of Pakistan on Students' Perceptions and Attitudes

ERIC Educational Resources Information Center

Alam, Qutbi

2017-01-01

This paper examines the impact of School Outreach Tour (SOT-A) program,one of the projects of the Citizens Archive of Pakistan (CAP), a non-profit organisation on the perceptions and attitudes of Grade-8 Students of partners' schools. The sample in this study consists of (n = 139) students of Grade-8, selected by convenience sampling from five…

Detection and Characterization of Circulating Tumour Cells from Frozen Peripheral Blood Mononuclear Cells

PubMed Central

Lu, David; Graf, Ryon P.; Harvey, Melissa; Madan, Ravi A.; Heery, Christopher; Marte, Jennifer; Beasley, Sharon; Tsang, Kwong Y.; Krupa, Rachel; Louw, Jessica; Wahl, Justin; Bales, Natalee; Landers, Mark; Marrinucci, Dena; Schlom, Jeffrey; Gulley, James L.; Dittamore, Ryan

2015-01-01

Retrospective analysis of patient tumour samples is a cornerstone of clinical research. CTC biomarker characterization offers a non-invasive method to analyse patient samples. However, current CTC technologies require prospective blood collection, thereby reducing the ability to utilize archived clinical cohorts with long-term outcome data. We sought to investigate CTC recovery from frozen, archived patient PBMC pellets. Matched samples from both mCRPC patients and mock samples, which were prepared by spiking healthy donor blood with cultured prostate cancer cell line cells, were processed “fresh” via Epic CTC Platform or from “frozen” PBMC pellets. Samples were analysed for CTC enumeration and biomarker characterization via immunofluorescent (IF) biomarkers, fluorescence in-situ hybridization (FISH) and CTC morphology. In the frozen patient PMBC samples, the median CTC recovery was 18%, compared to the freshly processed blood. However, abundance and localization of cytokeratin (CK) and androgen receptor (AR) protein, as measured by IF, were largely concordant between the fresh and frozen CTCs. Furthermore, a FISH analysis of PTEN loss showed high concordance in fresh vs. frozen. The observed data indicate that CTC biomarker characterization from frozen archival samples is feasible and representative of prospectively collected samples. PMID:28936240

Superoxide dismutases in chronic gastritis.

PubMed

Švagelj, Dražen; Terzić, Velimir; Dovhanj, Jasna; Švagelj, Marija; Cvrković, Mirta; Švagelj, Ivan

2016-04-01

Human gastric diseases have shown significant changes in the activity and expression of superoxide dismutase (SOD) isoforms. The aim of this study was to detect Mn-SOD activity and expression in the tissue of gastric mucosa, primarily in chronic gastritis (immunohistochemical Helicobacter pylori-negative gastritis, without other pathohistological changes) and to evaluate their possible connection with pathohistological diagnosis. We examined 51 consecutive outpatients undergoing endoscopy for upper gastrointestinal symptoms. Patients were classified based on their histopathological examinations and divided into three groups: 51 patients (archive samples between 2004-2009) with chronic immunohistochemical Helicobacter pylori-negative gastritis (mononuclear cells infiltration were graded as absent, moderate, severe) divided into three groups. Severity of gastritis was graded according to the updated Sydney system. Gastric tissue samples were used to determine the expression of Mn-SOD with anti-Mn-SOD Ab immunohistochemically. The Mn-SOD expression was more frequently present in specimens with severe and moderate inflammation of gastric mucosa than in those with normal mucosa. In patients with normal histological finding, positive immunoreactivity of Mn-SOD was not found. Our results determine the changes in Mn-SOD expression occurring in the normal gastric mucosa that had undergone changes in the intensity of chronic inflammatory infiltrates in the lamina propria. © 2016 APMIS. Published by John Wiley & Sons Ltd.

VizieR Online Data Catalog: Ccompact group galaxies UV and IR SFR (Lenkic+, 2016)

NASA Astrophysics Data System (ADS)

Lenkic, L.; Tzanavaris, P.; Gallagher, S. C.; Desjardins, T. D.; Walker, L. M.; Johnson, K. E.; Fedotov, K.; Charlton, J.; Hornschemeier, A. E.; Durrell, P. R.; Gronwall, C.

2017-07-01

The sample of CGs studied here is the same sample studied by Walker et al. (2012AJ....143...69W) of 49 CGs: 33 Hickson Compact Groups and 16 Redshift Survey Compact Groups (RSCGs). The RSCG catalogue of 89 CGs was constructed by Barton et al. (1996AJ....112..871B). The data used in this study originated from 'fill-in' observations with UVOT's three UV filters (uvw2, uvm2, uvw1) as well as the bluest optical filter (u). All UV data (PI: Tzanavaris) were downloaded from the Swift archive. The Spitzer Infrared Array Camera images for our sample of CGs are archival data presented by Walker et al. (2012AJ....143...69W) Spitzer MIPS (24um) data were obtained from the Spitzer Heritage Archive. (4 data files).

[Quality of DNA from archival pathological samples of gallbladder cancer].

PubMed

Roa, Iván; de Toro, Gonzalo; Sánchez, Tamara; Slater, Jeannie; Ziegler, Anne Marie; Game, Anakaren; Arellano, Leonardo; Schalper, Kurt; de Aretxabala, Xabier

2013-12-01

The quality of the archival samples stored at pathology services could be a limiting factor for molecular biology studies. To determine the quality of DNA extracted from gallbladder cancer samples at different institutions. One hundred ninety four samples coming from five medical centers in Chile, were analyzed. DNA extraction was quantified determining genomic DNA concentration. The integrity of DNA was determined by polymerase chain reaction amplification of different length fragments of a constitutive gene (β-globin products of 110, 268 and 501 base pairs). The mean DNA concentration obtained in 194 gallbladder cancer samples was 48 ± 43.1 ng/µl. In 22% of samples, no amplification was achieved despite obtaining a mean DNA concentration of 58.3 ng/ul. In 81, 67 and 22% of samples, a DNA amplification of at least 110, 268 or 501 base pairs was obtained, respectively. No differences in DNA concentration according to the source of the samples were demonstrated. However, there were marked differences in DNA integrity among participating centers. Samples from public hospitals were of lower quality than those from private clinics. Despite some limitations, in 80% of cases, the integrity of DNA in archival samples from pathology services in our country would allow the use of molecular biology techniques.

Identification of forensic samples by using an infrared-based automatic DNA sequencer.

PubMed

Ricci, Ugo; Sani, Ilaria; Klintschar, Michael; Cerri, Nicoletta; De Ferrari, Francesco; Giovannucci Uzielli, Maria Luisa

2003-06-01

We have recently introduced a new protocol for analyzing all core loci of the Federal Bureau of Investigation's (FBI) Combined DNA Index System (CODIS) with an infrared (IR) automatic DNA sequencer (LI-COR 4200). The amplicons were labeled with forward oligonucleotide primers, covalently linked to a new infrared fluorescent molecule (IRDye 800). The alleles were displayed as familiar autoradiogram-like images with real-time detection. This protocol was employed for paternity testing, population studies, and identification of degraded forensic samples. We extensively analyzed some simulated forensic samples and mixed stains (blood, semen, saliva, bones, and fixed archival embedded tissues), comparing the results with donor samples. Sensitivity studies were also performed for the four multiplex systems. Our results show the efficiency, reliability, and accuracy of the IR system for the analysis of forensic samples. We also compared the efficiency of the multiplex protocol with ultraviolet (UV) technology. Paternity tests, undegraded DNA samples, and real forensic samples were analyzed with this approach based on IR technology and with UV-based automatic sequencers in combination with commercially-available kits. The comparability of the results with the widespread UV methods suggests that it is possible to exchange data between laboratories using the same core group of markers but different primer sets and detection methods.

European roe deer antlers as an environmental archive for fallout (236)U and (239)Pu.

PubMed

Froehlich, M B; Steier, P; Wallner, G; Fifield, L K

2016-01-01

Anthropogenic (236)U and (239)Pu were measured in European roe deer antlers hunted between 1955 and 1977 which covers and extends beyond the period of intensive nuclear weapons testing (1954-1962). The antlers were hunting trophies, and hence the hunting area, the year of shooting and the approximate age of each animal is given. Uranium and plutonium are known to deposit in skeletal tissue. Since antler histology is similar to bone, both elements were expected in antlers. Furthermore, roe deer shed their antlers annually, and hence antlers may provide a time-resolved environmental archive for fallout radionuclides. The radiochemical procedure is based on a Pu separation step by anion exchange (Dowex 1 × 8) and a subsequent U purification by extraction chromatography using UTEVA(®). The samples were measured by Accelerator Mass Spectrometry at the VERA facility (University of Vienna). In addition to the (236)U and (239)Pu concentrations, the (240)Pu/(239)Pu isotopic ratios were determined with a mean value of 0.172 ± 0.023 which is in agreement with the ratio of global fallout (∼0.18). Rather high (236)U/(238)U ratios of the order of 10(-6) were observed. These measured ratios, where the (236)U arises only from global fallout, have implications for the use of the (236)U/(238)U ratio as a fingerprint for nuclear accidents or releases from nuclear facilities. Our investigations have shown the potential to use antlers as a temporally resolved archive for the uptake of actinides from the environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crystal violet stain as a selective stain for the assessment of mitotic figures in oral epithelial dysplasia and oral squamous cell carcinoma.

PubMed

Jadhav, Kiran B; Ahmed Mujib, B R; Gupta, Nidhi

2012-01-01

Assessment of mitotic figures (MFs) is routinely practiced as prognostic indicator in oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC), but identification of MFs poses a problem in terms of staining characteristics. To evaluate effectiveness of crystal violet stain for staining of MFs and its comparison with hematoxylin and eosin (H and E) stain. Study sample includes archival tissues embedded in paraffin blocks diagnosed as OED (n = 30) and OSCC (n = 30). The control group comprised of tissue specimen from oral mucosa of healthy volunteers (n = 30). Two serial sections of each tissue specimen were stained separately with H and E stain and 1% crystal violet stain. The stained sections were observed under microscope for identification and counting of MFs. Data obtained was statistically analyzed by using the Man-Whitney U test. A significant increase in number of MFs was observed in OED and OSCC in comparison with normal oral mucosa. There was a highly significant increase in number of MFs in crystal violet stained tissue sections when compared with H and E stain. Metaphase is the most commonly observed phase of mitosis in crystal violet stain when compared with H and E stain for all three groups. Crystal violet stain can be considered as selective stain for mitotic figures.

Optimal extraction of quasar Lyman limit absorption systems from the IUE archive

NASA Technical Reports Server (NTRS)

Tytler, David

1992-01-01

The IUE archive contains a wealth of information on Lyman limit absorption systems (LLS) in quasar spectra. QSO spectra from the IUE data base were optimally extracted, coadded, and analyzed to yield a homogeneous samples of LLS at low red shifts. This sample comprise 36 LLS, twice the number previously analyzed low z samples. These systems are ideal for the determination of the origin, redshift evolution, ionization, velocity dispersions and the metal abundances of absorption systems. Two of them are also excellent targets for the primordial Deuterium to Hydrogen ratio.

Measurements of CO2 Mole Fractionand δ13C in Archived Air Samples from Cape Meares, Oregon (USA) 1977 - 1998

NASA Astrophysics Data System (ADS)

Clark, O.; Rice, A. L.

2017-12-01

Carbon dioxide (CO2) is the most abundant, anthropogenically forced greenhouse gas (GHG) in the global atmosphere. Emissions of CO2 account for approximately 75% of the world's total GHG emissions. Atmospheric concentrations of CO2 are higher now than they've been at any other time in the past 800,000 years. Currently, the global mean concentration exceeds 400 ppm. Today, global networks regularly monitor CO2 concentrations and isotopic composition (δ13C and δ18O). However, past data is sparse. Over 200 ambient air samples from Cape Meares, Oregon (45.5°N, 124.0°W), a coastal site in Western United States, were obtained by researchers at Oregon Institute of Science and Technology (OGI, now Oregon Health & Science University), between the years of 1977 and 1998 as part of a global monitoring program of six different sites in the polar, middle, and tropical latitudes of the Northern and Southern Hemispheres. Air liquefaction was used to compress approximately 1000L of air (STP) to 30bar, into 33L electropolished (SUMMA) stainless steel canisters. Select archived air samples from the original network are maintained at Portland State University (PSU) Department of Physics. These archived samples are a valuable look at changing atmospheric concentrations of CO2 and δ13C, which can contribute to a better understanding of changes in sources during this time. CO2 concentrations and δ13C of CO2 were measured at PSU, with a Picarro Cavity Ringdown Spectrometer, model G1101-i analytical system. This study presents the analytical methods used, calibration techniques, precision, and reproducibility. Measurements of select samples from the archive show rising CO2 concentrations and falling δ13C over the 1977 to 1998 period, compatible with previous observations and rising anthropogenic sources of CO2. The resulting data set was statistically analyzed in MATLAB. Results of preliminary seasonal and secular trends from the archive samples are presented.

The Cancer Digital Slide Archive - TCGA

Cancer.gov

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.

Expression of proinflammatory cytokine interleukin-6 in tissue samples of human prostate obtained by needle biopsy.

PubMed

Miličević, Nevenka; Mrčela, Milanka; Galić, Josip; Marjanović, Ksenija

2015-11-01

Interleukin-6 (IL-6) has been associated with the development of prostate cancer. The aim of the study was to clarify whether IL-6 expression in prostate tissue could be a useful marker in differentiation of prostate diseases in small foci by pathologist visual scoring. Archival paraffin-embedded specimens of benign prostate hyperplasia (BPH), high-grade prostatic intraepithelial neoplasia (PIN), prostatitis and prostate adenocarcinoma were studied by immunohistochemistry with a mouse monoclonal antibody IL-6 using the streptavidin-biotin method. Significantly, lower IL-6 immunoreactivity was observed in normal epithelial cells (p=0.000) and basal cells (p=0.000) in the samples of prostate adenocarcinoma in comparison to the samples with BPH, PIN and prostatitis. There was no significant difference in IL-6 expression in malignant and premalignant cells (p=0.814) as well as in stromal cells among the four diagnoses (p=0.22). IL-6 was expressed in normal epithelial cells, premalignant epithelial cells and malignant epithelial cells as well as in stromal cells. However, in our research IL-6 was of limited utility as a single marker for differential diagnosis of the prostate diseases in small foci needle biopsy by pathologist visual scoring. The standardization of immunohistochemical (IHC) staining protocol for IL-6 is required to determine IL-6 expression in order to avoid possible misinterpretation of the IHC results. Copyright © 2015 Elsevier GmbH. All rights reserved.

Dynamic molecular analysis and clinical correlates of tumor evolution within a phase II trial of panitumumab-based therapy in metastatic colorectal cancer.

PubMed

Siena, S; Sartore-Bianchi, A; Garcia-Carbonero, R; Karthaus, M; Smith, D; Tabernero, J; Van Cutsem, E; Guan, X; Boedigheimer, M; Ang, A; Twomey, B; Bach, B A; Jung, A S; Bardelli, A

2018-01-01

Mutations in rat sarcoma (RAS) genes may be a mechanism of secondary resistance in epidermal growth factor receptor inhibitor-treated patients. Tumor-tissue biopsy testing has been the standard for evaluating mutational status; however, plasma testing of cell-free DNA has been shown to be a more sensitive method for detecting clonal evolution. Archival pre- and post-treatment tumor biopsy samples from a phase II study of panitumumab in combination with irinotecan in patients with metastatic colorectal cancer (mCRC) that also collected plasma samples before, during, and after treatment were analyzed for emergence of mutations during/post-treatment by next-generation sequencing and BEAMing. The rate of emergence of tumor tissue RAS mutations was 9.5% by next-generation sequencing (n = 21) and 6.3% by BEAMing (n = 16). Plasma testing of cell-free DNA by BEAMing revealed a mutant RAS emergence rate of 36.7% (n = 39). Exploratory outcomes analysis of plasma samples indicated that patients who had emergent RAS mutations at progression had similar median progression-free survival to those patients who remained wild-type at progression. Serial analysis of plasma samples showed that the first detected emergence of RAS mutations preceded progression by a median of 3.6 months (range, -0.3 to 7.5 months) and that there did not appear to be a mutant RAS allele frequency threshold that could predict near-term outcomes. This first prospective analysis in mCRC showed that serial plasma biopsies are more inclusive than tissue biopsies for evaluating global tumor heterogeneity; however, the clinical utility of plasma testing in mCRC remains to be further explored. NCT00891930. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology.

Three Proposed Compendia for Genesis Solar Wind Samples: Science Results, Collector Materials Characterization and Cleaning Techniques

NASA Technical Reports Server (NTRS)

Allton, J. H.; Calaway, M. J.; Nyquist, L. E.; Jurewicz, A. J. G.; Burnett, D. S.

2018-01-01

Final Paper and not the abstract is attached. Introduction: Planetary material and cosmochemistry research using Genesis solar wind samples (including the development and implementation of cleaning and analytical techniques) has matured sufficiently that compilations on several topics, if made publically accessible, would be beneficial for researchers and reviewers. We propose here three compendia based on content, organization and source of documents (e.g. published peer-reviewed, published, internal memos, archives). For planning purposes, suggestions are solicited from potential users of Genesis solar wind samples for the type of science content and/or organizational style that would be most useful to them. These compendia are proposed as living documents, periodically updated. Similar to the existing compendia described below, the curation compendia are like library or archival finding aids, they are guides to published or archival documents and should not be cited as primary sources.

Identification of mycotoxins by UHPLC–QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, Nancy I.; Ibáñez, María; Beltrán, Eduardo

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquidmore » chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC–QTOF MS) under MS{sup E} mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC–QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC–MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. - Highlights: • Mold deterioration of historical documents is a frequent and complex phenomenon. • Samples of broths of fungal species isolated from Archive of Bogotá analyzed. • UHPLC–QTOF MS (MS{sup E}) applied for mycotoxins screening, without reference standards. • Customized home-made database for around 600 mycotoxins compiled. • 44 mycotoxins tentatively identified, 34 of which confirmed by LC–MS/MS.« less

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch; Gallati, Sabina, E-mail: sabina.gallati@insel.ch; Schaller, Andre, E-mail: andre.schaller@insel.ch

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serialmore » qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.« less

CDX2 immunostaining in primary and metastatic germ cell tumours of the testis.

PubMed

Oz Atalay, Fatma; Aytac Vuruskan, Berna; Vuruskan, Hakan

2016-12-01

Objective To evaluate the immunohistochemical staining pattern of caudal type homeobox 2 (CDX2) protein in germ cell tumours (GCTs) of the testis. Methods This study reassessed archival tissue samples collected from patients diagnosed with primary and metastatic testicular GCTs for CDX2 immunoreactivity using standard immunohistochemical techniques. Positive nuclear immunostaining was evaluated with regard to both the staining intensity and the extent of the staining. Results Tissue sections from primary and metastatic testicular GCTs ( n = 104), germ cell neoplasia in situ (GCNis) ( n = 5) and benign testicles ( n = 15) were analysed. The GCNis and benign testicular tissues showed no immunoreactivity for CDX2. Strong and diffuse staining of CDX2 was demonstrated only in the mature colonic epithelium of teratomas in both primary and metastatic GCTs. CDX2 positivity in other tumours (one pure yolk sac tumour, one yolk sac component of a mixed GCT and one pure seminoma) was infrequent, and was only weak and focal. Conclusions CDX2 immunostaining should be interpreted based on both the staining intensity and the extent of staining so as not to cause misdiagnosis. Teratomas with colonic-type epithelium should be considered in the differential diagnosis if a metastatic tumour with an unknown primary shows prominent CDX2 immunostaining.

Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.

PubMed

Sinicropi, Dominick; Qu, Kunbin; Collin, Francois; Crager, Michael; Liu, Mei-Lan; Pelham, Robert J; Pho, Mylan; Dei Rossi, Andrew; Jeong, Jennie; Scott, Aaron; Ambannavar, Ranjana; Zheng, Christina; Mena, Raul; Esteban, Jose; Stephans, James; Morlan, John; Baker, Joffre

2012-01-01

RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole transcriptome profiling from FFPE tissue. The chemistry accommodates low RNA inputs and sample multiplexing. These methods both enable rediscovery of RNA biomarkers for disease recurrence risk that were previously identified by RT-PCR analysis of a cohort of 136 patients, and also identify a high percentage of recurrence risk markers that were previously discovered using DNA microarrays in a separate cohort of patients, evidence that this RNA-Seq technology has sufficient precision and sensitivity for biomarker discovery. More than two thousand RNAs are strongly associated with breast cancer recurrence risk in the 136 patient cohort (FDR <10%). Many of these are intronic RNAs for which corresponding exons are not also associated with disease recurrence. A number of the RNAs associated with recurrence risk belong to novel RNA networks. It will be important to test the validity of these novel associations in whole transcriptome RNA-Seq screens of other breast cancer cohorts.

Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

PubMed Central

Sinicropi, Dominick; Qu, Kunbin; Collin, Francois; Crager, Michael; Liu, Mei-Lan; Pelham, Robert J.; Pho, Mylan; Rossi, Andrew Dei; Jeong, Jennie; Scott, Aaron; Ambannavar, Ranjana; Zheng, Christina; Mena, Raul; Esteban, Jose; Stephans, James; Morlan, John; Baker, Joffre

2012-01-01

RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole transcriptome profiling from FFPE tissue. The chemistry accommodates low RNA inputs and sample multiplexing. These methods both enable rediscovery of RNA biomarkers for disease recurrence risk that were previously identified by RT-PCR analysis of a cohort of 136 patients, and also identify a high percentage of recurrence risk markers that were previously discovered using DNA microarrays in a separate cohort of patients, evidence that this RNA-Seq technology has sufficient precision and sensitivity for biomarker discovery. More than two thousand RNAs are strongly associated with breast cancer recurrence risk in the 136 patient cohort (FDR <10%). Many of these are intronic RNAs for which corresponding exons are not also associated with disease recurrence. A number of the RNAs associated with recurrence risk belong to novel RNA networks. It will be important to test the validity of these novel associations in whole transcriptome RNA-Seq screens of other breast cancer cohorts. PMID:22808097

The Hubble Spectroscopic Legacy Archive

NASA Astrophysics Data System (ADS)

Peeples, M.; Tumlinson, J.; Fox, A.; Aloisi, A.; Fleming, S.; Jedrzejewski, R.; Oliveira, C.; Ayres, T.; Danforth, C.; Keeney, B.; Jenkins, E.

2017-04-01

With no future space ultraviolet instruments currently planned, the data from the UV spectrographs aboard the Hubble Space Telescope have a legacy value beyond their initial science goals. The goal of the Hubble Spectroscopic Legacy Archive(HSLA) is to provide to the community new science-grade combined spectra for all publicly available data obtained by the Cosmic Origins Spectrograph (COS)and the Space Telescope Imaging Spectrograph (STIS). These data are packaged into "smart archives" according to target type and scientific themes to facilitate the construction of archival samples for common science uses. A new "quick look" capability makes the data easy for users to quickly access, assess the quality of,and download for archival science. The first generation of these products for the far-ultraviolet (FUV) modes of COS was made available online via the Mikulski Archive for Space Telescopes (MAST) in early 2016 and updated in early 2017; future releases will include COS/NUV and STIS/UV data.

Identification of mycotoxins by UHPLC-QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá.

PubMed

Castillo, Nancy I; Ibáñez, María; Beltrán, Eduardo; Rivera-Monroy, Jhon; Ochoa, Juan Camilo; Páez-Castillo, Mónica; Posada-Buitrago, Martha L; Sulyok, Michael; Hernández, Félix

2016-01-01

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC-QTOF MS) under MS(E) mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC-QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC-MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. Copyright © 2015 Elsevier Inc. All rights reserved.

The Hubble Spectroscopic Legacy Archive

NASA Astrophysics Data System (ADS)

Peeples, Molly S.; Tumlinson, Jason; Fox, Andrew; Aloisi, Alessandra; Ayres, Thomas R.; Danforth, Charles; Fleming, Scott W.; Jenkins, Edward B.; Jedrzejewski, Robert I.; Keeney, Brian A.; Oliveira, Cristina M.

2016-01-01

With no future space ultraviolet instruments currently planned, the data from the UV spectrographs aboard the Hubble Space Telescope have a legacy value beyond their initial science goals. The Hubble Spectroscopic Legacy Archive will provide to the community new science-grade combined spectra for all publicly available data obtained by the Cosmic Origins Spectrograph (COS) and the Space Telescope Imaging Spectrograph (STIS). These data will be packaged into "smart archives" according to target type and scientific themes to facilitate the construction of archival samples for common science uses. A new "quick look" capability will make the data easy for users to quickly access, assess the quality of, and download for archival science starting in Cycle 24, with the first generation of these products for the FUV modes of COS available online via MAST in early 2016.

Archeological Echocardiography: Digitization and Speckle Tracking Analysis of Archival Echocardiograms in the HyperGEN Study.

PubMed

Aguilar, Frank G; Selvaraj, Senthil; Martinez, Eva E; Katz, Daniel H; Beussink, Lauren; Kim, Kwang-Youn A; Ping, Jie; Rasmussen-Torvik, Laura; Goyal, Amita; Sha, Jin; Irvin, Marguerite R; Arnett, Donna K; Shah, Sanjiv J

2016-03-01

Several large epidemiologic studies and clinical trials have included echocardiography, but images were stored in analog format and these studies predated tissue Doppler imaging (TDI) and speckle tracking echocardiography (STE). We hypothesized that digitization of analog echocardiograms, with subsequent quantification of cardiac mechanics using STE, is feasible, reproducible, accurate, and produces clinically valid results. In the NHLBI HyperGEN study (N = 2234), archived analog echocardiograms were digitized and subsequently analyzed using STE to obtain tissue velocities/strain. Echocardiograms were assigned quality scores and inter-/intra-observer agreement was calculated. Accuracy was evaluated in: (1) a separate second study (N = 50) comparing prospective digital strain versus post hoc analog-to-digital strain, and (2) in a third study (N = 95) comparing prospectively obtained TDI e' velocities with post hoc STE e' velocities. Finally, we replicated previously known associations between tissue velocities/strain, conventional echocardiographic measurements, and clinical data. Of the 2234 HyperGEN echocardiograms, 2150 (96.2%) underwent successful digitization and STE analysis. Inter/intra-observer agreement was high for all STE parameters, especially longitudinal strain (LS). In accuracy studies, LS performed best when comparing post hoc STE to prospective digital STE for strain analysis. STE-derived e' velocities correlated with, but systematically underestimated, TDI e' velocity. Several known associations between clinical variables and cardiac mechanics were replicated in HyperGEN. We also found a novel independent inverse association between fasting glucose and LS (adjusted β = -2.4 [95% CI -3.6, -1.2]% per 1-SD increase in fasting glucose; P < 0.001). Archeological echocardiography, the digitization and speckle tracking analysis of archival echocardiograms, is feasible and generates indices of cardiac mechanics similar to contemporary studies. © 2015, Wiley Periodicals, Inc.

Archeological Echocardiography: Digitization and Speckle-Tracking Analysis of Archival Echocardiograms in the HyperGEN Study

PubMed Central

Aguilar, Frank G.; Selvaraj, Senthil; Martinez, Eva E.; Katz, Daniel H.; Beussink, Lauren; Kim, Kwang-Youn A.; Ping, Jie; Rasmussen-Torvik, Laura; Goyal, Amita; Sha, Jin; Irvin, Marguerite R.; Arnett, Donna K.; Shah, Sanjiv J.

2015-01-01

Background Several large epidemiologic studies and clinical trials have included echocardiography, but images were stored in analog format and these studies predated tissue Doppler imaging (TDI) and speckle-tracking echocardiography (STE). We hypothesized that digitization of analog echocardiograms, with subsequent quantification of cardiac mechanics using STE, is feasible, reproducible, accurate, and produces clinically valid results. Methods In the NHLBI HyperGEN study (N=2234), archived analog echocardiograms were digitized and subsequently analyzed using STE to obtain tissue velocities/strain. Echocardiograms were assigned quality scores and inter/intraobserver agreement was calculated. Accuracy was evaluated in (1) a separate second study (N=50) comparing prospective digital strain vs. post-hoc analog-to-digital strain; and (2) in a third study (N=95) comparing prospectively-obtained TDI e′ velocities with post-hoc STE e′ velocities. Finally, we replicated previously known associations between tissue velocities/strain, conventional echocardiographic measurements, and clinical data. Results Of the 2234 HyperGEN echocardiograms, 2150 (96.2%) underwent successful digitization and STE analysis. Inter/intraobserver agreement was high for all STE parameters, especially longitudinal strain (LS). In accuracy studies, LS performed best when comparing post-hoc STE to prospective digital STE for strain analysis. STE-derived e′ velocities correlated with, but systematically underestimated, TDI e′ velocity. Several known associations between clinical variables and cardiac mechanics were replicated in HyperGEN. We also found a novel independent inverse association between fasting glucose and LS (adjusted β =−2.4 [95% CI −3.6,−1.2]% per 1-SD increase in fasting glucose; P<0.001). Conclusions Archeological echocardiography, the digitization and speckle-tracking analysis of archival echocardiograms, is feasible and generates parameters of cardiac mechanics similar to contemporary studies. PMID:26525308

Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.

PubMed

Janku, Filip; Zhang, Shile; Waters, Jill; Liu, Li; Huang, Helen J; Subbiah, Vivek; Hong, David S; Karp, Daniel D; Fu, Siqing; Cai, Xuyu; Ramzanali, Nishma M; Madwani, Kiran; Cabrilo, Goran; Andrews, Debra L; Zhao, Yue; Javle, Milind; Kopetz, E Scott; Luthra, Rajyalakshmi; Kim, Hyunsung J; Gnerre, Sante; Satya, Ravi Vijaya; Chuang, Han-Yu; Kruglyak, Kristina M; Toung, Jonathan; Zhao, Chen; Shen, Richard; Heymach, John V; Meric-Bernstam, Funda; Mills, Gordon B; Fan, Jian-Bing; Salathia, Neeraj S

2017-09-15

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy. Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care. Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did ( P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF ( P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03). Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR . ©2017 American Association for Cancer Research.

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

PubMed

Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

2011-04-01

Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

Immunohistochemical findings of the granulomatous reaction associated with tuberculosis.

PubMed

Karimi, Shirin; Shamaei, Masoud; Pourabdollah, Mihan; Sadr, Makan; Karbasi, Mehrdad; Kiani, Arda; Bahadori, Moslem

2016-12-01

The histological diagnosis of Mycobacterium tuberculosis (MTB) has long been a diagnostic challenge in the anatomical pathology field despite availability of different laboratory methods. Immunohistochemistry (IHC) could not only confirm granulomatous tissue involvement but also demonstrate MTB antigen immunolocalization. This study tries to clarify the details of IHC staining for MTB with pAbBCG. A total of 50 patients undergoing simultaneous biopsy and tissue culture with positive tissue culture for MTB during 2005-2009 were selected from the MRC Department at Masih Daneshvari Hospital, Tehran, Iran. Using the archives of the Pathology Department of this hospital, which is a referral center for pathological lung lesions, hematoxylin and eosin slides of the selected patients were evaluated. Twenty-three confirmed TB granulomatous tissue samples with adequate tissue and number of granulomas were chosen and studied by Ziehl-Neelsen and IHC staining with pAbBCG. A total of 23 cases were evaluated, of which 17 (73.9%) were males. The types of tissue obtained from study cases were as follows: pleura (9 cases, 39.1%), lymph node (cervical, axillary, and thoracic [9 cases, 39.1%]), and lung tissues (5 cases, 21.7%). IHC staining was positive in all samples, whereas Ziehl-Neelsen staining was positive in nine cases of 23 (39.1%). IHC showed positive coarse granular cytoplasmic and round, fragmented bacillary staining. In this study, epithelioid cells clearly showed more positive staining at the periphery rather than at the center of granuloma. There is also positive staining in endothelial cells, fibroblasts, plasma cells, macrophages, and lymphocytes outside the granuloma. Detection of TB in tissue slides is still based on the histological pattern of the granuloma, which has several differential diagnoses with different treatments. Presence of mycobacterial antigens and tissue morphology can be evaluated using the IHC technique. Considering the criteria of positive IHC staining of TB granulomatous reactions, this stain not only highlights the presence of mycobacterial antigens for tissue diagnosis, but also could morphologically localize their distribution in different cells. Pathologists must be familiar with adequate staining pattern, elimination of background staining, and type of selected antibody. This method is especially important for application in countries with high prevalence of TB as a technique with early diagnostic value in tissue specimens. Early diagnosis using this technique can reduce related morbidity and mortality and decrease the rate of complications due to misdiagnosis and mistreatment of TB. Copyright © 2016.

Multi-Center Evaluation of the Fully Automated PCR-Based Idylla™ KRAS Mutation Assay for Rapid KRAS Mutation Status Determination on Formalin-Fixed Paraffin-Embedded Tissue of Human Colorectal Cancer

PubMed Central

Solassol, Jérôme; Vendrell, Julie; Märkl, Bruno; Haas, Christian; Bellosillo, Beatriz; Montagut, Clara; Smith, Matthew; O’Sullivan, Brendan; D’Haene, Nicky; Le Mercier, Marie; Grauslund, Morten; Melchior, Linea Cecilie; Burt, Emma; Cotter, Finbarr; Stieber, Daniel; Schmitt, Fernando de Lander; Motta, Valentina; Lauricella, Calogero; Colling, Richard; Soilleux, Elizabeth; Fassan, Matteo; Mescoli, Claudia; Collin, Christine; Pagès, Jean-Christophe; Sillekens, Peter

2016-01-01

Since the advent of monoclonal antibodies against epidermal growth factor receptor (EGFR) in colorectal cancer therapy, the determination of RAS mutational status is needed for therapeutic decision-making. Most prevalent in colorectal cancer are KRAS exon 2 mutations (40% prevalence); lower prevalence is observed for KRAS exon 3 and 4 mutations (6%) and NRAS exon 2, 3, and 4 mutations (5%). The Idylla™ KRAS Mutation Test on the molecular diagnostics Idylla™ platform is a simple (<2 minutes hands-on time), highly reliable, and rapid (approximately 2 hours turnaround time) in vitro diagnostic sample-to-result solution. This test enables qualitative detection of 21 mutations in codons 12, 13, 59, 61, 117, and 146 of the KRAS oncogene being clinically relevant according to the latest clinical guidelines. Here, the performance of the Idylla™ KRAS Mutation Assay, for Research Use Only, was assessed on archived formalin-fixed paraffin-embedded (FFPE) tissue sections by comparing its results with the results previously obtained by routine reference approaches for KRAS genotyping. In case of discordance, samples were assessed further by additional methods. Among the 374 colorectal cancer FFPE samples tested, the overall concordance between the Idylla™ KRAS Mutation Assay and the confirmed reference routine test results was found to be 98.9%. The Idylla™ KRAS Mutation Assay enabled detection of 5 additional KRAS-mutated samples not detected previously with reference methods. As conclusion the Idylla™ KRAS Mutation Test can be applied as routine tool in any clinical setting, without needing molecular infrastructure or expertise, to guide the personalized treatment of colorectal cancer patients. PMID:27685259

Rapid spread and association of Schmallenberg virus with ruminant abortions and foetal death in Austria in 2012/2013.

PubMed

Steinrigl, Adolf; Schiefer, Peter; Schleicher, Corina; Peinhopf, Walter; Wodak, Eveline; Bagó, Zoltán; Schmoll, Friedrich

2014-10-15

Schmallenberg virus (SBV) has emerged in summer-autumn 2011 in north-western Europe. Since then, SBV has been continuously spreading over Europe, including Austria, where antibodies to SBV, as well as SBV genome, were first detected in autumn 2012. This study was performed to demonstrate the dynamics of SBV spread within Austria, after its probable first introduction in summer 2012. True seroprevalence estimates for cattle and small ruminates were calculated to demonstrate temporal and regional differences of infection. Furthermore, the probability of SBV genome detection in foetal tissues of aborted or stillborn cattle and small ruminants as well as in allantoic fluid samples from cows with early foetal losses was retrospectively assessed. SBV first reached Austria most likely in July-August 2012, as indicated by retrospective detection of SBV antibodies and SBV genome in archived samples. From August to October 2012, a rapid increase in seroprevalence to over 98% in cattle and a contemporaneous peak in the detection of SBV genome in foetal tissues and allantoic fluid samples was noted, indicating widespread acute infections. Notably, foetal malformations were absent in RT-qPCR positive foetuses at this time of the epidemic. SBV spread within Austrian cattle reached a plateau phase as early as October 2012, without significant regional differences in SBV seroprevalence (98.4-100%). Estimated true seroprevalences among small ruminates were comparatively lower than in cattle and regionally different (58.3-95.6% in October 2012), potentially indicating an eastward spread of the infection, as well as different infection dynamics between cattle and small ruminants. Additionally, the probability of SBV genome detection over time differed significantly between small ruminant and cattle samples subjected to RT-qPCR testing. Copyright © 2014 Elsevier B.V. All rights reserved.

Exploitation of FTA cartridges for the sampling, long-term storage, and DNA-based analyses of plant-parasitic nematodes.

PubMed

Marek, Martin; Zouhar, Miloslav; Douda, Ondřej; Maňasová, Marie; Ryšánek, Pavel

2014-03-01

The use of DNA-based analyses in molecular plant nematology research has dramatically increased over recent decades. Therefore, the development and adaptation of simple, robust, and cost-effective DNA purification procedures are required to address these contemporary challenges. The solid-phase-based approach developed by Flinders Technology Associates (FTA) has been shown to be a powerful technology for the preparation of DNA from different biological materials, including blood, saliva, plant tissues, and various human and plant microbial pathogens. In this work, we demonstrate, for the first time, that this FTA-based technology is a valuable, low-cost, and time-saving approach for the sampling, long-term archiving, and molecular analysis of plant-parasitic nematodes. Despite the complex structure and anatomical organization of the multicellular bodies of nematodes, we report the successful and reliable DNA-based analysis of nematode high-copy and low-copy genes using the FTA technology. This was achieved by applying nematodes to the FTA cards either in the form of a suspension of individuals, as intact or pestle-crushed nematodes, or by the direct mechanical printing of nematode-infested plant tissues. We further demonstrate that the FTA method is also suitable for the so-called "one-nematode-assay", in which the target DNA is typically analyzed from a single individual nematode. More surprisingly, a time-course experiment showed that nematode DNA can be detected specifically in the FTA-captured samples many years after initial sampling occurs. Collectively, our data clearly demonstrate the applicability and the robustness of this FTA-based approach for molecular research and diagnostics concerning phytonematodes; this research includes economically important species such as the stem nematode (Ditylenchus dipsaci), the sugar beet nematode (Heterodera schachtii), and the Northern root-knot nematode (Meloidogyne hapla).

Chemical Analysis Results for Potable Water from ISS Expeditions 21 Through 25

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Schultz, John R.; McCoy, J. Torin

2011-01-01

The Johnson Space Center Water and Food Analytical Laboratory (WAFAL) performed detailed ground-based analyses of archival water samples for verification of the chemical quality of the International Space Station (ISS) potable water supplies for Expeditions 21 through 25. Over a 14-month period the Space Shuttle visited the ISS on four occasions to complete construction and deliver supplies. The onboard supplies of potable water available for consumption by the Expeditions 21 to 25 crews consisted of Russian ground-supplied potable water, Russian potable water regenerated from humidity condensate, and US potable water recovered from urine distillate and condensate. Chemical archival water samples that were collected with U.S. hardware during Expeditions 21 to 25 were returned on Shuttle flights STS-129 (ULF3), STS-130 (20A), STS-131 (19A), and STS-132 (ULF4), as well as on Soyuz flights 19-23. This paper reports the analytical results for these returned potable water archival samples and their compliance with ISS water quality standards.

Evaluation of sampling and storage procedures on preserving the community structure of stool microbiota: A simple at-home toilet-paper collection method.

PubMed

Al, Kait F; Bisanz, Jordan E; Gloor, Gregory B; Reid, Gregor; Burton, Jeremy P

2018-01-01

The increasing interest on the impact of the gut microbiota on health and disease has resulted in multiple human microbiome-related studies emerging. However, multiple sampling methods are being used, making cross-comparison of results difficult. To avoid additional clinic visits and increase patient recruitment to these studies, there is the potential to utilize at-home stool sampling. The aim of this pilot study was to compare simple self-sampling collection and storage methods. To simulate storage conditions, stool samples from three volunteers were freshly collected, placed on toilet tissue, and stored at four temperatures (-80, 7, 22 and 37°C), either dry or in the presence of a stabilization agent (RNAlater®) for 3 or 7days. Using 16S rRNA gene sequencing by Illumina, the effect of storage variations for each sample was compared to a reference community from fresh, unstored counterparts. Fastq files may be accessed in the NCBI Sequence Read Archive: Bioproject ID PRJNA418287. Microbial diversity and composition were not significantly altered by any storage method. Samples were always separable based on participant, regardless of storage method suggesting there was no need for sample preservation by a stabilization agent. In summary, if immediate sample processing is not feasible, short term storage of unpreserved stool samples on toilet paper offers a reliable way to assess the microbiota composition by 16S rRNA gene sequencing. Copyright © 2017 Elsevier B.V. All rights reserved.

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

PubMed Central

Carrick, Danielle Mercatante; Mehaffey, Michele G.; Sachs, Michael C.; Altekruse, Sean; Camalier, Corinne; Chuaqui, Rodrigo; Cozen, Wendy; Das, Biswajit; Hernandez, Brenda Y.; Lih, Chih-Jian; Lynch, Charles F.; Makhlouf, Hala; McGregor, Paul; McShane, Lisa M.; Phillips Rohan, JoyAnn; Walsh, William D.; Williams, Paul M.; Gillanders, Elizabeth M.; Mechanic, Leah E.; Schully, Sheri D.

2015-01-01

Next Generation Sequencing (NGS) technologies are used to detect somatic mutations in tumors and study germ line variation. Most NGS studies use DNA isolated from whole blood or fresh frozen tissue. However, formalin-fixed paraffin-embedded (FFPE) tissues are one of the most widely available clinical specimens. Their potential utility as a source of DNA for NGS would greatly enhance population-based cancer studies. While preliminary studies suggest FFPE tissue may be used for NGS, the feasibility of using archived FFPE specimens in population based studies and the effect of storage time on these specimens needs to be determined. We conducted a study to determine whether DNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries Residual Tissue Repositories (RTR) was present in sufficient quantity and quality for NGS assays. Fifty-nine FFPE tissues, stored from 3 to 32 years, were obtained from three SEER RTR sites. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing (WES). Following DNA extraction, 58 of 59 specimens (98%) yielded DNA and moved on to the library generation step followed by WES. Specimens stored for longer periods of time had significantly lower coverage of the target region (6% lower per 10 years, 95% CI: 3-10%) and lower average read depth (40x lower per 10 years, 95% CI: 18-60), although sufficient quality and quantity of WES data was obtained for data mining. Overall, 90% (53/59) of specimens provided usable NGS data regardless of storage time. This feasibility study demonstrates FFPE specimens acquired from SEER registries after varying lengths of storage time and under varying storage conditions are a promising source of DNA for NGS. PMID:26222067

The GIK-Archive of sediment core radiographs with documentation

NASA Astrophysics Data System (ADS)

Grobe, Hannes; Winn, Kyaw; Werner, Friedrich; Driemel, Amelie; Schumacher, Stefanie; Sieger, Rainer

2017-12-01

The GIK-Archive of radiographs is a collection of X-ray negative and photographic images of sediment cores based on exposures taken since the early 1960s. During four decades of marine geological work at the University of Kiel, Germany, several thousand hours of sampling, careful preparation and X-raying were spent on producing a unique archive of sediment radiographs from several parts of the World Ocean. The archive consists of more than 18 500 exposures on chemical film that were digitized, geo-referenced, supplemented with metadata and archived in the data library PANGAEA®. With this publication, the images have become available open-access for use by the scientific community at https://doi.org/10.1594/PANGAEA.854841.

A Novel Porcine Circovirus Distantly Related to Known Circoviruses Is Associated with Porcine Dermatitis and Nephropathy Syndrome and Reproductive Failure.

PubMed

Palinski, Rachel; Piñeyro, Pablo; Shang, Pengcheng; Yuan, Fangfeng; Guo, Rui; Fang, Ying; Byers, Emily; Hause, Ben M

2017-01-01

Porcine circovirus-associated disease (PCVAD) is clinically manifested by postweaning multisystemic wasting syndrome (PMWS), respiratory and enteric disease, reproductive failure, and porcine dermatitis and nephropathy syndrome (PDNS). Porcine circovirus 2 (PCV2) is an essential component of PCVAD, although an etiologic role in PDNS is not well established. Here, a novel circovirus, designated porcine circovirus 3 (PCV3), was identified in sows that died acutely with PDNS-like clinical signs. The capsid and replicase proteins of PCV3 are only 37% and 55% identical to PCV2 and bat circoviruses, respectively. Aborted fetuses from sows with PDNS contained high levels of PCV3 (7.57 × 10 7 genome copies/ml), and no other viruses were detected by PCR and metagenomic sequencing. Immunohistochemistry (IHC) analysis of sow tissue samples identified PCV3 antigen in skin, kidney, lung, and lymph node samples localized in typical PDNS lesions, including necrotizing vasculitis, glomerulonephritis, granulomatous lymphadenitis, and bronchointerstitial pneumonia. Further study of archived PDNS tissue samples that were negative for PCV2 by IHC analysis identified 45 of 48 that were PCV3 positive by quantitative PCR (qPCR), with 60% of a subset also testing positive for PCV3 by IHC analysis. Analysis by qPCR of 271 porcine respiratory disease diagnostic submission samples identified 34 PCV3-positive cases (12.5%), and enzyme-linked immunosorbent assay detection of anti-PCV3 capsid antibodies in serum samples found that 46 (55%) of 83 samples tested were positive. These results suggest that PCV3 commonly circulates within U.S. swine and may play an etiologic role in reproductive failure and PDNS. Because of the high economic impact of PCV2, this novel circovirus warrants further studies to elucidate its significance and role in PCVAD. While porcine circovirus 2 (PCV2) was first identified in sporadic cases of postweaning multisystemic wasting syndrome in Canada in the early 1990s, an epidemic of severe systemic disease due to PCV2 spread worldwide in the ensuing decade. Despite being effectively controlled by commercial vaccines, PCV2 remains one of the most economically significant viruses of swine. Here, a novel porcine circovirus (PCV3) that is distantly related to known circoviruses was identified in sows with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCV2, which has previously been associated with these clinical presentations, was not identified. High levels of PCV3 nucleic acid were observed in aborted fetuses by quantitative PCR, and PCV3 antigen was localized in histologic lesions typical of PDNS in sows by immunohistochemistry (IHC) analysis. PCV3 was also identified in archival PDNS diagnostic samples that previously tested negative for PCV2 by IHC analysis. The emergence of PCV3 warrants further investigation. Copyright © 2016 American Society for Microbiology.

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Radiation Fibrosis of the Vocal Fold: From Man to Mouse

PubMed Central

Johns, Michael M.; Kolachala, Vasantha; Berg, Eric; Muller, Susan; Creighton, Frances X.; Branski, Ryan C.

2013-01-01

Objectives To characterize fundamental late tissue effects in the human vocal fold following radiation therapy. To develop a murine model of radiation fibrosis to ultimately develop both treatment and prevention paradigms. Design Translational study using archived human and fresh murine irradiated vocal fold tissue. Methods 1) Irradiated vocal fold tissue from patients undergoing laryngectomy for loss of function from radiation fibrosis were identified from pathology archives. Histomorphometry, immunohistochemistry, and whole-genome microarray as well as real-time transcriptional analyses was performed. 2) Focused radiation to the head and neck was delivered to mice in a survival fashion. One month following radiation, vocal fold tissue was analyzed with histomorphometry, immunohistochemistry, and real-time PCR transcriptional analysis for selected markers of fibrosis. Results Human irradiated vocal folds demonstrated increased collagen transcription with increased deposition and disorganization of collagen in both the thyroarytenoid muscle and the superficial lamina propria. Fibronectin were increased in the superficial lamina propria. Laminin decreased in the thyroarytenoid muscle. Whole genome microarray analysis demonstrated increased transcription of markers for fibrosis, oxidative stress, inflammation, glycosaminoglycan production and apoptosis. Irradiated murine vocal folds demonstrated increases in collagen and fibronectin transcription and deposition in the lamina propria. Transforming growth factor (TGF)-β increased in the lamina propria. Conclusion Human irradiated vocal folds demonstrate molecular changes leading to fibrosis that underlie loss of vocal fold pliability that occurs in patients following laryngeal irradiation. Irradiated murine tissue demonstrates similar findings, and this mouse model may have utility in creating prevention and treatment strategies for vocal fold radiation fibrosis. PMID:23242839

A single digital droplet PCR assay to detect multiple KIT exon 11 mutations in tumor and plasma from patients with gastrointestinal stromal tumors.

PubMed

Boonstra, Pieter A; Ter Elst, Arja; Tibbesma, Marco; Bosman, Lisette J; Mathijssen, Ron; Atrafi, Florence; van Coevorden, Frits; Steeghs, Neeltje; Farag, Sheima; Gelderblom, Hans; van der Graaf, Winette T A; Desar, Ingrid M E; Maier, Jacqueline; Overbosch, Jelle; Suurmeijer, Albert J H; Gietema, Jourik; Schuuring, Ed; Reyners, Anna K L

2018-03-02

Gastrointestinal stromal tumors (GISTs) are characterized by oncogenic KIT mutations that cluster in two exon 11 hotspots. The aim of this study was to develop a single, sensitive, quantitative digital droplet PCR (ddPCR) assay for the detection of common exon 11 mutations in both GIST tumor tissue and in circulating tumor DNA (ctDNA) isolated from GIST patients' plasma. A ddPCR assay was designed using two probes that cover both hotspots. Available archival FFPE tumor tissue from 27 consecutive patients with known KIT exon 11 mutations and 9 randomly selected patients without exon 11 mutations were tested. Plasma samples were prospectively collected in a multicenter bio-databank from December 2014. ctDNA was analyzed of 22 patients with an exon 11 mutation and a baseline plasma sample. The ddPCR assay detected the exon 11 mutation in 21 of 22 tumors with exon 11 mutations covered by the assay. Mutations in ctDNA were detected at baseline in 13 of 14 metastasized patients, but in only 1 of 8 patients with localized disease. In serial plasma samples from 11 patients with metastasized GIST, a decrease in mutant droplets was detected during treatment. According to RECIST 1.1, 10 patients had radiological treatment response and one patient stable disease. A single ddPCR assay for the detection of multiple exon 11 mutations in ctDNA is a feasible, promising tool for monitoring treatment response in patients with metastasized GIST and should be further evaluated in a larger cohort.

An Optimized Set of Fluorescence In Situ Hybridization Probes for Detection of Pancreatobiliary Tract Cancer in Cytology Brush Samples.

PubMed

Barr Fritcher, Emily G; Voss, Jesse S; Brankley, Shannon M; Campion, Michael B; Jenkins, Sarah M; Keeney, Matthew E; Henry, Michael R; Kerr, Sarah M; Chaiteerakij, Roongruedee; Pestova, Ekaterina V; Clayton, Amy C; Zhang, Jun; Roberts, Lewis R; Gores, Gregory J; Halling, Kevin C; Kipp, Benjamin R

2015-12-01

Pancreatobiliary cancer is detected by fluorescence in situ hybridization (FISH) of pancreatobiliary brush samples with UroVysion probes, originally designed to detect bladder cancer. We designed a set of new probes to detect pancreatobiliary cancer and compared its performance with that of UroVysion and routine cytology analysis. We tested a set of FISH probes on tumor tissues (cholangiocarcinoma or pancreatic carcinoma) and non-tumor tissues from 29 patients. We identified 4 probes that had high specificity for tumor vs non-tumor tissues; we called this set of probes pancreatobiliary FISH. We performed a retrospective analysis of brush samples from 272 patients who underwent endoscopic retrograde cholangiopancreatography for evaluation of malignancy at the Mayo Clinic; results were available from routine cytology and FISH with UroVysion probes. Archived residual specimens were retrieved and used to evaluate the pancreatobiliary FISH probes. Cutoff values for FISH with the pancreatobiliary probes were determined using 89 samples and validated in the remaining 183 samples. Clinical and pathologic evidence of malignancy in the pancreatobiliary tract within 2 years of brush sample collection was used as the standard; samples from patients without malignancies were used as negative controls. The validation cohort included 85 patients with malignancies (46.4%) and 114 patients with primary sclerosing cholangitis (62.3%). Samples containing cells above the cutoff for polysomy (copy number gain of ≥2 probes) were classified as positive in FISH with the UroVysion and pancreatobiliary probes. Multivariable logistic regression was used to estimate associations between clinical and pathology findings and results from FISH. The combination of FISH probes 1q21, 7p12, 8q24, and 9p21 identified cancer cells with 93% sensitivity and 100% specificity in pancreatobiliary tissue samples and were therefore included in the pancreatobiliary probe set. In the validation cohort of brush samples, pancreatobiliary FISH identified samples from patients with malignancy with a significantly higher level of sensitivity (64.7%) than the UroVysion probes (45.9%) (P < .001) or routine cytology analysis (18.8%) (P < .001), but similar specificity (92.9%, 90.8%, and 100.0% respectively). Factors significantly associated with detection of carcinoma, in adjusted analyses, included detection of polysomy by pancreatobiliary FISH (P < .001), a mass by cross-sectional imaging (P < .001), cancer cells by routine cytology (overall P = .003), as well as absence of primary sclerosing cholangitis (P = .011). We identified a set of FISH probes that detects cancer cells in pancreatobiliary brush samples from patients with and without primary sclerosing cholangitis with higher levels of sensitivity than UroVysion probes. Cytologic brushing test results and clinical features were independently associated with detection of cancer and might be used to identify patients with pancreatobiliary cancers. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.

PubMed

Auerbach, Scott S; Phadke, Dhiral P; Mav, Deepak; Holmgren, Stephanie; Gao, Yuan; Xie, Bin; Shin, Joo Heon; Shah, Ruchir R; Merrick, B Alex; Tice, Raymond R

2015-07-01

Formalin-fixed, paraffin-embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic-based biomarker discovery. We present here a comparison of results from a whole transcriptome RNA-Seq analysis of RNA extracted from fresh frozen and FFPE livers. The samples were derived from rats exposed to aflatoxin B1 (AFB1 ) and a corresponding set of control animals. Principal components analysis indicated that samples were separated in the two groups representing presence or absence of chemical exposure, both in fresh frozen and FFPE sample types. Sixty-five percent of the differentially expressed transcripts (AFB1 vs. controls) in fresh frozen samples were also differentially expressed in FFPE samples (overlap significance: P < 0.0001). Genomic signature and gene set analysis of AFB1 differentially expressed transcript lists indicated highly similar results between fresh frozen and FFPE at the level of chemogenomic signatures (i.e., single chemical/dose/duration elicited transcriptomic signatures), mechanistic and pathology signatures, biological processes, canonical pathways and transcription factor networks. Overall, our results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples. These results indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature-based biomarker discovery and mechanistic characterization of toxicity. Copyright © 2014 John Wiley & Sons, Ltd.

BCOR-CCNB3 Fusions Are Frequent in Undifferentiated Sarcomas of Male Children

PubMed Central

Peters, Tricia L.; Kumar, Vijetha; Polikepahad, Sumanth; Lin, Frank Y.; Sarabia, Stephen F.; Liang, Yu; Wang, Wei-Lien; Lazar, Alexander J.; Doddapaneni, Harsha Vardhan; Chao, Hsu; Muzny, Donna M.; Wheeler, David A.; Okcu, M. Fatih; Plon, Sharon E.; Hicks, M. John; López-Terrada, Dolores; Parsons, D. Williams; Roy, Angshumoy

2014-01-01

The BCOR-CCNB3 fusion gene, resulting from a chromosome X paracentric inversion, was recently described in translocation-negative ‘Ewing-like’ sarcomas arising in bone and soft tissue. Genetic subclassification of undifferentiated unclassified sarcomas may potentially offer markers for reproducible diagnosis and substrates for therapy. Using whole transcriptome paired end RNA sequencing (RNA-seq) we unexpectedly identified BCOR-CCNB3 fusion transcripts in an undifferentiated spindle cell sarcoma. RNA-seq results were confirmed through direct RT-PCR of tumor RNA and cloning of the genomic breakpoints from tumor DNA. Five additional undifferentiated sarcomas with BCOR-CCNB3 fusions were identified in a series of 42 pediatric and adult unclassified sarcomas. Genomic breakpoint analysis demonstrated unique breakpoint locations in each case at the DNA level even though the resulting fusion mRNA was identical in all cases. All patients with BCOR-CCNB3 sarcoma were males diagnosed in mid-childhood (7-13 years of age). Tumors were equally distributed between axial and extra-axial locations. Five of the six tumors were soft tissue lesions with either predominant spindle cell morphology or spindle cell areas interspersed with ovoid to round cells. CCNB3 immunohistochemistry showed strong nuclear positivity in 5 tumors prior to oncologic therapy, but was patchy to negative in post-treatment tumor samples. An RT-PCR assay developed to detect the fusion transcript in archival formalin-fixed tissue was positive in all 6 cases, with high sensitivity and specificity in both pre- and post-treated samples. This study adds to recent reports on the clinicopathologic spectrum of BCOR-CCNB3 fusion-positive sarcomas, a newly-emerging entity within the undifferentiated unclassified sarcoma category, and describes a simple RT-PCR assay that in conjunction with CCNB3 immunohistochemistry can be useful in diagnosing these tumors. PMID:25360585

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

PubMed Central

Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

2010-01-01

Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues.

PubMed

Chen, Jing; Guo, Liping; Peiffer, Daniel A; Zhou, Lixin; Chan, Owen Tsan Mo; Bibikova, Marina; Wickham-Garcia, Eliza; Lu, Shih-Hsin; Zhan, Qimin; Wang-Rodriguez, Jessica; Jiang, Wei; Fan, Jian-Bing

2008-05-15

We employed the BeadArraytrade mark technology to perform a genetic analysis in 33 formalin-fixed, paraffin-embedded (FFPE) human esophageal carcinomas, mostly squamous-cell-carcinoma (ESCC), and their adjacent normal tissues. A total of 1,432 single nucleotide polymorphisms (SNPs) derived from 766 cancer-related genes were genotyped with partially degraded genomic DNAs isolated from these samples. This directly targeted genomic profiling identified not only previously reported somatic gene amplifications (e.g., CCND1) and deletions (e.g., CDKN2A and CDKN2B) but also novel genomic aberrations. Among these novel targets, the most frequently deleted genomic regions were chromosome 3p (including tumor suppressor genes FANCD2 and CTNNB1) and chromosome 5 (including tumor suppressor gene APC). The most frequently amplified genomic region was chromosome 3q (containing DVL3, MLF1, ABCC5, BCL6, AGTR1 and known oncogenes TNK2, TNFSF10, FGF12). The chromosome 3p deletion and 3q amplification occurred coincidently in nearly all of the affected cases, suggesting a molecular mechanism for the generation of somatic chromosomal aberrations. We also detected significant differences in germline allele frequency between the esophageal cohort of our study and normal control samples from the International HapMap Project for 10 genes (CSF1, KIAA1804, IL2, PMS2, IRF7, FLT3, NTRK2, MAP3K9, ERBB2 and PRKAR1A), suggesting that they might play roles in esophageal cancer susceptibility and/or development. Taken together, our results demonstrated the utility of the BeadArray technology for high-throughput genetic analysis in FFPE tumor tissues and provided a detailed genetic profiling of cancer-related genes in human esophageal cancer. (c) 2008 Wiley-Liss, Inc.

VizieR Online Data Catalog: Galaxies and QSOs FIR size and surface brightness (Lutz+, 2016)

NASA Astrophysics Data System (ADS)

Lutz, D.; Berta, S.; Contursi, A.; Forster Schreiber, N. M.; Genzel, R.; Gracia-Carpio, J.; Herrera-Camus, R.; Netzer, H.; Sturm, E.; Tacconi, L. J.; Tadaki, K.; Veilleux, S.

2016-08-01

We use 70, 100, and 160um images from scan maps obtained with PACS on board Herschel, collecting archival data from various projects. In order to cover a wide range of galaxy properties, we first obtain an IR-selected local sample ranging from normal galaxies up to (ultra)luminous infrared galaxies. For that purpose, we searched the Herschel archive for all cz>=2000km/s objects from the IRAS Revised Bright Galaxy Sample (RBGS, Sanders et al., 2003, Cat. J/AJ/126/1607). (1 data file).

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

PubMed

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.

Not the time or the place: the missing spatio-temporal link in publicly available genetic data.

PubMed

Pope, Lisa C; Liggins, Libby; Keyse, Jude; Carvalho, Silvia B; Riginos, Cynthia

2015-08-01

Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be 'repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data. © 2015 John Wiley & Sons Ltd.

High-resolution elemental mapping of human placental chorionic villi using synchrotron X-ray fluorescence spectroscopy

DOE PAGES

Punshon, Tracy; Chen, Si; Finney, Lydia; ...

2015-07-03

The placenta is the organ that mediates transport of nutrients and waste materials between mother and fetus. Synchrotron X-ray fluorescence (SXRF) microanalysis is a tool for imaging the distribution and quantity of elements in biological tissue, which can be used to study metal transport across biological membranes. Our aims were to pilot placental biopsy specimen preparation techniques that could be integrated into an ongoing epidemiology birth cohort study without harming rates of sample acquisition. We studied the effects of fixative (formalin or glutaraldehyde) and storage duration (30 days or immediate processing) on metal distribution and abundance and investigated a thaw-fixationmore » protocol for archived specimens stored at -80° C. We measured fixative elemental composition with and without a placental biopsy via inductively coupled plasma mass spectrometry (ICP-MS) to quantify fixative-induced elemental changes. Formalin-fixed specimens showed hemolysis of erythrocytes. The glutaraldehyde-paraformaldehyde solution in HEPES buffer (GTA-HEPES) had superior anatomical preservation, avoided hemolysis, and minimized elemental loss, although some cross-linking of exogenous Zn was evident. Elemental loss from tissue stored in fixative for 1 month showed variable losses (≈ 40 % with GTA-HEPES), suggesting storage duration be controlled for. Lastly, thawing of tissue held at -80 °C in a GTA-HEPES solution provided high-quality visual images and elemental images« less

Diet induced differences in carbon isotope fractionation between sirenians and terrestrial ungulates

USGS Publications Warehouse

Clementz, M.T.; Koch, P.L.; Beck, C.A.

2007-01-01

Carbon isotope differences (??13C) between bioapatite and diet, collagen and diet, and bioapatite and collagen were calculated for four species of sirenians, Dugong dugon (Mu??ller), Trichechus manatus (Linnaeus), Trichechus inunguis (Natterer), and the extinct Hydrodamalis gigas (Zimmerman). Bone and tooth samples were taken from archived materials collected from populations during the mid eighteenth century (H. gigas), between 1978 and 1984 (T. manatus, T. inunguis), and between 1997 and 1999 (D. dugon). Mean ??13C values were compared with those for terrestrial ungulates, carnivores, and six species of carnivorous marine mammals (cetaceans = 1; pinnipeds = 4; mustelids = 1). Significant differences in mean ??13C values among species for all tissue types were detected that separated species or populations foraging on freshwater plants or attached marine macroalgae (??13C values -4???; ??13Cbioapatite-diet ???11???). Likewise, ??13Cbioapatite-collagen values for freshwater and algal-foraging species (???7???) were greater than those for seagrass-foraging species (???5???). Variation in ??13C values calculated between tissues and between tissues and diet among species may relate to the nutritional composition of a species' diet and the extent and type of microbial fermentation that occurs during digestion of different types of plants. These results highlight the complications that can arise when making dietary interpretations without having first determined species-specific ??13Ctissue-diet values. ?? 2007 Springer-Verlag.

Applications and challenges of digital pathology and whole slide imaging.

PubMed

Higgins, C

2015-07-01

Virtual microscopy is a method for digitizing images of tissue on glass slides and using a computer to view, navigate, change magnification, focus and mark areas of interest. Virtual microscope systems (also called digital pathology or whole slide imaging systems) offer several advantages for biological scientists who use slides as part of their general, pharmaceutical, biotechnology or clinical research. The systems usually are based on one of two methodologies: area scanning or line scanning. Virtual microscope systems enable automatic sample detection, virtual-Z acquisition and creation of focal maps. Virtual slides are layered with multiple resolutions at each location, including the highest resolution needed to allow more detailed review of specific regions of interest. Scans may be acquired at 2, 10, 20, 40, 60 and 100 × or a combination of magnifications to highlight important detail. Digital microscopy starts when a slide collection is put into an automated or manual scanning system. The original slides are archived, then a server allows users to review multilayer digital images of the captured slides either by a closed network or by the internet. One challenge for adopting the technology is the lack of a universally accepted file format for virtual slides. Additional challenges include maintaining focus in an uneven sample, detecting specimens accurately, maximizing color fidelity with optimal brightness and contrast, optimizing resolution and keeping the images artifact-free. There are several manufacturers in the field and each has not only its own approach to these issues, but also its own image analysis software, which provides many options for users to enhance the speed, quality and accuracy of their process through virtual microscopy. Virtual microscope systems are widely used and are trusted to provide high quality solutions for teleconsultation, education, quality control, archiving, veterinary medicine, research and other fields.

Occurrence and genotypic analysis of Trichinella species in Alaska marine-associated mammals of the Bering and Chukchi seas.

PubMed

Seymour, J; Horstmann-Dehn, L; Rosa, C; Lopez, J A

2014-02-24

The zoonotic parasite Trichinella is the causative agent of trichinellosis outbreaks in the circumpolar Arctic. Subsistence communities are particularly prone to trichinellosis due to traditional meat preparation methods and regional presence of a freeze-tolerant Trichinella species (Trichinella nativa). This study is the first application of a validated artificial digestion method in determining incidence of Trichinella sp. in Alaskan mammals. Infection incidence in pinniped species (Erignathus barbatus, Eumetopias jubatus, Odobenus rosmarus divergens, and Pusa hispida) was low, with only 1/57 ringed seals infected. Polymerase Chain Reaction assays indicate T. nativa as the only species present in northern Alaska. Analysis of an archived polar bear (Ursus maritimus) muscle sample shows freeze-tolerance and longevity for T. nativa to -20°C for 10 years and short-term freeze resistance to -80°C when morphology was used to determine presence of live larvae. However, larval motility suggests 0% survival. An approach that combines artificial digestion with PCR based species identification has excellent potential for Trichinella sp. detection and identification of archived tissues. Overall, Trichinella in Alaskan mammals, particularly marine mammals of subsistence importance, appears to be a minor problem. These modern diagnostic techniques provide accurate insight into the presence of Trichinella in the Alaskan marine environment. Copyright © 2013 Elsevier B.V. All rights reserved.

University Counseling Center Clients' Expressed Preferences for Counselors: A Four Year Archival Exploration

ERIC Educational Resources Information Center

Speight, Suzette L.; Vera, Elizabeth M.

2005-01-01

This archival study explored patterns of client preferences from a randomized sample of 881 clients at a Midwestern university counseling center. Information from client intake forms was collected for a four year time frame. Results showed that 61% of the clients did not express preferences for particular types of counselors when asked on intake…

Selected Guidelines for the Management of Records and Archives: A RAMP Reader.

ERIC Educational Resources Information Center

Walne, Peter, Comp.

The guidelines contained in this book are taken from studies published by UNESCO's Records and Archives Management Program (RAMP) between 1981 and 1987. Each set of guidelines is accompanied by an introduction to provide chronological or methodological context. The guidelines are titled as follows: (1) "The Use of Sampling Techniques in the…

DATA QUALITY OBJECTIVES FOR SELECTING WASTE SAMPLES FOR THE BENCH STEAM REFORMER TEST

DOE Office of Scientific and Technical Information (OSTI.GOV)

BANNING DL

2010-08-03

This document describes the data quality objectives to select archived samples located at the 222-S Laboratory for Fluid Bed Steam Reformer testing. The type, quantity and quality of the data required to select the samples for Fluid Bed Steam Reformer testing are discussed. In order to maximize the efficiency and minimize the time to treat Hanford tank waste in the Waste Treatment and Immobilization Plant, additional treatment processes may be required. One of the potential treatment processes is the fluid bed steam reformer (FBSR). A determination of the adequacy of the FBSR process to treat Hanford tank waste is required.more » The initial step in determining the adequacy of the FBSR process is to select archived waste samples from the 222-S Laboratory that will be used to test the FBSR process. Analyses of the selected samples will be required to confirm the samples meet the testing criteria.« less

[A study on feeding ecology and migration patterns of Dosidicus gigas off Peru using stable isotope analysis].

PubMed

Gong, Yi; Chen, Xin-jun; Li, Yun-kai; Han, Meng-jie

2015-09-01

As a pelagic cephalopod and one of the main target species of Chinese distant water fishery, jumbo squids (Dosidicus gigas) play a major role in the marine ecosystems of the eastern Pacific. Understanding the feeding ecology and migration patterns of jumbo squids is of importance for better utilizing the resources. The isotopic signatures of gladius, have been proved to be a powerful tool to reveal high resolution and ontogenic variations in individual foraging strategies of squids; which is an archival tissue with no elemental turnover after formation. In this study, the growth equation of gladius proostracum was established based on the age information determined by statolith. Gladius was cut successionally by the growth curve of gladius proostracum, the stable isotopic values of the gladius profiles were determined, and the feeding ecology and migration patterns of jumbo squids during its growth process were investigated. Results showed that the jumbo squids began to migrate after 180 days of postnatal, and their trophic levels tended to decrease throughout the life span. These results demonstrated the feasibility of using continuous sampling hard tissue to study the feeding ecology and habitat transfer of jumbo squids.

The AMBRE project: Parameterisation of FGK-type stars from the ESO:HARPS archived spectra

NASA Astrophysics Data System (ADS)

De Pascale, M.; Worley, C. C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Bijaoui, A.

2014-10-01

Context. The AMBRE project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Côte d'Azur (OCA). It has been established to determine the stellar atmospheric parameters of the archived spectra of four ESO spectrographs. Aims: The analysis of the ESO:HARPS archived spectra for the determination of their atmospheric parameters (effective temperature, surface gravity, global metallicities, and abundance of α-elements over iron) is presented. The sample being analysed (AMBRE:HARPS) covers the period from 2003 to 2010 and is comprised of 126 688 scientific spectra corresponding to ~17 218 different stars. Methods: For the analysis of the AMBRE:HARPS spectral sample, the automated pipeline developed for the analysis of the AMBRE:FEROS archived spectra has been adapted to the characteristics of the HARPS spectra. Within the pipeline, the stellar parameters are determined by the MATISSE algorithm, which has been developed at OCA for the analysis of large samples of stellar spectra in the framework of galactic archaeology. In the present application, MATISSE uses the AMBRE grid of synthetic spectra, which covers FGKM-type stars for a range of gravities and metallicities. Results: We first determined the radial velocity and its associated error for the ~15% of the AMBRE:HARPS spectra, for which this velocity had not been derived by the ESO:HARPS reduction pipeline. The stellar atmospheric parameters and the associated chemical index [α/Fe] with their associated errors have then been estimated for all the spectra of the AMBRE:HARPS archived sample. Based on key quality criteria, we accepted and delivered the parameterisation of 93 116 (74% of the total sample) spectra to ESO. These spectra correspond to ~10 706 stars; each are observed between one and several hundred times. This automatic parameterisation of the AMBRE:HARPS spectra shows that the large majority of these stars are cool main-sequence dwarfs with metallicities greater than -0.5 dex (as expected, given that HARPS has been extensively used for planet searches around GK-stars).

Whole genome amplification of DNA extracted from FFPE tissues.

PubMed

Bosso, Mira; Al-Mulla, Fahd

2011-01-01

Whole genome amplification systems were developed to meet the increasing research demands on DNA resources and to avoid DNA shortage. The technology enables amplification of nanogram amounts of DNA into microgram quantities and is increasingly used in the amplification of DNA from multiple origins such as blood, fresh frozen tissue, formalin-fixed paraffin-embedded tissues, saliva, buccal swabs, bacteria, and plant and animal sources. This chapter focuses on the use of GenomePlex(®) tissue Whole Genome Amplification Kit, to amplify DNA directly from archived tissue. In addition, this chapter documents our unique experience with the utilization of GenomePlex(®) amplified DNA using several molecular techniques including metaphase Comparative Genomic Hybridization, array Comparative Genomic Hybridization, and real-time quantitative polymerase chain reaction assays. GenomePlex(®) is a registered trademark of Rubicon Genomics Incorporation.

The importance of long‐term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience

PubMed Central

Johnston, A. E.

2018-01-01

Summary Long‐term field experiments that test a range of treatments and are intended to assess the sustainability of crop production, and thus food security, must be managed actively to identify any treatment that is failing to maintain or increase yields. Once identified, carefully considered changes can be made to the treatment or management, and if they are successful yields will change. If suitable changes cannot be made to an experiment to ensure its continued relevance to sustainable crop production, then it should be stopped. Long‐term experiments have many other uses. They provide a field resource and samples for research on plant and soil processes and properties, especially those properties where change occurs slowly and affects soil fertility. Archived samples of all inputs and outputs are an invaluable source of material for future research, and data from current and archived samples can be used to develop models to describe soil and plant processes. Such changes and uses in the Rothamsted experiments are described, and demonstrate that with the appropriate crop, soil and management, acceptable yields can be maintained for many years, with either organic manure or inorganic fertilizers. Highlights Long‐term experiments demonstrate sustainability and increases in crop yield when managed to optimize soil fertility.Shifting individual response curves into coincidence increases understanding of the factors involved.Changes in inorganic and organic pollutants in archived crop and soil samples are related to inputs over time.Models describing soil processes are developed from current and archived soil data. PMID:29527119

Impact of a western diet on the ovarian and serum metabolome.

PubMed

Dhungana, Suraj; Carlson, James E; Pathmasiri, Wimal; McRitchie, Susan; Davis, Matt; Sumner, Susan; Appt, Susan E

2016-10-01

The objective of this investigation was to determine differences in the profiles of endogenous metabolites (metabolomics) among ovaries and serum derived from Old World nonhuman primates fed prudent or Western diets. A retrospective, observational study was done using archived ovarian tissue and serum from midlife cynomolgus monkeys (Macaca fasicularis). Targeted and broad spectrum metabolomics analysis was used to compare ovarian tissue and serum from monkeys that had been exposed to a prudent diet or a Western diet. Monkeys in the prudent diet group (n=13) were research naïve and had been exposed only to a commercial monkey chow diet (low in cholesterol and saturated fats, high in complex carbohydrates). Western diet monkeys (n=8) had consumed a diet that was high in cholesterol, saturated animal fats and soluble carbohydrates for 2 years prior to ovarian tissue and serum collection. Metabolomic analyses were done on extracts of homogenized ovary tissue samples, and extracts of serum. Targeted analysis was conducted using the Biocrates p180 kit and broad spectrum analysis was conducted using UPLC-TOF-MS, resulting in the detection of 3500 compound ions. Using metabolomics methods, which capture thousands of signals for metabolites, 64 metabolites were identified in serum and 47 metabolites were identified in ovarian tissue that differed by diet. Quantitative targeted analysis revealed 13 amino acids, 6 acrylcarnitines, and 2 biogenic amines that were significantly (p<0.05) different between the two diet groups for serum extracts, and similar results were observed for the ovary extracts. These data demonstrate that dietary exposure had a significant impact on the serum and ovarian metabolome, and demonstrated perturbation in carnitine, lipids/fatty acid, and amino acid metabolic pathways. Published by Elsevier Ireland Ltd.

Epstein-Barr virus latent membrane protein-1 (LMP-1) 30-bp deletion and Xho I-loss is associated with type III nasopharyngeal carcinoma in Malaysia

PubMed Central

See, Hui Shien; Yap, Yoke Yeow; Yip, Wai Kien; Seow, Heng Fong

2008-01-01

Background Nasopharyngeal carcinoma (NPC) is a human epithelial tumour with high prevalence amongst Chinese in Southern China and South East Asia and is associated with the Epstein-Barr virus (EBV). The viral genome harbours an oncogene, namely, the latent membrane protein 1 (LMP1) gene and known variants such as the 30-bp deletion and loss of XhoI restriction site have been found. Less is known about the relationship between these variants and the population characteristics and histological type. Methods In this study, the EBV LMP1 gene variants from 42 NPC and 10 non-malignant archived formalin fixed, paraffin-embedded tissues, as well as plasma from another 35 patients with nasopharyngeal carcinoma were determined by using Polymerase Chain Reaction (PCR). Statistical analysis was performed by using SPSS programme. Results LMP1 30-bp deletion was detected in 19/34 (55.9%) of NPC tissues, 7/29 (24.1%) of plasma but absent in non-malignant tissues (8/8). Coexistence of variants with and without 30bp deletion was found only in 5/29 (17.2%) plasma samples but not in NPC tissues. The loss of XhoI restriction site in LMP1 gene was found in 34/39 (87.2%) of the NPC tissues and 11/30 (36.7%) of plasma samples. None of the non-malignant nasopharyngeal tissues (8/8) harbour XhoI-loss variants. LMP1 30-bp deletion was detected in 16/18 Chinese versus 3/15 Malays and 13/16 type III (undifferentiated carcinoma) versus 1/6 type I (keratinizing squamous cell carcinoma). XhoI-loss was found in 19/19 Chinese versus 14/19 Malays and 18/18 type III (undifferentiated) versus 2/5 type I (keratinizing squamous cell carcinoma). Statistical analysis showed that these variants were associated with ethnic race (30-bp deletion, p < 0.05; XhoI-loss, p = 0.046) and histological type of NPC (30-bp deletion, p = 0.011; XhoI-loss, p = 0.006). Nineteen out of 32 NPC tissues (19/32; 59.4%) and 6/24 (25%) of plasma samples showed the coexistence of both the 30-bp deletion and the loss of XhoI restriction site. A significant relationship was found with the Chinese race but not histological type. Conclusion The incidence rate of 56% for LMP1 30-bp deletion was lower compared to previously reported rates of 75–100% in NPC tissues. Coexistence of variants with and without 30-bp deletion was found only in 5/29 plasma samples. The incidence rate of XhoI restriction site loss in NPC was comparable to other studies from endemic regions such as Southern China. For the first time, the presence of LMP1 30-bp deletion or XhoI-loss was associated with the Chinese race and type III NPC. Both these variants were not found in non-malignant tissues. The influence of these variants on disease progression and outcome in Chinese and type III NPC requires further investigation. PMID:18275617

Final Technical Report for DE-SC0002014- July 29, 2011

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramirez, NC

2011-07-29

The project titled “National Biorepository for Children’s and Women’s Cancer”. The funding received by the Biopathology Center (BPC) at the Research Institute at Nationwide Children’s Hospital was utilized to procure equipment and add resources to establish a national digital archive of tissues of children and women’s cancers to advance treatment and research. As planned in the proposal, the project allowed the BPC to procure two high-speed imaging robots and hire imaging technicians to scan a large collection of Children’s and Women’s cancer tissues. The BPC team focused on completed clinical trials, with some dating back nearly 30 years, conducted bymore » the Children’s Oncology Group (and its precursor groups) as well as the Gynecologic Oncology Group. A total of 139 clinical trials were imaged as part of the archive project allowing the team to generate 29, 488 images that are currently stored at the Ohio Supercomputer Center located in Columbus Ohio. The images are now integrated with the Virtual Imaging for Pathology, Education and Research (VIPER) application. The VIPER application allows the BPC to make the digital archive available via the Internet to approved researchers remotely eliminating the use of glass slides for this collection. The elimination of glass slides reduces costs associated with shipping, reduces breakage of glass slides and allows for the review of these cases quickly by experts on a standard desktop computer.« less

The Digital Fish Library: Using MRI to Digitize, Database, and Document the Morphological Diversity of Fish

PubMed Central

Berquist, Rachel M.; Gledhill, Kristen M.; Peterson, Matthew W.; Doan, Allyson H.; Baxter, Gregory T.; Yopak, Kara E.; Kang, Ning; Walker, H. J.; Hastings, Philip A.; Frank, Lawrence R.

2012-01-01

Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators. PMID:22493695

The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish.

PubMed

Berquist, Rachel M; Gledhill, Kristen M; Peterson, Matthew W; Doan, Allyson H; Baxter, Gregory T; Yopak, Kara E; Kang, Ning; Walker, H J; Hastings, Philip A; Frank, Lawrence R

2012-01-01

Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.

Utility of Cytospin and Cell block Technology in Evaluation of Body Fluids and Urine Samples: A Comparative Study.

PubMed

Qamar, Irmeen; Rehman, Suhailur; Mehdi, Ghazala; Maheshwari, Veena; Ansari, Hena A; Chauhan, Sunanda

2018-01-01

Cytologic examination of body fluids commonly involves the use of direct or sediment smears, cytocentrifuge preparations, membrane filter preparations, or cell block sections. Cytospin and cell block techniques are extremely useful in improving cell yield of thin serous effusions and urine samples, and ensure high diagnostic efficacy. We studied cytospin preparations and cell block sections prepared from 180 samples of body fluids and urine samples to compare the relative efficiency of cell retrieval, preservation of cell morphology, ease of application of special stains, and diagnostic efficacy. Samples were collected and processed to prepare cytospin smears and cell block sections. We observed that overall, cell yield and preservation of individual cell morphology were better in cytospin preparations as compared to cell blocks, while preservation of architectural pattern was better in cell block sections. The number of suspicious cases also decreased on cell block sections, with increased detection of malignancy. It was difficult to prepare cell blocks from urine samples due to low cellularity. Cytospin technology is a quick, efficient, and cost-effective method of increasing cell yield in hypocellular samples, with better preservation of cell morphology. Cell blocks are better prepared from high cellularity fluids; however, tissue architecture is better studied, with improved rate of diagnosis and decrease in ambiguous results. Numerous sections can be prepared from a small amount of material. Special stains and immunochemical stains can be easily applied to cell blocks. It also provides a source of archival material.

The Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) Framework: Encouraging Reduction, Replacement, and Refinement in Animal Research.

PubMed

Morrissey, Bethny; Blyth, Karen; Carter, Phil; Chelala, Claude; Jones, Louise; Holen, Ingunn; Speirs, Valerie

2017-01-01

While significant medical breakthroughs have been achieved through using animal models, our experience shows that often there is surplus material remaining that is frequently never revisited but could be put to good use by other scientists. Recognising that most scientists are willing to share this material on a collaborative basis, it makes economic, ethical, and academic sense to explore the option to utilise this precious resource before generating new/additional animal models and associated samples. To bring together those requiring animal tissue and those holding this type of archival material, we have devised a framework called Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) with the aim of making remaining material derived from animal studies in biomedical research more visible and accessible to the scientific community. We encourage journals, funding bodies, and scientists to unite in promoting a new way of approaching animal research by adopting the SEARCH framework.

The Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) Framework: Encouraging Reduction, Replacement, and Refinement in Animal Research

PubMed Central

Morrissey, Bethny; Blyth, Karen; Carter, Phil; Chelala, Claude; Jones, Louise; Holen, Ingunn; Speirs, Valerie

2017-01-01

While significant medical breakthroughs have been achieved through using animal models, our experience shows that often there is surplus material remaining that is frequently never revisited but could be put to good use by other scientists. Recognising that most scientists are willing to share this material on a collaborative basis, it makes economic, ethical, and academic sense to explore the option to utilise this precious resource before generating new/additional animal models and associated samples. To bring together those requiring animal tissue and those holding this type of archival material, we have devised a framework called Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) with the aim of making remaining material derived from animal studies in biomedical research more visible and accessible to the scientific community. We encourage journals, funding bodies, and scientists to unite in promoting a new way of approaching animal research by adopting the SEARCH framework. PMID:28081116

Microbiological contamination with moulds in work environment in libraries and archive storage facilities.

PubMed

Zielinska-Jankiewicz, Katarzyna; Kozajda, Anna; Piotrowska, Malgorzata; Szadkowska-Stanczyk, Irena

2008-01-01

Microbiological contamination with fungi, including moulds, can pose a significant health hazard to those working in archives or museums. The species involved include Aspergillus, Penicillium, Geotrichum, Alternaria, Cladosporium, Mucor, Rhizopus, Trichoderma, Fusarium which are associated mostly with allergic response of different types. The aim of the study was to analyse, both in quantitative and qualitative terms, workplace air samples collected in a library and archive storage facilities. Occupational exposure and the related health hazard from microbiological contamination with moulds were assessed in three archive storage buildings and one library. Air samples (total 60) were collected via impact method before work and at hourly intervals during work performance. Surface samples from the artifacts were collected by pressing a counting (RODAC) plate filled with malt extract agar against the surface of the artifacts. The air sample and surface sample analyses yielded 36 different mould species, classified into 19 genera, of which Cladosporium and Penicillium were the most prevalent. Twelve species were regarded as potentially pathogenic for humans: 8 had allergic and 11 toxic properties, the latter including Aspergillus fumigatus. Quantitative analysis revealed air microbiological contamination with moulds at the level ranging from 1.8 x 10(2)-2.3 x 10(3) cfu/m(3). In surface samples from library and archive artifacts, 11 fungal species were distinguished; the number of species per artifact varying from 1-6 and colony count ranging from 4 x 10(1) to 8-10(1) cfu/100 cm(2). Higher contamination levels were found only for Cladosporium cladosporioides (1.48 x 10(3) cfu/100 cm(2)) and Paecillomyces varioti (1.2 x 10(2) cfu/100 cm(2)). At the workposts examined, although no clearly visible signs of mould contamination could be found, the study revealed abundant micromycetes, with the predominant species of Cladosporium and Penicillium. The detected species included also potentially pathogenic microorganisms which can cause allergic and toxic effects, such as Aspergillus fumigatus, that could be hazardous to workers' health. For some species, the concentration levels exceeded the values considered the proposed hygienic standards for total microscopical fungi in occupational settings. The findings of the study point to unsatisfactory hygienic conditions at the worksites examined, resulting in microbiological contamination with moulds, as well as the necessity for prompt remedial activities on the part of the employers.

Nedd4L expression is decreased in ovarian epithelial cancer tissues compared to ovarian non-cancer tissue.

PubMed

Yang, Qiuyun; Zhao, Jinghe; Cui, Manhua; Gi, Shuting; Wang, Wei; Han, Xiaole

2015-12-01

Recent studies have demonstrated that the neural precursor cell expressed, developmentally downregulated 4-like (Nedd4L) gene plays a role in the progression of various cancers. However, reports describing Nedd4L expression in ovarian cancer tissues are limited. A cohort (n = 117) of archival formalin-fixed, paraffin embedded resected normal ovarian epithelial tissues (n = 10), benign ovarian epithelial tumor tissues (n = 10), serous borderline ovarian epithelial tumor tissues (n = 14), mucous borderline ovarian epithelial tumor tissues (n = 11), and invasive ovarian epithelial cancer tissues (n = 72) were assessed for Nedd4L protein expression using immunohistochemistry. Nedd4L protein expression was significantly decreased in invasive ovarian epithelial cancer tissues compared to non-cancer tissues (P < 0.05). Decreased Nedd4L protein expression correlated with clinical stage, pathological grade, lymph node metastasis and survival (P < 0.05). Nedd4L protein expression may be an independent prognostic marker of ovarian cancer development. © 2015 Japan Society of Obstetrics and Gynecology.

Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma.

PubMed

Anderson, Bradley W; Suh, Yun-Suhk; Choi, Boram; Lee, Hyuk-Joon; Yab, Tracy C; Taylor, William; Dukek, Brian A; Berger, Calise K; Cao, Xiaoming; Foote, Patrick H; Devens, Mary E; Boardman, Lisa A; Kisiel, John B; Mahoney, Douglas W; Slettedahl, Seth W; Allawi, Hatim T; Lidgard, Graham P; Smyrk, Thomas C; Yang, Han-Kwang; Ahlquist, David A

2018-05-29

Gastric adenocarcinoma (GAC) is the third most common cause of cancer mortality worldwide. Accurate and affordable non-invasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDMs) for GAC, validate their discrimination for GAC in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from GAC cases and normal controls. Following discovery by unbiased whole methylome sequencing, candidate MDMs were validated by blinded methylation-specific PCR in archival case-control tissues from U.S. and South Korean patients. Top MDMs were then assayed by an analytically sensitive method (quantitative real-time allele-specific target and signal amplification) in a blinded pilot study on archival plasma from GAC cases and normal controls. Whole methylome discovery yielded novel and highly discriminant candidate MDMs. In tissue, a panel of candidate MDMs detected GAC in 92-100% of U.S. and S. Korean cohorts at 100% specificity. Levels of most MDMs increased progressively from normal mucosa through metaplasia, adenoma, and GAC with variation in points of greatest marker acquisition. In plasma, a 3 marker panel ( ELMO1 , ZNF569 , C13orf18) detected 86% (95% CI 71-95%) of GACs at 95% specificity. Novel MDMs appear to accurately discriminate GAC from normal controls in both tissue and plasma. The point of aberrant methylation during oncogenesis varies by MDM, which may have relevance to marker selection in clinical applications. Further exploration of these MDMs for GAC screening and surveillance is warranted. Copyright ©2018, American Association for Cancer Research.

Past and present mercury accumulation in the Lake Baikal seal: Temporal trends, effects of life history, and toxicological implications.

PubMed

Poste, Amanda E; Pastukhov, Mikhail V; Braaten, Hans Fredrik Veiteberg; Ozersky, Ted; Moore, Marianne

2018-05-01

Despite global efforts to reduce anthropogenic mercury (Hg) emissions, the timescale and degree to which Hg concentrations in the environment and biota respond to decreased emissions remain challenging to assess or predict. In the present study we characterize long-term trends and life-history patterns in Hg accumulation and toxicological implications of Hg contamination for a freshwater seal from one of the world's largest lakes (Lake Baikal, Siberia, Russia) using contemporary tissues and archival teeth. Stable isotope analysis and Hg analyses of soft tissues (muscle, liver, kidney, blood, brain, heart) and teeth from 22 contemporary seals revealed rapid changes in diet and Hg accumulation in the first year of life with a stable diet and increase in tissue Hg throughout the rest of life. Although maternal transfer of Hg was an important source of Hg to seal pups, reproduction and lactation by female seals did not appear to result in sex-related differences in Hg concentrations or age-related accumulation in adult seals. Based on Hg analysis of archival teeth (n = 114) and reconstructed values for soft tissues, we also assessed temporal trends in seal Hg between the years 1960 and 2013. Seal Hg concentrations in hard (teeth) and soft (e.g., muscle, liver) tissues were highest in the 1960s and 1970s, followed by a decrease. The decline in seal Hg concentrations in recent decades was most likely driven by a reduction in Hg inputs to the lake, suggesting that global and regional efforts to reduce Hg emissions have been successful at reducing ecosystem and human health risks posed by Hg in Lake Baikal. Environ Toxicol Chem 2018;37:1476-1486. © 2018 SETAC. © 2018 SETAC.

MGMT-STP27 methylation status as predictive marker for response to PCV in anaplastic Oligodendrogliomas and Oligoastrocytomas. A report from EORTC study 26951.

PubMed

van den Bent, Martin J; Erdem-Eraslan, Lale; Idbaih, Ahmed; de Rooi, Johan; Eilers, Paul H C; Spliet, Wim G M; den Dunnen, Wilfred F A; Tijssen, Cees; Wesseling, Pieter; Sillevis Smitt, Peter A E; Kros, Johan M; Gorlia, Thierry; French, Pim J

2013-10-01

The long-term follow-up results from the EORTC-26951 trial showed that the addition of procarbazine, CCNU, and vincristine (PCV) after radiotherapy increases survival in anaplastic oligodendrogliomas/oligoastrocytomas (AOD/AOA). However, some patients appeared to benefit more from PCV treatment than others. We conducted genome-wide methylation profiling of 115 samples included in the EORTC-26951 trial and extracted the CpG island hypermethylated phenotype (CIMP) and MGMT promoter methylation (MGMT-STP27) status. We first show that methylation profiling can be conducted on archival tissues with a performance that is similar to snap-frozen tissue samples. We then conducted methylation profiling on EORTC-26951 clinical trial samples. Univariate analysis indicated that CIMP+ or MGMT-STP27 methylated tumors had an improved survival compared with CIMP- and/or MGMT-STP27 unmethylated tumors [median overall survival (OS), 1.05 vs. 6.46 years and 1.06 vs. 3.8 years, both P < 0.0001 for CIMP and MGMT-STP27 status, respectively]. Multivariable analysis indicates that CIMP and MGMT-STP27 are significant prognostic factors for survival in presence of age, sex, performance score, and review diagnosis in the model. CIMP+ and MGMT-STP27 methylated tumors showed a clear benefit from adjuvant PCV chemotherapy: the median OS of CIMP+ samples in the RT and RT-PCV arms was 3.27 and 9.51 years, respectively (P = 0.0033); for MGMT-STP27 methylated samples, it was 1.98 and 8.65 years. There was no such benefit for CIMP- or for MGMT-STP27 unmethylated tumors. MGMT-STP27 status remained significant in an interaction test (P = 0.003). Statistical analysis of microarray (SAM) identified 259 novel CpGs associated with treatment response. MGMT-STP27 may be used to guide treatment decisions in this tumor type. ©2013 AACR.

Multi-site evaluation of the LN34 pan-lyssavirus real-time RT-PCR assay for post-mortem rabies diagnostics

PubMed Central

Dettinger, Lisa; Powell, James W.; Seiders, Melanie; Condori, Rene Edgar Condori; Griesser, Richard; Okogi, Kenneth; Carlos, Maria; Pesko, Kendra; Breckenridge, Mike; Simon, Edson Michael M.; Chu, Maria Yna Joyce V.; Davis, April D.; Brunt, Scott J.; Orciari, Lillian; Yager, Pamela; Carson, William C.; Hartloge, Claire; Saliki, Jeremiah T.; Deldari, Mojgan; Hsieh, Kristina; Wadhwa, Ashutosh; Wilkins, Kimberly; Rabideau, Patricia; Gruhn, Nina; Cadet, Rolain; Isloor, Shrikrishna; Nath, Sujith S.; Joseph, Tomy; Gao, Jinxin; Wallace, Ryan; Reynolds, Mary; Olson, Victoria A.

2018-01-01

Rabies is a fatal zoonotic disease that requires fast, accurate diagnosis to prevent disease in an exposed individual. The current gold standard for post-mortem diagnosis of human and animal rabies is the direct fluorescent antibody (DFA) test. While the DFA test has proven sensitive and reliable, it requires high quality antibody conjugates, a skilled technician, a fluorescence microscope and diagnostic specimen of sufficient quality. The LN34 pan-lyssavirus real-time RT-PCR assay represents a strong candidate for rabies post-mortem diagnostics due to its ability to detect RNA across the diverse Lyssavirus genus, its high sensitivity, its potential for use with deteriorated tissues, and its simple, easy to implement design. Here, we present data from a multi-site evaluation of the LN34 assay in 14 laboratories. A total of 2,978 samples (1,049 DFA positive) from Africa, the Americas, Asia, Europe, and the Middle East were tested. The LN34 assay exhibited low variability in repeatability and reproducibility studies and was capable of detecting viral RNA in fresh, frozen, archived, deteriorated and formalin-fixed brain tissue. The LN34 assay displayed high diagnostic specificity (99.68%) and sensitivity (99.90%) when compared to the DFA test, and no DFA positive samples were negative by the LN34 assay. The LN34 assay produced definitive findings for 80 samples that were inconclusive or untestable by DFA; 29 were positive. Five samples were inconclusive by the LN34 assay, and only one sample was inconclusive by both tests. Furthermore, use of the LN34 assay led to the identification of one false negative and 11 false positive DFA results. Together, these results demonstrate the reliability and robustness of the LN34 assay and support a role for the LN34 assay in improving rabies diagnostics and surveillance. PMID:29768505

An Archive of Spectra from the Mayall Fourier Transform Spectrometer at Kitt Peak

NASA Astrophysics Data System (ADS)

Pilachowski, C. A.; Hinkle, K. H.; Young, M. D.; Dennis, H. B.; Gopu, A.; Henschel, R.; Hayashi, S.

2017-02-01

We describe the SpArc science gateway for spectral data obtained using the Fourier Transform Spectrometer (FTS) in operation at the Mayall 4-m telescope at the Kitt Peak National Observatory during the period from 1975 through 1995. SpArc is hosted by Indiana University Bloomington and is available for public access. The archive includes nearly 10,000 individual spectra of more than 800 different astronomical sources including stars, nebulae, galaxies, and solar system objects. We briefly describe the FTS instrument itself and summarize the conversion of the original interferograms into spectral data and the process for recovering the data into FITS files. The architecture of the archive is discussed and the process for retrieving data from the archive is introduced. Sample use cases showing typical FTS spectra are presented.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 formore » 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« less

Global tropospheric experiment at the Hong Kong Atmosphere Chemistry Measurement Station

NASA Technical Reports Server (NTRS)

Carroll, Mary Ann; Wang, Tao

1995-01-01

The major activities of the Global Tropospheric Experiment at the Hong Kong Atmospheric Chemistry Measurement Station are presented for the period 1 January - 31 December 1995. Activities included data analysis, reduction, and archiving of atmospheric measurements and sampling. Sampling included O3, CO, SO2, NO, TSP, RSP, and ozone column density. A data archive was created for the surface meteorological data. Exploratory data analysis was performed, including examination of time series, frequency distributions, diurnal variations and correlation. The major results have been or will be published in scientific journals as well as presented at conferences/workshops. Abstracts are attached.

On a path towards long-term sampling following the Deepwater Horizon: Initial insights

NASA Astrophysics Data System (ADS)

Reddy, C. M.

2012-12-01

During the past two decades in the United States, few areas contaminated from an oil spill have been revisited on the time scales from months to years. The lack of sampling is a missed opportunity to shine light on long-term processes, evaluate recovery, identify compounds most likely to persist, and apply new chemical and biological techniques. To address this issue, my laboratory has begun a land-based effort to collect oiled samples from the Gulf of Mexico beaches from the Deepwater Horizon disaster. Each sample is archived, analyzed, and available for others via an online repository. Detailed analysis of many of these samples has already been fruitful on determining the fate of the spilled oil, which will be discussed. This meeting is an ideal time to discuss strategies for long-term sampling and archiving. With support from the Gulf Research Initiative for the next nine years, the opportunities to use these samples will be frequent.

Chemical Analysis Results for Potable Water from ISS Expeditions 21 to 25

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Schultz, John R.; McCoy, J. Torin

2010-01-01

The Johnson Space Center Water and Food Analytical Laboratory (WAFAL) performed detailed ground-based analyses of archival water samples for verification of the chemical quality of the International Space Station (ISS) potable water supplies for Expeditions 21 to 25. Over a 14-month period, the Space Shuttle visited the ISS on five occasions to complete construction and deliver supplies. The onboard supplies of potable water available for consumption by the Expeditions 21 to 25 crews consisted of Russian ground-supplied potable water, Russian potable water regenerated from humidity condensate, and US potable water recovered from urine distillate and condensate. Chemical archival water samples that were collected with U.S. hardware during Expeditions 21 to 25 were returned on Shuttle flights STS-129 (ULF3), STS-130 (20A), STS-131 (19A), STS-132 (ULF4) and STS-133 (ULF5), as well as on Soyuz flights 19-22. This paper reports the analytical results for the returned archival water samples and evaluates their compliance with ISS water quality standards. The WAFAL also received and analyzed aliquots of some Russian potable water samples collected in-flight and pre-flight samples of Rodnik potable water delivered to the Station on the Russian Progress vehicle during Expeditions 21 to 25. These additional analytical results are also reported and discussed in this paper.

Digital Archive Issues from the Perspective of an Earth Science Data Producer

NASA Technical Reports Server (NTRS)

Barkstrom, Bruce R.

2004-01-01

Contents include the following: Introduction. A Producer Perspective on Earth Science Data. Data Producers as Members of a Scientific Community. Some Unique Characteristics of Scientific Data. Spatial and Temporal Sampling for Earth (or Space) Science Data. The Influence of the Data Production System Architecture. The Spatial and Temporal Structures Underlying Earth Science Data. Earth Science Data File (or Relation) Schemas. Data Producer Configuration Management Complexities. The Topology of Earth Science Data Inventories. Some Thoughts on the User Perspective. Science Data User Communities. Spatial and Temporal Structure Needs of Different Users. User Spatial Objects. Data Search Services. Inventory Search. Parameter (Keyword) Search. Metadata Searches. Documentation Search. Secondary Index Search. Print Technology and Hypertext. Inter-Data Collection Configuration Management Issues. An Archive View. Producer Data Ingest and Production. User Data Searching and Distribution. Subsetting and Supersetting. Semantic Requirements for Data Interchange. Tentative Conclusions. An Object Oriented View of Archive Information Evolution. Scientific Data Archival Issues. A Perspective on the Future of Digital Archives for Scientific Data. References Index for this paper.

Evaluation of sample preservation methods for space mission

NASA Technical Reports Server (NTRS)

Schubert, W.; Rohatgi, N.; Kazarians, G.

2002-01-01

For interplanetary spacecraft that will travel to destinations where future life detection experiments may be conducted or samples are to be returned to earth, we should archive and preserve relevant samples from the spacecraft and cleanrooms for evaluation at a future date.

Long-term data archiving

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, David Steven

2009-01-01

Long term data archiving has much value for chemists, not only to retain access to research and product development records, but also to enable new developments and new discoveries. There are some recent regulatory requirements (e.g., FDA 21 CFR Part 11), but good science and good business both benefit regardless. A particular example of the benefits of and need for long term data archiving is the management of data from spectroscopic laboratory instruments. The sheer amount of spectroscopic data is increasing at a scary rate, and the pressures to archive come from the expense to create the data (or recreatemore » it if it is lost) as well as its high information content. The goal of long-term data archiving is to save and organize instrument data files as well as any needed meta data (such as sample ID, LIMS information, operator, date, time, instrument conditions, sample type, excitation details, environmental parameters, etc.). This editorial explores the issues involved in long-term data archiving using the example of Raman spectral databases. There are at present several such databases, including common data format libraries and proprietary libraries. However, such databases and libraries should ultimately satisfy stringent criteria for long term data archiving, including readability for long times into the future, robustness to changes in computer hardware and operating systems, and use of public domain data formats. The latter criterion implies the data format should be platform independent and the tools to create the data format should be easily and publicly obtainable or developable. Several examples of attempts at spectral libraries exist, such as the ASTM ANDI format, and the JCAMP-DX format. On the other hand, proprietary library spectra can be exchanged and manipulated using proprietary tools. As the above examples have deficiencies according to the three long term data archiving criteria, Extensible Markup Language (XML; a product of the World Wide Web Consortium, an independent standards body) as a new data interchange tool is being investigated and implemented. In order to facilitate data archiving, Raman data needs calibration as well as some other kinds of data treatment. Figure 1 illustrates schematically the present situation for Raman data calibration in the world-wide Raman spectroscopy community, and presents some of the terminology used.« less

Coupling Meteorology, Metal Concentrations, and Pb Isotopes for Source Attribution in Archived Precipitation Samples

EPA Science Inventory

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 16 ...

Cores to the rescue: how old cores enable new science

NASA Astrophysics Data System (ADS)

Ito, E.; Noren, A. J.; Brady, K.

2016-12-01

The value of archiving scientific specimens and collections for the purpose of enabling further research using new analytical techniques, resolving conflicting results, or repurposing them for entirely new research, is often discussed in abstract terms. We all agree that samples with adequate metadata ought to be archived systematically for easy access, for a long time and stored under optimal conditions. And yet, as storage space fills, there is a temptation to cull the collection, or when a researcher retires, to discard the collection unless the researcher manages to make his or her own arrangement for the collection to be accessioned elsewhere. Nobody has done anything with these samples in over 20 years! Who would want them? It turns out that plenty of us do want them, if we know how to find them and if they have sufficient metadata to assess past work and suitability for new analyses. The LacCore collection holds over 33 km of core from >6700 sites in diverse geographic locations worldwide with samples collected as early as 1950s. From these materials, there are many examples to illustrate the scientific value of archiving geologic samples. One example that benefitted Ito personally were cores from Lakes Mirabad and Zeribar, Iran, acquired in 1963 by Herb Wright and his associates. Several doctoral and postdoctoral students generated and published paleoecological reconstructions based on cladocerans, diatoms, pollen or plant macrofossils, mostly between 1963 and 1967. The cores were resampled in 1990s by a student being jointly advised by Wright and Ito for oxygen isotope analysis of endogenic calcite. The results were profitably compared with pollen and the results published in 2001 and 2006. From 1979 until very recently, visiting Iran for fieldwork was not pallowed for US scientists. Other examples will be given to further illustrate the power of archived samples to advance science.

The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine.

PubMed

Elliott, Paul; Peakman, Tim C

2008-04-01

UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided. The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process. The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.

An Archival Search For Young Globular Clusters in Galaxies

NASA Astrophysics Data System (ADS)

Whitmore, Brad

1995-07-01

One of the most intriguing results from HST has been the discovery of ultraluminous star clusters in interacting and merging galaxies. These clusters have the luminosities, colors, and sizes that would be expected of young globular clusters produced by the interaction. We propose to use the data in the HST Archive to determine how prevalent this phenomena is, and to determine whether similar clusters are produced in other environments. Three samples will be extracted and studied in a systematic and consistent manner: 1} interacting and merging galaxies, 2} starburst galaxies, 3} a control sample of ``normal'' galaxies. A preliminary search of the archives shows that there are at least 20 galaxies in each of these samples, and the number will grow by about 50 observations become available. The data will be used to determine the luminosity function, color histogram , spatial distribution, and structural properties of the clusters using the same techniques employed in our study of NGC 7252 {``Atoms -for-Peace'' galaxy} and NGC 4038/4039 {``The Antennae''}. Our ultimate goals are: 1} to understand how globular clusters form, and 2} to use the clusters as evolutionary tracers to unravel the histories of interacting galaxies.

Development of a Climatology of Vertically Complete Wind Profiles from Doppler Radar Wind Profiler Systems

NASA Technical Reports Server (NTRS)

Barbre, Robert E., Jr.

2015-01-01

This paper describes in detail the QC and splicing methodology for KSC's 50- and 915-MHz DRWP measurements that generates an extensive archive of vertically complete profiles from 0.20-18.45 km. The concurrent POR from each archive extends from April 2000 to December 2009. MSFC NE applies separate but similar QC processes to each of the 50- and 915-MHz DRWP archives. DRWP literature and data examination provide the basis for developing and applying the automated and manual QC processes on both archives. Depending on the month, the QC'ed 50- and 915-MHz DRWP archives retain 52-65% and 16-30% of the possible data, respectively. The 50- and 915-MHz DRWP QC archives retain 84-91% and 85-95%, respectively, of all the available data provided that data exist in the non- QC'ed archives. Next, MSFC NE applies an algorithm to splice concurrent measurements from both DRWP sources. Last, MSFC NE generates a composite profile from the (up to) five available spliced profiles to effectively characterize boundary layer winds and to utilize all possible 915-MHz DRWP measurements at each timestamp. During a given month, roughly 23,000-32,000 complete profiles exist from 0.25-18.45 km from the composite profiles' archive, and approximately 5,000- 27,000 complete profiles exist from an archive utilizing an individual 915-MHz DRWP. One can extract a variety of profile combinations (pairs, triplets, etc.) from this sample for a given application. The sample of vertically complete DRWP wind measurements not only gives launch vehicle customers greater confidence in loads and trajectory assessments versus using balloon output, but also provides flexibility to simulate different DOL situations across applicable altitudes. In addition to increasing sample size and providing more flexibility for DOL simulations in the vehicle design phase, the spliced DRWP database provides any upcoming launch vehicle program with the capability to utilize DRWP profiles on DOL to compute vehicle steering commands, provided the program applies the procedures that this report describes to new DRWP data on DOL. Decker et al. (2015) details how SLS is proposing to use DRWP data and splicing techniques on DOL. Although automation could enhance the current DOL 50-MHz DRWP QC process and could streamline any future DOL 915-MHz DRWP QC and splicing process, the DOL community would still require manual intervention to ensure that the vehicle only uses valid profiles. If a program desires to use high spatial resolution profiles, then the algorithm could randomly add high-frequency components to the DRWP profiles. The spliced DRWP database provides lots of flexibility in how one performs DOL simulations, and the algorithms that this report provides will assist the aerospace and atmospheric communities that are interested in utilizing the DRWP.

GATA6 expression in Barrett's oesophagus and oesophageal adenocarcinoma.

PubMed

Pavlov, Kirill; Honing, Judith; Meijer, Coby; Boersma-van Ek, Wytske; Peters, Frans T M; van den Berg, Anke; Karrenbeld, Arend; Plukker, John T M; Kruyt, Frank A E; Kleibeuker, Jan H

2015-01-01

Barrett's oesophagus can progress towards oesophageal adenocarcinoma through a metaplasia-dysplasia-carcinoma sequence, but the underlying mechanisms are poorly understood. The transcription factor GATA6 is known to be involved in columnar differentiation and proliferation, and GATA6 gene amplification was recently linked with poor survival in oesophageal adenocarcinoma. To study the expression of GATA6 during Barrett's oesophagus development and malignant transformation. To determine the prognostic value of GATA6 in oesophageal adenocarcinoma. Two retrospective cohorts were derived from the pathological archive of the University Medical Center Groningen. The first cohort contained 130 tissue samples of normal squamous epithelium, metaplasia, dysplasia and oesophageal adenocarcinoma. The second cohort consisted of a tissue microarray containing tissue from 92 oesophageal adenocarcinoma patients. Immunohistochemistry was used to examine GATA6 protein expression and to correlate GATA6 expression in oesophageal adenocarcinoma with overall and disease-free survival. The percentage of GATA6-positive cells was low in squamous epithelium (10%) but increased progressively in Barrett's oesophagus (30%, P < 0.001) and high-grade dysplasia (82%, P = 0.005). GATA6 expression was not associated with overall or disease-free survival in oesophageal adenocarcinoma patients (P = 0.599 and P = 0.700 respectively). GATA6 expression is progressively increased during Barrett's oesophagus development and its malignant transformation. However, no prognostic value of GATA6 expression could be found in oesophageal adenocarcinoma. Copyright © 2014 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

PubMed

Deck, John; Gaither, Michelle R; Ewing, Rodney; Bird, Christopher E; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J; Crandall, Eric D

2017-08-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

PubMed Central

Deck, John; Gaither, Michelle R.; Ewing, Rodney; Bird, Christopher E.; Davies, Neil; Meyer, Christopher; Riginos, Cynthia; Toonen, Robert J.; Crandall, Eric D.

2017-01-01

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science. PMID:28771471

A novel presenilin 1 mutation (Ala275Val) as cause of early-onset familial Alzheimer disease.

PubMed

Luedecke, Daniel; Becktepe, Jos S; Lehmbeck, Jan T; Finckh, Ulrich; Yamamoto, Raina; Jahn, Holger; Boelmans, Kai

2014-04-30

Mutations in the presenilin 1 (PS1) gene (PSEN1) are associated with familial Alzheimer disease (FAD). Here, we report on a 50-year-old patient presenting with progressive deterioration of his short-term memory and a family history of early-onset dementia. Diagnostic workup included a neuropsychological examination, structural magnetic resonance (MR) imaging, cerebrospinal fluid (CSF) biomarkers including total tau, phosphorylated tau, and Aβ42 levels, as well as sequencing relevant fragments of the genes PSEN1, PSEN2, and APP. Additionally, we were able to obtain archival paraffin-embedded cerebellar tissue from the patient's father for cosegregation analysis. Clinical, neuropsychological and MR imaging data were indicative of early-onset Alzheimer disease. Furthermore, CSF biomarkers showed a typical pattern for Alzheimer disease. DNA sequencing revealed a heterozygous nucleotide transition (c.824C>T) in exon 8 of PSEN1, leading to an amino acid change from alanine to valine at codon 275 (Ala275Val). The same mutation was found in an archival brain specimen of the patient's demented father, but not in a blood sample of the non-demented mother. This mutation alters a conserved residue in the large hydrophilic loop of PS1, suggesting pathogenic relevance. Cosegregegation analysis and the structural as well as the presumed functional role of the mutated and highly conserved residue suggest FAD causing characteristics of the novel PSEN1 mutation Ala275Val. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Automated Extraction of Formalin-Fixed, Paraffin-Embedded Tissue for High-Risk Human Papillomavirus Testing of Head and Neck Squamous Cell Carcinomas Using the Roche Cobas 4800 System.

PubMed

Kerr, Darcy A; Sweeney, Brenda; Arpin, Ronald N; Ring, Melissa; Pitman, Martha B; Wilbur, David C; Faquin, William C

2016-08-01

-Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed. -To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry. -Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction. -Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas. -Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.

Utility of Cytospin and Cell block Technology in Evaluation of Body Fluids and Urine Samples: A Comparative Study

PubMed Central

Qamar, Irmeen; Rehman, Suhailur; Mehdi, Ghazala; Maheshwari, Veena; Ansari, Hena A.; Chauhan, Sunanda

2018-01-01

Background: Cytologic examination of body fluids commonly involves the use of direct or sediment smears, cytocentrifuge preparations, membrane filter preparations, or cell block sections. Cytospin and cell block techniques are extremely useful in improving cell yield of thin serous effusions and urine samples, and ensure high diagnostic efficacy. Materials and Methods: We studied cytospin preparations and cell block sections prepared from 180 samples of body fluids and urine samples to compare the relative efficiency of cell retrieval, preservation of cell morphology, ease of application of special stains, and diagnostic efficacy. Samples were collected and processed to prepare cytospin smears and cell block sections. Results: We observed that overall, cell yield and preservation of individual cell morphology were better in cytospin preparations as compared to cell blocks, while preservation of architectural pattern was better in cell block sections. The number of suspicious cases also decreased on cell block sections, with increased detection of malignancy. It was difficult to prepare cell blocks from urine samples due to low cellularity. Conclusions: Cytospin technology is a quick, efficient, and cost-effective method of increasing cell yield in hypocellular samples, with better preservation of cell morphology. Cell blocks are better prepared from high cellularity fluids; however, tissue architecture is better studied, with improved rate of diagnosis and decrease in ambiguous results. Numerous sections can be prepared from a small amount of material. Special stains and immunochemical stains can be easily applied to cell blocks. It also provides a source of archival material. PMID:29643653

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

EPA Science Inventory

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...

It's Time to Develop a New "Draft Test Protocol" for a Mars Sample Return Mission (or Two....)

NASA Astrophysics Data System (ADS)

Rummel, J. D.

2018-04-01

A Mars Sample Return (MSR) will involve analysis of those samples in containment, including their safe receiving, handling, testing, and archiving. With an MSR planned for the end of the next decade, it is time to update the existing MSR protocol.

DATA QUALITY OBJECTIVES FOR SELECTING WASTE SAMPLES FOR BENCH-SCALE REFORMER TREATABILITY STUDIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

BANNING DL

2011-02-11

This document describes the data quality objectives to select archived samples located at the 222-S Laboratory for Bench-Scale Reforming testing. The type, quantity, and quality of the data required to select the samples for Fluid Bed Steam Reformer testing are discussed. In order to maximize the efficiency and minimize the time to treat Hanford tank waste in the Waste Treatment and Immobilization Plant, additional treatment processes may be required. One of the potential treatment processes is the fluidized bed steam reformer. A determination of the adequacy of the fluidized bed steam reformer process to treat Hanford tank waste is required.more » The initial step in determining the adequacy of the fluidized bed steam reformer process is to select archived waste samples from the 222-S Laboratory that will be used in a bench scale tests. Analyses of the selected samples will be required to confirm the samples meet the shipping requirements and for comparison to the bench scale reformer (BSR) test sample selection requirements.« less

Harvey Cushing Treated the First Known Patient With Carney Complex.

PubMed

Tsay, Cynthia J; Stratakis, Constantine A; Faucz, Fabio Rueda; London, Edra; Stathopoulou, Chaido; Allgauer, Michael; Quezado, Martha; Dagradi, Terry; Spencer, Dennis D; Lodish, Maya

2017-10-01

Carney complex (CNC) is a syndrome characterized by hyperplasia of endocrine organs and may present with clinical features of Cushing syndrome and acromegaly due to functional adrenal and pituitary gland tumors. CNC has been linked to mutations in the regulatory subunit of protein kinase A type I-alpha ( PRKAR1A ) gene. Tissue samples were taken from the hypothalamus or thalamus or tumors of patients with pituitary adenomas seen and operated on by neurosurgeon Harvey Cushing between 1913 and 1932. Following DNA extraction, sequencing for genes of interest was attempted, including PRKAR1A , AIP , USP8 , GNAS1 , and GPR101 , to explore the possibility that these mutations associated with acromegaly, CNC, and Cushing syndrome have been conserved over time. We report a patient described by Dr. Cushing in 1914 with a clinical presentation and postmortem findings suggestive of CNC. Genetic sequencing of the hypothalamus and pituitary adenoma revealed a germline heterozygous p.Arg74His mutation in the PRKAR1A gene, a codon previously described as mutated in CNC, but with a novel amino acid change. This patient is, to our knowledge, the first molecularly confirmed individual with CNC. This case demonstrates the power of modern genetics in studying archived tissues and the importance of recording detailed clinical notes in the diagnosis of disease.

Image standards in tissue-based diagnosis (diagnostic surgical pathology).

PubMed

Kayser, Klaus; Görtler, Jürgen; Goldmann, Torsten; Vollmer, Ekkehard; Hufnagl, Peter; Kayser, Gian

2008-04-18

Progress in automated image analysis, virtual microscopy, hospital information systems, and interdisciplinary data exchange require image standards to be applied in tissue-based diagnosis. To describe the theoretical background, practical experiences and comparable solutions in other medical fields to promote image standards applicable for diagnostic pathology. THEORY AND EXPERIENCES: Images used in tissue-based diagnosis present with pathology-specific characteristics. It seems appropriate to discuss their characteristics and potential standardization in relation to the levels of hierarchy in which they appear. All levels can be divided into legal, medical, and technological properties. Standards applied to the first level include regulations or aims to be fulfilled. In legal properties, they have to regulate features of privacy, image documentation, transmission, and presentation; in medical properties, features of disease-image combination, human-diagnostics, automated information extraction, archive retrieval and access; and in technological properties features of image acquisition, display, formats, transfer speed, safety, and system dynamics. The next lower second level has to implement the prescriptions of the upper one, i.e. describe how they are implemented. Legal aspects should demand secure encryption for privacy of all patient related data, image archives that include all images used for diagnostics for a period of 10 years at minimum, accurate annotations of dates and viewing, and precise hardware and software information. Medical aspects should demand standardized patients' files such as DICOM 3 or HL 7 including history and previous examinations, information of image display hardware and software, of image resolution and fields of view, of relation between sizes of biological objects and image sizes, and of access to archives and retrieval. Technological aspects should deal with image acquisition systems (resolution, colour temperature, focus, brightness, and quality evaluation procedures), display resolution data, implemented image formats, storage, cycle frequency, backup procedures, operation system, and external system accessibility. The lowest third level describes the permitted limits and threshold in detail. At present, an applicable standard including all mentioned features does not exist to our knowledge; some aspects can be taken from radiological standards (PACS, DICOM 3); others require specific solutions or are not covered yet. The progress in virtual microscopy and application of artificial intelligence (AI) in tissue-based diagnosis demands fast preparation and implementation of an internationally acceptable standard. The described hierarchic order as well as analytic investigation in all potentially necessary aspects and details offers an appropriate tool to specifically determine standardized requirements.

Detection of viral sequences in archival spinal cords from fatal cases of poliomyelitis in 1951-1952.

PubMed

Rekand, Tiina; Male, Rune; Myking, Andreas O; Nygaard, Svein J T; Aarli, Johan A; Haarr, Lars; Langeland, Nina

2003-12-01

Poliovirus (PV) subjected to genetic characterization is often isolated from faecal carriage. Such virus is not necessarily identical to the virus causing paralytic disease since genetic modifications may occur during replication outside the nervous system. We have searched for poliovirus genomes in the 14 fatal cases occurring during the last epidemics in Norway in 1951-1952. A method was developed for isolation and analysis of poliovirus RNA from formalin-fixed and paraffin-embedded archival tissue. RNA was purified by incubation with Chelex-100 and heating followed by treatment with the proteinase K and chloroform extraction. Viral sequences were amplified by a reverse transcriptase-polymerase chain reaction (RT-PCR), the products subjected to TA cloning and sequenced. RNA from the beta-actin gene, as a control, was identified in 13 cases, while sequences specific for poliovirus were achieved in 11 cases. The sequences from the 2C region of poliovirus were rather conserved while those in the 5'-untranslated region were variable. The developed method should be suitable also for other genetic studies of old archival material.

Studying The Spectral Shape And The X-ray/uv Variability Of Active Galactic Nuclei With Data From Swift And Xmm Archives

NASA Astrophysics Data System (ADS)

Turriziani, Sara

2011-01-01

Many efforts have been made in understanding the underlying origin of variability in Active Galactic Nuclei (AGN), but at present they could give still no conclusive answers. Since a deeper knowledge of variability will enable to understand better the accretion process onto supermassive black holes, I built the first ensemble struction function analysis of the X-ray variability of samples of quasars with data from Swift and XMM-Newton archives in order to study the average properties of their variability. Moreover, it is known that UV and X-ray luminosities of quasars are correlated and recent studies quantified this relation across 5 orders of magnitude. In this context, I presents results on the X-ray/UV ratio from simultaneous observations in UV and X-ray bands of a sample of quasars with data from XMM-Newton archive. Lastly, I will present a complete sample of Swift/SDSS faint blazars and other non-thermal dominated AGNs. I used this sample to calculate the general statistical properties of faint blazars and radio galaxies and in particular their Radio LogN-LogS with fluxes down to 10 mJy, in order to gain knowledge on the contribution to Cosmic Microwave Background (CMB) and gamma-ray background radiation from the faint tail of the radio population. I acknowledge financial support through Grant ASI I/088/06/0.

Downregulation of toll-like receptor-mediated signalling pathways in oral lichen planus.

PubMed

Sinon, Suraya H; Rich, Alison M; Parachuru, Venkata P B; Firth, Fiona A; Milne, Trudy; Seymour, Gregory J

2016-01-01

The objective of this study was to investigate the expression of Toll-like receptors (TLR) and TLR-associated signalling pathway genes in oral lichen planus (OLP). Initially, immunohistochemistry was used to determine TLR expression in 12 formalin-fixed archival OLP tissues with 12 non-specifically inflamed oral tissues as controls. RNA was isolated from further fresh samples of OLP and non-specifically inflamed oral tissue controls (n = 6 for both groups) and used in qRT(2)-PCR focused arrays to determine the expression of TLRs and associated signalling pathway genes. Genes with a statistical significance of ±two-fold regulation (FR) and a P-value < 0.05 were considered as significantly regulated. Significantly more TLR4(+) cells were present in the inflammatory infiltrate in OLP compared with the control tissues (P < 0.05). There was no statistically significant difference in the numbers of TLR2(+) and TLR8(+) cells between the groups. TLR3 was significantly downregulated in OLP (P < 0.01). TLR8 was upregulated in OLP, but the difference between the groups was not statistically significant. The TLR-mediated signalling-associated protein genes MyD88 and TIRAP were significantly downregulated (P < 0.01 and P < 0.05), as were IRAK1 (P < 0.05), MAPK8 (P < 0.01), MAP3K1 (P < 0.05), MAP4K4 (P < 0.05), REL (P < 0.01) and RELA (P < 0.01). Stress proteins HMGB1 and the heat shock protein D1 were significantly downregulated in OLP (P < 0.01). These findings suggest a downregulation of TLR-mediated signalling pathways in OLP lesions. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A loss of telocytes accompanies fibrosis of multiple organs in systemic sclerosis

PubMed Central

Manetti, Mirko; Rosa, Irene; Messerini, Luca; Guiducci, Serena; Matucci-Cerinic, Marco; Ibba-Manneschi, Lidia

2014-01-01

Systemic sclerosis (SSc) is a complex connective tissue disease characterized by fibrosis of the skin and various internal organs. In SSc, telocytes, a peculiar type of stromal (interstitial) cells, display severe ultrastructural damages and are progressively lost from the clinically affected skin. The aim of the present work was to investigate the presence and distribution of telocytes in the internal organs of SSc patients. Archival paraffin-embedded samples of gastric wall, myocardium and lung from SSc patients and controls were collected. Tissue sections were stained with Masson's trichrome to detect fibrosis. Telocytes were studied on tissue sections subjected to CD34 immunostaining. CD34/CD31 double immunofluorescence was performed to unequivocally differentiate telocytes (CD34-positive/CD31-negative) from vascular endothelial cells (CD34-positive/CD31-positive). Few telocytes entrapped in the fibrotic extracellular matrix were found in the muscularis mucosae and submucosa of SSc gastric wall. In the muscle layers and myenteric plexus, the network of telocytes was discontinuous or even completely absent around smooth muscle cells and ganglia. Telocytes were almost completely absent in fibrotic areas of SSc myocardium. In SSc fibrotic lung, few or no telocytes were observed in the thickened alveolar septa, around blood vessels and in the interstitial space surrounding terminal and respiratory bronchioles. In SSc, the loss of telocytes is not restricted to the skin, but it is a widespread process affecting multiple organs targeted by the fibrotic process. As telocytes are believed to be key players in the regulation of tissue/organ homoeostasis, our data suggest that telocyte loss might have important pathophysiological implications in SSc. PMID:24467430

Detection of Helicobacter pylori in Oral Lesions

PubMed Central

Irani, Soussan; Monsef Esfahani, Alireza; Bidari Zerehpoush, Farahnaz

2013-01-01

Background and aims. Helicobacter pylori is a microaerophilic gram-negative spiral organism. It is recognized as the etiologic factor for peptic ulcers, gastric adenocarcinoma and gastric lymphoma. Recently, it has been isolated from dental plaque and the dorsum of the tongue. This study was designed to assess the association between H. pylori and oral lesions such as ulcerative/inflammatory lesions, squamous cell carcinoma (SCC) and primary lymphoma. Materials and methods. A total of 228 biopsies diagnosed as oral ulcerative/inflammatory lesions, oral squamous cell carcinoma (OSCC) and oral primary lymphoma were selected from the archives of the Pathology Department. Thirty-two samples that were diagnosed as being without any pathological changes were selected as the control group. All the paraffin blocks were cut for hematoxylin and eosin staining to confirm the diagnoses and then the samples were prepared for immunohistochemistry staining. Data were collected and analyzed. Results. Chi-squared test showed significant differences between the frequency of H. pylori positivity in normal tissue and the lesions were examined (P=0.000). In addition, there was a statistically significant difference between the lesions examined (P=0.042). Chi-squared test showed significant differences between H. pylori positivity and different tissue types except inside the muscle layer as follows: in epithelium and in lamina propria (P=0.000), inside the blood vessels (P=0.003), inside the salivary gland duct (P=0.036), and muscle layer (P=0.122). Conclusion. There might be a relation between the presence of H. pylori and oral lesions. Therefore, early detection and eradication of H. pylori in high-risk patients are suggested. PMID:24578822

NASA's Rodent Research Project: Validation of Capabilities for Conducting Long Duration Experiments in Space

NASA Technical Reports Server (NTRS)

Choi, Sungshin Y.; Cole, Nicolas; Reyes, America; Lai, San-Huei; Klotz, Rebecca; Beegle, Janet E.; Wigley, Cecilia L.; Pletcher, David; Globus, Ruth K.

2015-01-01

Research using rodents is an essential tool for advancing biomedical research on Earth and in space. Prior rodent experiments on the Shuttle were limited by the short flight duration. The International Space Station (ISS) provides a new platform for conducting rodent experiments under long duration conditions. Rodent Research (RR)-1 was conducted to validate flight hardware, operations, and science capabilities that were developed at the NASA Ames Research Center. Twenty C57BL6J adult female mice were launched on Sept 21, 2014 in a Dragon Capsule (SpaceX-4), then transferred to the ISS for a total time of 21-22 days (10 commercial mice) or 37 days (10 validation mice). Tissues collected on-orbit were either rapidly frozen or preserved in RNAlater at -80C (n2group) until their return to Earth. Remaining carcasses on-orbit were rapidly frozen for dissection post-flight. The three controls groups at Kennedy Space Center consisted of: Basal mice euthanized at the time of launch, Vivarium controls housed in standard cages, and Ground Controls (GC) housed in flight hardware within an environmental chamber. Upon return to Earth, there were no differences in body weights between Flight (FLT) and GC at the end of the 37 days in space. Liver enzyme activity levels of FLT mice and all control mice were similar in magnitude to those of the samples that were processed under optimal conditions in the laboratory. Liver samples dissected on-orbit yielded high quality RNA (RIN8.99+-0.59, n7). Liver samples dissected post-flight from the intact, frozen FLT carcasses yielded RIN of 7.27 +- 0.52 (n6). Additionally, wet weights of various tissues were measured. Adrenal glands and spleen showed no significant differences in FLT compared to GC although thymus and livers weights were significantly greater in FLT compared to GC. Over 3,000 tissue aliquots collected post-flight from the four groups of mice were deposited into the Ames Life Science Data Archives for future Biospecimen Sharing Program. Together, the RR validation flight successfully demonstrates the capability to support long-duration experimentation on the ISS to achieve both basic science and biomedical objectives.

Exome capture sequencing reveals new insights into hepatitis B virus-induced hepatocellular carcinoma at the early stage of tumorigenesis.

PubMed

Chen, Yong; Wang, Lijuan; Xu, Hexiang; Liu, Xingxiang; Zhao, Yingren

2013-10-01

Hepatocellular carcinoma (HCC), the most common type of liver cancer, is the third primary cause of cancer-related mortality worldwide. The molecular mechanisms underlying the initiation and formation of HCC remain obscure. In the present study, we performed exome sequencing using tumor and normal tissues from 3 hepatitis B virus (HBV)-positive BCLC stage A HCC patients. Bioinformatic analysis was performed to find candidate protein-altering somatic mutations. Eighty damaging mutations were validated and 59 genes were reported to be mutated in HBV-related HCCs for the first time here. Further analysis using whole genome sequencing (WGS) data of 88 HBV-related HCC patients from the European Genome-phenome Archive database showed that mutations in 33 of the 59 genes were also detected in other samples. Variants of two newly found genes, ZNF717 and PARP4, were detected in more than 10% of the WGS samples. Several other genes, such as FLNA and CNTN2, are also noteworthy. Thus, the exome sequencing analysis of three BCLC stage A patients provides new insights into the molecular events governing the early steps of HBV-induced HCC tumorigenesis.

Use of routine histopathology and factor VIII-related antigen/von Willebrand factor immunohistochemistry to differentiate primary hemangiosarcoma of bone from telangiectatic osteosarcoma in 54 dogs.

PubMed

Giuffrida, M A; Bacon, N J; Kamstock, D A

2017-12-01

Hemangiosarcoma (HSA) of bone and telangiectatic osteosarcoma (tOSA) can appear similar histologically, but differ in histogenesis (malignant endothelial cells versus osteoblasts), and may warrant different treatments. Immunohistochemistry (IHC) for endothelial cell marker factor VIII-related antigen/von Willebrand factor (FVIII-RAg/vWF) is a well-documented ancillary test to confirm HSA diagnoses in soft tissues, but its use in osseous HSA is rarely described. Archived samples of 54 primary appendicular bone tumours previously diagnosed as HSA or tOSA were evaluated using combination routine histopathology (RHP) and IHC. Approximately 20% of tumours were reclassified on the basis of FVIII-RAg/vWF immunoreactivity, typically from an original diagnosis of tOSA to a reclassified diagnosis of HSA. No sample with tumour osteoid clearly identified on RHP was immunopositive for FVIII-RAg/vWF. RHP alone was specific but not sensitive for diagnosis of HSA, compared with combination RHP and IHC. Routine histopathological evaluation in combination with FVIII-RAg/vWF IHC can help differentiate canine primary appendicular HSA from tOSA. © 2016 John Wiley & Sons Ltd.

Comparison between single PCR and nested PCR in detection of human papilloma viruses in paraffin-embedded OSCC and fresh oral mucosa.

PubMed

Jalouli, Miranda; Jalouli, Jamshid; Ibrahim, Salah O; Hirsch, Jan-Michaél; Sand, Lars

2015-01-01

Infection with human papilloma virus (HPV) has been implicated as one of the risk factors for the development of oropharyngeal cancer. Many different HPV tests exist, and information regarding their specific technical, analytical, and clinical properties is increasing. This study aimed to compare the level of detection of HPV using two reliable polymerase chain reaction (PCR) methods, nested PCR (NPCR) and single PCR (SPCR), in archival paraffin-embedded oral squamous cell carcinoma (OSCC) samples and fresh oral mucosa specimens. The presence of HPV genome in two groups of tissue samples was analyzed: (i) 57 paraffin-embedded OSCC samples from Sudan and (ii) eight healthy fresh oral mucosal samples from Swedish volunteers. The specimens were tested by SPCR with primer pair MY9/MY11 and NPCR using GP5+/GP6+ primer sets. Eighteen (32%) out of the 57 paraffin-embedded OSCC samples, and five (62%) out of the eight fresh clinically healthy samples were found to be HPV-positive with NPCR. With SPCR, four (7%) out of the paraffin-embedded OSCC samples were HPV-positive. A statistically significant difference between HPV-positive and -negative samples was found when comparing NPCR and SPCR in OSCC and fresh oral mucosa (p<0.0001). The comparative test between SPCR and NPCR showed 100% sensitivity and 69% specificity for OSCC. The use of the GP5+/GP6+ nested PCR increased the positivity rate, efficiency rate and sensitivity of HPV detection in oral samples significantly and should be considered as the method of choice. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue

PubMed Central

2010-01-01

Background The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months. Methods RNA from fresh frozen (FF) and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospectively selected genes and computing scores representing the functions of the estrogen receptor (eight genes, ER_8), the progesterone receptor (five genes, PGR_5), Her2 (two genes, HER2_2), and proliferation (ten genes, PRO_10) by quantitative reverse transcription PCR (qRT-PCR) on TaqMan Low Density Arrays. Molecular scores were computed for each category and ER_8, PGR_5, HER2_2, and PRO_10 scores were combined into a RISK_25 score. Results Pearson correlation coefficients between FF- and FFPE-derived scores were at least 0.94 and high concordance was observed between molecular scores and immunohistochemical data. The HER2_2, PGR_5, PRO_10 and RISK_25 scores were significant predictors of disease free-survival (DFS) in univariate Cox proportional hazard regression. PRO_10 and RISK_25 scores predicted DFS in patients with histological grade II breast cancer and in lymph node positive disease. The PRO_10 and PGR_5 scores were independent predictors of DFS in multivariate Cox regression models incorporating clinical risk indicators; PRO_10 outperformed Ki-67 labeling index in multivariate Cox proportional hazard analyses. Conclusions Scores representing the endocrine responsiveness and proliferation status of breast cancers were developed from gene expression analyses based on RNA derived from FFPE tissues. The validation of the molecular scores with tumor samples of participants of the BIG 1-98 trial demonstrates that such scores can serve as independent prognostic factors to estimate disease free survival (DFS) in postmenopausal patients with estrogen receptor positive breast cancer. Trial Registration Current Controlled Trials: NCT00004205 PMID:20144231

Final report for project "Effects of Low-Dose Irradiation on NFkB Signaling Networks and Mitochondria"

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woloschak, Gayle E; Grdina, David; Li, Jian-Jian

Low dose ionizing radiation effects are difficult to study in human population because of the numerous confounding factors such as genetic and lifestyle differences. Research in mammalian model systems and in vitro is generally used in order to overcome this difficulty. In this program project three projects have joined together to investigate effects of low doses of ionizing radiation. These are doses at and below 10 cGy of low linear energy transfer ionizing radiation such as X-ray and gamma rays. This project was focused on cellular signaling associated with nuclear factor kappa B (NFkB) and mitochondria - subcellular organelles criticalmore » for cell aging and aging-like changes induced by ionizing radiation. In addition to cells in culture this project utilized animal tissues accumulated in a radiation biology tissue archive housed at Northwestern University (http://janus.northwestern.edu/janus2/index.php). Major trust of Project 1 was to gather all of the DoE sponsored irradiated animal (mouse, rat and dog) data and tissues under one roof and investigate mitochondrial DNA changes and micro RNA changes in these samples. Through comparison of different samples we were trying to delineate mitochondrial DNA quantity alterations and micro RNA expression differences associated with different doses and dose rates of radiation. Historic animal irradiation experiments sponsored by DoE were done in several national laboratories and universities between 1950’s and 1990’s; while these experiments were closed data and tissues were released to Project 1. Project 2 used cells in culture to investigate effects that low doses or radiation have on NFκB and its target genes manganese superoxide dismutase (MnSOD) and genes involved in cell cycle: Cyclins (B1 and D1) and cyclin dependent kinases (CDKs). Project 3 used cells in culture such as “normal” human cells (breast epithelial cell line MCF10A cells and skin keratinocyte cells HK18) and mouse embryo fibroblast (mef) cells to focus on role of NFkB protein and several other proteins such as survivin (BIRC5) in radiation dependent regulation of tumor necrosis factor alpha (TNFα) and its downstream signaling.« less

Repurposing Archival Samples for Investigating Toxicological Modes of Action

EPA Science Inventory

Little is known about formalin fixation induced genomic artifacts, limiting the use of formalin-fixed paraffin-embedded (FFPE) samples in toxicological and clinical studies. Previously, we identified a consistent shift in transcriptional profiles between paired frozen and FFPE sa...

Equine insulin receptor and insulin-like growth factor-1 receptor expression in digital lamellar tissue and insulin target tissues.

PubMed

Kullmann, A; Weber, P S; Bishop, J B; Roux, T M; Norby, B; Burns, T A; McCutcheon, L J; Belknap, J K; Geor, R J

2016-09-01

Hyperinsulinaemia is implicated in the pathogenesis of endocrinopathic laminitis. Insulin can bind to different receptors: two insulin receptor isoforms (InsR-A and InsR-B), insulin-like growth factor-1 receptor (IGF-1R) and InsR/IGF-1R hybrid receptor (Hybrid). Currently, mRNA expression of these receptors in equine tissues and the influence of body type and dietary carbohydrate intake on expression of these receptors is not known. The study objectives were to characterise InsR-A, InsR-B, IGF-1R and Hybrid expression in lamellar tissue (LT) and insulin responsive tissues from horses and examine the effect of dietary nonstructural carbohydrate (NSC) on mRNA expression of these receptors in LT, skeletal muscle, liver and two adipose tissue (AT) depots of lean and obese ponies. In vivo experiment. Lamellar tissue samples were evaluated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) for receptor mRNA expression (n = 8) and immunoblotting for protein expression (n = 3). Archived LT, skeletal muscle, liver and AT from lean and obese mixed-breed ponies fed either a low (~7% NSC as dry matter; 5 lean, 5 obese) or high NSC diet (~42% NSC as dry matter; 6 lean, 6 obese) for 7 days were evaluated by RT-qPCR to determine the effect of body condition and diet on expression of the receptors in different tissues. Significance was set at P≤0.05. Lamellar tissue expresses both InsR isoforms, IGF-1R and Hybrid. LT IGF-1R gene expression was greater than either InsR isoform and InsR-A expression was greater than InsR-B (P≤0.05). Obesity significantly lowered IGF-1R, InsR-A and InsR-B mRNA expression in LT and InsR-A in tailhead AT. High NSC diet lowered expression of all three receptor types in liver; IGF-1R and InsR-A in LT and InsR-A in tailhead AT. Lamellar tissue expresses IGF-1R, InsR isoforms and Hybrids. The functional characteristics of these receptors and their role in endocrinopathic laminitis warrants further investigation. © 2015 EVJ Ltd.

Chroni - an Android Application for Geochronologists to Access Archived Sample Analyses from the NSF-Funded Geochron.Org Data Repository.

NASA Astrophysics Data System (ADS)

Nettles, J. J.; Bowring, J. F.

2014-12-01

NSF requires data management plans as part of funding proposals and geochronologists, among other scientists, are archiving their data and results to the public cloud archives managed by the NSF-funded Integrated Earth Data Applications, or IEDA. GeoChron is a database for geochronology housed within IEDA. The software application U-Pb_Redux developed at the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES.org) at the College of Charleston provides seamless connectivity to GeoChron for uranium-lead (U-Pb) geochronologists to automatically upload and retrieve their data and results. U-Pb_Redux also manages publication-quality documents including report tables and graphs. CHRONI is a lightweight mobile application for Android devices that provides easy access to these archived data and results. With CHRONI, U-Pb geochronologists can view archived data and analyses downloaded from the Geochron database, or any other location, in a customizable format. CHRONI uses the same extensible markup language (XML) schema and documents used by U-Pb_Redux and GeoChron. Report Settings are special XML files that can be customized in U-Pb_Redux, stored in the cloud, and then accessed and used in CHRONI to create the same customized data display on the mobile device. In addition to providing geologists effortless and mobile access to archived data and analyses, CHRONI allows users to manage their GeoChron credentials, quickly download private and public files via a specified IEDA International Geo Sample Number (IGSN) or URL, and view specialized graphics associated with particular IGSNs. Future versions of CHRONI will be developed to support iOS compatible devices. CHRONI is an open source project under the Apache 2 license and is hosted at https://github.com/CIRDLES/CHRONI. We encourage community participation in its continued development.

PRDM1 expression on the epithelial component but not on ectopic lymphoid tissues of Warthin tumour.

PubMed

Wang, Y; Zhou, J; Zhang, Y; Wang, L; Liu, Y; Fan, L; Zhu, J; Xu, X; Huang, G; Li, X; Xun, W

2015-05-01

To determine the role of PRDM1, a key molecule for modulating the immune cells, in Warthin tumour (WT) pathogenesis. Forty paraffin-embedded parotid tissues of patients (mean age: 62.08 ± 11.90) with WT were retrieved from the pathology archives of Qindu Hospital from January 2012 to December 2012. The PRDM1 expression was investigated in a cohort of WT by immunohistochemistry. PRDM1 was expressed only on the epithelial component but not on ectopic lymphoid tissue of the tumour. Statistically, PRDM1 expression rates between WT glandular epithelial cells (40/40 cases) and the tumour-adjacent tissues (0/9 cases), and WT germinal centres (0/34 cases) and tonsil tissues (10/10 cases) were significantly different (P < 0.001), respectively. The PRDM1 expression appeared to play an essential role in WT pathogenesis. A better understanding of it might give options for revealing possible novel management strategies. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Foliar and soil chemistry at red spruce sites in the Monongahela National Forest

Treesearch

Stephanie J. Connolly

2010-01-01

In 2005, soil and foliar chemistry were sampled from 10 sites in the Monongahela National Forest which support red spruce. Soils were sampled from hand-dug pits, by horizon, from the O-horizon to bedrock or 152 cm, and each pit was described fully. Replicate, archived samples also were collected.

ISS Potable Water Sampling and Chemical Analysis Results for 2016

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Wallace William T.; Alverson, James T.; Benoit, Mickie J.; Gillispie, Robert L.; Hunter, David; Kuo, Mike; Rutz, Jeffrey A.; Hudson, Edgar K.;

ISS Potable Water Sampling and Chemical Analysis Results for 2016

NASA Technical Reports Server (NTRS)

Straub, John E., II; Plumlee, Debrah K.; Wallace, William T.; Alverson, James T.; Benoit, Mickie J.; Gillispie, Robert L.; Hunter, David; Kuo, Mike; Rutz, Jeffrey A.; Hudson, Edgar K.;

Exploring Hominin and Non-hominin Primate Dental Fossil Remains with Neutron Microtomography

NASA Astrophysics Data System (ADS)

Zanolli, Clément; Schillinger, Burkhard; Beaudet, Amélie; Kullmer, Ottmar; Macchiarelli, Roberto; Mancini, Lucia; Schrenk, Friedemann; Tuniz, Claudio; Vodopivec, Vladimira

Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on X-ray microfocus sources (X-μCT) and Synchrotron Radiation (SR-μCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through high-resolution ;virtual histology;. Nonetheless, depending on the degree of alterations undergone during fossilization, X-ray analyses of tooth tissues do not always provide distinct imaging contrasts, thus preventing the extraction of essential morphological and anatomical details. We illustrate here by three examples the successful application of neutron microtomography (n-μCT) in cases where X-rays have previously failed to deliver contrasts between dental tissues of fossilized specimen.

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform.

PubMed

Kim, Claire H; Tworoger, Shelley S; Stampfer, Meir J; Dillon, Simon T; Gu, Xuesong; Sawyer, Sherilyn J; Chan, Andrew T; Libermann, Towia A; Eliassen, A Heather

2018-05-30

The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses' Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours after collection, as well as those of samples collected from the same individuals 1 year apart. CVs were <20% for 99% of proteins overall and <10% for 92% of proteins in heparin samples compared to 66% for EDTA samples. We observed ICC or Spearman r (comparing immediate vs. 24-hour delayed processing) ≥0.75 for 61% of proteins, with some variation by anticoagulant (56% for heparin and 70% for EDTA) and protein class (ranging from 49% among kinases to 83% among hormones). Within-person stability over 1 year was good (ICC or Spearman r ≥ 0.4) for 91% of proteins. These results demonstrate the feasibility of SOMAscan for analyses of archived plasma samples.

The Index to Marine and Lacustrine Geological Samples: Improving Sample Accessibility and Enabling Current and Future Research

NASA Astrophysics Data System (ADS)

Moore, C.

2011-12-01

The Index to Marine and Lacustrine Geological Samples is a community designed and maintained resource enabling researchers to locate and request sea floor and lakebed geologic samples archived by partner institutions. Conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center (NGDC) at a 1977 meeting convened by the National Science Foundation (NSF), the Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. Form and content of underlying vocabularies and metadata continue to evolve according to the needs of the community, as do supporting technologies and access methodologies. The Curators Consortium, now international in scope, meets at partner institutions biennially to share ideas and discuss best practices. NGDC serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the herculean task of creating and contributing metadata for over 195,000 sea floor and lakebed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images; 1) at participating institutions, 2) in the NGDC archive, and 3) at sites such as the Rolling Deck to Repository (R2R) and the System for Earth Sample Registration (SESAR). Over 34,000 International GeoSample Numbers (IGSNs) linking to SESAR are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. To promote interoperability and broaden exposure via the semantic web, NGDC is publishing lithologic classification schemes and terminology used in the Index as Simple Knowledge Organization System (SKOS) vocabularies, coordinating with R2R and the Consortium for Ocean Leadership for consistency. Availability in SKOS form will also facilitate use of the vocabularies in International Standards Organization (ISO) 19115-2 compliant metadata records. NGDC provides stewardship for the Index on behalf of U.S. repositories as the NSF designated "appropriate National Data Center" for data and metadata pertaining to sea floor samples as specified in the 2011 Division of Ocean Sciences Sample and Data Policy, and on behalf of international partners via a collocated World Data Center. NGDC operates on the Open Archival Information System (OAIS) reference model. Active Partners: Antarctic Marine Geology Research Facility, Florida State University; British Ocean Sediment Core Research Facility; Geological Survey of Canada; Integrated Ocean Drilling Program; Lamont-Doherty Earth Observatory; National Lacustrine Core Repository, University of Minnesota; Oregon State University; Scripps Institution of Oceanography; University of Rhode Island; U.S. Geological Survey; Woods Hole Oceanographic Institution.

Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II.

PubMed

Herrmann, Daland C; Maksimov, Pavlo; Hotop, Andrea; Groß, Uwe; Däubener, Walter; Liesenfeld, Oliver; Pleyer, Uwe; Conraths, Franz J; Schares, Gereon

2014-10-01

Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany. Copyright © 2014 Elsevier GmbH. All rights reserved.

VizieR Online Data Catalog: M67 variable stars from Kepler/K2-Campaign-5 (Gonzalez, 2016)

NASA Astrophysics Data System (ADS)

Gonzalez, G.

2017-06-01

M 67 was observed continuously between 2015 April 27 and July 10 during the Kepler/K2-Campaign-5 (hereafter, 'Campaign-5 field'). It includes 28 850 long-cadence, 204 short-cadence, and several other special targets. Several data products for the Campaign-5 field were released to the public on the NASA Barbara A. Mikulski Archive for Space Telescopes (MAST) website on 2015 October 30 (https://archive.stsci.edu/k2/). We downloaded tar files containing all the long-cadence light-curve (CLC) files of the Campaign-5 targets from the MAST archive. In addition, we downloaded the comprehensive K2 input catalogue (EPIC) for the Campaign-5 field. We supplemented the NASA K2 data with ground-based data, of which Nardiello et al. (2016, Cat. J/MNRAS/455/2337) is our primary source. Nardiello et al. (2016, Cat. J/MNRAS/455/2337) list the positions and white-light magnitudes for 6905 objects in the M 67 field, but they only list BVRI magnitudes, proper motions and membership probabilities for a subset of this large sample. Cross-referencing (using coordinates) the Campaign-5 input catalogue with the Nardiello et al. (2016, Cat. J/MNRAS/455/2337) catalogue resulted in 3201 matches. Of these, 639 have light curves available in the MAST Campaign-5 archive. This will be the working sample. (1 data file).

Evaluating Trends in Historical PM2.5 Element Concentrations by Reanalyzing a 15-Year Sample Archive

NASA Astrophysics Data System (ADS)

Hyslop, N. P.; White, W. H.; Trzepla, K.

2014-12-01

The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors aerosol concentrations at 170 remote sites throughout the United States. Twenty-four-hour filter samples of particulate matter are collected every third day and analyzed for chemical composition. About 30 of the sites have operated continuously since 1988, and the sustained data record (http://views.cira.colostate.edu/web/) offers a unique window on regional aerosol trends. All elemental analyses have been performed by Crocker Nuclear Laboratory at the University of California in Davis, and sample filters collected since 1995 are archived on campus. The suite of reported elements has remained constant, but the analytical methods employed for their determination have evolved. For example, the elements Na - Mn were determined by PIXE until November 2001, then by XRF analysis in a He-flushed atmosphere through 2004, and by XRF analysis in vacuum since January 2005. In addition to these fundamental changes, incompletely-documented operational factors such as detector performance and calibration details have introduced variations in the measurements. Because the past analytical methods were non-destructive, the archived filters can be re-analyzed with the current analytical systems and protocols. The 15-year sample archives from Great Smoky Mountains (GRSM), Mount Rainier (MORA), and Point Reyes National Parks (PORE) were selected for reanalysis. The agreement between the new analyses and original determinations varies with element and analytical era. The graph below compares the trend estimates for all the elements measured by IMPROVE based on the original and repeat analyses; the elements identified in color are measured above the detection limit more than 90% of the time. The trend estimates are sensitive to the treatment of non-detect data. The original and reanalysis trends are indistinguishable (have overlapping confidence intervals) for most of the well-detected elements.

Reanalysis of a 15-year Archive of IMPROVE Samples

NASA Astrophysics Data System (ADS)

Hyslop, N. P.; White, W. H.; Trzepla, K.

2013-12-01

The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors aerosol concentrations at 170 remote sites throughout the United States. Twenty-four-hour filter samples of particulate matter are collected every third day and analyzed for chemical composition. About 30 of the sites have operated continuously since 1988, and the sustained data record (http://views.cira.colostate.edu/web/) offers a unique window on regional aerosol trends. All elemental analyses have been performed by Crocker Nuclear Laboratory at the University of California in Davis, and sample filters collected since 1995 are archived on campus. The suite of reported elements has remained constant, but the analytical methods employed for their determination have evolved. For example, the elements Na - Mn were determined by PIXE until November 2001, then by XRF analysis in a He-flushed atmosphere through 2004, and by XRF analysis in vacuum since January 2005. In addition to these fundamental changes, incompletely-documented operational factors such as detector performance and calibration details have introduced variations in the measurements. Because the past analytical methods were non-destructive, the archived filters can be re-analyzed with the current analytical systems and protocols. The 15-year sample archives from Great Smoky Mountains, Mount Rainier, and Point Reyes National Parks were selected for reanalysis. The agreement between the new analyses and original determinations varies with element and analytical era (Figure 1). Temporal trends for some elements are affected by these changes in measurement technique while others are not (Figure 2). Figure 1. Repeatability of analyses for sulfur and vanadium at Great Smoky Mountains National Park. Each point shows the ratio of mass loadings determined by the original analysis and recent reanalysis. Major method distinctions are indicated at the top. Figure 2. Trends, based on Thiel-Sen regression, in lead concentrations based on the original and reanalysis data.

Integration of In-Flight and Post-Flight Water Monitoring Resources in Addressing the U.S. Water Processor Assembly Total Organic Carbon (TOC) Anomaly

NASA Technical Reports Server (NTRS)

Straub, John E., II; McCly, J. Torin

2011-01-01

Beginning in June of 2010, the total organic carbon (TOC) concentration in the U.S. Water Processor Assembly (WPA) product water started to increase. A surprisingly consistent upward TOC trend was observed through weekly ISS total organic carbon analyzer (TOCA) monitoring. As TOC is a general organic compound indicator, return of water archive samples was needed to make better-informed crew health decisions on the specific compounds of concern and to aid in WPA troubleshooting. TOCA-measured TOC was more than halfway to the health-based screening limit of 3,000 g/L before archive samples were returned. Archive samples were returned on 22 Soyuz in September 2010 and on ULF5 in November of 2010. The samples were subjected to extensive analysis. Although TOC was confirmed to be elevated, somewhat surprisingly, none of the typical target compounds were detected at high levels. After some solid detective work, it was confirmed that the TOC was associated with a compound known as dimethylsilanediol (DMSD). DMSD is believed to be a breakdown product of siloxanes which are thought to be ubiquitous in the ISS atmosphere. A toxicological limit was set for DMSD and a forward plan was developed for conducting operations in the context of understanding the composition of the TOC measured in flight. This required careful consideration of existing ISS flight rules, coordination with ISS stakeholders, and development of a novel approach for the blending of inflight TOCA data with archive results to protect crew health. Among other challenges, team members had to determine how to utilize TOCA readings when making decisions about crew consumption of WPA water. This involved balancing very real concerns associated with the assumption that TOC would continue to be comprised of only DMSD. Demonstrated teamwork, multidisciplinary awareness, and innovative problem-solving were required to respond effectively to this anomaly.

Interrogating trees as archives of sulphur deposition

NASA Astrophysics Data System (ADS)

Wynn, P. M.; Loader, N. J.; Fairchild, I. J.

2012-04-01

A principal driver of climatic variability over the past 1,000 years and essential forcing mechanism for climate, are the changes in atmospheric composition resulting from sulphur aerosols. Natural and anthropogenic aerosols released into the atmosphere disrupt the radiative balance through backscattering and absorption of incoming solar radiation and increase cloud albedo by acting as condensation nuclei. Understanding the impact of sulphur emissions upon climate beyond the last few hundred years however is not straightforward and natural archives of environmental information must be explored. Tree-rings represent one such archive as they are widely distributed and preserve environmental information within a precisely dateable, annually resolved timescale. Until recently the sulphur contained within tree-rings has largely remained beyond the reach of environmental scientists and climate modelers owing to difficulties associated with the extraction of a robust signal and uncertainties regarding post-depositional mobility. Our recent work using synchrotron radiation has established that the majority of non-labile sulphur in two conifer species is preserved within the cellular structure of the woody tissue after uptake and demonstrates an increasing trend in sulphur concentration during the 20th century and during known volcanic events. Due to the clear isotopic distinction between marine (+21), geological (+10 to +30), atmospheric pollution (-3 to +9 ) and volcanic sources of sulphur (0 to +5), isotopic ratios provide a diagnostic tool with which changes in the source of atmospheric sulphur can be detected in a more reliable fashion than concentration alone. Sulphur isotopes should thereby provide a fingerprint of short lived events including volcanic activity when extracted at high resolution and in conjunction with high resolution S concentrations defining the event. Here we present methodologies associated with extracting the sulphur isotopic signal from tree-rings using both elemental analyser isotope ratio mass spectrometry and ion probe technology. Preliminary data indicate success at extracting the sulphur isotopic signal from woody tissues at 2-3 year resolution. In conjunction with analytical developments in ion probe technology, high resolution records of localised sulphur forcing from tree-ring archives, including volcanic activity, no longer seem too far beyond the reach of climate scientists.

Rapid Multiplex PCR Assay To Identify Respiratory Viral Pathogens: Moving Forward Diagnosing The Common Cold

PubMed Central

Gordon, Sarah M; Elegino-Steffens, Diane U; Agee, Willie; Barnhill, Jason; Hsue, Gunther

2013-01-01

Upper respiratory tract infections (URIs) can be a serious burden to the healthcare system. The majority of URIs are viral in etiology, but definitive diagnosis can prove difficult due to frequently overlapping clinical presentations of viral and bacterial infections, and the variable sensitivity, and lengthy turn-around time of viral culture. We tested new automated nested multiplex PCR technology, the FilmArray® system, in the TAMC department of clinical investigations, to determine the feasibility of replacing the standard viral culture with a rapid turn-around system. We conducted a feasibility study using a single-blinded comparison study, comparing PCR results with archived viral culture results from a convenience sample of cryopreserved archived nasopharyngeal swabs from acutely ill ED patients who presented with complaints of URI symptoms. A total of 61 archived samples were processed. Viral culture had previously identified 31 positive specimens from these samples. The automated nested multiplex PCR detected 38 positive samples. In total, PCR was 94.5% concordant with the previously positive viral culture results. However, PCR was only 63.4% concordant with the negative viral culture results, owing to PCR detection of 11 additional viral pathogens not recovered on viral culture. The average time to process a sample was 75 minutes. We determined that an automated nested multiplex PCR is a feasible alternative to viral culture in an acute clinical setting. We were able to detect at least 94.5% as many viral pathogens as viral culture is able to identify, with a faster turn-around time. PMID:24052914

Molecular Phylogeny of Hantaviruses Harbored by Insectivorous Bats in Côte d’Ivoire and Vietnam

PubMed Central

Gu, Se Hun; Lim, Burton K.; Kadjo, Blaise; Arai, Satoru; Kim, Jeong-Ah; Nicolas, Violaine; Lalis, Aude; Denys, Christiane; Cook, Joseph A.; Dominguez, Samuel R.; Holmes, Kathryn V.; Urushadze, Lela; Sidamonidze, Ketevan; Putkaradze, Davit; Kuzmin, Ivan V.; Kosoy, Michael Y.; Song, Jin-Won; Yanagihara, Richard

2014-01-01

The recent discovery of genetically distinct hantaviruses in multiple species of shrews and moles prompted a further exploration of their host diversification by analyzing frozen, ethanol-fixed and RNAlater®-preserved archival tissues and fecal samples from 533 bats (representing seven families, 28 genera and 53 species in the order Chiroptera), captured in Asia, Africa and the Americas in 1981–2012, using RT-PCR. Hantavirus RNA was detected in Pomona roundleaf bats (Hipposideros pomona) (family Hipposideridae), captured in Vietnam in 1997 and 1999, and in banana pipistrelles (Neoromicia nanus) (family Vespertilionidae), captured in Côte d’Ivoire in 2011. Phylogenetic analysis, based on the full-length S- and partial M- and L-segment sequences using maximum likelihood and Bayesian methods, demonstrated that the newfound hantaviruses formed highly divergent lineages, comprising other recently recognized bat-borne hantaviruses in Sierra Leone and China. The detection of bat-associated hantaviruses opens a new era in hantavirology and provides insights into their evolutionary origins. PMID:24784569

454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples

PubMed Central

Altimari, Annalisa; de Biase, Dario; De Maglio, Giovanna; Gruppioni, Elisa; Capizzi, Elisa; Degiovanni, Alessio; D’Errico, Antonia; Pession, Annalisa; Pizzolitto, Stefano; Fiorentino, Michelangelo; Tallini, Giovanni

2013-01-01

Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues. PMID:23950653

Aberrant microRNA-137 promoter methylation is associated with lymph node metastasis and poor clinical outcomes in non-small cell lung cancer

PubMed Central

Min, Lingfeng; Wang, Fang; Hu, Suwei; Chen, Yong; Yang, Junjun; Liang, Sudong; Xu, Xingxiang

2018-01-01

MicroRNA-137 (miR-137) functions as a tumor suppressor and is silenced by aberrant promoter methylation. Previous studies have demonstrated that miR-137 is downregulated in lung cancer. The purpose of the present study was to investigate miR-137 promoter methylation and to assess its prognostic value in non-small cell lung cancer (NSCLC). The expression of miR-137 was analyzed inhuman lung cancer A549 and H1299 cells and normal bronchial epithelial BEAS-2B cells, 10 paired formalin-fixed paraffin-embedded lung cancer and normal tissue samples, and 56 archived paraffin-embedded lung cancer tissues. Quantitative methylation-specific polymerase chain reaction analysis was used to assess the miR-137 methylation status. The associations between miR-137 promoter methylation and the clinicopathological features and prognosis of patients with NSCLC (n=56) were analyzed using analysis of variance. miR-137 was markedly downregulated in lung cancer cells and lung cancer tissue specimens compared with expression in BEAS-2B cells and matched adjacent normal lung tissues. A significant negative correlation between miR-137 expression and miR-137 promoter methylation was observed in human lung cancer tissues (r=−0.343; P=0.01). Smoking, lymph node metastasis and advanced clinical stage were associated with significantly lower expression of miR-137 in variance analysis. High levels of miR-137 promoter methylation were associated with a significantly poorer disease-free survival rate (P=0.034), but were not associated with overall survival, in Kaplan-Meier analysis and univariate analysis. In conclusion, the results of the present study indicated that miR-137 is downregulated and that its promoter is aberrantly methylated in lung cancer, and that high levels of miR-137 promoter methylation may have prognostic value for poor disease-free survival. PMID:29740491

Raman Spectroscopy Study of Prostatic Adenocarcinoma Bulk Tissues

NASA Astrophysics Data System (ADS)

Devpura, S.; Dai, H.; Thakur, J. S.; Naik, R.; Cao, A.; Pandya, A.; Auner, G. W.; Sarkar, F.; Sakr, W.; Naik, V.

2009-03-01

Prostate cancer is one of the most common types of cancer among men. The mortality rate for this disease can be dramatically reduced if it can be diagnosed in its early stages. Raman spectroscopy is one of the optical techniques which can provide fingerprints of a disease in terms of its molecular composition which changes due to the onset of disease. The aim of this project is to investigate the differences in the Raman spectra to identify benign epithelium (BE), prostatic intraepithelial neoplasia (PIN) and adenocarcinoma of various Gleason grades in archived bulk tissues embedded in paraffin wax. For each tissue, two adjacent tissue sections were cut and dewaxed, where one of the sections was stained using haematoxylin and eosin for histological examination and the other unstained adjacent section was used for Raman spectroscopic studies. We have collected Raman spectra from 10 prostatic adenocarcinoma dewaxed tissue sections using Raman microscope (785 nm excitation laser). The data were analyzed using statistical methods of principal component analysis and discriminant function analysis to classify the tissue regions. The results indicate that Raman Spectroscopy can differentiate between BE, PIN and Cancer regions.

Interrogating trees for isotopic archives of atmospheric sulphur deposition and comparison to speleothem records.

PubMed

Wynn, P M; Loader, N J; Fairchild, I J

2014-04-01

Palaeorecords which depict changes in sulphur dynamics form an invaluable resource for recording atmospheric pollution. Tree rings constitute an archive that are ubiquitously available and can be absolutely dated, providing the potential to explore local- to regional-scale trends in sulphur availability. Rapid isotopic analysis by a novel "on-line" method using elemental analyser isotope ratio mass spectrometry (EA-IRMS) is developed, achieving sample precision of <0.4‰ using sample sizes of 40 mg wood powder. Tree cores from NE Italy show trends in pollution, evidenced through increasing concentrations of sulphur towards the youngest growth, and inverse trends in sulphur isotopes differentiating modern growth with light sulphur isotopes (+0.7‰) from pre-industrial growth (+7.5‰) influenced by bedrock composition. Comparison with speleothem records from the same location demonstrate replication, albeit offset in isotopic value due to groundwater storage. Using EA-IRMS, tree ring archives form a valuable resource for understanding local- to regional-scale sulphur pollution dynamics. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nitrate deposition and preservation in the snowpack along a traverse from coast to the ice sheet summit (Dome A) in East Antarctica

NASA Astrophysics Data System (ADS)

Shi, Guitao; Hastings, Meredith G.; Yu, Jinhai; Ma, Tianming; Hu, Zhengyi; An, Chunlei; Li, Chuanjin; Ma, Hongmei; Jiang, Su; Li, Yuansheng

2018-04-01

Antarctic ice core nitrate (NO3-) can provide a unique record of the atmospheric reactive nitrogen cycle. However, the factors influencing the deposition and preservation of NO3- at the ice sheet surface must first be understood. Therefore, an intensive program of snow and atmospheric sampling was made on a traverse from the coast to the ice sheet summit, Dome A, East Antarctica. Snow samples in this observation include 120 surface snow samples (top ˜ 3 cm), 20 snow pits with depths of 150 to 300 cm, and 6 crystal ice samples (the topmost needle-like layer on Dome A plateau). The main purpose of this investigation is to characterize the distribution pattern and preservation of NO3- concentrations in the snow in different environments. Results show that an increasing trend of NO3- concentrations with distance inland is present in surface snow, and NO3- is extremely enriched in the topmost crystal ice (with a maximum of 16.1 µeq L-1). NO3- concentration profiles for snow pits vary between coastal and inland sites. On the coast, the deposited NO3- was largely preserved, and the archived NO3- fluxes are dominated by snow accumulation. The relationship between the archived NO3- and snow accumulation rate can be depicted well by a linear model, suggesting a homogeneity of atmospheric NO3- levels. It is estimated that dry deposition contributes 27-44 % of the archived NO3- fluxes, and the dry deposition velocity and scavenging ratio for NO3- were relatively constant near the coast. Compared to the coast, the inland snow shows a relatively weak correlation between archived NO3- and snow accumulation, and the archived NO3- fluxes were more dependent on concentration. The relationship between NO3- and coexisting ions (nssSO42-, Na+ and Cl-) was also investigated, and the results show a correlation between nssSO42- (fine aerosol particles) and NO3- in surface snow, while the correlation between NO3- and Na+ (mainly associated with coarse aerosol particles) is not significant. In inland snow, there were no significant relationships found between NO3- and the coexisting ions, suggesting a dominant role of NO3- recycling in determining the concentrations.

Toward Automatic Georeferencing of Archival Aerial Photogrammetric Surveys

NASA Astrophysics Data System (ADS)

Giordano, S.; Le Bris, A.; Mallet, C.

2018-05-01

Images from archival aerial photogrammetric surveys are a unique and relatively unexplored means to chronicle 3D land-cover changes over the past 100 years. They provide a relatively dense temporal sampling of the territories with very high spatial resolution. Such time series image analysis is a mandatory baseline for a large variety of long-term environmental monitoring studies. The current bottleneck for accurate comparison between epochs is their fine georeferencing step. No fully automatic method has been proposed yet and existing studies are rather limited in terms of area and number of dates. State-of-the art shows that the major challenge is the identification of ground references: cartographic coordinates and their position in the archival images. This task is manually performed, and extremely time-consuming. This paper proposes to use a photogrammetric approach, and states that the 3D information that can be computed is the key to full automation. Its original idea lies in a 2-step approach: (i) the computation of a coarse absolute image orientation; (ii) the use of the coarse Digital Surface Model (DSM) information for automatic absolute image orientation. It only relies on a recent orthoimage+DSM, used as master reference for all epochs. The coarse orthoimage, compared with such a reference, allows the identification of dense ground references and the coarse DSM provides their position in the archival images. Results on two areas and 5 dates show that this method is compatible with long and dense archival aerial image series. Satisfactory planimetric and altimetric accuracies are reported, with variations depending on the ground sampling distance of the images and the location of the Ground Control Points.

A 115-year δ15N record of cumulative nitrogen pollution in California serpentine grasslands

NASA Astrophysics Data System (ADS)

Vallano, D.; Zavaleta, E. S.

2010-12-01

Until the 1980s, California’s biodiverse serpentine grasslands were threatened primarily by development and protected by reserve creation. However, nitrogen (N) fertilization due to increasing fossil fuel emissions in the expanding Bay Area is thought to be contributing to rapid, recent invasion of these ecosystems by exotic annual grasses that are displacing rare and endemic serpentine species. Documenting the cumulative effects of N deposition in this ecosystem can direct policy and management actions to mitigate the role of N deposition in its transformation. Natural abundance stable isotopes of N in vegetation have been increasingly used as bio-indicators of N deposition patterns and subsequent changes to plant N cycling and assimilation. However, the long-term record of atmospheric reactive N enrichment and the resulting changes in ecosystem N dynamics have yet to be adequately reconstructed in many ecosystems. Museum archives of vascular plant tissue are valuable sources of materials to reconstruct temporal and spatial isotopic patterns of N inputs to ecosystems. Here, we present N stable isotope data from archived and current specimens of an endemic California serpentine grassland species, leather oak (Quercus durata), since 1895 across the greater San Francisco Bay region. We measured spatial and temporal trends in stable isotope composition (δ15N and δ13C) and concentration (%N and %C) of historical and current samples of leather oak leaves from sites within the Bay Area, impacted by increasing development, and sites northeast of the Bay Area, with significantly lower rates of urbanization and industrialization. Specifically, we sampled dry museum and fresh leaf specimens from serpentine sites within Lake (n=27) and Santa Clara (n=30) counties dating from 1895 to 2010. Leaf δ15N values were stable from 1895 to the 1950s and then decreased strongly throughout the last 50 years as fossil fuel emissions rapidly increased in the Bay Area, indicating that N pollution is being retained in serpentine grassland ecosystems. Leaf δ15N values in the high-deposition region declined at a rate of -0.041‰ yr-1, while leaf δ15N values in the low-deposition region did not show a strong pattern. In both regions, leaf δ13C values declined through time as atmospheric CO2 concentrations increased in response to fossil fuel combustion (the Suess effect). Leaf %N and %C values did not present any clear patterns at sites within or outside of the Bay Area. We conclude that using natural abundance stable isotope values in leaves can indicate variation in N pollution inputs across wide spatial and temporal scales and that archived plant samples can provide valuable baselines against which to assess changes in regional N cycling and subsequent ecological impacts on vegetation.

The Prevalence of PCR-Confirmed Pertussis Cases in Palestine From Archived Nasopharyngeal Samples.

PubMed

Dumaidi, Kamal; Al-Jawabreh, Amer

2018-05-01

Pertussis caused by Bordetella pertussis is a vaccine-preventable disease causing whooping cough in humans of all ages. This study reports infection rate of pertussis in Palestine between the years 2004-2008 from archived nasopharyngeal samples collected from clinically- suspected cases. A convenience archived DNA samples collected from 267 clinically-suspected pertussis cases were investigated for B. pertussis. Laboratory diagnosis was done by examining all DNA samples using polymerase chain reaction (PCR). Approximately 49% (130/267) were confirmed by PCR. A pertussis peak was shown to occur in 2008 with 77% (100/130) of PCR-confirmed cases isolated in that year. PCR-confirmed cases existed in all Palestinian districts with highest rate in Ramallah, Bethlehem, Jenin and Al-Khalil. Half of the PCR-confirmed cases (68/130) were less than 2 months old. The positivity rate among who had three doses of vaccine (at 2, 4 and 6 months) was 38%, and became 50% with the fourth dose at 12 months. The prevalence of pertussis was found to be significantly high among infants less than 2 months old. Active pertussis surveillance using rapid PCR assays is essential, as it is helpful in prompt diagnosis and treatment of patients with pertussis. © 2018 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Effects of Data Sampling on Graphical Depictions of Learning

ERIC Educational Resources Information Center

Carey, Mary-Katherine; Bourret, Jason C.

2014-01-01

Continuous and discontinuous data-collection methods were compared in the context of discrete-trial programming. Archival data sets were analyzed using trial sampling (1st 5 trials, 1st 3 trials, and 1st trial only) and session sampling (every other session, every 3rd session, and every 5th session). Results showed that trial sampling…

Comparison and evaluation of mitotic figures in oral epithelial dysplasia using crystal violet and Feulgen stain.

PubMed

Rao, Roopa S; Patil, Shankargouda; Agarwal, Anveeta

2014-05-01

Routine staining procedures often pose a problem in differentiating a mitotic cell from an apoptotic cell, deteriorating the reliability of histology grading. Although various new methods have been recommended for identifying mitotic figures (MFs) in tissues, the time factor and cost makes them less feasible. Thus, an attempt was made to evaluate the efficacy of crystal violet and Feulgen reaction in identifying MFs and also to see for any variation in the number of MFs in various grades of Epithelial dysplasia. 1. Using crystal violet and Feulgen stain in the identification and counting of MFs on diagnosed cases of epithelial dysplasia and thereby to evaluate their efficacy. 2. To evaluate the variation in the number of MFs in various grades of epithelial dysplasia. The study sample includes retrieval of 30 formalin fixed paraffin embedded tissue sections diagnosed for different grades of epithelial dysplasia (WHO grading system, 2005) from the archives, Department of Oral Pathology, MSRDC, Bengaluru. Ten tissue sections each of mild, moderate and severe epithelial dysplasia were stained with H&E, Feulgen and 1% crystal violet stains and the number of MFs were counted. Five cases of cervical carcinoma were taken as control. Stained sections were compared, and data obtained was statistically analyzed using the Kruskal-Wallis test. A significant increase in the number of MFs (p = 0.02) was observed in Feulgen stained sections as compared to H&E stain. Feulgen stain can be considered as a simple, reliable, cost-effective and reproducible method of staining MFs.

UK National Data Centre archive of seismic recordings of (presumed) underground nuclear tests 1964-1996

NASA Astrophysics Data System (ADS)

Young, John; Peacock, Sheila

2016-04-01

The year 1996 has particular significance for forensic seismologists. This was the year when the Comprehensive Test Ban Treaty (CTBT) was signed in September at the United Nations, setting an international norm against nuclear testing. Blacknest, as a long time seismic centre for research into detecting and identifying underground explosions using seismology, provided significant technical advice during the CTBT negotiations. Since 1962 seismic recordings of both presumed nuclear explosions and earthquakes from the four seismometer arrays Eskdalemuir, Scotland (EKA), Yellowknife, Canada (YKA), Gauribidanur, India (GBA), and Warramunga, Australia (WRA) have been copied, digitised, and saved. There was a possibility this archive would be lost. It was decided to process the records and catalogue them for distribution to other groups and institutions. This work continues at Blacknest but the archive is no longer under threat. In addition much of the archive of analogue tape recordings has been re-digitised with modern equipment, allowing sampling rates of 100 rather than 20 Hz.

Multiple hot-deck imputation for network inference from RNA sequencing data.

PubMed

Imbert, Alyssa; Valsesia, Armand; Le Gall, Caroline; Armenise, Claudia; Lefebvre, Gregory; Gourraud, Pierre-Antoine; Viguerie, Nathalie; Villa-Vialaneix, Nathalie

2018-05-15

Network inference provides a global view of the relations existing between gene expression in a given transcriptomic experiment (often only for a restricted list of chosen genes). However, it is still a challenging problem: even if the cost of sequencing techniques has decreased over the last years, the number of samples in a given experiment is still (very) small compared to the number of genes. We propose a method to increase the reliability of the inference when RNA-seq expression data have been measured together with an auxiliary dataset that can provide external information on gene expression similarity between samples. Our statistical approach, hd-MI, is based on imputation for samples without available RNA-seq data that are considered as missing data but are observed on the secondary dataset. hd-MI can improve the reliability of the inference for missing rates up to 30% and provides more stable networks with a smaller number of false positive edges. On a biological point of view, hd-MI was also found relevant to infer networks from RNA-seq data acquired in adipose tissue during a nutritional intervention in obese individuals. In these networks, novel links between genes were highlighted, as well as an improved comparability between the two steps of the nutritional intervention. Software and sample data are available as an R package, RNAseqNet, that can be downloaded from the Comprehensive R Archive Network (CRAN). alyssa.imbert@inra.fr or nathalie.villa-vialaneix@inra.fr. Supplementary data are available at Bioinformatics online.

Hepatitis C virus genotyping of organ donor samples to aid in transplantation of HCV-positive organs.

PubMed

Gentile, Caren; Van Deerlin, Vivianna M; Goldberg, David S; Reese, Peter P; Hasz, Richard D; Abt, Peter; Blumberg, Emily; Farooqi, Midhat S

2018-02-01

Given the availability of new highly efficacious anti-HCV therapies, some clinicians have advocated for wider use of kidneys from hepatitis C virus-positive (HCV+) donors, including transplanting them into HCV-negative recipients. As treatment regimens for HCV are commonly guided by genotype, pretransplant HCV genotyping of tissue donors would be beneficial. To our knowledge, donor HCV genotyping has never been reported. We retrieved archived frozen plasma samples for 17 previous organ donors through a local organ procurement organization. We performed HCV genotyping using the eSensor HCVg Direct Test (GenMark Diagnostics) and also by Sanger sequencing, for confirmation (Retrogen). In addition, viral loads were measured using the COBAS AmpliPrep/TaqMan system (Roche Diagnostics). We found that most of the samples (n = 14) were HCV Genotype 1a with the remainder being Genotype 2b (n = 1) or Genotype 3 (n = 2). All genotyping results were concordant with Sanger sequencing. The average HCV viral load in the sample group was ~ 1.6 million IU/mL (range: ~16 000 IU/mL to 7 million IU/mL). We demonstrate that viral RNA from organ donor plasma can be successfully genotyped for HCV. This ability suggests that transplantation of HCV+ kidneys into HCV-negative recipients, followed by genotype-guided antiviral therapy, could be feasible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Outbreaks of abortions by Coxiella burnetii in small ruminant flocks and a longitudinal serological approach on archived bulk tank milk suggest Q fever emergence in Central Portugal.

PubMed

Cruz, Rita; Esteves, Fernando; Vasconcelos-Nóbrega, Carmen; Santos, Carla; Ferreira, Ana S; Mega, Cristina; Coelho, Ana C; Vala, Helena; Mesquita, João R

2018-05-25

Q fever is a worldwide zoonotic infectious disease caused by Coxiella burnetii and sheep and goats are known to be the main reservoir for human infection. This study describes the epidemiological and laboratory findings of C. burnetii outbreaks affecting sheep and goat flocks and also provides the results of a prospective serosurvey in bulk tank milk samples to assess C. burnetii circulation in a population of sheep living in close contact to the human population in Central Portugal. In the epizooties, C. burnetii was identified in tissues of the resulting abortions by qPCR. As for the serological survey, 10.2% (95%CI: 4.5-19.2) of the 78 bulk tank milk samples collected in 2015 presented IgG antibodies against C. burnetii. The same farms were visited and sampled in 2016 and 25.6% (95%CI: 16.4-36.8) were positive. This steep increase in the number of anti-C. burnetii farms between the 2015 and 2016 collections showed to be statistically significant (p = 0.020) and is strongly suggestive of Q fever emergence in Central Portugal. Measures on animal health and on disease spread control to the human population should be considered. © 2018 Blackwell Verlag GmbH.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas.

PubMed

Chang, P; Grinband, J; Weinberg, B D; Bardis, M; Khy, M; Cadena, G; Su, M-Y; Cha, S; Filippi, C G; Bota, D; Baldi, P; Poisson, L M; Jain, R; Chow, D

2018-05-10

The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation. MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 ( IDH1 ) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase ( MGMT ) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification. Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features. Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training. © 2018 by American Journal of Neuroradiology.

VizieR Online Data Catalog: Astrometric monitoring of ultracool dwarf binaries (Dupuy+, 2017)

NASA Astrophysics Data System (ADS)

Dupuy, T. J.; Liu, M. C.

2017-09-01

In Table 1 we list all 33 binaries in our Keck+CFHT astrometric monitoring sample, along with three other binaries that have published orbit and parallax measurements. We began obtaining resolved Keck AO astrometry in 2007-2008, and we combined our new astrometry with available data in the literature or public archives (e.g., HST and Gemini) to refine our orbital period estimates and thereby our prioritization for Keck observations. We present here new Keck/NIRC2 AO imaging and non-redundant aperture-masking observations, in addition to a re-analysis of our own previously published data and publicly available archival data for our sample binaries. Table 2 gives our measured astrometry and flux ratios for all Keck AO data used in our orbital analysis spanning 2003 Apr 15 to 2016 May 13. In total there are 339 distinct measurements (unique bandpass and epoch for a given target), where 302 of these are direct imaging and 37 are non-redundant aperture masking. Eight of the imaging measurements are from six unpublished archival data sets. See section 3.1.1 for further details. In addition to our Keck AO monitoring, we also obtained data for three T dwarf binaries over a three-year HST program using the Advanced Camera for Surveys (ACS) Wide Field Camera (WFC) in the F814W bandpass. See section 3.1.2 for further details. Many of our sample binaries have HST imaging data in the public archive. We have re-analyzed the available archival data coming from the WFPC2 Planetary Camera (WFPC2-PC1), ACS High Resolution Channel (ACS-HRC), and NICMOS Camera 1 (NICMOS-NIC1). See section 3.1.3 for further details. We present here an updated analysis of our data from the Hawaii Infrared Parallax Program that uses the CFHT facility infrared camera WIRCam. Our observing strategy and custom astrometry pipeline are described in detail in Dupuy & Liu (2012, J/ApJS/201/19). See section 3.2 for further explanations. (10 data files).

Prolonged Outbreak of Mycobacterium chimaera Infection After Open-Chest Heart Surgery.

PubMed

Sax, Hugo; Bloemberg, Guido; Hasse, Barbara; Sommerstein, Rami; Kohler, Philipp; Achermann, Yvonne; Rössle, Matthias; Falk, Volkmar; Kuster, Stefan P; Böttger, Erik C; Weber, Rainer

2015-07-01

Invasive Mycobacterium chimaera infections were diagnosed in 2012 in 2 heart surgery patients on extracorporeal circulation. We launched an outbreak investigation to identify the source and extent of the potential outbreak and to implement preventive measures. We collected water samples from operating theaters, intensive care units, and wards, including air samples from operating theaters. Mycobacterium chimaera strains were characterized by randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). Case detection was performed based on archived histopathology samples and M. chimaera isolates since 2006, and the patient population at risk was prospectively surveyed. We identified 6 male patients aged between 49 and 64 years with prosthetic valve endocarditis or vascular graft infection due to M. chimaera, which became clinically manifest with a latency of between 1.5 and 3.6 years after surgery. Mycobacterium chimaera was isolated from cardiac tissue specimens, blood cultures, or other biopsy specimens. We were able also to culture M. chimaera from water circuits of heater-cooler units connected to the cardiopulmonary bypass, and air samples collected when the units were in use. RAPD-PCR demonstrated identical patterns among M. chimaera strains from heater-cooler unit water circuits and air samples, and strains in 2 patient clusters. The epidemiological and microbiological features of this prolonged outbreak provided evidence for the airborne transmission of M. chimaera from contaminated heater-cooler unit water tanks to patients during open-heart surgery. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Let Archived Paraffin Blocks Be Utilized for Research with Waiver of Informed Consent.

PubMed

Kim, Yong-Jin; Park, Jeong Sik; Ko, Karam; Jeong, Chang Rok

2018-05-01

Advances in biomedical and genetic research have contributed to more effective public health improvement via bench-to-bed research and the emergence of personalized medicine. This has certainly showcased the importance of archived human tissues, especially paraffin-embedded blocks in pathology. Currently in Korea, undue legislative regulations of the Bioethics and Safety Act suspend and at times discourage studies from taking place. In this paper, the authors underline the value of paraffin blocks in the era of personalized and translational medicine. We discuss detailed clauses regarding the applicability of paraffin blocks from a legal perspective and compare Korea's regulations with those of other countries. The necessity for allowing waived consent and Institutional Review Board (IRB) approval will be argued throughout. The authors suggest that researchers declare the following to obtain IRB approval and waiver of informed consents: research could not be practically carried out without a waiver of consent; the proposed research presents no more than minimal risk of harm to subjects, and the waiver of consent will not adversely affect the rights and welfare of subjects; and research will not utilize a tissue block if only 1 is available for each subject, to allow future clinical use such as re-evaluation or further studies.

Characteristics and Hypothesized Functions of Challenging Behavior in a Community-Based Sample

ERIC Educational Resources Information Center

Petursdottir, Anna Ingeborg; Esch, John W.; Sautter, Rachael A.; Stewart, Kelise K.

2010-01-01

An archival study was conducted to document (a) types of challenging behavior, and (b) functional assessment outcomes, for a sample of persons with developmental disabilities who were referred to community-practicing behavior analysts for assessment and treatment of challenging behavior. Functional assessment reports, prepared by 17 behavior…

Pharmaceuticals and Personal Care Products in Archived U.S. Biosolids from the 2001 EPA National Sewage Sludge Survey

PubMed Central

McClellan, Kristin; Halden, Rolf U.

2010-01-01

In response to the U.S. National Academies’ call for a better assessment of chemical pollutants contained in the approximately 6.9 million dry tons of digested municipal sludge produced annually in the United States, the mean concentration of 72 pharmaceuticals and personal care products (PPCP) were determined in 110 biosolids samples collected by the U.S. Environmental Protection Agency (EPA) in its 2001 National Sewage Sludge Survey. Composite samples of archived biosolids, collected at 94 U.S. wastewater treatment plants from 32 states and the District of Columbia, were analyzed by liquid chromatography tandem mass spectrometry using EPA Method 1694. Thirty-eight (54%) of the 72 analytes were detected in at least one composite sample at concentrations ranging from 0.002 to 48 mg kg−1 dry weight. Triclocarban and triclosan were the most abundant analytes with mean concentrations of 36 ± 8 and 12.6 ± 3.8 mg kg−1 (n = 5), respectively, accounting for 65% of the total PPCP mass found. The loading to U.S. soils from nationwide biosolids recycling was estimated at 210–250 metric tons per year for the sum of the 72 PPCPs investigated. The results of this nationwide reconnaissance of PPCPs in archived U.S. biosolids mirror in contaminant occurrences, frequencies and concentrations, those reported by the U.S. EPA for samples collected in 2006/07. This demonstrates that PPCP releases in U.S. biosolids have been ongoing for many years and the most abundant PPCPs appear to show limited fluctuations in mass over time when assessed on a nationwide basis. The here demonstrated use of five mega composite samples holds promise for conducting cost-effective, routine monitoring on a regional basis. PMID:20106500

Recent advances and opportunities in proteomic analyses of tumour heterogeneity.

PubMed

Bateman, Nicholas W; Conrads, Thomas P

2018-04-01

Solid tumour malignancies comprise a highly variable admixture of tumour and non-tumour cellular populations, forming a complex cellular ecosystem and tumour microenvironment. This tumour heterogeneity is not incidental, and is known to correlate with poor patient prognosis for many cancer types. Indeed, non-malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumour biology, and represent targets of emerging therapeutics, such as antiangiogenesis and immune checkpoint inhibitors. The biochemical interplay between these cellular populations and how they contribute to molecular tumour heterogeneity remains enigmatic, particularly from the perspective of the tumour proteome. This review focuses on recent advances in proteomic methods, namely imaging mass spectrometry, single-cell proteomic techniques, and preanalytical sample processing, that are uniquely positioned to enable detailed analysis of discrete cellular populations within tumours to improve our understanding of tumour proteomic heterogeneity. This review further emphasizes the opportunity afforded by the application of these techniques to the analysis of tumour heterogeneity in formalin-fixed paraffin-embedded archival tumour tissues, as these represent an invaluable resource for retrospective analyses that is now routinely accessible, owing to recent technological and methodological advances in tumour tissue proteomics. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Harvey Cushing Treated the First Known Patient With Carney Complex

PubMed Central

Tsay, Cynthia J.; Stratakis, Constantine A.; Faucz, Fabio Rueda; London, Edra; Stathopoulou, Chaido; Allgauer, Michael; Quezado, Martha; Dagradi, Terry; Spencer, Dennis D.

2017-01-01

Context: Carney complex (CNC) is a syndrome characterized by hyperplasia of endocrine organs and may present with clinical features of Cushing syndrome and acromegaly due to functional adrenal and pituitary gland tumors. CNC has been linked to mutations in the regulatory subunit of protein kinase A type I-alpha (PRKAR1A) gene. Design: Tissue samples were taken from the hypothalamus or thalamus or tumors of patients with pituitary adenomas seen and operated on by neurosurgeon Harvey Cushing between 1913 and 1932. Following DNA extraction, sequencing for genes of interest was attempted, including PRKAR1A, AIP, USP8, GNAS1, and GPR101, to explore the possibility that these mutations associated with acromegaly, CNC, and Cushing syndrome have been conserved over time. Results: We report a patient described by Dr. Cushing in 1914 with a clinical presentation and postmortem findings suggestive of CNC. Genetic sequencing of the hypothalamus and pituitary adenoma revealed a germline heterozygous p.Arg74His mutation in the PRKAR1A gene, a codon previously described as mutated in CNC, but with a novel amino acid change. Conclusions: This patient is, to our knowledge, the first molecularly confirmed individual with CNC. This case demonstrates the power of modern genetics in studying archived tissues and the importance of recording detailed clinical notes in the diagnosis of disease. PMID:29264456

[Significance of MUC5B antibody in differential diagnosis between Aspergillus species and Mucorales of fungal sinusitis].

PubMed

Piao, Ying-shi; Liu, Hong-gang; Liu, Xian-jun

2008-04-01

To differentiate between Aspergillus species and Mucorales of fungal sinusitis by immunohistochemistry. Formalin-fixed paraffin-embedded tissue blocks of 66 cases of fungal sinusitis were retrieved from the archival files of Department of Pathology of Beijing Tongren Hospital during the period from 2001 to 2006. The samples included 29 cases of fungal balls, 12 cases of allergic fungal sinusitis, 24 cases of chronic invasive fungal sinusitis and 1 case of acute invasive fungal sinusitis. The types of fungi were 44 Aspergillus species (31 cases of A. fumigatus, 7 cases of A. flavus and 6 cases of A. terreus) and 22 Mucorales (14 cases of Mucor species and 8 cases of Rhizopus species). Immunohistochemistry was performed with MUC2, MUC5AC and MUC5B antibodies. The results were compared with histochemical study for periodic acid-Schiff (PAS) and Grocott methenamine silver (GMS) stains. Immunohistochemical study for MUC5B showed that the positive rate of Aspergillus species was 90.9%, in contrast to 4.5% in Mucorales (P < 0.001). The expression of MUC2 and MUC5AC was completely negative, whereas PAS and GMS stains were positive in all cases. MUC5B antibody appears to be a useful immunohistochemical marker for identifying fungal types in tissue sections, especially in distinguishing between Aspergillus species and Mucorales in fungal sinusitis.

All lesions great and small, part 2. Diagnostic cytology in veterinary medicine.

PubMed

Sharkey, Leslie C; Seelig, Davis M; Overmann, Jed

2014-06-01

This is the second in a two-part review of diagnostic cytopathology in veterinary medicine. As in human medicine, cytopathology is a minimally invasive, rapid, and cost-effective diagnostic modality with broad utilization. In this second part, the diagnostic applications of cytology in respiratory, gastrointestinal, genitourinary, endocrine, ocular, and central nervous system tissues are discussed with a section describing fluid analysis in veterinary medicine. As noted in the previous manuscript, which characterized the cytology of the skin/subcutis, musculoskeletal, and lymphoid tissues, the interpretation of veterinary cytology samples must be undertaken with extensive knowledge of the breadth of animal species, including familiarity with the frequency and clinical progression of diseases, both of which can be influenced by species, breed, and husbandry conditions. Similar to part one, this review focuses on the most common domestic companion animal species (dog, cat, and horse) and highlights lesions that are either unique to veterinary species or have relevant correlates in people. The cytologic features and biological behavior of similar lesions are compared, and selected mechanisms of disease and ancillary diagnostics are reviewed when appropriate. Supporting figures illustrate a subset of lesions. While not an exhaustive archive of veterinary cytology, the goal is to give cytopathologists working in human medicine a general impression of correlates and unique entities in veterinary practice. Copyright © 2014 Wiley Periodicals, Inc.

Performance Evaluation of the Operational Air Quality Monitor for Water Testing Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Wallace, William T.; Limero, Thomas F.; Gazda, Daniel B.; Macatangay, Ariel V.; Dwivedi, Prabha; Fernandez, Facundo M.

2014-01-01

In the history of manned spaceflight, environmental monitoring has relied heavily on archival sampling. For short missions, this type of sample collection was sufficient; returned samples provided a snapshot of the presence of chemical and biological contaminants in the spacecraft air and water. However, with the construction of the International Space Station (ISS) and the subsequent extension of mission durations, soon to be up to one year, the need for enhanced, real-time environmental monitoring became more pressing. The past several years have seen the implementation of several real-time monitors aboard the ISS, complemented with reduced archival sampling. The station air is currently monitored for volatile organic compounds (VOCs) using gas chromatography-differential mobility spectrometry (Air Quality Monitor [AQM]). The water on ISS is analyzed to measure total organic carbon and biocide concentrations using the Total Organic Carbon Analyzer (TOCA) and the Colorimetric Water Quality Monitoring Kit (CWQMK), respectively. The current air and water monitors provide important data, but the number and size of the different instruments makes them impractical for future exploration missions. It is apparent that there is still a need for improvements in environmental monitoring capabilities. One such improvement could be realized by modifying a single instrument to analyze both air and water. As the AQM currently provides quantitative, compound-specific information for target compounds present in air samples, and many of the compounds are also targets for water quality monitoring, this instrument provides a logical starting point to evaluate the feasibility of this approach. In this presentation, we will discuss our recent studies aimed at determining an appropriate method for introducing VOCs from water samples into the gas phase and our current work, in which an electro-thermal vaporization unit has been interfaced with the AQM to analyze target analytes at the relevant concentrations at which they are routinely detected in archival water samples from the ISS.

Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation.

PubMed

Azimzadeh, Omid; Scherthan, Harry; Yentrapalli, Ramesh; Barjaktarovic, Zarko; Ueffing, Marius; Conrad, Marcus; Neff, Frauke; Calzada-Wack, Julia; Aubele, Michaela; Buske, Christian; Atkinson, Michael J; Hauck, Stefanie M; Tapio, Soile

2012-04-18

Qualitative proteome profiling of formalin-fixed, paraffin-embedded (FFPE) tissue is advancing the field of clinical proteomics. However, quantitative proteome analysis of FFPE tissue is hampered by the lack of an efficient labelling method. The usage of conventional protein labelling on FFPE tissue has turned out to be inefficient. Classical labelling targets lysine residues that are blocked by the formalin treatment. The aim of this study was to establish a quantitative proteomics analysis of FFPE tissue by combining the label-free approach with optimised protein extraction and separation conditions. As a model system we used FFPE heart tissue of control and exposed C57BL/6 mice after total body irradiation using a gamma ray dose of 3 gray. We identified 32 deregulated proteins (p≤0.05) in irradiated hearts 24h after the exposure. The proteomics data were further evaluated and validated by bioinformatics and immunoblotting investigation. In good agreement with our previous results using fresh-frozen tissue, the analysis indicated radiation-induced alterations in three main biological pathways: respiratory chain, lipid metabolism and pyruvate metabolism. The label-free approach enables the quantitative measurement of radiation-induced alterations in FFPE tissue and facilitates retrospective biomarker identification using clinical archives. Copyright © 2012 Elsevier B.V. All rights reserved.

Isolation of Cardiomyocyte Nuclei from Post-mortem Tissue

PubMed Central

Bergmann, Olaf; Jovinge, Stefan

2012-01-01

Identification of cardiomyocyte nuclei has been challenging in tissue sections as most strategies rely only on cytoplasmic marker proteins1. Rare events in cardiac myocytes such as proliferation and apoptosis require an accurate identification of cardiac myocyte nuclei to analyze cellular renewal in homeostasis and in pathological conditions2. Here, we provide a method to isolate cardiomyocyte nuclei from post mortem tissue by density sedimentation and immunolabeling with antibodies against pericentriolar material 1 (PCM-1) and subsequent flow cytometry sorting. This strategy allows a high throughput analysis and isolation with the advantage of working equally well on fresh tissue and frozen archival material. This makes it possible to study material already collected in biobanks. This technique is applicable and tested in a wide range of species and suitable for multiple downstream applications such as carbon-14 dating3, cell-cycle analysis4, visualization of thymidine analogues (e.g. BrdU and IdU)4, transcriptome and epigenetic analysis. PMID:22805241

Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis

PubMed Central

Tsujikawa, Takahiro; Kumar, Sushil; Borkar, Rohan N.; Azimi, Vahid; Thibault, Guillaume; Chang, Young Hwan; Balter, Ariel; Kawashima, Rie; Choe, Gina; Sauer, David; El Rassi, Edward; Clayburgh, Daniel R.; Kulesz-Martin, Molly F.; Lutz, Eric R.; Zheng, Lei; Jaffee, Elizabeth M.; Leyshock, Patrick; Margolin, Adam A.; Mori, Motomi; Gray, Joe W.; Flint, Paul W.; Coussens, Lisa M.

2017-01-01

SUMMARY Here we describe a multiplexed immunohistochemical platform, with computational image processing workflows including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas, and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination, and revealed that response to therapy correlated with degree of mono-myelocytic cell density, and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification, and provide digital image processing pipelines (https://github.com/multiplexIHC/cppipe) to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to thus improve biomarker discovery and assessment. PMID:28380359

Detection of hepatitis "C" virus in formalin-fixed liver tissue by nested polymerase chain reaction.

PubMed

Sallie, R; Rayner, A; Portmann, B; Eddleston, A L; Williams, R

1992-08-01

Interpretation of antibody to hepatitis C virus (HCV) in patients with liver disease is difficult due to false-positive reactivity in some conditions. To evaluate the feasibility of HCV in archival material, HCV was sought in formalin-fixed, paraffin-embedded liver biopsy specimens. Nested polymerase chain reaction was used to detect hepatitis C virus in formalin-fixed, paraffin-embedded liver biopsy specimens after total RNA was extracted from tissue by proteinase K digestion and phenol/chloroform purification. The relative efficiency of amplification of HCV RNA from formalin-fixed material was estimated semiquantitatively by serial dilution of cDNA synthesised from RNA extracted from fresh and formalin-fixed sections from the same liver. Although HCV RNA could be detected in formalin-fixed liver tissue by nested PCR in 5/5 cases in which HCV was detected in serum, amplification was approximately 5-fold less efficient than when HCV was amplified from fresh tissue. Nevertheless, nested PCR of HCV from formalin-fixed liver tissue represents a useful technique in addressing some important questions related to the pathogenesis of liver disease.

Method And Apparatus For Examining A Tissue Using The Spectral Wing Emission Therefrom Induced By Visible To Infrared Photoexcitation.

DOEpatents

Alfano, Robert R.; Demos, Stavros G.; Zhang, Gang

2003-12-16

Method and an apparatus for examining a tissue using the spectral wing emission therefrom induced by visible to infrared photoexcitation. In one aspect, the method is used to characterize the condition of a tissue sample and comprises the steps of (a) photoexciting the tissue sample with substantially monochromatic light having a wavelength of at least 600 nm; and (b) using the resultant far red and near infrared spectral wing emission (SW) emitted from the tissue sample to characterize the condition of the tissue sample. In one embodiment, the substantially monochromatic photoexciting light is a continuous beam of light, and the resultant steady-state far red and near infrared SW emission from the tissue sample is used to characterize the condition of the tissue sample. In another embodiment, the substantially monochromatic photoexciting light is a light pulse, and the resultant time-resolved far red and near infrared SW emission emitted from the tissue sample is used to characterize the condition of the tissue sample. In still another embodiment, the substantially monochromatic photoexciting light is a polarized light pulse, and the parallel and perpendicular components of the resultant polarized time-resolved SW emission emitted from the tissue sample are used to characterize the condition of the tissue sample.

Evaluation of a Gas Chromatograph-Differential Mobility Spectrometer for Potential Water Monitoring on the International Space Station

NASA Technical Reports Server (NTRS)

Wallace, William T.; Limero, Thomas F.; Gazda, Daniel B.; Macatangay, Ariel V.; Dwivedi, Prabha; Fernandez, Facundo M.

2015-01-01

Environmental monitoring for manned spaceflight has long depended on archival sampling, which was sufficient for short missions. However, the longer mission durations aboard the International Space Station (ISS) have shown that enhanced, real-time monitoring capabilities are necessary in order to protect both the crewmembers and the spacecraft systems. Over the past several years, a number of real-time environmental monitors have been deployed on the ISS. Currently, volatile organic compounds (VOCs) in the station air are monitored by the Air Quality Monitor (AQM), a small, lightweight gas chromatograph-differential mobility spectrometer. For water monitoring, real-time monitors are used for total organic carbon (TOC) and biocide analysis. No information on the actual makeup of the TOC is provided presently, however. An improvement to the current state of environmental monitoring could be realized by modifying a single instrument to analyze both air and water. As the AQM currently provides quantitative, compound-specific information for VOCs in air samples, this instrument provides a logical starting point to evaluate the feasibility of this approach. The major hurdle for this effort lies in the liberation of the target analytes from the water matrix. In this presentation, we will discuss our recent studies, in which an electro-thermal vaporization unit has been interfaced with the AQM to analyze target VOCs at the concentrations at which they are routinely detected in archival water samples from the ISS. We will compare the results of these studies with those obtained from the instrumentation routinely used to analyze archival water samples.

National Aeronautics and Space Administration Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, Kathleen A.; Pietrzyk, Robert a.; Johnson, Mary Anne

2008-01-01

The National Aeronautics and Space Administration Biological Specimen Repository (Repository) is a storage bank that is used to maintain biological specimens over extended periods of time and under well-controlled conditions. Samples from the International Space Station (ISS), including blood and urine, will be collected, processed and archived during the preflight, inflight and postflight phases of ISS missions. This investigation has been developed to archive biosamples for use as a resource for future space flight related research. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can study space flight related changes and investigate physiological markers. The development of the National Aeronautics and Space Administration Biological Specimen Repository will allow for the collection, processing, storage, maintenance, and ethical distribution of biosamples to meet goals of scientific and programmatic relevance to the space program. Archiving of the biosamples will provide future research opportunities including investigating patterns of physiological changes, analysis of components unknown at this time or analyses performed by new methodologies.

Chemical contamination in aquatic ecosystems.

PubMed

Iwata, Hisato; Kim, Eun-Young; Yamauchi, Masanobu; Inoue, Suguru; Agusa, Tetsuro; Tanabe, Shinsuke

2007-03-01

The 21st Century's Center of Excellence (COE) Program "Coastal Marine Environmental Research" in Ehime University, funded by the Ministry of Education, Culture, Sports, Science and Technology, Government of Japan, started its activities in October 2002. One of the core projects of the COE Program in Ehime University is "studies on environmental behavior of hazardous chemicals and their toxic effects on wildlife". This core project deals with studies of the local and global distribution of environmental contaminants in aquatic ecosystems, retrospective analysis of such chemicals, their toxicokinetics in humans and wildlife, molecular mechanisms to determine species-specific reactions, and sensitivity of chemically induced effects, and with the development of methodology for risk assessment for the conservation of ecological and species diversity. This presentation describes our recent achievements of this project, including research on contamination by arsenic and organohalogen pollutants in the Mekong River basin and molecular mechanisms of morphologic deformities in dioxin-exposed red seabream (Pagrus major) embryos. We established the Environmental Specimen Bank (es-BANK) in Ehime University in 2004, archiving approximately 100000 cryogenic samples containing tissues of wildlife and humans that have been collected for the past 40 years. The CMES homepage offers details of samples through online database retrieval. The es-BANK facility was in operation by the end of 2005.

Piscine reovirus in wild and farmed salmonids in British Columbia, Canada: 1974-2013.

PubMed

Marty, G D; Morrison, D B; Bidulka, J; Joseph, T; Siah, A

2015-08-01

Piscine reovirus (PRV) was common among wild and farmed salmonids in British Columbia, western Canada, from 1987 to 2013. Salmonid tissues tested for PRV by real-time rRT-PCR included sections from archived paraffin blocks from 1974 to 2008 (n = 363) and fresh-frozen hearts from 2013 (n = 916). The earliest PRV-positive sample was from a wild-source steelhead trout, Oncorhynchus mykiss (Walbaum), from 1977. By histopathology (n = 404), no fish had lesions diagnostic for heart and skeletal muscle inflammation (HSMI). In some groups, lymphohistiocytic endocarditis affected a greater proportion of fish with PRV than fish without PRV, but the range of Ct values among affected fish was within the range of Ct values among unaffected fish. Also, fish with the lowest PRV Ct values (18.4-21.7) lacked endocarditis or any other consistent lesion. From 1987 to 1994, the proportion of PRV positives was not significantly different between farmed Atlantic salmon, Salmo salar L. (44% of 48), and wild-source salmonids (31% of 45). In 2013, the proportion of PRV positives was not significantly different between wild coho salmon, Oncorhynchus kisutch (Walbaum), sampled from British Columbia (5.0% of 60) or the reference region, Alaska, USA (10% of 58). © 2014 John Wiley & Sons Ltd.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Bono, Hidemasa

2017-01-01

Abstract It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. PMID:28449062

Benign Breast Disease: Toward Molecular Prediction of Breast Cancer Risk

DTIC Science & Technology

2006-06-01

with benign breast disease ( BBD ) (1967-1991); 2) the application of potential biomarkers of risk to this archival tissue set; and 3) the discovery...of new, potentially relevant biomarkers of risk in fresh and frozen specimens of BBD . The Center includes a multi-institutional team of basic...State). I. Task 1: Establish Retrospective Cohort of BBD and Nested Case-Control Study A. Complete cohort follow-up We provide here an update of

Function of cell-cycle regulators in predicting silent pituitary adenoma progression following surgical resection

PubMed Central

Park, Sung Hyun; Jang, Ji Hwan; Lee, Young Min; Kim, Joon Soo; Kim, Kyu Hong; Kim, Young Zoon

2017-01-01

The present study investigated the use of cell-cycle regulators for predicting the progression of silent pituitary adenoma (SPA) following surgical resection, via immunohistochemical analysis of tumor samples obtained by surgical resection. The medical records of patients diagnosed with SPA between January 2000 and December 2013 in the Samsung Changwon Hospital, Sungkyunkwan University School of Medicine (Changwon, South Korea) were reviewed. Immunohistochemical staining was performed on sections of the archived, paraffin-embedded tissues obtained by surgery, with all tissues stained for cell-cycle regulatory proteins p16, p15, p21, cyclin-dependent kinase (CDK)4, CDK6, retinoblastoma protein (pRb) and cyclin D1, as well as E3 ubiquitin-protein ligase mib1 (MIB-1) antigen and p53. The primary end-point was to investigate the expression of cell-cycle regulatory proteins in SPA. The secondary end-point was to estimate the progression-free survival of patients with SPA following surgical resection and to identify its association with the expression of cell-cycle regulatory proteins. Of the 127 SPA samples, 44 (34.6%) were from patients with progression during a mean follow-up period of 62.4 months (range, 24.2–118.9 months). Immunohistochemical overexpression was identified in 61 samples (48.0%) for p16, 38 samples (29.9%) for p15, 19 samples (15.0%) for p21, 49 samples (38.6%) for CDK4, 17 samples (13.4%) for CDK6, 57 samples (44.9%) for pRb and in 65 samples (51.2%) for cyclin D1. Multivariate analysis revealed that null cell adenoma [95% confidence interval (CI), 0.276–0.808], somatotroph SPAs (95% CI, 1.296–3.121), corticotroph SPAs (95% CI, 1.811–4.078), pluripotent SPAs (95% CI, 2.264–5.194), decreased expression of p16 (95% CI, 2.724–5.588), overexpression of pRb (95% CI, 2.557–5.333), cyclin D1 (95% CI, 1.894–4.122) and MIB-1 (95% CI, 1.561–4.133), increased mitotic index (95% CI, 1.228–4.079), increased p53 expression (95% CI, 1.307–4.065) and invasion into the cavernous sinus (95% CI, 3.842–7.502) predicted SPA progression following resection. The results of the present study suggested that specific cell-cycle regulators, including p16, cyclin D1 and pRb, were associated with SPA progression. PMID:29344143

Stable Water Isotope Climate Archives in Springs from the Olympic Mountains, Washington

EPA Science Inventory

The ¹⁸O and ²H (HDO) compositions are summarized for sampled springs (n = 81) within the Elwha watershed (≈ 692 km²) on the northern Olympic Peninsula. Samples, collected during 2001–2009, of springs (n = 158), precipitation (n = 520), streams (n...

The possible role of soils in the global cycling of PCBs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lead, W.A.; Jones, K.C.; Steinnes, E.

Archived soil and humus samples collected between 1950 and 1974 from 50 remote sites across the U.K. have been analyzed for a range of PCB congeners. The same sites have been revisited and contemporary samples taken. Results show increasing {Sigma}PCB concentrations up until the late 1960s after which there has been a dramatic reduction in the soil {Sigma}PCB concentration. These trends are indicative of the changes in use of these compounds over time. There are also temporal changes in the congener profiles, with the percentage contribution of the heavier homologue groups (hepta and octa -chlorinated) increasing. Samples of contemporary humusmore » from 12 rural Norwegian sites have also been screened for a range of congeners and the results compared with those of the U.K. soils and humus samples. Results for the Norway/U.K. comparison and the trends in the congener profiles for the archived/contemporary soil comparison suggest that PCBs are volatilizing from temperate areas and undergoing long range transport and subsequent global fractionation.« less

Novel Insight for Organic Matter Sourcing: Interest of Time Resolved Fluorescence to Qualify and Quantify PAH Content of Solid Matrix at High Resolution

NASA Astrophysics Data System (ADS)

Quiers, M.; Perrette, Y.; Jacq, K.; Pousset, E.; Plassart, G.

2017-12-01

OM fluorescence is today a well-developed tool used to characterize and quantify organic matter (OM), but also to evaluate and discriminate OM fate and changes related to climate and environmental modifications. While fluorescence measurements on water and soils extracts provide information about organic fluxes today, solid phase fluorescence using natural archives allows to obtain high resolution records of OM evolution during time. These evolutions can be discussed in regards of climate and environmental perturbations detected in archives using different proxies, and thus provide keys for understanding factors driving carbon fluxes mechanisms. Among fluorescent organic species, Polycyclic Aromatic Hydrocarbons (PAH) have been used as probe molecules for organic contamination tracking. Moreover, monitoring studies have shown that PAH could also be used as markers to discriminates atmospheric and erosion factors leading to PAH and organic matter fluxes to the aquifer. PAH records in soils and natural archives appear as a promising proxy to follow both past atmospheric contamination and soil erosion. But, PAH fluorescence is difficult to discriminate from bulk OM fluorescence using steady-state fluorescence (SSF) technics as their fluorescence domains recover. Time resolved emission spectroscopy (TRES) increases the information provided by SSF technic, adding a time dimension to measurements and allowing to discriminate PAH fluorescence. We report here a first application of this technic on natural archives. The challenge is to obtain TRES signature along the sample, including for low PAH concentrations. This study aims to evaluate the reliability of high resolution TRES measurement as PAH carbon fluxes sources. Method is based on LIF instrument for solid phase fluorescence measurement. An instrument coupling an excitation system constituting by 2 pulsed lasers (266 and 355 nm) and a detection system was developed. This measurement provides high resolution record of PAH fluorescence. Preliminary results on stalagmite samples, lake sediments and soils will be reported. PAH content variations along the sample were compared with PAH concentration and with bulk OM content deduced from SSF records. The accuracy of the PAH fluorescence as source marker of fluxes will be discussed for each type of sample.

Distinct microbiological signatures associated with triple negative breast cancer.

PubMed

Banerjee, Sagarika; Wei, Zhi; Tan, Fei; Peck, Kristen N; Shih, Natalie; Feldman, Michael; Rebbeck, Timothy R; Alwine, James C; Robertson, Erle S

2015-10-15

Infectious agents are the third highest human cancer risk factor and may have a greater role in the origin and/or progression of cancers, and related pathogenesis. Thus, knowing the specific viruses and microbial agents associated with a cancer type may provide insights into cause, diagnosis and treatment. We utilized a pan-pathogen array technology to identify the microbial signatures associated with triple negative breast cancer (TNBC). This technology detects low copy number and fragmented genomes extracted from formalin-fixed paraffin embedded archival tissues. The results, validated by PCR and sequencing, define a microbial signature present in TNBC tissue which was underrepresented in normal tissue. Hierarchical clustering analysis displayed two broad microbial signatures, one prevalent in bacteria and parasites and one prevalent in viruses. These signatures demonstrate a new paradigm in our understanding of the link between microorganisms and cancer, as causative or commensal in the tumor microenvironment and provide new diagnostic potential.

The role of metalloendopeptidases in oropharyngeal carcinomas assessed by tissue microarray.

PubMed

Ribeiro, Daniel A; Nascimento, Fabio D; Fracalossi, Ana Carolina C; Noguti, Juliana; Oshima, Celina T F; Ihara, Silvia S M; Franco, Marcello F

2011-01-01

The goal of this study was to investigate the expression of some metalloendopeptidases in squamous cell carcinomas of the oropharynx as well as its relation to histological differentiation, staging of disease, and prognosis. Paraffin blocks from 21 primary tumors were obtained from archives of the Department of Pathology, Paulista Medical School, Federal University of Sao Paulo, UNIFESP/EPM. Immunohistochemistry was used to detect the expression of EP24.15 and EP24.16 by means of tissue microarrays. Expression of EP24.15 or EP24.16 was not correlated with the stage of disease, histopathological grading or recurrence in squamous cell carcinomas of the oropharynx. In summary, our results support the notion that EP24.15 and EP24.16 are expressed in carcinoma of the oropharynx; however, these do not appear to be suitable biomarkers for histological grading, disease stage or recurrence as depicted by tissue microarrays and immunohistochemistry.

Base rate of performance invalidity among non-clinical undergraduate research participants.

PubMed

Silk-Eglit, Graham M; Stenclik, Jessica H; Gavett, Brandon E; Adams, Jason W; Lynch, Julie K; Mccaffrey, Robert J

2014-08-01

Neuropsychological research frequently uses non-clinical undergraduate participants to evaluate neuropsychological tests. However, a recent study by An and colleagues (2012, Archives of Clinical Neuropsychology, 27, 849-857) called into question that the extent to which the interpretation of these participants' performance on neuropsychological tests is valid. This study found that in a sample of 36 participants, 55.6% exhibited performance invalidity at an initial session and 30.8% exhibited performance invalidity at a follow-up session. The current study attempted to replicate these findings in a larger, more representative sample using a more rigorous methodology. Archival data from 133 non-clinical undergraduate research participants were analyzed. Participants were classified as performance invalid if they failed any one PVT. In the current sample, only 2.26% of participants exhibited performance invalidity. Thus, concerns regarding insufficient effort and performance invalidity when using undergraduate research participants appear to be overstated. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Persistence of perfluoroalkyl acid precursors in AFFF-impacted groundwater and soil.

PubMed

Houtz, Erika F; Higgins, Christopher P; Field, Jennifer A; Sedlak, David L

2013-08-06

Several classes of polyfluorinated chemicals that are potential precursors to the perfluorinated carboxylates and sulfonates are present in aqueous film-forming foams (AFFF). To assess the persistence of these AFFF-derived precursors, groundwater, soil, and aquifer solids were obtained in 2011 from an unlined firefighter training area at a U.S. Air Force Base where AFFF was regularly used between 1970 and 1990. To measure the total concentration of perfluorinated carboxylate and sulfonate precursors in archived AFFF formulations and AFFF-impacted environmental samples, a previously developed assay that uses hydroxyl radical to oxidize precursors to perfluorinated carboxylates was adapted for these media. This assay was employed along with direct measurement of 22 precursors found in AFFF and a suite of other poly- and perfluoroalkyl substances (PFASs). On a molar basis, precursors accounted for 41-100% of the total concentration of PFASs in archived AFFF formulations. In the training area, precursors measured by the oxidation assay accounted for an average of 23% and 28% of total PFASs (i.e., precursors and perfluorinated carboxylates and sulfonates) in groundwater and solids samples, respectively. One precursor in AFFF, perfluorohexane sulfonamide amine, was observed on several highly contaminated soil and aquifer solids samples, but no other precursors present in AFFF formulations were detected in any samples at this field site. Suspected intermediate transformation products of precursors in AFFF that were directly measured accounted for approximately half of the total precursor concentration in samples from the training site. The fraction of PFASs consisting of perfluorinated carboxylates and sulfonates was greater in groundwater and solid samples than in any archived AFFF formulations, suggesting that much of the mass of precursors released at the site was converted to perfluorinated carboxylates and sulfonates. The precursors that have persisted at this site may generate significant amounts of additional perfluorinated carboxylates and sulfonates upon remediation of contaminated groundwater or aquifer solids.

Endometrial Polyps and Benign Endometrial Hyperplasia Present Increased Prevalence of DNA Fragmentation Factors 40 and 45 (DFF40 and DFF45) Together With the Antiapoptotic B-Cell Lymphoma (Bcl-2) Protein Compared With Normal Human Endometria.

PubMed

Banas, Tomasz; Pitynski, Kazimierz; Mikos, Marcin; Cielecka-Kuszyk, Joanna

2017-09-13

DNA fragmentation factor 40 (DFF40) is a key executor of apoptosis. It localizes to the nucleus together with DNA fragmentation factor 45 (DFF45), which acts as a DFF40 inhibitor and chaperone. B-cell lymphoma (Bcl-2) protein is a proven antiapoptotic factor present in the cytoplasm. In this study, we aimed to investigate DFF40, DFF45, and Bcl-2 immunoexpression in endometrial polyps (EPs) and benign endometrial hyperplasia (BEH) tissue compared with that in normal proliferative endometrium (NPE) and normal secretory endometrium (NSE) as well as normal post menopausal endometrium (NAE). This study used archived samples from 65 and 62 cases of EPs and BEH, respectively. The control group consisted of 52 NPE, 54 NSE, and 54 NAE specimens. Immunohistochemistry was used to detect DFF40, DFF45, and Bcl-2. DFF40, DFF45, and Bcl-2 were more highly expressed in the glandular layer of EPs and BEH compared with the stroma, and this was not influenced by menopausal status. Both glandular and stromal expression of DFF40, DFF45, and Bcl-2 were significantly higher in EPs compared with NPE, NSE, and NAE. Glandular BEH tissue showed significantly higher DFF40, DFF45, and Bcl-2 expression than in NPE, NSE, and NAE. No differences in the glandular expression of DFF40, DFF45, and Bcl-2 were observed between EP and BEH tissues, while Bcl-2 stromal expression in BEH was significantly lower than in EPs. Glandular, menopause-independent DFF40, DFF45, and Bcl-2 overexpression may play an important role in the pathogenesis of EPs and BEH.

Longitudinal and contemporaneous manganese exposure in apartheid-era South Africa: Implications for the past and future.

PubMed

Hess, Catherine A; Smith, Martin J; Trueman, Clive; Schutkowski, Holger

2015-03-01

Manganese is a potent environmental toxin, with significant effects on human health. Manganese exposure is of particular concern in South Africa where in the last decade, lead in gasoline has been replaced by methylcyclopentadienyl manganese tricarbonyl (MMT). We investigated recent historical levels of manganese exposure in urban Gauteng, South Africa prior to the introduction of MMT in order to generate heretofore non-existent longitudinal public health data on manganese exposure in urban South Africans. Cortical bone manganese concentration was measured by inductively coupled plasma mass spectrometer in 211 deceased adults with skeletal material from a fully identified archived tissue collection at the University of Pretoria, South Africa. All tissues came from individuals who lived and died in urban Gauteng (Transvaal), between 1958 and 1998. Median Mn concentration within the sampled tissues was 0.3μgg -1 , which is within reported range for bone manganese concentration in non-occupationally exposed populations and significantly below that reported in individuals environmentally exposed to MMT. No significant differences were seen in bone Mn between men and women or in individuals of different ethnicity, which further suggests environmental, as opposed to occupational exposure. There were no significant temporal or geographic differences in bone Mn. The results suggest that Mn exposure was low and uniformly distributed across the whole population prior to the introduction of MMT as a gasoline additive. In addition, should manganese exposure follow the same patterns as vehicle-emitted lead, a clear pattern of exposure will emerge with individuals in the urban core facing the greatest manganese exposure. Copyright © 2014 Elsevier Inc. All rights reserved.

Unmasking of complements using proteinase-K in formalin fixed paraffin embedded renal biopsies.

PubMed

Nada, R; Kumar, A; Kumar, V G; Gupta, K L; Joshi, K

2016-01-01

Renal biopsy interpretation requires histopathology, direct immunofluorescence (DIF) and electron microscopy. Formalin-fixed, paraffin-embedded tissue (FFPE) sent for light microscopy can be used for DIF after antigen retrieval. However, complement staining has not been satisfactory. We standardized DIF using proteinase-K for antigen retrieval in FFPE renal biopsies. A pilot study was conducted on known cases of membranous glomerulonephritis (MGN), membranoproliferative type-1 (MPGN-1), immunoglobulin A nephropathy (IgAN), and anti-glomerular basement disease (anti-GBM). Immunofluorescence panel included fluorescein isothiocyanate (FITC) conjugated IgG, IgA, IgM, complements (C3 and C1q), light chains (kappa, lambda) and fibrinogen antibodies. After standardization of the technique, 75 renal biopsies and 43 autopsies cases were stained. Out of 43 autopsy cases, immune-complex mediated glomerulonephritis (GN) was confirmed in 18 cases (Lupus nephritis-11, IgAN-6, MGN-1), complement-mediated dense deposit disease (DDD-1) and monoclonal diseases in 4 cases (amyloidosis-3, cast nephropathy-1). Immune-mediated injury was excluded in 17 cases (focal segmental glomerulosclerosis -3, crescentic GN-6 [pauci-immune-3, anti-GBM-3], thrombotic microangiopathy-5, atherosclerosis-3). Renal biopsies (n-75) where inadequate or no frozen sample was available; this technique classified 52 mesangiocapillary pattern as MPGN type-1-46, DDD-2 and (C3GN-4). Others were diagnosed as IgAN-3, lupus nephritis-2, MGN-4, diffuse proliferative glomerulonephritis (DPGN)-1, Non-IC crescentic GN-1, monoclonal diseases-3. In nine cases, DIF on FFPE tissue could not help in making diagnosis. Proteinase-K enzymatic digestion of FFPE renal biopsies can unmask complements (both C3 and C1q) in immune-complexes mediated and complement-mediated diseases. This method showed good results on autopsy tissues archived for as long as 15 years.

Sensitive molecular detection of small nodal metastasis in uterine cervical cancer using HPV16-E6/CK19/MUC1 cancer biomarkers.

PubMed

Samouëlian, Vanessa; Mechtouf, Nawel; Leblanc, Eric; Cardin, Guillaume B; Lhotellier, Valérie; Querleu, Denis; Révillion, Françoise; Rodier, Francis

2018-04-24

Metastatic nodal involvement is a critical prognostic factor in uterine cervical cancer (UCC). To improve current methods of detecting UCC metastases in lymph nodes (LNs), we used quantitative PCR (qPCR) to assess mRNA expression of potential metastatic biomarkers. We found that expression of HPV16-E6, cytokeratin19 (CK19), and mucin1 (MUC1) is consistently upregulated in tumors and metastatic tissues, supporting a role for these genes in UCC progression. These putative biomarkers were able to predict the presence of histologically positive metastatic LNs with respective sensitivities and specificities of 82% and 99% (CK19), 76% and 95% (HPV16-E6), and 76% and 78% (MUC1). While the biomarkers failed to detect 1.7% to 2.2% of the histologically positive LNs when used individually, combining CK19 and HPV16-E6 enhanced sensitivity and specificity to 100% and 94%, respectively. To explore the sensitivity of qPCR-based detection of varying proportions of invading HPV16-positive UCC cells, we designed a LN metastasis model that achieved a fresh cell detection limit of 0.008% (1:12500 HPV16-positive to HPV16-negative cells), and a paraffin-embedded, formalin-fixed (PEFF) detection limit of 0.02% (1:5000 HPV16-positive to HPV16-negative cells), both of which are within the theoretical detection limit for micrometastasis. Thus, HPV E6/E7 oncogenes may be useful targets for the ultrasensitive detection of nodal involvements like micrometastases in fresh or archived tissue samples. Moreover, our results suggest that the biomarker combination of CK19/HPV-E6 could support a real-time intraoperative strategy for the detection of small, but potentially lethal, metastatic nodal involvements in fresh UCC tissues.

Investigation of the "true" extraction recovery of analytes from multiple types of tissues and its impact on tissue bioanalysis using two model compounds.

PubMed

Yuan, Long; Ma, Li; Dillon, Lisa; Fancher, R Marcus; Sun, Huadong; Zhu, Mingshe; Lehman-McKeeman, Lois; Aubry, Anne-Françoise; Ji, Qin C

2016-11-16

LC-MS/MS has been widely applied to the quantitative analysis of tissue samples. However, one key remaining issue is that the extraction recovery of analyte from spiked tissue calibration standard and quality control samples (QCs) may not accurately represent the "true" recovery of analyte from incurred tissue samples. This may affect the accuracy of LC-MS/MS tissue bioanalysis. Here, we investigated whether the recovery determined using tissue QCs by LC-MS/MS can accurately represent the "true" recovery from incurred tissue samples using two model compounds: BMS-986104, a S1P 1 receptor modulator drug candidate, and its phosphate metabolite, BMS-986104-P. We first developed a novel acid and surfactant assisted protein precipitation method for the extraction of BMS-986104 and BMS-986104-P from rat tissues, and determined their recoveries using tissue QCs by LC-MS/MS. We then used radioactive incurred samples from rats dosed with 3 H-labeled BMS-986104 to determine the absolute total radioactivity recovery in six different tissues. The recoveries determined using tissue QCs and incurred samples matched with each other very well. The results demonstrated that, in this assay, tissue QCs accurately represented the incurred tissue samples to determine the "true" recovery, and LC-MS/MS assay was accurate for tissue bioanalysis. Another aspect we investigated is how the tissue QCs should be prepared to better represent the incurred tissue samples. We compared two different QC preparation methods (analyte spiked in tissue homogenates or in intact tissues) and demonstrated that the two methods had no significant difference when a good sample preparation was in place. The developed assay showed excellent accuracy and precision, and was successfully applied to the quantitative determination of BMS-986104 and BMS-986104-P in tissues in a rat toxicology study. Copyright © 2016 Elsevier B.V. All rights reserved.

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

Principles, Techniques, and Applications of Tissue Microfluidics

NASA Technical Reports Server (NTRS)

Wade, Lawrence A.; Kartalov, Emil P.; Shibata, Darryl; Taylor, Clive

2011-01-01

The principle of tissue microfluidics and its resultant techniques has been applied to cell analysis. Building microfluidics to suit a particular tissue sample would allow the rapid, reliable, inexpensive, highly parallelized, selective extraction of chosen regions of tissue for purposes of further biochemical analysis. Furthermore, the applicability of the techniques ranges beyond the described pathology application. For example, they would also allow the posing and successful answering of new sets of questions in many areas of fundamental research. The proposed integration of microfluidic techniques and tissue slice samples is called tissue microfluidics because it molds the microfluidic architectures in accordance with each particular structure of each specific tissue sample. Thus, microfluidics can be built around the tissues, following the tissue structure, or alternatively, the microfluidics can be adapted to the specific geometry of particular tissues. By contrast, the traditional approach is that microfluidic devices are structured in accordance with engineering considerations, while the biological components in applied devices are forced to comply with these engineering presets. The proposed principles represent a paradigm shift in microfluidic technology in three important ways: Microfluidic devices are to be directly integrated with, onto, or around tissue samples, in contrast to the conventional method of off-chip sample extraction followed by sample insertion in microfluidic devices. Architectural and operational principles of microfluidic devices are to be subordinated to suit specific tissue structure and needs, in contrast to the conventional method of building devices according to fluidic function alone and without regard to tissue structure. Sample acquisition from tissue is to be performed on-chip and is to be integrated with the diagnostic measurement within the same device, in contrast to the conventional method of off-chip sample prep and subsequent insertion into a diagnostic device. A more advanced form of tissue integration with microfluidics is tissue encapsulation, wherein the sample is completely encapsulated within a microfluidic device, to allow for full surface access. The immediate applications of these approaches lie with diagnostics of tissue slices and biopsy samples e.g. for cancer but the approaches would also be very useful in comparative genomics and other areas of fundamental research involving heterogeneous tissue samples.

Gonadotropin suppression in men leads to a reduction in claudin-11 at the Sertoli cell tight junction.

PubMed

McCabe, M J; Tarulli, G A; Laven-Law, G; Matthiesson, K L; Meachem, S J; McLachlan, R I; Dinger, M E; Stanton, P G

2016-04-01

Are Sertoli cell tight junctions (TJs) disrupted in men undergoing hormonal contraception? Localization of the key Sertoli cell TJ protein, claudin-11, was markedly disrupted by 8 weeks of gonadotropin suppression, the degree of which was related to the extent of adluminal germ cell suppression. Sertoli cell TJs are vital components of the blood-testis barrier (BTB) that sequester developing adluminal meiotic germ cells and spermatids from the vascular compartment. Claudin-11 knockout mice are infertile; additionally claudin-11 is spatially disrupted in chronically gonadotropin-suppressed rats coincident with a loss of BTB function, and claudin-11 is disorganized in various human testicular disorders. These data support the Sertoli cell TJ as a potential site of hormonal contraceptive action. BTB proteins were assessed by immunohistochemistry (n = 16 samples) and mRNA (n = 18 samples) expression levels in available archived testis tissue from a previous study of 22 men who had undergone 8 weeks of gonadotropin suppression and for whom meiotic and post-meiotic germ cell numbers were available. The gonadotropin suppression regimens were (i) testosterone enanthate (TE) plus the GnRH antagonist, acyline (A); (ii) TE + the progestin, levonorgestrel, (LNG); (iii) TE + LNG + A or (iv) TE + LNG + the 5α-reductase inhibitor, dutasteride (D). A control group consisted of seven additional men, with three archived samples available for this study. Immunohistochemical localization of claudin-11 (TJ) and other junctional type markers [ZO-1 (cytoplasmic plaque), β-catenin (adherens junction), connexin-43 (gap junction), vinculin (ectoplasmic specialization) and β-actin (cytoskeleton)] and quantitative PCR was conducted using matched frozen testis tissue. Claudin-11 formed a continuous staining pattern at the BTB in control men. Regardless of gonadotropin suppression treatment, claudin-11 localization was markedly disrupted and was broadly associated with the extent of meiotic/post-meiotic germ cell suppression; claudin-11 staining was (i) punctate (i.e. 'spotty' appearance) at the basal aspect of tubules when the average numbers of adluminal germ cells were <15% of control, (ii) presented as short fragments with cytoplasmic extensions when numbers were 15-25% of control or (iii) remained continuous when numbers were >40% of control. Changes in localization of connexin-43 and vinculin were also observed (smaller effects than for claudin-11) but ZO-1, β-catenin and β-actin did not differ, compared with control. Claudin-11 was the only Sertoli cell TJ protein investigated, but it is considered to be the most pivotal of constituent proteins given its known implication in infertility and BTB function. We were limited to testis samples which had been gonadotropin-suppressed for 8 weeks, shorter than the 74-day spermatogenic wave, which may account for the heterogeneity in claudin-11 and germ cell response observed among the men. Longer suppression (12-24 weeks) is known to suppress germ cells further and claudin-11 disruption may be more uniform, although we could not access such samples. These findings are important for our understanding of the sites of action of male hormonal contraception, because they suggest that BTB function could be ablated following long-term hormone suppression treatment. National Health and Medical Research Council (Australia) Program Grants 241000 and 494802; Research Fellowship 1022327 (to R.I.M.) and the Victorian Government's Operational Infrastructure Support Program. None of the authors have any conflicts to disclose. Not applicable. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Investigating the potential role of persistent organic pollutants in Hawaiian green sea turtle fibropapillomatosis

USGS Publications Warehouse

Keller, Jennifer M.; Balazs, George H.; Nilsen, Frances; Rice, Marc; Work, Thierry M.; Jensen, Brenda A.

2014-01-01

It has been hypothesized for decades that environmental pollutants may contribute to green sea turtle fibropapillomatosis (FP), possibly through immunosuppression leading to greater susceptibility to the herpesvirus, the putative causative agent of this tumor-forming disease. To address this question, we measured concentrations of 164 persistent organic pollutants (POPs) and halogenated phenols in 53 Hawaiian green turtle (Chelonia mydas) plasma samples archived by the Biological and Environmental Monitoring and Archival of Sea Turtle Tissues (BEMAST) project at the National Institute of Standards and Technology Marine Environmental Specimen Bank. Four groups of turtles were examined: free-ranging turtles from Kiholo Bay (0% FP, Hawaii), Kailua Bay (low FP, 8%, Oahu), and Kapoho Bay (moderate FP, 38%, Hawaii) and severely tumored stranded turtles that required euthanasia (high FP, 100%, Main Hawaiian Islands). Four classes of POPs and seven halogenated phenols were detected in at least one of the turtles, and concentrations were low (often <200 pg/g wet mass). The presence of halogenated phenols in sea turtles is a novel discovery; their concentrations were higher than most man-made POPs, suggesting that the source of most of these compounds was likely natural (produced by the algal turtle diet) rather than metabolites of man-made POPs. None of the compounds measured increased in concentration with increasing prevalence of FP across the four groups of turtles, suggesting that these 164 compounds are not likely primary triggers for the onset of FP. However, the stranded, severely tumored, emaciated turtle group (n = 14) had the highest concentrations of POPs, which might suggest that mobilization of contaminants with lipids into the blood during late-stage weight loss could contribute to the progression of the disease. Taken together, these data suggest that POPs are not a major cofactor in causing the onset of FP.

Investigating the potential role of persistent organic pollutants in Hawaiian green sea turtle fibropapillomatosis.

PubMed

Keller, Jennifer M; Balazs, George H; Nilsen, Frances; Rice, Marc; Work, Thierry M; Jensen, Brenda A

2014-07-15

It has been hypothesized for decades that environmental pollutants may contribute to green sea turtle fibropapillomatosis (FP), possibly through immunosuppression leading to greater susceptibility to the herpesvirus, the putative causative agent of this tumor-forming disease. To address this question, we measured concentrations of 164 persistent organic pollutants (POPs) and halogenated phenols in 53 Hawaiian green turtle (Chelonia mydas) plasma samples archived by the Biological and Environmental Monitoring and Archival of Sea Turtle Tissues (BEMAST) project at the National Institute of Standards and Technology Marine Environmental Specimen Bank. Four groups of turtles were examined: free-ranging turtles from Kiholo Bay (0% FP, Hawaii), Kailua Bay (low FP, 8%, Oahu), and Kapoho Bay (moderate FP, 38%, Hawaii) and severely tumored stranded turtles that required euthanasia (high FP, 100%, Main Hawaiian Islands). Four classes of POPs and seven halogenated phenols were detected in at least one of the turtles, and concentrations were low (often <200 pg/g wet mass). The presence of halogenated phenols in sea turtles is a novel discovery; their concentrations were higher than most man-made POPs, suggesting that the source of most of these compounds was likely natural (produced by the algal turtle diet) rather than metabolites of man-made POPs. None of the compounds measured increased in concentration with increasing prevalence of FP across the four groups of turtles, suggesting that these 164 compounds are not likely primary triggers for the onset of FP. However, the stranded, severely tumored, emaciated turtle group (n=14) had the highest concentrations of POPs, which might suggest that mobilization of contaminants with lipids into the blood during late-stage weight loss could contribute to the progression of the disease. Taken together, these data suggest that POPs are not a major cofactor in causing the onset of FP.

Understanding the Calcium Isotope and Trace Metal Composition of Elasmobranch Teeth: Implications for Recreating the δ44/40Ca of Seawater

NASA Astrophysics Data System (ADS)

Akhtar, A.; Higgins, J. A.

2017-12-01

Non-traditional stable isotopes in marine fossils have the potential to act as archives of paleo-seawater chemistry, biological evolution, and ancient ecosystems. In particular, bioapatite in elasmobranch enamel has been shown to be a robust proxy for environmental, geochemical and ecological reconstructions through Earth history due to its temporal range (from Devonian to present day) and resistance to diagenetic alteration. Moreover, frequent replacement rates of teeth in individuals, and high species level diversity and global distribution ensure a sample suite that encompasses a wide range of geographies and ecosystems. Here we present δ44/40Ca, δ87/86Sr and trace element (e.g. Sr/Ca, Mg/Ca) data from a suite of 300 teeth spanning the Cretaceous to present day and representing primary, secondary and tertiary piscivores. Modern teeth analyzed as part of this study have an average δ44/40Ca value of -2.07±0.48‰ (2s, n = 80) and Sr/Ca ratio of 2.30±0.24 mmol/mol (2s, n = 40), both offset from present day seawater (0 permil and 8.6 mmol/mol, respectively) due to a combination of inorganic (e.g. mineral precipitation) and biological (e.g. ionic regulation) effects. The total range in δ44/40Ca values in modern teeth is 1.19‰, the same order as that expected for variations in the δ44/40Ca value of ancient seawater. Using results from synthetic apatite synthesis experiments, mathematical modeling, and measurements of shark soft-tissue (e.g. blood and flesh), we explore sources of Ca isotope variability in shark teeth and evaluate their potential as archives of ancient seawater chemistry.

Association of microRNA-200c expression levels with clinicopathological factors and prognosis in endometrioid endometrial cancer.

PubMed

Wilczynski, Milosz; Danielska, Justyna; Domanska-Senderowska, Daria; Dzieniecka, Monika; Szymanska, Bozena; Malinowski, Andrzej

2018-05-01

MicroRNAs (miRNAs) are regulators of gene expression, which play an important role in many critical cellular processes including apoptosis, proliferation and cell differentiation. Aberrant miRNA expression has been reported in a variety of human malignancies. Therefore, miRNAs may be potentially used as cancer biomarkers. miRNA-200c, which is a member of the miRNA-200 family, might play an essential role in tumor progression. The purpose of this study was to evaluate the prognostic and clinical significance of miRNA-200c in women with endometrioid endometrial cancer. Total RNA extraction from 90 archival formalin-fixed paraffin-embedded tissue samples of endometri-oid endometrial cancer and 10 normal endometrium samples was performed. After cDNA synthesis, real-time polymerase chain reaction was conducted and relative expression of miRNA-200c was assessed. Then, miRNA-200c expression levels were evaluated with regard to clinicopathological characteristics. The expression levels of miRNA-200c were significantly increased in endometrioid endometrial cancer samples. Expression of miRNA-200c maintained at significantly higher levels in the early stage endometrioid endometrial cancer compared with more advanced stages. In the Kaplan-Meier analysis, lower levels of miRNA-200c expression were associated with inferior survival. Expression levels of miRNA-200c might be associated with clinicopathological factors and survival in endometrioid endometrial cancer. © 2018 Nordic Federation of Societies of Obstetrics and Gynecology.

DNA extraction from formalin-fixed, paraffin-embedded tissues: protein digestion as a limiting step for retrieval of high-quality DNA.

PubMed

Díaz-Cano, S J; Brady, S P

1997-12-01

Several DNA extraction methods have been used for formalin-fixed, paraffin-embedded tissues, with variable results being reported regarding the suitability of DNA obtained from such sources to serve as template in polymerase chain reaction (PCR)-based genetic analyses. We present a method routinely used for archival material in our laboratory that reliably yields DNA of sufficient quality for PCR studies. This method is based on extended proteinase K digestion (250 micrograms/ml in an EDTA-free calcium-containing buffer supplemented with mussel glycogen) followed by phenol-chloroform extraction. Agarose gel electrophoresis of both digestion buffer aliquots and PCR amplification of the beta-globin gene tested the suitability of the retrieved DNA for PCR amplification.

Ber-H2 (CD30) immunohistochemical staining in malignant melanoma.

PubMed

Polski, J M; Janney, C G

1999-09-01

Malignant melanoma can be included in the differential diagnosis of Hodgkin's disease, anaplastic large cell lymphoma, or embryonal carcinoma These malignancies express CD30, a marker of diagnostic value. A retrospective immunohistochemical study was undertaken to determine the frequency of immunoreactivity of Ber-H2 (anti-CD30 monoclonal antibody) in malignant melanoma Archival paraffin-embedded tissue from 24 primary and metastatic lesions was used. No Ber-H2 labeling was observed in the majority of the studied cases. Variable weak cytoplasmic staining was present in only one case. The findings are compared with the previous reports claiming frequent CD30 expression in malignant melanoma. We discuss issues pertaining to the interpretation of the Ber-H2 IHC staining in formalin-fixed, paraffin-embedded tissue.

Juvenile Delinquency Recidivism: Are Black and White Youth Vulnerable to the Same Risk Factors?

ERIC Educational Resources Information Center

Barrett, David E.; Katsiyannis, Antonis

2015-01-01

Using large-sample, archival data from the state of South Carolina's juvenile justice agency, we examine the question of race differences in predictors of repeat offending for a sample of approximately 100,000 youth who had been referred for criminal offenses. Independent variables relating to background, adverse parenting, mental health,…

Characterizing and Targeting Bone Marrow-Derived Inflammatory Cells in Driving the Malignancy and Progression of Childhood Astrocytic Brain Tumors

DTIC Science & Technology

2015-09-01

to C57/Bl6 mice to create allograft glioma. In addition, xenograft models with human glioma cell lines are also utilized. Furthermore, we also have...of low-grade astrocytoma patients (LGA) vs glioblastoma patients (GBM). Figure 2. IHC of CD11b (infiltrated myeloid cells) on archived...paraffin embedded tumor tissue from low-grade astrocytoma patients (grade II) vs glioblastoma patients (grade IV). 6 Figure 3. Characterizing

SEA: a super-enhancer archive.

PubMed

Wei, Yanjun; Zhang, Shumei; Shang, Shipeng; Zhang, Bin; Li, Song; Wang, Xinyu; Wang, Fang; Su, Jianzhong; Wu, Qiong; Liu, Hongbo; Zhang, Yan

2016-01-04

Super-enhancers are large clusters of transcriptional enhancers regarded as having essential roles in driving the expression of genes that control cell identity during development and tumorigenesis. The construction of a genome-wide super-enhancer database is urgently needed to better understand super-enhancer-directed gene expression regulation for a given biology process. Here, we present a specifically designed web-accessible database, Super-Enhancer Archive (SEA, http://sea.edbc.org). SEA focuses on integrating super-enhancers in multiple species and annotating their potential roles in the regulation of cell identity gene expression. The current release of SEA incorporates 83 996 super-enhancers computationally or experimentally identified in 134 cell types/tissues/diseases, including human (75 439, three of which were experimentally identified), mouse (5879, five of which were experimentally identified), Drosophila melanogaster (1774) and Caenorhabditis elegans (904). To facilitate data extraction, SEA supports multiple search options, including species, genome location, gene name, cell type/tissue and super-enhancer name. The response provides detailed (epi)genetic information, incorporating cell type specificity, nearby genes, transcriptional factor binding sites, CRISPR/Cas9 target sites, evolutionary conservation, SNPs, H3K27ac, DNA methylation, gene expression and TF ChIP-seq data. Moreover, analytical tools and a genome browser were developed for users to explore super-enhancers and their roles in defining cell identity and disease processes in depth. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Verification of out-of-control situations detected by "average of normal" approach.

PubMed

Liu, Jiakai; Tan, Chin Hon; Loh, Tze Ping; Badrick, Tony

2016-11-01

"Average of normal" (AoN) or "moving average" is increasingly used as an adjunct quality control tool in laboratory practice. Little guidance exists on how to verify if an out-of-control situation in the AoN chart is due to a shift in analytical performance, or underlying patient characteristics. Through simulation based on clinical data, we examined 1) the location of the last apparently stable period in the AoN control chart after an analytical shift, and 2) an approach to verify if the observed shift is related to an analytical shift by repeat testing of archived patient samples from the stable period for 21 common analytes. The number of blocks of results to look back for the stable period increased with the duration of the analytical shift, and was larger when smaller AoN block sizes were used. To verify an analytical shift, 3 archived samples from the analytically stable period should be retested. In particular, the process is deemed to have shifted if a difference of >2 analytical standard deviations (i.e. 1:2s rejection rule) between the original and retested results are observed in any of the 3 samples produced. The probability of Type-1 error (i.e., false rejection) and power (i.e., detecting true analytical shift) of this rule are <0.1 and >0.9, respectively. The use of appropriately archived patient samples to verify an apparent analytical shift is preferred to quality control materials. Nonetheless, the above findings may also apply to quality control materials, barring matrix effects. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Documenting of Geologic Field Activities in Real-Time in Four Dimensions: Apollo 17 as a Case Study for Terrestrial Analogues and Future Exploration

NASA Technical Reports Server (NTRS)

Feist, B.; Bleacher, J. E.; Petro, N. E.; Niles, P. B.

2018-01-01

During the Apollo exploration of the lunar surface, thousands of still images, 16 mm videos, TV footage, samples, and surface experiments were captured and collected. In addition, observations and descriptions of what was observed was radioed to Mission Control as part of standard communications and subsequently transcribed. The archive of this material represents perhaps the best recorded set of geologic field campaigns and will serve as the example of how to conduct field work on other planetary bodies for decades to come. However, that archive of material exists in disparate locations and formats with varying levels of completeness, making it not easily cross-referenceable. While video and audio exist for the missions, it is not time synchronized, and images taken during the missions are not time or location tagged. Sample data, while robust, is not easily available in a context of where the samples were collected, their descriptions by the astronauts are not connected to them, or the video footage of their collection (if available). A more than five year undertaking to reconstruct and reconcile the Apollo 17 mission archive, from launch through splashdown, has generated an integrated record of the entire mission, resulting in searchable, synchronized image, voice, and video data, with geologic context provided at the time each sample was collected. Through www.apollo17.org the documentation of the field investigation conducted by the Apollo 17 crew is presented in chronologic sequence, with additional context provided by high-resolution Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images and a corresponding digital terrain model (DTM) of the Taurus-Littrow Valley.

The MATISSE analysis of large spectral datasets from the ESO Archive

NASA Astrophysics Data System (ADS)

Worley, C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Vernisse, Y.; Ordenovic, C.; Bijaoui, A.

2010-12-01

The automated stellar classification algorithm, MATISSE, has been developed at the Observatoire de la Côte d'Azur (OCA) in order to determine stellar temperatures, gravities and chemical abundances for large datasets of stellar spectra. The Gaia Data Processing and Analysis Consortium (DPAC) has selected MATISSE as one of the key programmes to be used in the analysis of the Gaia Radial Velocity Spectrometer (RVS) spectra. MATISSE is currently being used to analyse large datasets of spectra from the ESO archive with the primary goal of producing advanced data products to be made available in the ESO database via the Virtual Observatory. This is also an invaluable opportunity to identify and address issues that can be encountered with the analysis large samples of real spectra prior to the launch of Gaia in 2012. The analysis of the archived spectra of the FEROS spectrograph is currently underway and preliminary results are presented.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

PubMed

Ohta, Tazro; Nakazato, Takeru; Bono, Hidemasa

2017-06-01

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. © The Authors 2017. Published by Oxford University Press.

76 FR 28421 - Marine Mammals; File No. 15646

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... Rebecca Dickhut, Ph.D., Virginia Institute of Marine Science, P.O. Box 1346, Route 1208 Greate Road... following archived samples will be imported from the Swedish Museum of Natural History: fur, blood, and fat...

High-resolution nitrogen stable isotope sclerochronology of bivalve shell carbonate-bound organics

NASA Astrophysics Data System (ADS)

Gillikin, David P.; Lorrain, Anne; Jolivet, Aurélie; Kelemen, Zita; Chauvaud, Laurent; Bouillon, Steven

2017-03-01

Nitrogen stable isotope ratios (δ15N) of organic material have successfully been used to track food-web dynamics, nitrogen baselines, pollution, and nitrogen cycling. Extending the δ15N record back in time has not been straightforward due to a lack of suitable substrates in which δ15N records are faithfully preserved, thus sparking interest in utilizing skeletal carbonate-bound organic matter (CBOM) in mollusks, corals, and foraminifera. Here we test if calcite Pecten maximus shells from the Bay of Brest and the French continental shelf can be used as an archive of δ15N values over a large environmental gradient and at a high temporal resolution (approximately weekly). Bulk CBOM δ15N values from the growing tip of shells collected over a large nitrogen isotope gradient were strongly correlated with adductor muscle tissue δ15N values (R2 = 0.99, n = 6, p < 0.0001). We were able to achieve weekly resolution (on average) over the growing season from sclerochronological profiles of three shells, which showed large seasonal variations up to 3.4‰. However, there were also large inter-specimen differences (up to 2.5‰) between shells growing at the same time and location. Generally, high-resolution shell δ15N values follow soft-tissue δ15N values, but soft-tissues integrate more time, hence soft-tissue data are more time-averaged and smoothed. Museum-archived shells from the 1950s, 1965, and 1970s do not show a large difference in δ15N values through time despite expected increasing N loading to the Bay over this time, which could be due to anthropogenic N sources with contrasting values. Compiling shell CBOM δ15N data from several studies suggests that the offset between soft-tissue and shell δ15N values (Δtissue-shell) differs between calcite and aragonite shells. We hypothesize that this difference is caused by differences in amino acids used in constructing the different minerals, which should be specific to the CaCO3 polymorph being constructed. Future work should use compound specific isotope analyses (CSIA) to test this hypothesis, and to determine whether certain amino acids could specifically track N sources or possibly identify amino acids that are more resistant to diagenesis in fossil shells. In conclusion, bivalve shell CBOM δ15N values can be used in a similar manner to soft-tissue δ15N values, and can track various biogeochemical events at a very high-resolution.

CUBIC pathology: three-dimensional imaging for pathological diagnosis.

PubMed

Nojima, Satoshi; Susaki, Etsuo A; Yoshida, Kyotaro; Takemoto, Hiroyoshi; Tsujimura, Naoto; Iijima, Shohei; Takachi, Ko; Nakahara, Yujiro; Tahara, Shinichiro; Ohshima, Kenji; Kurashige, Masako; Hori, Yumiko; Wada, Naoki; Ikeda, Jun-Ichiro; Kumanogoh, Atsushi; Morii, Eiichi; Ueda, Hiroki R

2017-08-24

The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.

A metadata-aware application for remote scoring and exchange of tissue microarray images

PubMed Central

2013-01-01

Background The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations. Results We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. Conclusion The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery. PMID:23635078

Human papillomavirus in normal conjunctival tissue and in conjunctival papilloma: types and frequencies in a large series.

PubMed

Sjö, Nicolai Christian; von Buchwald, Christian; Cassonnet, Patricia; Norrild, Bodil; Prause, Jan Ulrik; Vinding, Troels; Heegaard, Steffen

2007-08-01

To examine conjunctival papilloma and normal conjunctival tissue for the presence of human papillomavirus (HPV). Archival paraffin wax-embedded tissue from 165 conjunctival papillomas and from 20 histological normal conjunctival biopsy specimens was analysed for the presence of HPV by PCR. Specimens considered HPV positive using consensus primers, but with a negative or uncertain PCR result using type-specific HPV probes, were analysed with DNA sequencing. HPV was present in 86 of 106 (81%) beta-globin-positive papillomas. HPV type 6 was positive in 80 cases, HPV type 11 was identified in 5 cases and HPV type 45 was present in a single papilloma. All the 20 normal conjunctival biopsy specimens were beta-globin positive and HPV negative. There is a strong association between HPV and conjunctival papilloma. The study presents the largest material of conjunctival papilloma investigated for HPV and the first investigation of HPV in normal conjunctival tissue. HPV types 6 and 11 are the most common HPV types in conjunctival papilloma. This also is the first report of HPV type 45 in conjunctival papilloma.

Dioxins and dibenzofurans in adipose tissue of US Vietnam veterans and controls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, H.K.; Watanabe, K.K.; Breen, J.

1991-03-01

The primary reason for concern about the adverse effects of exposure to Agent Orange is attributable to its toxic contaminant, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or dioxin. We studied adipose tissues from 36 Vietnam veterans, a similar group of 79 non-Vietnam veterans, and 80 civilians; the tissue specimens were selected from the 8,000 archived tissues collected from the non-institutionalized general population by the US Environmental Protection Agency. The geometric mean (+/- standard deviation) dioxin levels in adipose tissue for Vietnam veterans, non-Vietnam veterans, and civilian controls were 11.7 (+/- 1.7), 10.9 (+/- 1.7), and 12.4 (+/- 1.9) parts per trillion on a lipidmore » weight basis, respectively. The mean levels for these groups were not significantly different from each other with or without adjustment for age of individuals, body mass index, and specimen collection year. In addition, none of the surrogate measures of Agent Orange exposure such as military branch, service within specific geographic region, military occupation, and troop location in relation to recorded Agent Orange spray was associated with the dioxin levels in adipose tissue of Vietnam veterans. Our results suggest that heavy exposure to Agent Orange or dioxin for most US troops was unlikely.« less

Interpretation of ANA Indirect Immunofluorescence Test Outside the Darkroom Using NOVA View Compared to Manual Microscopy

PubMed Central

Copple, Susan S.; Jaskowski, Troy D.; Giles, Rashelle; Hill, Harry R.

2014-01-01

Objective. To evaluate NOVA View with focus on reading archived images versus microscope based manual interpretation of ANA HEp-2 slides by an experienced, certified medical technologist. Methods. 369 well defined sera from: 44 rheumatoid arthritis, 50 systemic lupus erythematosus, 35 scleroderma, 19 Sjögren's syndrome, and 10 polymyositis patients as well as 99 healthy controls were examined. In addition, 12 defined sera from the Centers for Disease Control and 100 random patient sera sent to ARUP Laboratories for ANA HEp-2 IIF testing were included. Samples were read using the archived images on NOVA View and compared to results obtained from manual reading. Results. At a 1 : 40/1 : 80 dilution the resulting comparison demonstrated 94.8%/92.9% positive, 97.4%/97.4% negative, and 96.5%/96.2% total agreements between manual IIF and NOVA View archived images. Agreement of identifiable patterns between methods was 97%, with PCNA and mixed patterns undetermined. Conclusion. Excellent agreements were obtained between reading archived images on NOVA View and manually on a fluorescent microscope. In addition, workflow benefits were observed which need to be analyzed in future studies. PMID:24741573

The SAMI Galaxy Survey: A prototype data archive for Big Science exploration

NASA Astrophysics Data System (ADS)

Konstantopoulos, I. S.; Green, A. W.; Foster, C.; Scott, N.; Allen, J. T.; Fogarty, L. M. R.; Lorente, N. P. F.; Sweet, S. M.; Hopkins, A. M.; Bland-Hawthorn, J.; Bryant, J. J.; Croom, S. M.; Goodwin, M.; Lawrence, J. S.; Owers, M. S.; Richards, S. N.

2015-11-01

We describe the data archive and database for the SAMI Galaxy Survey, an ongoing observational program that will cover ≈3400 galaxies with integral-field (spatially-resolved) spectroscopy. Amounting to some three million spectra, this is the largest sample of its kind to date. The data archive and built-in query engine use the versatile Hierarchical Data Format (HDF5), which precludes the need for external metadata tables and hence the setup and maintenance overhead those carry. The code produces simple outputs that can easily be translated to plots and tables, and the combination of these tools makes for a light system that can handle heavy data. This article acts as a contextual companion to the SAMI Survey Database source code repository, samiDB, which is freely available online and written entirely in Python. We also discuss the decisions related to the selection of tools and the creation of data visualisation modules. It is our aim that the work presented in this article-descriptions, rationale, and source code-will be of use to scientists looking to set up a maintenance-light data archive for a Big Science data load.

Guidelines for Contracting Microfilming Services.

ERIC Educational Resources Information Center

Byrne, Sherry

1986-01-01

Outlines the process involved in selecting an outside filming agent for the purpose of preserving a library's or archive's holdings. Guidelines include project planning, selecting a filming agent, and contract preparation and maintenance. A sample contract is included. (Author/EM)

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

PubMed Central

Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Hoopen, Petra ten; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert D.

2016-01-01

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans. PMID:26582919

Climatically driven loss of calcium in steppe soil as a sink for atmospheric carbon

Treesearch

A.G. Lapenis; G.B. Lawrence; S.W. Bailey; B.F. Aparin; A.I. Shiklomanov; N.A. Speranskaya; M.S. Torn; M. Calef

2008-01-01

During the last several thousand years the semi-arid, cold climate of the Russian steppe formed highly fertile soils rich in organic carbon and calcium (classified as Chernozems in the Russian system). Analysis of archived soil samples collected in Kemannaya Steppe Preserve in 1920, 1947, 1970, and fresh samples collected in 1998 indicated that the native steppe...

A study of hydrocarbons associated with brines from DOE geopressured wells. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keeley, D.F.

1993-07-01

Accomplishments are summarized on the following tasks: distribution coefficients and solubilities, DOE design well sampling, analysis of well samples, review of theoretical models of geopressured reservoir hydrocarbons, monitor for aliphatic hydrocarbons, development of a ph meter probe, DOE design well scrubber analysis, removal and disposition of gas scrubber equipment at Pleasant Bayou Well, and disposition of archived brines.

Archive of Samples for Long-Term Preservation of RNA and Other Nucleic Acids

DTIC Science & Technology

2016-05-15

shaker platform whi le making sure that the tubes are held solidly in the rack. 6.3.4 Transfer the sample from the RNA tubes to the corresponding...well polypropylene u-bottom plate (Final_1) onto position P15. - 25- 6.3.15 Click the green "Play" arrow at the bottom right of the RNAdvance method

A study of hydrocarbons associated with brines from DOE geopressured wells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keeley, D.F.

1993-01-01

Accomplishments are summarized on the following tasks: distribution coefficients and solubilities, DOE design well sampling, analysis of well samples, review of theoretical models of geopressured reservoir hydrocarbons, monitor for aliphatic hydrocarbons, development of a ph meter probe, DOE design well scrubber analysis, removal and disposition of gas scrubber equipment at Pleasant Bayou Well, and disposition of archived brines.

Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues

PubMed Central

Kennedy, Jacob J.; Whiteaker, Jeffrey R.; Schoenherr, Regine M.; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N.; Baird, Geoffrey Stuart; Paulovich, Amanda G.

2016-01-01

Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring-mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e. 9 processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R2 = 0.94) and immuno-MRM (R2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens. PMID:27462933

Expression of connective tissue growth factor is a prognostic marker for patients with intrahepatic cholangiocarcinoma.

PubMed

Gardini, A; Corti, B; Fiorentino, M; Altimari, A; Ercolani, G; Grazi, G L; Pinna, A D; Grigioni, W F; D'Errico Grigioni, A

2005-04-01

Connective tissue growth factor is a member of the 'CCN' protein family. Consistent with its profibrotic properties, it is over-expressed in several human epithelial malignancies. We have retrospectively evaluated by immunohistochemistry the presence of connective tissue growth factor in archival tissues from 55 resected intrahepatic cholangiocarcinomas and compared its expression to the main pathological parameters, disease free and overall survival. Tumours were scored as high and low/absent expressers (> or =50%, 0-50% cells, respectively). Thirty-three of 55 cholangiocarcinomas (60%) were high and 22 (40%) low expressers. No significant correlation was found between connective tissue growth factor and tumour grade, tumour location, vascular and perineural invasion. Eighteen of 22 (82%) low/absent expressers and 12/33 (36%) high expressers had recurrence of disease (P=0.001). Low/absent expressers showed a poor disease free and overall survival compared with the higher expressers (P<0.001). Vascular invasion was related to tumour recurrence (P=0.025) and to decreased disease free survival (P<0.05). During proportional hazard regression analysis, only connective tissue growth factor was found to influence disease free survival (P=0.01). Expression of connective tissue growth factor is an independent prognostic indicator of both tumour recurrence and overall survival for intrahepatic cholangiocarcinoma patients regardless of tumour location, tumour grade, vascular and perineural invasion.

The AMBRE Project: Stellar parameterisation of the ESO:UVES archived spectra

NASA Astrophysics Data System (ADS)

Worley, C. C.; de Laverny, P.; Recio-Blanco, A.; Hill, V.; Bijaoui, A.

2016-06-01

Context. The AMBRE Project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Côte d'Azur (OCA) that has been established to determine the stellar atmospheric parameters for the archived spectra of four ESO spectrographs. Aims: The analysis of the UVES archived spectra for their stellar parameters was completed in the third phase of the AMBRE Project. From the complete ESO:UVES archive dataset that was received covering the period 2000 to 2010, 51 921 spectra for the six standard setups were analysed. These correspond to approximately 8014 distinct targets (that comprise stellar and non-stellar objects) by radial coordinate search. Methods: The AMBRE analysis pipeline integrates spectral normalisation, cleaning and radial velocity correction procedures in order that the UVES spectra can then be analysed automatically with the stellar parameterisation algorithm MATISSE to obtain the stellar atmospheric parameters. The synthetic grid against which the MATISSE analysis is carried out is currently constrained to parameters of FGKM stars only. Results: Stellar atmospheric parameters are reported for 12 403 of the 51 921 UVES archived spectra analysed in AMBRE:UVES. This equates to ~23.9% of the sample and ~3708 stars. Effective temperature, surface gravity, metallicity, and alpha element to iron ratio abundances are provided for 10 212 spectra (~19.7%), while effective temperature at least is provided for the remaining 2191 spectra. Radial velocities are reported for 36 881 (~71.0%) of the analysed archive spectra. While parameters were determined for 32 306 (62.2%) spectra these parameters were not considered reliable (and thus not reported to ESO) for reasons such as very low S/N, too poor radial velocity determination, spectral features too broad for analysis, and technical issues from the reduction. Similarly the parameters of a further 7212 spectra (13.9%) were also not reported to ESO based on quality criteria and error analysis which were determined within the automated parameterisation process. Those tests lead us to expect that multi-component stellar systems will return high errors in radial velocity and fitting to the synthetic spectra and therefore will not have parameters reported to ESO. Typical external errors of σTeff ~ 110 dex, σlog g ~ 0.18 dex, σ[ M/H ] ~ 0.13 dex, and σ[ α/ Fe ] ~ 0.05 dex with some variation between giants and dwarfs and between setups are reported. Conclusions: UVES is used to observe an extensive collection of stellar and non-stellar objects all of which have been included in the archived dataset provided to OCA by ESO. The AMBRE analysis extracts those objects that lie within the FGKM parameter space of the AMBRE slow-rotating synthetic spectra grid. Thus by homogeneous blind analysis AMBRE has successfully extracted and parameterised the targeted FGK stars (23.9% of the analysed sample) from within the ESO:UVES archive.

Detecting oscillatory patterns and time lags from proxy records with non-uniform sampling: Some pitfalls and possible solutions

NASA Astrophysics Data System (ADS)

Donner, Reik

2013-04-01

Time series analysis offers a rich toolbox for deciphering information from high-resolution geological and geomorphological archives and linking the thus obtained results to distinct climate and environmental processes. Specifically, on various time-scales from inter-annual to multi-millenial, underlying driving forces exhibit more or less periodic oscillations, the detection of which in proxy records often allows linking them to specific mechanisms by which the corresponding drivers may have affected the archive under study. A persistent problem in geomorphology is that available records do not present a clear signal of the variability of environmental conditions, but exhibit considerable uncertainties of both the measured proxy variables and the associated age model. Particularly, time-scale uncertainty as well as the heterogeneity of sampling in the time domain are source of severe conceptual problems that may lead to false conclusions about the presence or absence of oscillatory patterns and their mutual phasing in different archives. In my presentation, I will discuss how one can cope with non-uniformly sampled proxy records to detect and quantify oscillatory patterns in one or more data sets. For this purpose, correlation analysis is reformulated using kernel estimates which are found superior to classical estimators based on interpolation or Fourier transform techniques. In order to characterize non-stationary or noisy periodicities and their relative phasing between different records, an extension of continuous wavelet transform is utilized. The performance of both methods is illustrated for different case studies. An extension to explicitly considering time-scale uncertainties by means of Bayesian techniques is briefly outlined.

Exploring the Potential of a Global Emerging Contaminant Early Warning Network through the Use of Retrospective Suspect Screening with High-Resolution Mass Spectrometry.

PubMed

Alygizakis, Nikiforos A; Samanipour, Saer; Hollender, Juliane; Ibáñez, María; Kaserzon, Sarit; Kokkali, Varvara; van Leerdam, Jan A; Mueller, Jochen F; Pijnappels, Martijn; Reid, Malcolm J; Schymanski, Emma L; Slobodnik, Jaroslav; Thomaidis, Nikolaos S; Thomas, Kevin V

2018-05-01

A key challenge in the environmental and exposure sciences is to establish experimental evidence of the role of chemical exposure in human and environmental systems. High resolution and accurate tandem mass spectrometry (HRMS) is increasingly being used for the analysis of environmental samples. One lauded benefit of HRMS is the possibility to retrospectively process data for (previously omitted) compounds that has led to the archiving of HRMS data. Archived HRMS data affords the possibility of exploiting historical data to rapidly and effectively establish the temporal and spatial occurrence of newly identified contaminants through retrospective suspect screening. We propose to establish a global emerging contaminant early warning network to rapidly assess the spatial and temporal distribution of contaminants of emerging concern in environmental samples through performing retrospective analysis on HRMS data. The effectiveness of such a network is demonstrated through a pilot study, where eight reference laboratories with available archived HRMS data retrospectively screened data acquired from aqueous environmental samples collected in 14 countries on 3 different continents. The widespread spatial occurrence of several surfactants (e.g., polyethylene glycols ( PEGs ) and C12AEO-PEGs ), transformation products of selected drugs (e.g., gabapentin-lactam, metoprolol-acid, carbamazepine-10-hydroxy, omeprazole-4-hydroxy-sulfide, and 2-benzothiazole-sulfonic-acid), and industrial chemicals (3-nitrobenzenesulfonate and bisphenol-S) was revealed. Obtaining identifications of increased reliability through retrospective suspect screening is challenging, and recommendations for dealing with issues such as broad chromatographic peaks, data acquisition, and sensitivity are provided.

Recovery and archiving key Arctic Alaska vegetation map and plot data for the Arctic-Boreal Vulnerability Field Experiment (ABoVE)

NASA Astrophysics Data System (ADS)

Walker, D. A.; Breen, A. L.; Broderson, D.; Epstein, H. E.; Fisher, W.; Grunblatt, J.; Heinrichs, T.; Raynolds, M. K.; Walker, M. D.; Wirth, L.

2013-12-01

Abundant ground-based information will be needed to inform remote-sensing and modeling studies of NASA's Arctic-Boreal Vulnerability Experiment (ABoVE). A large body of plot and map data collected by the Alaska Geobotany Center (AGC) and collaborators from the Arctic regions of Alaska and the circumpolar Arctic over the past several decades is being archived and made accessible to scientists and the public via the Geographic Information Network of Alaska's (GINA's) 'Catalog' display and portal system. We are building two main types of data archives: Vegetation Plot Archive: For the plot information we use a Turboveg database to construct the Alaska portion of the international Arctic Vegetation Archive (AVA) http://www.geobotany.uaf.edu/ava/. High quality plot data and non-digital legacy datasets in danger of being lost have highest priority for entry into the archive. A key aspect of the database is the PanArctic Species List (PASL-1), developed specifically for the AVA to provide a standard of species nomenclature for the entire Arctic biome. A wide variety of reports, documents, and ancillary data are linked to each plot's geographic location. Geoecological Map Archive: This database includes maps and remote sensing products and links to other relevant data associated with the maps, mainly those produced by the Alaska Geobotany Center. Map data include GIS shape files of vegetation, land-cover, soils, landforms and other categorical variables and digital raster data of elevation, multispectral satellite-derived data, and data products and metadata associated with these. The map archive will contain all the information that is currently in the hierarchical Toolik-Arctic Geobotanical Atlas (T-AGA) in Alaska http://www.arcticatlas.org, plus several additions that are in the process of development and will be combined with GINA's already substantial holdings of spatial data from northern Alaska. The Geoecological Atlas Portal uses GINA's Catalog tool to develop a web interface to view and access the plot and map data. The mapping portal allows visualization of GIS data, sample-point locations and imagery and access to the map data. Catalog facilitates the discovery and dissemination of science-based information products in support of analysis and decision-making concerned with development and climate change and is currently used by GINA in several similar archive/distribution portals.

PD-L1 expression and presence of TILs in small intestinal neuroendocrine tumours

PubMed Central

Lamarca, Angela; Nonaka, Daisuke; Breitwieser, Wolfgang; Ashton, Garry; Barriuso, Jorge; McNamara, Mairéad G.; Moghadam, Sharzad; Rogan, Jane; Mansoor, Wasat; Hubner, Richard A.; Clark, Christopher; Chakrabarty, Bipasha; Valle, Juan W.

2018-01-01

Background The extent of resistance to immune surveillance in patients with well-differentiated (Wd) (grade 1/2) small-intestinal neuroendocrine tumours (Si-NETs) is unknown. Methods Patients diagnosed with Wd Si-NETs (excluding appendix, which are considered to have a different biology to other midgut NETs) were eligible. Tumoural programmed death (PD)-ligand(L) 1 (PD-L1)/PD-L2/PD-1 and tumour infiltrating lymphocytes (TILs) [presence and phenotype] were analysed in archival tissue by immunohistochemistry (IHC); reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used for confirmation of IHC results. Results Of 109 patients screened, 62 were eligible: 54.8% were male; median age was 63.7 years (95%-CI 59.7-67.2); disease stage II: 4.8%, III: 40.3% and IV: 54.8%; 41.9% were functional. Analysed samples (67.1% from primary tumours, 32.9% from metastases) were of grade 1 (67.1%) or 2 (32.86%) with a median Ki-67 of 2%. From the total of 62 eligible patients, 70 and 63 samples were suitable for IHC and RT-qPCR analysis, respectively. PD-L1 expression within tumour cells and TILs were identified in 12.8% and 24.3% of samples respectively; 30% of samples showed PD-L1 expression within tumour cells and/or TILs. PD-1 was present in TILs in 22.8% of samples. Majority of samples showed significant presence of CD4+ (focal 42.86%; moderate 2.86%) and CD8+ (focal 92.86%; moderate 4.29%) TILs. IHC findings were confirmed with RT-qPCR; which showed higher expression levels of PD-L1 (p-value 0.007) and PD-1 (p-value 0.001) in samples positive for IHC compared to negative-IHC. Conclusions Thirty-percent of patients express PD-L1 within tumour cells and/or TILs. Identification of presence of TILs was also significant and warrant the investigation of immunotherapy in this setting. PMID:29599916

TEAM Webinar Series | EGRP/DCCPS/NCI/NIH

Cancer.gov

View archived webinars from the Transforming Epidemiology through Advanced Methods (TEAM) Webinar Series, hosted by NCI's Epidemiology and Genomics Research Program. Topics include participant engagement, data coordination, mHealth tools, sample selection, and instruments for diet & physical activity assessment.

Detection and identification of Variola virus in fixed human tissue after prolonged archival storage.

PubMed

Schoepp, Randal J; Morin, Michelle D; Martinez, Mark J; Kulesh, David A; Hensley, Lisa; Geisbert, Thomas W; Brady, Daniel R; Jahrling, Peter B

2004-01-01

Smallpox disease has been eradicated from the human population since 1979, but is again a concern because of its potential use as an agent of bioterrorism or biowarfare. World Health Organization-sanctioned repositories of infectious Variola virus are known to occur in both Russia and the United States, but many believe other undeclared and unregulated sources of the virus could exist. Thus, validation of improved methods for definitive identification of smallpox virus in diagnostic specimens is urgently needed. In this paper, we describe the discovery of suspected Variola infected human tissue, fixed and preserved for decades in largely unknown solutions, and the use of routine histology, electron microscopy, and ultimately DNA extraction and fluorogenic 5' nuclease (TaqMan) assays for its identification and confirmation.

The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.

PubMed

Gutman, David A; Khalilia, Mohammed; Lee, Sanghoon; Nalisnik, Michael; Mullen, Zach; Beezley, Jonathan; Chittajallu, Deepak R; Manthey, David; Cooper, Lee A D

2017-11-01

Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software. In this article, we describe the Digital Slide Archive (DSA), an open-source web-based platform for digital pathology. DSA allows investigators to manage large collections of histologic images and integrate them with clinical and genomic metadata. The open-source model enables DSA to be extended to provide additional capabilities. Cancer Res; 77(21); e75-78. ©2017 AACR . ©2017 American Association for Cancer Research.

NASA's Planetary Data System: Support for the Delivery of Derived Data Sets at the Atmospheres Node

NASA Astrophysics Data System (ADS)

Chanover, Nancy J.; Beebe, Reta; Neakrase, Lynn; Huber, Lyle; Rees, Shannon; Hornung, Danae

2015-11-01

NASA’s Planetary Data System is charged with archiving electronic data products from NASA planetary missions that are sponsored by NASA’s Science Mission Directorate. This archive, currently organized by science disciplines, uses standards for describing and storing data that are designed to enable future scientists who are unfamiliar with the original experiments to analyze the data, and to do this using a variety of computer platforms, with no additional support. These standards address the data structure, description contents, and media design. The new requirement in the NASA ROSES-2015 Research Announcement to include a Data Management Plan will result in an increase in the number of derived data sets that are being delivered to the PDS. These data sets may come from the Planetary Data Archiving, Restoration and Tools (PDART) program, other Data Analysis Programs (DAPs) or be volunteered by individuals who are publishing the results of their analysis. In response to this increase, the PDS Atmospheres Node is developing a set of guidelines and user tools to make the process of archiving these derived data products more efficient. Here we provide a description of Atmospheres Node resources, including a letter of support for the proposal stage, a communication schedule for the planned archive effort, product label samples and templates in extensible markup language (XML), documentation templates, and validation tools necessary for producing a PDS4-compliant derived data bundle(s) efficiently and accurately.

VizieR Online Data Catalog: Star formation in active and normal galaxies (Tsai+, 2015)

NASA Astrophysics Data System (ADS)

Tsai, M.; Hwang, C.-Y.

2015-11-01

We selected 104 active galaxies from the lists of Melendez et al. (2010MNRAS.406..493M), Condon et al. 1991 (cat. J/ApJ/378/65), and Ho & Ulvestad 2001 (cat. J/ApJS/133/77). Most of the sources are identified as Active Galactic Nuclei (AGNs), and a few of them are classified as Luminous InfraRed Galaxies (LIRGs). We obtained 3.6 and 8μm infrared images of these galaxies from the Spitzer Archive (http://sha.ipac.caltech.edu/applications/Spitzer/SHA/) and 8GHz images from the VLA archive (http://archive.nrao.edu/archive/archiveimage.html). We also selected a nearby AGN sub-sample containing 21 radio-selected AGNs for further spatial analysis. We selected 25 nearby AGNs exhibiting no detected radio emission in order to compare with the results of the radio-selected sources. For comparison, we also selected normal galaxies with distances less than 15Mpc from the catalog of Tully 1994 (see cat. VII/145). We only selected the galaxies that have Spitzer archive data and are not identified as AGNs in either the Veron-Cetty & Veron 2006 (see cat. VII/258) AGN catalog or in the NED database (http://ned.ipac.caltech.edu/). Our results for the radio-selected and the non-radio-selected active galaxies are listed in Table1, and those for the normal galaxies are listed in Table2. (2 data files).

Expression profiling of cell cycle regulatory proteins in oropharyngeal carcinomas using tissue microarrays.

PubMed

Ribeiro, Daniel A; Nascimento, Fabio D; Fracalossi, Ana Carolina C; Gomes, Thiago S; Oshima, Celina T F; Franco, Marcello F

2010-01-01

The aim of this study was to investigate the expressions of cell cycle regulatory proteins such as p53, p16, p21, and Rb in squamous cell carcinoma of the oropharynx and their relation to histological differentiation, staging of disease, and prognosis. Paraffin blocks from 21 primary tumors were obtained from archives of the Department of Pathology, Paulista Medical School, Federal University of Sao Paulo, UNIFESP/EPM. Immunohistochemistry was used to detect the expression of p53, p16, p21, and Rb by means of tissue microarrays. Expression of p53, p21, p16 and Rb was not correlated with the stage of disease, histopathological grading or recurrence in squamous cell carcinoma of the oropharynx. Taken together, our results suggest that p53, p16, p21 and Rb are not reliable biomarkers for prognosis of the tumor severity or recurrence in squamous cell carcinoma of the oropharynx as depicted by tissue microarrays and immunohistochemistry.

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

PubMed Central

Krishnaswami, Suguna Rani; Grindberg, Rashel V; Novotny, Mark; Venepally, Pratap; Lacar, Benjamin; Bhutani, Kunal; Linker, Sara B; Pham, Son; Erwin, Jennifer A; Miller, Jeremy A; Hodge, Rebecca; McCarthy, James K; Kelder, Martin; McCorrison, Jamison; Aevermann, Brian D; Fuertes, Francisco Diez; Scheuermann, Richard H; Lee, Jun; Lein, Ed S; Schork, Nicholas; McConnell, Michael J; Gage, Fred H; Lasken, Roger S

2016-01-01

A protocol is described for sequencing the transcriptome of a cell nucleus. Nuclei are isolated from specimens and sorted by FACS, cDNA libraries are constructed and RNA-seq is performed, followed by data analysis. Some steps follow published methods (Smart-seq2 for cDNA synthesis and Nextera XT barcoded library preparation) and are not described in detail here. Previous single-cell approaches for RNA-seq from tissues include cell dissociation using protease treatment at 30 °C, which is known to alter the transcriptome. We isolate nuclei at 4 °C from tissue homogenates, which cause minimal damage. Nuclear transcriptomes can be obtained from postmortem human brain tissue stored at −80 °C, making brain archives accessible for RNA-seq from individual neurons. The method also allows investigation of biological features unique to nuclei, such as enrichment of certain transcripts and precursors of some noncoding RNAs. By following this procedure, it takes about 4 d to construct cDNA libraries that are ready for sequencing. PMID:26890679

Trace-Element Concentrations in Tissues of Aquatic Organisms from Rivers and Streams of the United States, 1992-1999

USGS Publications Warehouse

DeWeese, Lawrence R.; Stephens, Verlin C.; Short, Terry M.; Dubrovsky, Neil M.

2007-01-01

The U.S. Geological Survey National Water-Quality Assessment Program collected tissue samples from a variety of aquatic organisms during 1992-1999 within 47 study units across the United States. These tissue samples were collected to determine the occurrence and distribution of 20 major and minor trace elements in aquatic organisms. This report presents the tissue trace-element concentration data, sample summaries, and concentration statistics for 1,457 tissue samples representing 76 species or groups of fish, aquatic invertebrates, and plants were collected at 824 sampling sites.

Determination of initial fuel state and number of reactor shutdowns in archived low-burnup uranium targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Byerly, Benjamin; Tandon, Lav; Hayes-Sterbenz, Anna

This article presents a method for destructive analysis of irradiated uranium (U) targets, with a focus on collection and measurement of long-lived (t 1/2 > ~10 years) and stable fission product isotopes of ruthenium and cesium. Long-lived and stable isotopes of these elements can provide information on reactor conditions (e.g. flux, irradiation time, cooling time) in old samples (> 5–10 years) whose short-lived fission products have decayed away. The separation and analytical procedures were tested on archived U reactor targets at Los Alamos National Laboratory as part of an effort to evaluate reactor models at low-burnup.

Determination of initial fuel state and number of reactor shutdowns in archived low-burnup uranium targets

DOE PAGES

Byerly, Benjamin; Tandon, Lav; Hayes-Sterbenz, Anna; ...

2015-10-26

This article presents a method for destructive analysis of irradiated uranium (U) targets, with a focus on collection and measurement of long-lived (t 1/2 > ~10 years) and stable fission product isotopes of ruthenium and cesium. Long-lived and stable isotopes of these elements can provide information on reactor conditions (e.g. flux, irradiation time, cooling time) in old samples (> 5–10 years) whose short-lived fission products have decayed away. The separation and analytical procedures were tested on archived U reactor targets at Los Alamos National Laboratory as part of an effort to evaluate reactor models at low-burnup.

Small sarcocysts can be a feature of experimental infections with Sarcocystis neurona merozoites.

PubMed

Marsh, Antoinette E; Chaney, Sarah B; Howe, Daniel K; Saville, William J; Reed, Stephen M

2017-10-15

Several reports indicate the presence of small tissue cysts associated with Sarcocystis neurona infections. Several failed attempts to develop tissue cysts in potential intermediate host using in vitro derived parasites originally isolated from horses with equine protozoal myeloencephalitis suggest that the experimental methods to achieve bradyzoites with those isolates was not possible. Those prior studies reported the lack of detectable sarcocysts based on histology and in vivo feeding trials. A recent report of successful production and detection of small sarcocysts triggered us to review archived tissues from earlier experimental infection studies. The retrospective review sought to determine if small sized sarcocysts were not detected due to their relatively smaller size and infrequency as compared to larger sized sarcocysts produced with other isolates in these experimental inoculation trials. Tissues from two prior in vivo inoculation studies, involving in vitro-produced parasites inoculated into laboratory-reared cats and raccoons, were re-examined by immunohistochemistry staining to more easily detect the tissue cysts. In the experimental cat study no small tissue cysts were seen, consistent with the original publication results. However, in the experimental raccoon study, one raccoon inoculated with an EPM-derived isolate, SN-UCD1, had small sarcocysts not reported in the original publication. This retrospective study suggests that much closer scrutiny of tissues, including the use of immunohistochemistry on tissue sections is required to detect the smaller S. neurona sarcocysts associated with the experimental inoculations of the isolates originally derived from horses with EPM. Published by Elsevier B.V.

Kindlin-2 Expression in Arsenite and Cadmium Transformed Bladder Cancer Cell Lines and in Archival Specimens of Human Bladder Cancer

PubMed Central

Talaat, Sherine; Somji, Seema; Toni, Conrad; Garrett, Scott H.; Zhou, Xu Dong; Sens, Mary Ann; Sens, Donald A.

2011-01-01

Objective The goal of this study was to confirm a microarray study that suggested that Kindlin-2 might play a role in the development and progression of bladder cancer. There has been no previous examination of Kindlin-2 expression in human bladder cancer. Methods A combination of real time PCR, western analysis and immunohistochemistry was used to characterize Kindlin-2 expression in arsenite (As+3) and cadmium (Cd+2) transformed human cell lines, their tumor transplants in immune-compromised mice, and in archival specimens of human bladder and bladder cancer. Results The results show that the Kindlin-2 expression patterns in the cell lines were not duplicated in the tumor tissues. However, it was shown that Kindlin-2 was expressed in the stromal element of all the transplanted tumors and archival specimens of human bladder cancer. It was also shown that a small number of high grade invasive urothelial cancers have focal expression of Kindlin-2 in the tumor cells. Conclusion Kindlin-2 is expressed in the stromal component of most, if not all, human bladder cancers. Kindlin-2 is not expressed in normal urothelium. Kindlin-2 is expressed in a small subset of high grade invasive bladder cancers and may have potential as a prognostic marker for tumor progression. PMID:21624607

A survey of avian paramyxovirus type 1 infections among backyard poultry in New Zealand.

PubMed

Dunowska, M; Zheng, T; Perrott, M R; Christensen, N

2013-11-01

To determine the presence and the pathotype of avian paramyxovirus type 1 (APMV-1), as well as the prevalence of APMV-1 antibodies, among backyard flocks of poultry in selected New Zealand locations. Archival pooled (n = 162) tracheal and cloacal swabs collected from backyard poultry were tested for the presence of APMV-1 RNA by real-time and conventional reverse transcription (RT)-PCR assays. Archival blood samples (n = 240) from a subpopulation of the same birds were tested for the presence of the APMV-1 antibody using a commercial ELISA assay. The archival samples were collected from geographical areas close to bodies of water, in the Bay of Plenty or Wairarapa regions of the North Island of New Zealand, with the high likelihood of interactions between wild waterfowl and domestic poultry. Avian paramyxovirus type 1 RNA was not detected in any of the swabs tested. Antibodies to APMV-1 were detected on 18/19 farms, in 71/240 (29.5%) blood samples tested. The percentage of seropositive birds varied between seropositive farms and ranged from 8.3 to 100%. The percentage of seropositive birds on each farm was not statistically correlated with the flock size, the number of birds sampled, the number of farmed waterfowl, or with the distance to the closest lake/river. However, all chickens from the farm with the highest number of farmed ducks were seropositive for APMV-1. Lack of detection of APMV-1 in any of the samples indicates that APMV-1 was not circulating among the poultry at the time of sampling. However, detection of APMV-1 antibodies in a proportion of birds on each farm indicates that infection with APMV-1, or antigenically related APMV, is common among backyard poultry. On-going proactive surveillance and characterisation of circulating APMV-1 is important for monitoring changes in circulating genotypes of APMV-1 and for understanding the regional ecology of these viruses for the purpose of planning appropriate disease control and prevention strategies. Our data suggest that backyard flocks should be considered as potential reservoirs of APMV. Chickens from backyard farms with multiple bird species may provide good targets for surveillance purposes.

Quantification of HCV RNA in Liver Tissue by bDNA Assay.

PubMed

Dailey, P J; Collins, M L; Urdea, M S; Wilber, J C

1999-01-01

With this statement, Sherlock and Dooley have described two of the three major challenges involved in quantitatively measuring any analyte in tissue samples: the distribution of the analyte in the tissue; and the standard of reference, or denominator, with which to make comparisons between tissue samples. The third challenge for quantitative measurement of an analyte in tissue is to ensure reproducible and quantitative recovery of the analyte on extraction from tissue samples. This chapter describes a method that can be used to measure HCV RNA quantitatively in liver biopsy and tissue samples using the bDNA assay. All three of these challenges-distribution, denominator, and recovery-apply to the measurement of HCV RNA in liver biopsies.

Gains in efficiency and scientific potential of continental climate reconstruction provided by the LRC LacCore Facility, University of Minnesota

NASA Astrophysics Data System (ADS)

Noren, A.; Brady, K.; Myrbo, A.; Ito, E.

2007-12-01

Lacustrine sediment cores comprise an integral archive for the determination of continental paleoclimate, for their potentially high temporal resolution and for their ability to resolve spatial variability in climate across vast sections of the globe. Researchers studying these archives now have a large, nationally-funded, public facility dedicated to the support of their efforts. The LRC LacCore Facility, funded by NSF and the University of Minnesota, provides free or low-cost assistance to any portion of research projects, depending on the specific needs of the project. A large collection of field equipment (site survey equipment, coring devices, boats/platforms, water sampling devices) for nearly any lacustrine setting is available for rental, and Livingstone-type corers and drive rods may be purchased. LacCore staff can accompany field expeditions to operate these devices and curate samples, or provide training prior to device rental. The Facility maintains strong connections to experienced shipping agents and customs brokers, which vastly improves transport and importation of samples. In the lab, high-end instrumentation (e.g., multisensor loggers, high-resolution digital linescan cameras) provides a baseline of fundamental analyses before any sample material is consumed. LacCore staff provide support and training in lithological description, including smear-slide, XRD, and SEM analyses. The LRC botanical macrofossil reference collection is a valuable resource for both core description and detailed macrofossil analysis. Dedicated equipment and space for various subsample analyses streamlines these endeavors; subsamples for several analyses may be submitted for preparation or analysis by Facility technicians for a fee (e.g., carbon and sulfur coulometry, grain size, pollen sample preparation and analysis, charcoal, biogenic silica, LOI, freeze drying). The National Lacustrine Core Repository now curates ~9km of sediment cores from expeditions around the world, and stores metadata and analytical data for all cores processed at the facility. Any researcher may submit sample requests for material in archived cores. Supplies for field (e.g., polycarbonate pipe, endcaps), lab (e.g., sample containers, pollen sample spike), and curation (e.g., D-tubes) are sold at cost. In collaboration with facility users, staff continually develop new equipment, supplies, and procedures as needed in order to provide the best and most comprehensive set of services to the research community.

Developments in Seismic Data Quality Assessment Using MUSTANG at the IRIS DMC

NASA Astrophysics Data System (ADS)

Sharer, G.; Keyson, L.; Templeton, M. E.; Weertman, B.; Smith, K.; Sweet, J. R.; Tape, C.; Casey, R. E.; Ahern, T.

2017-12-01

MUSTANG is the automated data quality metrics system at the IRIS Data Management Center (DMC), designed to help characterize data and metadata "goodness" across the IRIS data archive, which holds 450 TB of seismic and related earth science data spanning the past 40 years. It calculates 46 metrics ranging from sample statistics and miniSEED state-of-health flag counts to Power Spectral Densities (PSDs) and Probability Density Functions (PDFs). These quality measurements are easily and efficiently accessible to users through the use of web services, which allows users to make requests not only by station and time period but also to filter the results according to metric values that match a user's data requirements. Results are returned in a variety of formats, including XML, JSON, CSV, and text. In the case of PSDs and PDFs, results can also be retrieved as plot images. In addition, there are several user-friendly client tools available for exploring and visualizing MUSTANG metrics: LASSO, MUSTANG Databrowser, and MUSTANGular. Over the past year we have made significant improvements to MUSTANG. We have nearly complete coverage over our archive for broadband channels with sample rates of 20-200 sps. With this milestone achieved, we are now expanding to include higher sample rate, short-period, and strong-motion channels. Data availability metrics will soon be calculated when a request is made which guarantees that the information reflects the current state of the archive and also allows for more flexibility in content. For example, MUSTANG will be able to return a count of gaps for any arbitrary time period instead of being limited to 24 hour spans. We are also promoting the use of data quality metrics beyond the IRIS archive through our recent release of ISPAQ, a Python command-line application that calculates MUSTANG-style metrics for users' local miniSEED files or for any miniSEED data accessible through FDSN-compliant web services. Finally, we will explore how researchers are using MUSTANG in real-world situations to select data, improve station data quality, anticipate station outages and servicing, and characterize site noise and environmental conditions.

Anatomical structure overrides temperature controls on magnesium uptake - calcification in the Arctic/subarctic coralline algae Leptophytum laeve and Kvaleya epilaeve (Rhodophyta; Corallinales)

NASA Astrophysics Data System (ADS)

Nash, Merinda C.; Adey, Walter

2018-02-01

Calcified coralline red algae are ecologically key organisms in photic benthic environments. In recent decades they have become important climate proxies, especially in the Arctic and subarctic. It has been widely accepted that magnesium content in coralline tissues is directly a function of ambient temperature, and this is a primary basis for their value as a climate archive. In this paper we show for two genera of Arctic/subarctic corallines, Leptophytum laeve and Kvaleya epilaeve, that previously unrecognised complex tissue and cell wall anatomy bears a variety of basal signatures for Mg content, with the accepted temperature relationship being secondary. The interfilament carbonate has lower Mg than adjacent cell walls and the hypothallial cell walls have the highest Mg content. The internal structure of the hypothallial cell walls can differ substantially from the perithallial radial cell wall structure. Using high-magnification scanning electron microscopy and etching we expose the nanometre-scale structures within the cell walls and interfilament. Fibrils concentrate at the internal and external edges of the cell walls. Fibrils ˜ 10 nm thick appear to thread through the radial Mg-calcite grains and form concentric bands within the cell wall. This banding may control Mg distribution within the cell. Similar fibril banding is present in the hypothallial cell walls but not the interfilament. Climate archiving with corallines can achieve greater precision with recognition of these parameters.

Combined Bisulfite Restriction Analysis for brain tissue identification.

PubMed

Samsuwan, Jarunya; Muangsub, Tachapol; Yanatatsaneejit, Pattamawadee; Mutirangura, Apiwat; Kitkumthorn, Nakarin

2018-05-01

According to the tissue-specific methylation database (doi: 10.1016/j.gene.2014.09.060), methylation at CpG locus cg03096975 in EML2 has been preliminarily proven to be specific to brain tissue. In this study, we enlarged sample size and developed a technique for identifying brain tissue in aged samples. Combined Bisulfite Restriction Analysis-for EML2 (COBRA-EML2) technique was established and validated in various organ samples obtained from 108 autopsies. In addition, this technique was also tested for its reliability, minimal DNA concentration detected, and use in aged samples and in samples obtained from specific brain compartments and spinal cord. COBRA-EML2 displayed 100% sensitivity and specificity for distinguishing brain tissue from other tissues, showed high reliability, was capable of detecting minimal DNA concentration (0.015ng/μl), could be used for identifying brain tissue in aged samples. In summary, COBRA-EML2 is a technique to identify brain tissue. This analysis is useful in criminal cases since it can identify the vital organ tissues from small samples acquired from criminal scenes. The results from this analysis can be counted as a medical and forensic marker supporting criminal investigations, and as one of the evidences in court rulings. Copyright © 2018 Elsevier B.V. All rights reserved.

The Story Behind the Numbers: Lessons Learned from the Integration of Monitoring Resources in Addressing an ISS Water Quality Anomaly

NASA Technical Reports Server (NTRS)

McCoy, Torin; Flint, Stephanie; Straub, John, II; Gazda, Dan; Schultz, John

2011-01-01

Beginning in June of 2010 an environmental mystery was unfolding on the International Space Station (ISS). The U.S. Water Processor Assembly (WPA) began to produce water with increasing levels of total organic carbon (TOC). A surprisingly consistent upward TOC trend was observed through weekly in-flight total organic carbon analyzer (TOCA) monitoring. As TOC is a general organics indicator, return of water archive samples was needed to make better-informed crew health decisions and to aid in WPA troubleshooting. TOCA-measured TOC was more than halfway to its health-based screening limit before archive samples could be returned on Soyuz 22 and analyzed. Although TOC was confirmed to be elevated, somewhat surprisingly, none of the typical target compounds were the source. After some solid detective work, it was confirmed that the TOC was associated with a compound known as dimethylsilanediol (DMSD). DMSD is believed to be a breakdown product of silicon-containing compounds present on ISS. A toxicological limit was set for DMSD and a forward plan developed for operations given this new understanding of the source of the TOC. This required extensive coordination with ISS stakeholders and innovative use of available in-flight and archive monitoring resources. Behind the numbers and scientific detail surrounding this anomaly, there exists a compelling story of multi-disciplinary awareness, teamwork, and important environmental lessons learned.

Tissue spray ionization mass spectrometry for rapid recognition of human lung squamous cell carcinoma

NASA Astrophysics Data System (ADS)

Wei, Yiping; Chen, Liru; Zhou, Wei; Chingin, Konstantin; Ouyang, Yongzhong; Zhu, Tenggao; Wen, Hua; Ding, Jianhua; Xu, Jianjun; Chen, Huanwen

2015-05-01

Tissue spray ionization mass spectrometry (TSI-MS) directly on small tissue samples has been shown to provide highly specific molecular information. In this study, we apply this method to the analysis of 38 pairs of human lung squamous cell carcinoma tissue (cancer) and adjacent normal lung tissue (normal). The main components of pulmonary surfactants, dipalmitoyl phosphatidylcholine (DPPC, m/z 757.47), phosphatidylcholine (POPC, m/z 782.52), oleoyl phosphatidylcholine (DOPC, m/z 808.49), and arachidonic acid stearoyl phosphatidylcholine (SAPC, m/z 832.43), were identified using high-resolution tandem mass spectrometry. Monte Carlo sampling partial least squares linear discriminant analysis (PLS-LDA) was used to distinguish full-mass-range mass spectra of cancer samples from the mass spectra of normal tissues. With 5 principal components and 30 - 40 Monte Carlo samplings, the accuracy of cancer identification in matched tissue samples reached 94.42%. Classification of a tissue sample required less than 1 min, which is much faster than the analysis of frozen sections. The rapid, in situ diagnosis with minimal sample consumption provided by TSI-MS is advantageous for surgeons. TSI-MS allows them to make more informed decisions during surgery.

Application of ribonucleoside vanadyl complex (RVC) for developing a multifunctional tissue preservative solution

PubMed Central

Yu, Cheng-Chia; Chen, Chin-Chuan

2018-01-01

The quality of biological samples greatly affects the accuracy of scientific results. However, RNA in cryopreserved tissues gradually degrades during storage, leading to errors in the results of subsequent experiments. A suitable sample preservative solution can prolong storage and enhance the research value of samples. Here, we developed a sample preservative solution using the properties of the ribonucleoside vanadyl complex (RVC) and compared its effects on RNA and DNA quality, protein activity, and tissue morphology with the commercially available and widely used RNAlater® Stabilization Solution. The results showed that both the RVC-based preservative solution and RNAlater can effectively delay RNA degradation in tissue samples stored at 4°C or −80°C compared with samples stored without any preservative solution. In contrast to RNAlater, the RVC-based preservative solution did not result in damage to the tissue morphology or a loss of protein activity. Additionally, the RVC-based preservative solution did not affect the RNA and genomic DNA contents of the tissue samples or the results of subsequent experimental analyses. An RVC-based reagent can be used as a multifunctional yet relatively inexpensive tissue preservative solution to provide a comprehensive and cost-effective method for preserving samples for tissue banks. PMID:29538436

Twenty years of Landsat data accessible through the national satellite land remote sensing data archive

USGS Publications Warehouse

Larsen, Dana M.

1993-01-01

The EROS Data Center has managed to National Satellite Land Remote Sensing Data Archive's (NSLRSDA) Landsat data since 1972. The NSLRSDA includes Landsat MSS data from 1972 through 1991 and T M data from 1982 through 1993. In response to many requests from multi-disciplined users for an enhanced insight into the availability and volume of Landsat data over specific worldwide land areas, numerous world plots and corresponding statical overviews have been prepared. These presentations include information related to image quality, cloud cover, various types of data overage (i.e. regions, countries, path, rows), acquisition station coverage areas, various archive media formats (i.e. wide band video tapes, computer compatible tapes, high density tapes, etc.) and acquisition time periods (i.e. years, seasons). Plans are to publish this information in a paper sample booklet at the Pecora 12 Symposium, in a USGS circular and on a Landsat CD-ROM; the data will be also be incorporated into GLIS.

Improving the security of international ISO container traffic by centralizing the archival of inspection results

NASA Astrophysics Data System (ADS)

Chalmers, Alex

2004-09-01

To increase the security and throughput of ISO traffic through international terminals more technology must be applied to the problem. A transnational central archive of inspection records is discussed that can be accessed by national agencies as ISO containers approach their borders. The intent is to improve the throughput and security of the cargo inspection process. A review of currently available digital media archiving technologies is presented and their possible application to the tracking of international ISO container shipments. Specific image formats employed by current x-ray inspection systems are discussed. Sample x-ray data from systems in use today are shown that could be entered into such a system. Data from other inspection technologies are shown to be easily integrated, as well as the creation of database records suitable for interfacing with other computer systems. Overall system performance requirements are discussed in terms of security, response time and capacity. Suggestions for pilot projects based on existing border inspection processes are made also.

HEROD: a human ethnic and regional specific omics database.

PubMed

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

System and method for controlling depth of imaging in tissues using fluorescence microscopy under ultraviolet excitation following staining with fluorescing agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demos, Stavros; Levenson, Richard

The present disclosure relates to a method for analyzing tissue specimens. In one implementation the method involves obtaining a tissue sample and exposing the sample to one or more fluorophores as contrast agents to enhance contrast of subcellular compartments of the tissue sample. The tissue sample is illuminated by an ultraviolet (UV) light having a wavelength between about 200 nm to about 400 nm, with the wavelength being selected to result in penetration to only a specified depth below a surface of the tissue sample. Inter-image operations between images acquired under different imaging parameters allow for improvement of the imagemore » quality via removal of unwanted image components. A microscope may be used to image the tissue sample and provide the image to an image acquisition system that makes use of a camera. The image acquisition system may create a corresponding image that is transmitted to a display system for processing and display.« less

Investigation of real tissue water equivalent path lengths using an efficient dose extinction method

NASA Astrophysics Data System (ADS)

Zhang, Rongxiao; Baer, Esther; Jee, Kyung-Wook; Sharp, Gregory C.; Flanz, Jay; Lu, Hsiao-Ming

2017-07-01

For proton therapy, an accurate conversion of CT HU to relative stopping power (RSP) is essential. Validation of the conversion based on real tissue samples is more direct than the current practice solely based on tissue substitutes and can potentially address variations over the population. Based on a novel dose extinction method, we measured water equivalent path lengths (WEPL) on animal tissue samples to evaluate the accuracy of CT HU to RSP conversion and potential variations over a population. A broad proton beam delivered a spread out Bragg peak to the samples sandwiched between a water tank and a 2D ion-chamber detector. WEPLs of the samples were determined from the transmission dose profiles measured as a function of the water level in the tank. Tissue substitute inserts and Lucite blocks with known WEPLs were used to validate the accuracy. A large number of real tissue samples were measured. Variations of WEPL over different batches of tissue samples were also investigated. The measured WEPLs were compared with those computed from CT scans with the Stoichiometric calibration method. WEPLs were determined within  ±0.5% percentage deviation (% std/mean) and  ±0.5% error for most of the tissue surrogate inserts and the calibration blocks. For biological tissue samples, percentage deviations were within  ±0.3%. No considerable difference (<1%) in WEPL was observed for the same type of tissue from different sources. The differences between measured WEPLs and those calculated from CT were within 1%, except for some bony tissues. Depending on the sample size, each dose extinction measurement took around 5 min to produce ~1000 WEPL values to be compared with calculations. This dose extinction system measures WEPL efficiently and accurately, which allows the validation of CT HU to RSP conversions based on the WEPL measured for a large number of samples and real tissues.

Development of a Climatology of Vertically Complete Wind Profiles from Doppler Radar Wind Profiler Systems

NASA Technical Reports Server (NTRS)

Barbre, Robert, Jr.

2015-01-01

Assessment of space vehicle loads and trajectories during design requires a large sample of wind profiles at the altitudes where winds affect the vehicle. Traditionally, this altitude region extends from near 8-14 km to address maximum dynamic pressure upon ascent into space, but some applications require knowledge of measured wind profiles at lower altitudes. Such applications include crew capsule pad abort and plume damage analyses. Two Doppler Radar Wind Profiler (DRWP) systems exist at the United States Air Force (USAF) Eastern Range and at the National Aeronautics and Space Administration's Kennedy Space Center. The 50-MHz DRWP provides wind profiles every 3-5 minutes from roughly 2.5-18.5 km, and five 915-MHz DRWPs provide wind profiles every 15 minutes from approximately 0.2-3.0 km. Archived wind profiles from all systems underwent rigorous quality control (QC) processes, and concurrent measurements from the QC'ed 50- and 915-MHz DRWP archives were spliced into individual profiles that extend from about 0.2-18.5 km. The archive contains combined profiles from April 2000 to December 2009, and thousands of profiles during each month are available for use by the launch vehicle community. This paper presents the details of the QC and splice methodology, as well as some attributes of the archive.

Enhancement of spectral quality of archival aerial photographs using satellite imagery for detection of land cover

NASA Astrophysics Data System (ADS)

Siok, Katarzyna; Jenerowicz, Agnieszka; Woroszkiewicz, Małgorzata

2017-07-01

Archival aerial photographs are often the only reliable source of information about the area. However, these data are single-band data that do not allow unambiguous detection of particular forms of land cover. Thus, the authors of this article seek to develop a method of coloring panchromatic aerial photographs, which enable increasing the spectral information of such images. The study used data integration algorithms based on pansharpening, implemented in commonly used remote sensing programs: ERDAS, ENVI, and PCI. Aerial photos and Landsat multispectral data recorded in 1987 and 2016 were chosen. This study proposes the use of modified intensity-hue-saturation and Brovey methods. The use of these methods enabled the addition of red-green-blue (RGB) components to monochrome images, thus enhancing their interpretability and spectral quality. The limitations of the proposed method relate to the availability of RGB satellite imagery, the accuracy of mutual orientation of the aerial and the satellite data, and the imperfection of archival aerial photographs. Therefore, it should be expected that the results of coloring will not be perfect compared to the results of the fusion of recent data with a similar ground sampling resolution, but still, they will allow a more accurate and efficient classification of land cover registered on archival aerial photographs.

Fermilab Today - Related Content

Science.gov Websites

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Micro-organisms isolated from cadaveric samples of allograft musculoskeletal tissue.

PubMed

Varettas, Kerry

2013-12-01

Allograft musculoskeletal tissue is commonly used in orthopaedic surgical procedures. Cadaveric donors of musculoskeletal tissue supply multiple allografts such as tendons, ligaments and bone. The microbiology laboratory of the South Eastern Area Laboratory Services (SEALS, Australia) has cultured cadaveric allograft musculoskeletal tissue samples for bacterial and fungal isolates since 2006. This study will retrospectively review the micro-organisms isolated over a 6-year period, 2006-2011. Swab and tissue samples were received for bioburden testing and were inoculated onto agar and/or broth culture media. Growth was obtained from 25.1 % of cadaveric allograft musculoskeletal tissue samples received. The predominant organisms isolated were coagulase-negative staphylococci and coliforms, with the heaviest bioburden recovered from the hemipelvis. The rate of bacterial and fungal isolates from cadaveric allograft musculoskeletal tissue samples is higher than that from living donors. The type of organism isolated may influence the suitability of the allograft for transplant.

Phenotypic characterization of glioblastoma identified through shape descriptors

NASA Astrophysics Data System (ADS)

Chaddad, Ahmad; Desrosiers, Christian; Toews, Matthew

2016-03-01

This paper proposes quantitatively describing the shape of glioblastoma (GBM) tissue phenotypes as a set of shape features derived from segmentations, for the purposes of discriminating between GBM phenotypes and monitoring tumor progression. GBM patients were identified from the Cancer Genome Atlas, and quantitative MR imaging data were obtained from the Cancer Imaging Archive. Three GBM tissue phenotypes are considered including necrosis, active tumor and edema/invasion. Volumetric tissue segmentations are obtained from registered T1˗weighted (T1˗WI) postcontrast and fluid-attenuated inversion recovery (FLAIR) MRI modalities. Shape features are computed from respective tissue phenotype segmentations, and a Kruskal-Wallis test was employed to select features capable of classification with a significance level of p < 0.05. Several classifier models are employed to distinguish phenotypes, where a leave-one-out cross-validation was performed. Eight features were found statistically significant for classifying GBM phenotypes with p <0.05, orientation is uninformative. Quantitative evaluations show the SVM results in the highest classification accuracy of 87.50%, sensitivity of 94.59% and specificity of 92.77%. In summary, the shape descriptors proposed in this work show high performance in predicting GBM tissue phenotypes. They are thus closely linked to morphological characteristics of GBM phenotypes and could potentially be used in a computer assisted labeling system.

CODIFI (Concordance in Diabetic Foot Ulcer Infection): a cross-sectional study of wound swab versus tissue sampling in infected diabetic foot ulcers in England.

PubMed

Nelson, Andrea; Wright-Hughes, Alexandra; Backhouse, Michael Ross; Lipsky, Benjamin A; Nixon, Jane; Bhogal, Moninder S; Reynolds, Catherine; Brown, Sarah

2018-01-31

To determine the extent of agreement and patterns of disagreement between wound swab and tissue samples in patients with an infected diabetic foot ulcer (DFU). Multicentre, prospective, cross-sectional study. Primary and secondary care foot ulcer/diabetic outpatient clinics and hospital wards across England. Inclusion criteria: consenting patients aged ≥18 years; diabetes mellitus; suspected infected DFU. clinically inappropriate to take either sample. Wound swab obtained using Levine's technique; tissue samples collected using a sterile dermal curette or scalpel. Coprimary: reported presence, and number, of pathogens per sample; prevalence of resistance to antimicrobials among likely pathogens. Secondary: recommended change in antibiotic therapy based on blinded clinical review; adverse events; sampling costs. 400 consenting patients (79% male) from 25 centres.Most prevalent reported pathogens were Staphylococcus aureus (43.8%), Streptococcus (16.7%) and other aerobic Gram-positive cocci (70.6%). At least one potential pathogen was reported from 70.1% of wound swab and 86.1% of tissue samples. Pathogen results differed between sampling methods in 58% of patients, with more pathogens and fewer contaminants reported from tissue specimens.The majority of pathogens were reported significantly more frequently in tissue than wound swab samples (P<0.01), with equal disagreement for S. aureus and Pseudomonas aeruginosa. Blinded clinicians more often recommended a change in antibiotic regimen based on tissue compared with wound swab results (increase of 8.9%, 95% CI 2.65% to 15.3%). Ulcer pain and bleeding occurred more often after tissue collection versus wound swabs (pain: 9.3%, 1.3%; bleeding: 6.8%, 1.5%, respectively). Reports of tissue samples more frequently identified pathogens, and less frequently identified non-pathogens compared with wound swab samples. Blinded clinicians more often recommended changes in antibiotic therapy based on tissue compared with wound swab specimens. Further research is needed to determine the effect of the additional information provided by tissue samples. ISRCTN52608451. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Cell block samples from malignant pleural effusion might be valid alternative samples for anaplastic lymphoma kinase detection in patients with advanced non-small-cell lung cancer.

PubMed

Zhou, Jianya; Yao, Hongtian; Zhao, Jing; Zhang, Shumeng; You, Qihan; Sun, Ke; Zou, Yinying; Zhou, Caicun; Zhou, Jianying

2015-06-01

To evaluate the clinical value of cell block samples from malignant pleural effusion (MPE) as alternative samples to tumour tissue for anaplastic lymphoma kinase (ALK) detection in patients with advanced non-small-cell lung cancer (NSCLC). Fifty-two matched samples were eligible for analysis. ALK status was detected by Ventana immunohistochemistry (IHC) (with the D5F3 clone), reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH) in MPE cell block samples, and by FISH in tumour tissue block samples. In total, ALK FISH results were obtained for 52 tumour tissue samples and 41 MPE cell block samples. Eight cases (15.4%) were ALK-positive in tumour tissue samples by FISH, and among matched MPE cell block samples, five were ALK-positive by FISH, seven were ALK-positive by RT-PCR, and eight were ALK-positive by Ventana IHC. The ALK status concordance rates between tumour tissue and MPE cell block samples were 78.9% by FISH, 98.1% by RT-PCR, and 100% by Ventana IHC. In MPE cell block samples, the sensitivity and specificity of Ventana IHC (100% and 100%) and RT-PCR (87.5% and 100%) were higher than those of FISH (62.5% and 100%). Malignant pleural effusion cell block samples had a diagnostic performance for ALK detection in advanced NSCLC that was comparable to that of tumour tissue samples. MPE cell block samples might be valid alternative samples for ALK detection when tissue is not available. Ventana IHC could be the most suitable method for ALK detection in MPE cell block samples. © 2014 John Wiley & Sons Ltd.

A workflow to preserve genome-quality tissue samples from plants in botanical gardens and arboreta.

PubMed

Gostel, Morgan R; Kelloff, Carol; Wallick, Kyle; Funk, Vicki A

2016-09-01

Internationally, gardens hold diverse living collections that can be preserved for genomic research. Workflows have been developed for genomic tissue sampling in other taxa (e.g., vertebrates), but are inadequate for plants. We outline a workflow for tissue sampling intended for two audiences: botanists interested in genomics research and garden staff who plan to voucher living collections. Standard herbarium methods are used to collect vouchers, label information and images are entered into a publicly accessible database, and leaf tissue is preserved in silica and liquid nitrogen. A five-step approach for genomic tissue sampling is presented for sampling from living collections according to current best practices. Collecting genome-quality samples from gardens is an economical and rapid way to make available for scientific research tissue from the diversity of plants on Earth. The Global Genome Initiative will facilitate and lead this endeavor through international partnerships.

Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma

PubMed Central

2013-01-01

Background Human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) represents a distinct clinical and epidemiological condition compared with HPV-negative (HPV-) HNSCC. To test the possible involvement of epigenetic modulation by HPV in HNSCC, we conducted a genome-wide DNA-methylation analysis. Methods Using laser-capture microdissection of 42 formalin-fixed paraffin wax-embedded (FFPE) HNSCCs, we generated DNA-methylation profiles of 18 HPV+ and 14 HPV- samples, using Infinium 450 k BeadArray technology. Methylation data were validated in two sets of independent HPV+/HPV- HNSCC samples (fresh-frozen samples and cell lines) using two independent methods (Infinium 450 k and whole-genome methylated DNA immunoprecipitation sequencing (MeDIP-seq)). For the functional analysis, an HPV- HNSCC cell line was transduced with lentiviral constructs containing the two HPV oncogenes (E6 and E7), and effects on methylation were assayed using the Infinium 450 k technology. Results and discussion Unsupervised clustering over the methylation variable positions (MVPs) with greatest variation showed that samples segregated in accordance with HPV status, but also that HPV+ tumors are heterogeneous. MVPs were significantly enriched at transcriptional start sites, leading to the identification of a candidate CpG island methylator phenotype in a sub-group of the HPV+ tumors. Supervised analysis identified a strong preponderance (87%) of MVPs towards hypermethylation in HPV+ HNSCC. Meta-analysis of our HNSCC and publicly available methylation data in cervical and lung cancers confirmed the observed DNA-methylation signature to be HPV-specific and tissue-independent. Grouping of MVPs into functionally more significant differentially methylated regions identified 43 hypermethylated promoter DMRs, including for three cadherins of the Polycomb group target genes. Integration with independent expression data showed strong negative correlation, especially for the cadherin gene-family members. Combinatorial ectopic expression of the two HPV oncogenes (E6 and E7) in an HPV- HNSCC cell line partially phenocopied the hypermethylation signature seen in HPV+ HNSCC tumors, and established E6 as the main viral effector gene. Conclusions Our data establish that archival FFPE tissue is very suitable for this type of methylome analysis, and suggest that HPV modulates the HNSCC epigenome through hypermethylation of Polycomb repressive complex 2 target genes such as cadherins, which are implicated in tumor progression and metastasis. PMID:23419152

SPRUCE Deep Peat Heat (DPH) Metagenomes for Peat Samples Collected June 2015

DOE Data Explorer

Klumber, Laurel A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Yang, Zamin K. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2015-01-01

This data set provides links to the results of metagenomic analyses of 38 peat core samples collected on 16 June 2015 from SPRUCE experiment treatment plots after approximately one year of belowground heating. These metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system and are available at the accession numbers provided in the accompanying inventory file.

Validity of the MMPI-2-RF (Restructured Form) L-r and K-r Scales in Detecting Underreporting in Clinical and Nonclinical Samples

ERIC Educational Resources Information Center

Sellbom, Martin; Bagby, R. Michael

2008-01-01

In the current investigation, the authors examined the validity of the L-r and K-r scales on the recently developed Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Y. S. Ben-Porath & A. Tellegen, in press) in measuring underreported response bias. Three archival samples previously collected for examining MMPI-2…

Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors.

PubMed

Paasinen-Sohns, Aino; Koelzer, Viktor H; Frank, Angela; Schafroth, Julian; Gisler, Aline; Sachs, Melanie; Graber, Anne; Rothschild, Sacha I; Wicki, Andreas; Cathomas, Gieri; Mertz, Kirsten D

2017-03-01

Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Lyman Limit Absorbers in GALEX Spectra

NASA Astrophysics Data System (ADS)

Williger, Gerard M.; Haberzettl, Lutz G.; Ribaudo, Joseph; Kuchner, Marc J.; Burchett, Joseph; Clowes, Roger G.; Lauroesch, James T.; Mills, Brianna; Borden, Jeremy

2018-01-01

We describe the method and early results for crowdsourcing a search for low-redshift partial and complete Lyman Limit Systems (pLLSs and LLSs) in the GALEX spectral archive. LLSs have been found in large numbers at z>3 and traced to lower redshift through a relatively small number of QSO spectra from spaced-based telescopes. From a sample of 44 pLLSs and 11 LLSs at 0.1 = -0.32 +/- 0.07 and the low-metallicity portion centered at <[X/H]> = -1.87 +/- 0.11.The GALEX spectral archive offers a vast dataset potentially containing hundreds of LLSs, which may be leveraged to search for such a bimodality and track its evolution within the unconstrained near-UV gap at 1

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

PubMed

Gautam, Aarti; Kumar, Raina; Dimitrov, George; Hoke, Allison; Hammamieh, Rasha; Jett, Marti

2016-10-01

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

JAMSTEC DARWIN Database Assimilates GANSEKI and COEDO

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Toyoda, Y.; Horikawa, H.; Sasaki, T.; Fukuda, K.; Hase, H.; Saito, H.

2017-12-01

Introduction: Japan Agency for Marine-Earth Science and Technology (JAMSTEC) archives data and samples obtained by JAMSTEC research vessels and submersibles. As a common property of the human society, JAMSTEC archive is open for public users with scientific/educational purposes [1]. For publicizing its data and samples online, JAMSTEC is operating NUUNKUI data sites [2], a group of several databases for various data and sample types. For years, data and metadata of JAMSTEC rock samples, sediment core samples and cruise/dive observation were publicized through databases named GANSEKI, COEDO, and DARWIN, respectively. However, because they had different user interfaces and data structures, these services were somewhat confusing for unfamiliar users. Maintenance costs of multiple hardware and software were also problematic for performing sustainable services and continuous improvements. Database Integration: In 2017, GANSEKI, COEDO and DARWIN were integrated into DARWIN+ [3]. The update also included implementation of map-search function as a substitute of closed portal site. Major functions of previous systems were incorporated into the new system; users can perform the complex search, by thumbnail browsing, map area, keyword filtering, and metadata constraints. As for data handling, the new system is more flexible, allowing the entry of variety of additional data types. Data Management: After the DARWIN major update, JAMSTEC data & sample team has been dealing with minor issues of individual sample data/metadata which sometimes need manual modification to be transferred to the new system. Some new data sets, such as onboard sample photos and surface close-up photos of rock samples, are getting available online. Geochemical data of sediment core samples will supposedly be added in the near future. Reference: [1] http://www.jamstec.go.jp/e/database/data_policy.html [2] http://www.godac.jamstec.go.jp/jmedia/portal/e/ [3] http://www.godac.jamstec.go.jp/darwin/e/

Blind Biobanking of the Prostatectomy Specimen: Critical Evaluation of the Existing Techniques and Development of the New 4-Level Tissue Extraction Model With High Sampling Efficacy.

PubMed

Tolkach, Yuri; Eminaga, Okyaz; Wötzel, Fabian; Huss, Sebastian; Bettendorf, Olaf; Eltze, Elke; Abbas, Mahmoud; Imkamp, Florian; Semjonow, Axel

2017-03-01

Fresh tissue is mandatory to perform high-quality translation studies. Several models for tissue extraction from prostatectomy specimens without guidance by frozen sections are already introduced. However, little is known about the sampling efficacy of these models, which should provide representative tissue in adequate volumes, account for multifocality and heterogeneity of tumor, not violate the routine final pathological examination, and perform quickly without frozen section-based histological control. The aim of the study was to evaluate the sampling efficacy of the existing tissue extraction models without guidance by frozen sections ("blind") and to develop an optimized model for tissue extraction. Five hundred thirty-three electronic maps of the tumor distribution in prostates from a single-center cohort of the patients subjected to radical prostatectomy were used for analysis. Six available models were evaluated in silico for their sampling efficacy. Additionally, a novel model achieving the best sampling efficacy was developed. The available models showed high efficacies for sampling "any part" from the tumor (up to 100%), but were uniformly low in efficacy to sample all tumor foci from the specimens (with the best technique sampling only 51.6% of the all tumor foci). The novel 4-level extraction model achieved a sampling efficacy of 93.1% for all tumor foci. The existing "blind" tissue extraction models from prostatectomy specimens without frozen sections control are suitable to target tumor tissues but these tissues do not represent the whole tumor. The novel 4-level model provides the highest sampling efficacy and a promising potential for integration into routine. Prostate 77: 396-405, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Label-free tissue scanner for colorectal cancer screening

NASA Astrophysics Data System (ADS)

Kandel, Mikhail E.; Sridharan, Shamira; Liang, Jon; Luo, Zelun; Han, Kevin; Macias, Virgilia; Shah, Anish; Patel, Roshan; Tangella, Krishnarao; Kajdacsy-Balla, Andre; Guzman, Grace; Popescu, Gabriel

2017-06-01

The current practice of surgical pathology relies on external contrast agents to reveal tissue architecture, which is then qualitatively examined by a trained pathologist. The diagnosis is based on the comparison with standardized empirical, qualitative assessments of limited objectivity. We propose an approach to pathology based on interferometric imaging of "unstained" biopsies, which provides unique capabilities for quantitative diagnosis and automation. We developed a label-free tissue scanner based on "quantitative phase imaging," which maps out optical path length at each point in the field of view and, thus, yields images that are sensitive to the "nanoscale" tissue architecture. Unlike analysis of stained tissue, which is qualitative in nature and affected by color balance, staining strength and imaging conditions, optical path length measurements are intrinsically quantitative, i.e., images can be compared across different instruments and clinical sites. These critical features allow us to automate the diagnosis process. We paired our interferometric optical system with highly parallelized, dedicated software algorithms for data acquisition, allowing us to image at a throughput comparable to that of commercial tissue scanners while maintaining the nanoscale sensitivity to morphology. Based on the measured phase information, we implemented software tools for autofocusing during imaging, as well as image archiving and data access. To illustrate the potential of our technology for large volume pathology screening, we established an "intrinsic marker" for colorectal disease that detects tissue with dysplasia or colorectal cancer and flags specific areas for further examination, potentially improving the efficiency of existing pathology workflows.

Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human.

PubMed

Kojima, Kyoko; Bowersock, Gregory J; Kojima, Chinatsu; Klug, Christopher A; Grizzle, William E; Mobley, James A

2012-11-01

A number of reports have recently emerged with focus on extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice (n = 8) were analyzed using 1D-nanoLC-MS(MS)(2) following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens (n = 11) as compared to uninvolved tissues (n = 8), where 47 potential pancreatic ductal adenocarcinoma markers were identified as significantly increased, of which 28 were previously reported. Further, these proteins share strongly overlapping pathway associations to pancreatic cancer that include estrogen receptor α. Together, these data support the validation of an approach for the proteomic analysis of FFPE tissues that is straightforward and highly robust, which can also be effectively applied toward translational studies of disease. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human papillomavirus in normal conjunctival tissue and in conjunctival papilloma: types and frequencies in a large series

PubMed Central

Sjö, Nicolai Christian; von Buchwald, Christian; Cassonnet, Patricia; Norrild, Bodil; Prause, Jan Ulrik; Vinding, Troels; Heegaard, Steffen

2007-01-01

Aim To examine conjunctival papilloma and normal conjunctival tissue for the presence of human papillomavirus (HPV). Methods Archival paraffin wax‐embedded tissue from 165 conjunctival papillomas and from 20 histological normal conjunctival biopsy specimens was analysed for the presence of HPV by PCR. Specimens considered HPV positive using consensus primers, but with a negative or uncertain PCR result using type‐specific HPV probes, were analysed with DNA sequencing. Results HPV was present in 86 of 106 (81%) β‐globin‐positive papillomas. HPV type 6 was positive in 80 cases, HPV type 11 was identified in 5 cases and HPV type 45 was present in a single papilloma. All the 20 normal conjunctival biopsy specimens were β‐globin positive and HPV negative. Conclusion There is a strong association between HPV and conjunctival papilloma. The study presents the largest material of conjunctival papilloma investigated for HPV and the first investigation of HPV in normal conjunctival tissue. HPV types 6 and 11 are the most common HPV types in conjunctival papilloma. This also is the first report of HPV type 45 in conjunctival papilloma. PMID:17166894

Comparison of hard tissues that are useful for DNA analysis in forensic autopsy.

PubMed

Kaneko, Yu; Ohira, Hiroshi; Tsuda, Yukio; Yamada, Yoshihiro

2015-11-01

Forensic analysis of DNA from hard tissues can be important when investigating a variety of cases resulting from mass disaster or criminal cases. This study was conducted to evaluate the most suitable tissues, method and sample size for processing of hard tissues prior to DNA isolation. We also evaluated the elapsed time after death in relation to the quantity of DNA extracted. Samples of hard tissues (37 teeth, 42 skull, 42 rib, and 39 nails) from 42 individuals aged between 50 and 83 years were used. The samples were taken from remains following forensic autopsy (from 2 days to 2 years after death). To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls for short tandem repeat profiles were compared between the hard tissues. DNA typing results indicated that until 1 month after death, any of the four hard tissue samples could be used as an alternative to teeth, allowing analysis of all of the loci. However, in terms of the sampling site, collection method and sample size adjustment, the rib appeared to be the best choice in view of the ease of specimen preparation. Our data suggest that the rib could be an alternative hard tissue sample for DNA analysis of human remains. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Physics and engineering aspects of cell and tissue imaging systems: microscopic devices and computer assisted diagnosis.

PubMed

Chen, Xiaodong; Ren, Liqiang; Zheng, Bin; Liu, Hong

2013-01-01

The conventional optical microscopes have been used widely in scientific research and in clinical practice. The modern digital microscopic devices combine the power of optical imaging and computerized analysis, archiving and communication techniques. It has a great potential in pathological examinations for improving the efficiency and accuracy of clinical diagnosis. This chapter reviews the basic optical principles of conventional microscopes, fluorescence microscopes and electron microscopes. The recent developments and future clinical applications of advanced digital microscopic imaging methods and computer assisted diagnosis schemes are also discussed.

Residual antibiotics in decontaminated human cardiovascular tissues intended for transplantation and risk of falsely negative microbiological analyses.

PubMed

Buzzi, Marina; Guarino, Anna; Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives.

Residual Antibiotics in Decontaminated Human Cardiovascular Tissues Intended for Transplantation and Risk of Falsely Negative Microbiological Analyses

PubMed Central

Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives. PMID:25397402

VizieR Online Data Catalog: Kepler multiple transiting planet systems (Wang+, 2015)

NASA Astrophysics Data System (ADS)

Wang, J.; Fischer, D. A.; Xie, J.-W.; Ciardi, D. R.

2017-10-01

The sample of MTPSs remains the same as that in Wang et al. (2014, J/ApJ/783/4). From the NASA Exoplanet Archive (http://exoplanetarchive.ipac.caltech.edu), we select Kepler objects of interest (KOIs) that satisfy the following criteria: (1) disposition of either Candidate or Confirmed; (2) with at least two planet candidates; (3) Kepler magnitude (KP) brighter than 13.5. The above selection criteria resulted in 138 MTPSs in Wang et al. (2014, J/ApJ/783/4). With the updated Exoplanet Archive, the selection criteria resulted in 208 MTPSs. In this paper, we focus on the 138 MTPSs to be consistent with previous work. (4 data files).

Archive of sediment data from vibracores collected in 2010 offshore of the Mississippi barrier islands

USGS Publications Warehouse

Kelso, Kyle W.; Flocks, James G.

2015-01-01

Selection of the core site locations was based on geophysical surveys conducted around the islands from 2008 to 2010. The surveys, using acoustic systems to image and interpret the nearsurface stratigraphy, were conducted to investigate the geologic controls on island evolution. This data series serves as an archive of sediment data collected from August to September 2010, offshore of the Mississippi barrier islands. Data products, including descriptive core logs, core photographs, results of sediment grain-size analyses, sample location maps, and geographic information system (GIS) data files with accompanying formal Federal Geographic Data Committee (FDGC) metadata can be downloaded from the data products and downloads page.

IMPACT OF SUBMERSIBLE PUMPS ON PB CONSTITUENTS IN RESIDENTIAL WELLS

EPA Science Inventory

Dissolved lead in 51 domestic wells screened from 18 m to 48 m in glacial tills and outwash deposits were examined, from archived samples collected during 2001-2004, in conjunction with respective submersible pump characteristics. Pb concentrations of these residential water supp...

30 CFR 784.14 - Hydrologic information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Hydrologic information. 784.14 Section 784.14... Hydrologic information. (a) Sampling and analysis. All water quality analyses performed to meet the... at the National Archives and Records Administration (NARA). For information on the availability of...

30 CFR 784.14 - Hydrologic information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Hydrologic information. 784.14 Section 784.14... Hydrologic information. (a) Sampling and analysis. All water quality analyses performed to meet the... at the National Archives and Records Administration (NARA). For information on the availability of...

The metagenomic data life-cycle: standards and best practices

PubMed Central

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder

2017-01-01

Abstract Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing. PMID:28637310

The metagenomic data life-cycle: standards and best practices

DOE Office of Scientific and Technical Information (OSTI.GOV)

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is stillmore » needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.« less

On the construction of a time base and the elimination of averaging errors in proxy records

NASA Astrophysics Data System (ADS)

Beelaerts, V.; De Ridder, F.; Bauwens, M.; Schmitz, N.; Pintelon, R.

2009-04-01

Proxies are sources of climate information which are stored in natural archives (e.g. ice-cores, sediment layers on ocean floors and animals with calcareous marine skeletons). Measuring these proxies produces very short records and mostly involves sampling solid substrates, which is subject to the following two problems: Problem 1: Natural archives are equidistantly sampled at a distance grid along their accretion axis. Starting from these distance series, a time series needs to be constructed, as comparison of different data records is only meaningful on a time grid. The time series will be non-equidistant, as the accretion rate is non-constant. Problem 2: A typical example of sampling solid substrates is drilling. Because of the dimensions of the drill, the holes drilled will not be infinitesimally small. Consequently, samples are not taken at a point in distance, but rather over a volume in distance. This holds for most sampling methods in solid substrates. As a consequence, when the continuous proxy signal is sampled, it will be averaged over the volume of the sample, resulting in an underestimation of the amplitude. Whether this averaging effect is significant, depends on the volume of the sample and the variations of interest of the proxy signal. Starting from the measured signal, the continuous signal needs to be reconstructed in order eliminate these averaging errors. The aim is to provide an efficient identification algorithm to identify the non-linearities in the distance-time relationship, called time base distortions, and to correct for the averaging effects. Because this is a parametric method, an assumption about the proxy signal needs to be made: the proxy record on a time base is assumed to be harmonic, this is an obvious assumption because natural archives often exhibit a seasonal cycle. In a first approach the averaging effects are assumed to be in one direction only, i.e. the direction of the axis on which the measurements were performed. The measured averaged proxy signal is modeled by following signal model: -- Δ ∫ n+12Δδ- y(n,θ) = δ- 1Δ- y(m,θ)dm n-2 δ where m is the position, x(m) = Δm; θ are the unknown parameters and y(m,θ) is the proxy signal we want to identify (the proxy signal as found in the natural archive), which we model as: y(m, θ) = A +∑H [A sin(kωt(m ))+ A cos(kωt(m ))] 0 k=1 k k+H With t(m): t(m) = mTS + g(m )TS Here TS = 1/fS is the sampling period, fS the sampling frequency, and g(m) the unknown time base distortion (TBD). In this work a splines approximation of the TBD is chosen: ∑ g(m ) = b blφl(m ) l=1 where, b is a vector of unknown time base distortion parameters, and φ is a set of splines. The estimates of the unknown parameters were obtained with a nonlinear least squares algorithm. The vessel density measured in the mangrove tree R mucronata was used to illustrate the method. The vessel density is a proxy for the rain fall in tropical regions. The proxy data on the newly constructed time base showed a yearly periodicity, this is what we expected and the correction for the averaging effect increased the amplitude by 11.18%.

Workshop report: Nucleic acid delivery devices for HIV vaccines: Workshop proceedings, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA, May 21, 2015.

PubMed

Weniger, Bruce G; Anglin, Ian E; Tong, Tina; Pensiero, Michael; Pullen, Jeffrey K

2018-01-25

On May 21st, 2015, the U.S. National Institute of Allergy and Infectious Diseases (NIAID) convened a workshop on delivery devices for nucleic acid (NA) as vaccines in order to review the landscape of past and future technologies for administering NA (e.g., DNA, RNA, etc.) as antigen into target tissues of animal models and humans. Its focus was on current and future applications for preventing and treating human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS) disease, among other infectious-disease priorities. Meeting participants presented the results and experience of representative clinical trials of NA vaccines using a variety of alternative delivery devices, as well as a broader group of methods studied in animal models and at bench top, to improve upon the performance and/or avoid the drawbacks of conventional needle-syringe (N-S) delivery. The subjects described and discussed included (1) delivery targeted into oral, cutaneous/intradermal, nasal, upper and lower respiratory, and intramuscular tissues; (2) devices and techniques for jet injection, solid, hollow, and dissolving microneedles, patches for topical passive diffusion or iontophoresis, electroporation, thermal microporation, nasal sprayers, aerosol upper-respiratory and pulmonary inhalation, stratum-corneum ablation by ultrasound, chemicals, and mechanical abrasion, and kinetic/ballistic delivery; (3) antigens, adjuvants, and carriers such as DNA, messenger RNA, synthesized plasmids, chemokines, wet and dry aerosols, and pollen-grain and microparticle vectors; and (4) the clinical experience and humoral, cellular, and cytokine immune responses observed for many of these target tissues, technologies, constructs, and carriers. This report summarizes the presentations and discussions from the workshop (https://web.archive.org/web/20160228112310/https://www.blsmeetings.net/NucleicAcidDeliveryDevices/), which was webcast live in its entirety and archived online (http://videocast.nih.gov/summary.asp?live=16059). Copyright © 2018.

Telocytes are reduced during fibrotic remodelling of the colonic wall in ulcerative colitis

PubMed Central

Manetti, Mirko; Rosa, Irene; Messerini, Luca; Ibba-Manneschi, Lidia

2015-01-01

Ulcerative colitis (UC) is characterized by chronic relapsing intestinal inflammation finally leading to extensive tissue fibrosis and resulting in a stiff colon unable to carry out peristalsis or to resorb fluids. Telocytes, a peculiar type of stromal cells, have been recently identified in the human gastrointestinal tract. Several roles have been proposed for telocytes, including mechanical support, intercellular signalling and modulation of intestinal motility. The aim of the present work was to investigate the presence and distribution of telocytes in colonic specimens from UC patients compared with controls. Archival paraffin-embedded samples of the left colon from UC patients who underwent elective bowel resection and controls were collected. Tissue sections were stained with Masson's trichrome to detect fibrosis. Telocytes were identified by CD34 immunohistochemistry. In early fibrotic UC cases, fibrosis affected the muscularis mucosae and submucosa, while the muscularis propria was spared. In advanced fibrotic UC cases, fibrosis extended to affect the muscle layers and the myenteric plexus. Few telocytes were found in the muscularis mucosae and submucosa of both early and advanced fibrotic UC colonic wall. In the muscle layers and myenteric plexus of early fibrotic UC, telocytes were preserved in their distribution. In the muscularis propria of advanced fibrotic UC, the network of telocytes was reduced or even completely absent around smooth muscle bundles and myenteric plexus ganglia, paralleling the loss of the network of interstitial cells of Cajal. In UC, a loss of telocytes accompanies the fibrotic remodelling of the colonic wall and might contribute to colonic dysmotility. PMID:25283476

Cyclooxygenase-2 expression in the eyes of cats with and without uveitis.

PubMed

Sim, Zhi Hui; Pinard, Chantale L; Plattner, Brandon L; Bienzle, Dorothee

2018-01-01

OBJECTIVE To characterize the distribution and intensity of cyclooxygenase (COX)-2 expression in the eyes of cats with and without uveitis and to determine whether COX-2 expression is correlated with severity of inflammation. SAMPLES Archived ocular tissue specimens from 51 cats with and 10 cats without ocular disease. PROCEDURES Specimens from only 1 eye were evaluated for each cat. Specimens were stained with H&E stain or immunohistochemical stain for detection of COX-2 and reviewed. For each eye, the type, severity, and distribution of inflammation and the distribution and intensity of COX-2 expression were determined for the uvea and other ocular tissues. Correlation between COX-2 expression and inflammation severity was also assessed. RESULTS COX-2 was not expressed in any nondiseased eye. Of the 51 diseased eyes, 20 had histologic evidence of lymphocytic-plasmacytic uveitis, 13 had neutrophilic uveitis, 11 had diffuse iris melanoma with uveitis, and 7 had diffuse iris melanoma without uveitis. Of the 44 eyes with uveitis, COX-2 was detected in the uvea of 16, including 11 eyes with lymphocytic-plasmacytic uveitis, 4 with neutrophilic uveitis, and 1 with diffuse iris melanoma-induced uveitis. Inflammation was severe, moderate, or mild in 10, 5, and 1 of those eyes, respectively. Cyclooxygenase-2 was detected in the cornea of 21 eyes with uveitis and 1 eye with diffuse iris melanoma without uveitis. Uveitis severity was positively correlated with COX-2 expression in both the uvea and cornea. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that COX-2 is an inflammatory mediator in feline uveitis but not diffuse iris melanoma.

Fatal pyogranulomatous myocarditis in 10 Boxer puppies.

PubMed

Detmer, Susan E; Bouljihad, Mostafa; Hayden, David W; Schefers, Jeremy M; Armien, Anibal; Wünschmann, Arno

2016-03-01

Over a period of 5 years, 10 pure-bred Boxer puppies, 9-16 weeks old, were presented with a history of sudden death and were diagnosed with pyogranulomatous myocarditis. The myocarditis was characterized by a mixed infiltrate composed predominantly of neutrophils and macrophages. In our retrospective study, original case records and archived materials were examined. All dogs were positive for Borrelia burgdorferi on immunohistochemistry (IHC). There was no evidence of infectious agents in formalin-fixed, paraffin-embedded (FFPE) heart tissue sections stained with hematoxylin and eosin, Ziehl-Neelsen, Gram, Grocott methenamine silver, Warthin-Starry, Von Kossa, and Steiner-Chapman stains. IHC for Chlamydia sp., Toxoplasma gondii, Neospora caninum, West Nile virus, and canine parvovirus also yielded a negative result in all dogs. Polymerase chain reaction testing for vector-borne pathogens on heart tissue from 9 of the dogs (1 frozen and 8 FFPE samples) yielded positive results for 1 dog with B. burgdorferi as well as Anaplasma phagocytophilum in another dog. Subsequently, 2 additional cases were found in a French Bulldog and a French Bulldog-Beagle mix that had identical morphology, test results, age, and seasonality to these 10 Boxer dogs. The similarities in the seasonality, signalment of the affected dogs, and the gross and microscopic lesions suggest a common etiology. Positive IHC and morphologic similarities to human Lyme carditis indicate that B. burgdorferi is likely the agent involved. An additional consideration for these cases is the possibility of a breed-specific autoimmune myocarditis or potential predisposition for cardiopathogenic agents in young Boxers. © 2016 The Author(s).

Swab or biopsy samples for bioburden testing of allograft musculoskeletal tissue?

PubMed

Varettas, Kerry

2014-12-01

Swab and biopsy samples of allograft musculoskeletal tissue are most commonly collected by tissue banks for bacterial and fungal bioburden testing. An in vitro study was performed using the National Committee for Clinical Laboratory Standards standard 'Quality control of microbiological transport systems' (2003) to validate and evaluate the recovery of six challenge organisms from swab and biopsy samples of allograft musculoskeletal tissue. On average, 8.4 to >100 and 7.2 to >100 % of the inoculum was recovered from swab and biopsy samples respectively. A retrospective review of donor episodes was also performed, consisting of paired swab and biopsy samples received in this laboratory during the period 2001-2012. Samples of allograft femoral heads were collected from living donors during hip operations. From the 3,859 donor episodes received, 21 paired swab and biopsy samples each recovered an isolate, 247 swab samples only and 79 biopsy samples only were culture positive. Low numbers of challenge organisms were recovered from inoculated swab and biopsy samples in the in vitro study and validated their use for bioburden testing of allograft musculoskeletal tissue. Skin commensals were the most common group of organisms isolated during a 12-year retrospective review of paired swab and biopsy samples from living donor allograft femoral heads. Paired swab and biopsy samples are a suitable representative sample of allograft musculoskeletal tissue for bioburden testing.

CANINE DISTEMPER VIRUS IN A WILD FAR EASTERN LEOPARD ( PANTHERA PARDUS ORIENTALIS).

PubMed

Sulikhan, Nadezhda S; Gilbert, Martin; Blidchenko, Ekaterina Yu; Naidenko, Sergei V; Ivanchuk, Galina V; Gorpenchenko, Tatiana Yu; Alshinetskiy, Mikhail V; Shevtsova, Elena I; Goodrich, John M; Lewis, John C M; Goncharuk, Mikhail S; Uphyrkina, Olga V; Rozhnov, Vyatcheslav V; Shedko, Sergey V; McAloose, Denise; Miquelle, Dale G

2018-01-01

The critically endangered population of Far Eastern leopards ( Panthera pardus orientalis) may number as few as 60 individuals and is at risk from stochastic processes such as infectious disease. During May 2015, a case of canine distemper virus (CDV) was diagnosed in a wild leopard exhibiting severe neurologic disease in the Russian territory of Primorskii Krai. Amplified sequences of the CDV hemagglutinin gene and phosphoprotein gene aligned within the Arctic-like clade of CDV, which includes viruses from elsewhere in Russia, China, Europe, and North America. Histologic examination of cerebral tissue revealed perivascular lymphoid cuffing and demyelination of the white matter consistent with CDV infection. Neutralizing antibodies against CDV were detected in archived serum from two wild Far Eastern leopards sampled during 1993-94, confirming previous exposure in the population. This leopard population is likely too small to maintain circulation of CDV, suggesting that infections arise from spillover from more-abundant domestic or wild carnivore reservoirs. Increasing the population size and establishment of additional populations of leopards would be important steps toward securing the future of this subspecies and reducing the risk posed by future outbreaks of CDV or other infectious diseases.

INHALATION TOXICOLOGY METHODS: The Generation and Characterization of Exposure Atmospheres and Inhalational Exposures

PubMed Central

Chen, Lung-Chi; Lippmann, Morton

2015-01-01

In this review, we outline the need for laboratory-based inhalation toxicology studies, the historical background on adverse health effects of airborne toxicants, and the benefits of advance planning for the building of analytic options into the study design to maximize the scientific gains to be derived from the investments in the study. We then discuss methods for: 1) the generation and characterization of exposure atmospheres for inhalation exposures in humans and laboratory animals; 2) their delivery and distribution into and within whole-body exposure chambers, head-only exposure chambers, face-masks, and mouthpieces or nasal catheters; 3) options for on-line functional assays during and between exposures; and 4) options for serial non-invasive assays of response. In doing so, we go beyond exposures to single agents and simple mixtures, and include methods for evaluating biological responses to complex environmental mixtures. We also emphasize that great care should be taken in the design and execution of such studies so that the scientific returns can be maximized both initially, and in follow-up utilization of archived samples of the exposure atmospheres, excreta, and tissues collected for histology. PMID:25645246

Pathological α-synuclein in gastrointestinal tissues from prodromal Parkinson disease patients.

PubMed

Stokholm, Morten Gersel; Danielsen, Erik Hvid; Hamilton-Dutoit, Stephen Jacques; Borghammer, Per

2016-06-01

It has been hypothesized that Lewy pathology initiates in the enteric nervous system years prior to debut of clinical motor symptoms in Parkinson disease patients. This study investigates whether Lewy pathology is present in various gastrointestinal tract tissues from Parkinson disease patients in the prodromal phase. We used the Danish National Pathology Registry to identify archived paraffin-embedded tissue blocks from 57 Parkinson disease patients (98 blocks) and 90 control subjects (98 blocks). We employed 2 different immunohistochemistry techniques visualizing aggregated α-synuclein and phosphorylated α-synuclein. Thirty-nine Parkinson disease patients contributed tissues obtained in the prodromal disease phase, whereas 18 Parkinson disease patients contributed tissues obtained solely after Parkinson diagnosis. Prodromal tissues were obtained on average 7.0 years prior to diagnosis (range = 20 years to 4 months), and postdiagnosis tissue on average 2.8 years after diagnosis (range = 2 days to 18 years). Phosphorylated α-synuclein positivity was seen in 22 of 39 (56%) prodromal Parkinson disease subjects and 30 of 67 (45%) prodromal tissue blocks. These fractions were significantly higher compared to control subjects (p = 0.0001 and p = 0.0032, respectively). In contrast, no significant difference was seen in the positivity rate between prodromal Parkinson disease patients and controls when using the aggregated α-synuclein immunohistochemistry technique. We detected Lewy pathology in the gastrointestinal tract of patients up to 20 years prior to their Parkinson disease diagnosis. These findings are in accordance with a hypothesized prodromal disease phase spanning 10 to 20 years. Ann Neurol 2016;79:940-949. © 2016 American Neurological Association.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doll, Stephanie R.; Bolling, Stacie D.

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), polarizedmore » 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.« less

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

PubMed Central

2014-01-01

Background Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers. PMID:24684698

A workflow to preserve genome-quality tissue samples from plants in botanical gardens and arboreta1

PubMed Central

Gostel, Morgan R.; Kelloff, Carol; Wallick, Kyle; Funk, Vicki A.

2016-01-01

Premise of the study: Internationally, gardens hold diverse living collections that can be preserved for genomic research. Workflows have been developed for genomic tissue sampling in other taxa (e.g., vertebrates), but are inadequate for plants. We outline a workflow for tissue sampling intended for two audiences: botanists interested in genomics research and garden staff who plan to voucher living collections. Methods and Results: Standard herbarium methods are used to collect vouchers, label information and images are entered into a publicly accessible database, and leaf tissue is preserved in silica and liquid nitrogen. A five-step approach for genomic tissue sampling is presented for sampling from living collections according to current best practices. Conclusions: Collecting genome-quality samples from gardens is an economical and rapid way to make available for scientific research tissue from the diversity of plants on Earth. The Global Genome Initiative will facilitate and lead this endeavor through international partnerships. PMID:27672517

Status of the TESS Science Processing Operations Center

NASA Astrophysics Data System (ADS)

Jenkins, Jon Michael; Caldwell, Douglas A.; Davies, Misty; Li, Jie; Morris, Robert L.; Rose, Mark; Smith, Jeffrey C.; Tenenbaum, Peter; Ting, Eric; Twicken, Joseph D.; Wohler, Bill

2018-06-01

The Transiting Exoplanet Survey Satellite (TESS) was selected by NASA’s Explorer Program to conduct a search for Earth’s closest cousins starting in 2018. TESS will conduct an all-sky transit survey of F, G and K dwarf stars between 4 and 12 magnitudes and M dwarf stars within 200 light years. TESS is expected to discover 1,000 small planets less than twice the size of Earth, and to measure the masses of at least 50 of these small worlds. The TESS science pipeline is being developed by the Science Processing Operations Center (SPOC) at NASA Ames Research Center based on the highly successful Kepler science pipeline. Like the Kepler pipeline, the TESS pipeline provides calibrated pixels, simple and systematic error-corrected aperture photometry, and centroid locations for all 200,000+ target stars observed over the 2-year mission, along with associated uncertainties. The pixel and light curve products are modeled on the Kepler archive products and will be archived to the Mikulski Archive for Space Telescopes (MAST). In addition to the nominal science data, the 30-minute Full Frame Images (FFIs) simultaneously collected by TESS will also be calibrated by the SPOC and archived at MAST. The TESS pipeline searches through all light curves for evidence of transits that occur when a planet crosses the disk of its host star. The Data Validation pipeline generates a suite of diagnostic metrics for each transit-like signature, and then extracts planetary parameters by fitting a limb-darkened transit model to each potential planetary signature. The results of the transit search are modeled on the Kepler transit search products (tabulated numerical results, time series products, and pdf reports) all of which will be archived to MAST. Synthetic sample data products are available at https://archive.stsci.edu/tess/ete-6.html.Funding for the TESS Mission has been provided by the NASA Science Mission Directorate.

Constraints on Rational Model Weighting, Blending and Selecting when Constructing Probability Forecasts given Multiple Models

NASA Astrophysics Data System (ADS)

Higgins, S. M. W.; Du, H. L.; Smith, L. A.

2012-04-01

Ensemble forecasting on a lead time of seconds over several years generates a large forecast-outcome archive, which can be used to evaluate and weight "models". Challenges which arise as the archive becomes smaller are investigated: in weather forecasting one typically has only thousands of forecasts however those launched 6 hours apart are not independent of each other, nor is it justified to mix seasons with different dynamics. Seasonal forecasts, as from ENSEMBLES and DEMETER, typically have less than 64 unique launch dates; decadal forecasts less than eight, and long range climate forecasts arguably none. It is argued that one does not weight "models" so much as entire ensemble prediction systems (EPSs), and that the marginal value of an EPS will depend on the other members in the mix. The impact of using different skill scores is examined in the limits of both very large forecast-outcome archives (thereby evaluating the efficiency of the skill score) and in very small forecast-outcome archives (illustrating fundamental limitations due to sampling fluctuations and memory in the physical system being forecast). It is shown that blending with climatology (J. Bröcker and L.A. Smith, Tellus A, 60(4), 663-678, (2008)) tends to increase the robustness of the results; also a new kernel dressing methodology (simply insuring that the expected probability mass tends to lie outside the range of the ensemble) is illustrated. Fair comparisons using seasonal forecasts from the ENSEMBLES project are used to illustrate the importance of these results with fairly small archives. The robustness of these results across the range of small, moderate and huge archives is demonstrated using imperfect models of perfectly known nonlinear (chaotic) dynamical systems. The implications these results hold for distinguishing the skill of a forecast from its value to a user of the forecast are discussed.

Fermilab History and Archives Project | Norman F. Ramsey

Science.gov Websites

Fermilab History and Archives Project Fermilab History and Archives Project Fermilab History and Archives Project Home About the Archives History and Archives Online Request Contact Us History & ; Archives Project Fermilab History and Archives Project Norman F. Ramsey Back to History and Archives

A seasonal comparison of surface sediment characteristics in Chincoteague Bay, Maryland and Virginia, USA

USGS Publications Warehouse

Ellis, Alisha M.; Marot, Marci E.; Wheaton, Cathryn J.; Bernier, Julie C.; Smith, Christopher G.

2016-02-03

This report is an archive for sedimentological data derived from the surface sediment of Chincoteague Bay. Data are available for the spring (March/April 2014) and fall (October 2014) samples collected. Downloadable data are provided as Excel spreadsheets and as JPEG files. Additional files include ArcGIS shapefiles of the sampling sites, detailed results of sediment grain-size analyses, and formal Federal Geographic Data Committee metadata (data downloads).

Expression of VEGF₁₆₅b, VEGFR1, VEGFR2 and CD34 in benign and malignant tumors of parotid glands.

PubMed

Błochowiak, Katarzyna J; Sokalski, Jerzy; Bodnar, Magdalena B; Trzybulska, Dorota; Marszałek, Andrzej K; Witmanowski, Henryk

2018-01-01

Vascular endothelial growth factor (VEGF) is an angiogenic factor and could be involved in the pathogenesis of salivary gland tumors. VEGF exerts its biological function by binding to its receptors, VEGFR1 and VEGFR2. An alternative splice variant of VEGF (VEGFxxxb) is an anti-angiogenic factor. Binding VEGF165b with VEGFR2 results in an impaired angiogenic response. The imbalance of VEGFxxx and VEGFxxxb isoforms can underpin pathological angiogenesis. The purpose of this study was to evaluate and compare the expression of VEGF165b, VEGFR1, VEGFR2, and CD34 in benign and malignant parotid gland tumors and to explore the possible correlations between their expression and clinicopathological features of tumors. The study was performed on archived paraffin-embedded tissue samples derived from 70 patients with benign and malignant parotid gland tumors (25 with malignant tumors, 23 with pleomorphic adenoma and 22 with Warthin's tumor). Immunohistochemical staining of selected tissue sections was performed using monoclonal antibodies. Immunohistochemical staining of selected molecules was used for evaluation of their expression in tissue sections. There were no statistically significant differences in the expression of the selected proteins localized in the tumor and surgical margin taken from the same patient. Expression of VEGFR2 correlated with VEGF165b in mixed tumors. There was a statistically significant difference in the expression of VEGFR1 in malignant tumors between females and males, and between the expression of VEGFR1 and the score of T classification in malignant tumors. VEGF165b cannot be treated as a prognostic factor. VEGF receptors correlated with selected clinicopathological data of malignant tumors, indicating their possible role as a prognostic marker. The balance of VEGF isoforms have a limited influence on the development of parotid glands tumors. The correlation between VEGF165b and VEGFR2 in mixed tumors suggests the existence of an additional antiangiogenic pathway in poorly vascularized mixed tumors.

Sensitive molecular detection of small nodal metastasis in uterine cervical cancer using HPV16-E6/CK19/MUC1 cancer biomarkers

PubMed Central

Samouëlian, Vanessa; Mechtouf, Nawel; Leblanc, Eric; Cardin, Guillaume B.; Lhotellier, Valérie; Querleu, Denis; Révillion, Françoise; Rodier, Francis

2018-01-01

Metastatic nodal involvement is a critical prognostic factor in uterine cervical cancer (UCC). To improve current methods of detecting UCC metastases in lymph nodes (LNs), we used quantitative PCR (qPCR) to assess mRNA expression of potential metastatic biomarkers. We found that expression of HPV16-E6, cytokeratin19 (CK19), and mucin1 (MUC1) is consistently upregulated in tumors and metastatic tissues, supporting a role for these genes in UCC progression. These putative biomarkers were able to predict the presence of histologically positive metastatic LNs with respective sensitivities and specificities of 82% and 99% (CK19), 76% and 95% (HPV16-E6), and 76% and 78% (MUC1). While the biomarkers failed to detect 1.7% to 2.2% of the histologically positive LNs when used individually, combining CK19 and HPV16-E6 enhanced sensitivity and specificity to 100% and 94%, respectively. To explore the sensitivity of qPCR-based detection of varying proportions of invading HPV16-positive UCC cells, we designed a LN metastasis model that achieved a fresh cell detection limit of 0.008% (1:12500 HPV16-positive to HPV16-negative cells), and a paraffin-embedded, formalin-fixed (PEFF) detection limit of 0.02% (1:5000 HPV16-positive to HPV16-negative cells), both of which are within the theoretical detection limit for micrometastasis. Thus, HPV E6/E7 oncogenes may be useful targets for the ultrasensitive detection of nodal involvements like micrometastases in fresh or archived tissue samples. Moreover, our results suggest that the biomarker combination of CK19/HPV-E6 could support a real-time intraoperative strategy for the detection of small, but potentially lethal, metastatic nodal involvements in fresh UCC tissues. PMID:29774091

Psychiatric Correlates of Nonsuicidal Cutting Behaviors in an Adolescent Inpatient Sample

ERIC Educational Resources Information Center

Swenson, Lance P.; Spirito, Anthony; Dyl, Jennifer; Kittler, Jennifer; Hunt, Jeffrey I.

2008-01-01

This archival study of 288 adolescent psychiatric inpatients examined the psychiatric correlates of cutting behavior. Participants were categorized into Threshold cutters (n = 61), Subthreshold cutters (n = 43), and Noncutters (n = 184). Groups were compared on psychiatric diagnoses, suicidality, and self-reported impairment. Results demonstrated…

Physics of Galaxy Clusters and How it Affects Cosmological Tests

NASA Technical Reports Server (NTRS)

Vikhlinin, Alexey; Oliversen, Ronald J. (Technical Monitor)

2002-01-01

We have worked on the analysis of the Chandra observations of the nearby and distant clusters of galaxies, and on the expansion of the sample of distant X-ray clusters based on the archival ROSAT PSPC data. Some of the scientific results are discussed.

42 CFR 37.44 - Approval of radiographic facilities that use digital radiography systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

... image acquisition, digitization, processing, compression, transmission, display, archiving, and... quality digital chest radiographs by submitting to NIOSH digital radiographic image files of a test object... digital radiographic image files from six or more sample chest radiographs that are of acceptable quality...

42 CFR 37.44 - Approval of radiographic facilities that use digital radiography systems.

Code of Federal Regulations, 2012 CFR

2012-10-01

... image acquisition, digitization, processing, compression, transmission, display, archiving, and... quality digital chest radiographs by submitting to NIOSH digital radiographic image files of a test object... digital radiographic image files from six or more sample chest radiographs that are of acceptable quality...

Changes in stable isotope composition in Lake Michigan trout ...

EPA Pesticide Factsheets

Researchers have frequently sought to use environmental archives of sediment, peat and glacial ice to try and assess historical trends in atmospheric mercury (Hg) deposition to aquatic ecosystems. While this information is valuable in the context of identifying temporal source trends, these types of assessments cannot account for likely changes in bioavailability of Hg sources that are tied to the formation of methylmercury (MeHg) and accumulation in fish tissues. For this study we propose the use of long-term fish archives and Hg stable isotope determination as an improved means to relate temporal changes in fish Hg levels to varying Hg sources in the Great Lakes. For this study we acquired 180 archived fish composites from Lake Michigan over a 40-year time period (1975 to 2014) from the Great Lakes Fish Monitoring and Surveillance Program, which were analyzed for their total Hg content and Hg isotope abundances. The results reveal that Hg sources to Lake Michigan trout (Salvelinus namaycush) have encountered considerable changes as well as a large shift in the food web trophic position as a result of the introduction of several invasive species, especially the recent invasion of dreissenid mussels. Total Hg concentrations span a large range (1,600 to 150 ng g-1) and exhibit large variations from 1975 to 1985. Ä199Hg signatures similarly exhibit large variation (3.2 to 6.9‰) until 1985, followed by less variation through the end of the data record in 2014.

Validation of Marek's disease diagnosis and monitoring of Marek's disease vaccines from samples collected in FTA cards.

PubMed

Cortes, Aneg L; Montiel, Enrique R; Gimeno, Isabel M

2009-12-01

The use of Flinders Technology Associates (FTA) filter cards to quantify Marek's disease virus (MDV) DNA for the diagnosis of Marek's disease (MD) and to monitor MD vaccines was evaluated. Samples of blood (43), solid tumors (14), and feather pulp (FP; 36) collected fresh and in FTA cards were analyzed. MDV DNA load was quantified by real-time PCR. Threshold cycle (Ct) ratios were calculated for each sample by dividing the Ct value of the internal control gene (glyceraldehyde-3-phosphate dehydrogenase) by the Ct value of the MDV gene. Statistically significant correlation (P < 0.05) within Ct ratios was detected between samples collected fresh and in FTA cards by using Pearson's correlation test. Load of serotype 1 MDV DNA was quantified in 24 FP, 14 solid tumor, and 43 blood samples. There was a statistically significant correlation between FP (r = 0.95), solid tumor (r = 0.94), and blood (r = 0.9) samples collected fresh and in FTA cards. Load of serotype 2 MDV DNA was quantified in 17 FP samples, and the correlation between samples collected fresh and in FTA cards was also statistically significant (Pearson's coefficient, r = 0.96); load of serotype 3 MDV DNA was quantified in 36 FP samples, and correlation between samples taken fresh and in FTA cards was also statistically significant (r = 0.84). MDV DNA samples extracted 3 days (t0) and 8 months after collection (t1) were used to evaluate the stability of MDV DNA in archived samples collected in FTA cards. A statistically significant correlation was found for serotype 1 (r = 0.96), serotype 2 (r = 1), and serotype 3 (r = 0.9). The results show that FTA cards are an excellent media to collect, transport, and archive samples for MD diagnosis and to monitor MD vaccines. In addition, FTA cards are widely available, inexpensive, and adequate for the shipment of samples nationally and internationally.

Soft-Tissue Sarcomas of the Abdomen and Pelvis: Radiologic-Pathologic Features, Part 1-Common Sarcomas: From the Radiologic Pathology Archives.

PubMed

Levy, Angela D; Manning, Maria A; Al-Refaie, Waddah B; Miettinen, Markku M

2017-01-01

Soft-tissue sarcomas are a diverse group of rare mesenchymal malignancies that can arise at any location in the body and affect all age groups. These sarcomas are most common in the extremities, trunk wall, retroperitoneum, and head and neck. In the adult population, soft-tissue sarcomas arising in the abdomen and pelvis are often large masses at the time of diagnosis because they are usually clinically silent or cause vague or mild symptoms until they invade or compress vital organs. In contrast, soft-tissue sarcomas arising from the abdominal wall come to clinical attention earlier in the course of disease because they cause a palpable mass, abdominal wall deformity, or pain that is more clinically apparent. The imaging features of abdominal and pelvic sarcomas and abdominal wall sarcomas can be nonspecific and overlap with more common pathologic conditions, making diagnosis difficult or, in some cases, delaying diagnosis. Liposarcoma (well-differentiated and dedifferentiated liposarcomas), leiomyosarcoma, and gastrointestinal stromal tumor (GIST) are the most common intra-abdominal primary sarcomas. Any soft-tissue sarcoma can arise in the abdominal wall. Knowledge of the classification and pathologic features of soft-tissue sarcomas, the anatomic locations where they occur, and their cross-sectional imaging features helps the radiologist establish the diagnosis or differential diagnosis so that patients with soft-tissue sarcomas can receive optimal treatment and management. In part 1 of this article, the most common soft-tissue sarcomas (liposarcoma, leiomyosarcoma, and GIST) are reviewed, with a discussion on anatomic locations, classification, clinical considerations, and differential diagnosis. Part 2 will focus on the remainder of the soft-tissue sarcomas occurring in the abdomen and pelvis.

Soft-Tissue Sarcomas of the Abdomen and Pelvis: Radiologic-Pathologic Features, Part 1—Common Sarcomas: From the Radiologic Pathology Archives

PubMed Central

Manning, Maria A.; Al-Refaie, Waddah B.; Miettinen, Markku M.

2017-01-01

Soft-tissue sarcomas are a diverse group of rare mesenchymal malignancies that can arise at any location in the body and affect all age groups. These sarcomas are most common in the extremities, trunk wall, retroperitoneum, and head and neck. In the adult population, soft-tissue sarcomas arising in the abdomen and pelvis are often large masses at the time of diagnosis because they are usually clinically silent or cause vague or mild symptoms until they invade or compress vital organs. In contrast, soft-tissue sarcomas arising from the abdominal wall come to clinical attention earlier in the course of disease because they cause a palpable mass, abdominal wall deformity, or pain that is more clinically apparent. The imaging features of abdominal and pelvic sarcomas and abdominal wall sarcomas can be nonspecific and overlap with more common pathologic conditions, making diagnosis difficult or, in some cases, delaying diagnosis. Liposarcoma (well-differentiated and dedifferentiated liposarcomas), leiomyosarcoma, and gastrointestinal stromal tumor (GIST) are the most common intra-abdominal primary sarcomas. Any soft-tissue sarcoma can arise in the abdominal wall. Knowledge of the classification and pathologic features of soft-tissue sarcomas, the anatomic locations where they occur, and their cross-sectional imaging features helps the radiologist establish the diagnosis or differential diagnosis so that patients with soft-tissue sarcomas can receive optimal treatment and management. In part 1 of this article, the most common soft-tissue sarcomas (liposarcoma, leiomyosarcoma, and GIST) are reviewed, with a discussion on anatomic locations, classification, clinical considerations, and differential diagnosis. Part 2 will focus on the remainder of the soft-tissue sarcomas occurring in the abdomen and pelvis. PMID:28287938

Clean and Cold Sample Curation

NASA Technical Reports Server (NTRS)

Allen, C. C.; Agee, C. B.; Beer, R.; Cooper, B. L.

2000-01-01

Curation of Mars samples includes both samples that are returned to Earth, and samples that are collected, examined, and archived on Mars. Both kinds of curation operations will require careful planning to ensure that the samples are not contaminated by the instruments that are used to collect and contain them. In both cases, sample examination and subdivision must take place in an environment that is organically, inorganically, and biologically clean. Some samples will need to be prepared for analysis under ultra-clean or cryogenic conditions. Inorganic and biological cleanliness are achievable separately by cleanroom and biosafety lab techniques. Organic cleanliness to the <50 ng/sq cm level requires material control and sorbent removal - techniques being applied in our Class 10 cleanrooms and sample processing gloveboxes.

Liquid Microjunction Surface Sampling Probe Electrospray Mass Spectrometry for Detection of Drugs and Metabolites in Thin Tissue Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Berkel, Gary J; Kertesz, Vilmos; Koeplinger, Kenneth A.

2008-01-01

A self-aspirating, liquid micro-junction surface sampling probe/electrospray emitter mass spectrometry system was demonstrated for use in the direct analysis of spotted and dosed drugs and their metabolites in thin tissue sections. Proof-of-principle sampling and analysis directly from tissue without the need for sample preparation was demonstrated first by raster scanning a region on a section of rat liver onto which reserpine was spotted. The mass spectral signal from selected reaction monitoring was used to develop a chemical image of the spotted drug on the tissue. The probe was also used to selectively spot sample areas of sagittal whole mouse bodymore » tissue sections that had been dosed orally (90 mg/kg) with R,S-sulforaphane 3 hrs prior to sacrifice. Sulforaphane and its glutathione and N-acetyl cysteine conjugates were monitored with selected reaction monitoring and detected in the stomach and various other tissues from the dosed mouse. No signal for these species was observed in the tissue from a control mouse. The same dosed tissue section was used to illustrate the possibility of obtaining a line scan across the whole body section. In total these results illustrate the potential for rapid screening of the distribution of drugs and metabolites in tissue sections with the micro-liquid junction surface sampling probe/electrospray mass spectrometry approach.« less

The value of intraoperative ultrasonography during the resection of relapsed irradiated malignant gliomas in the brain.

PubMed

Mursch, Kay; Scholz, Martin; Brück, Wolfgang; Behnke-Mursch, Julianne

2017-01-01

The aim of this study was to investigate whether intraoperative ultrasonography (IOUS) helped the surgeon navigate towards the tumor as seen in preoperative magnetic resonance imaging and whether IOUS was able to distinguish between tumor margins and the surrounding tissue. Twenty-five patients suffering from high-grade gliomas who were previously treated by surgery and radiotherapy were included. Intraoperatively, two histopathologic samples were obtained a sample of unequivocal tumor tissue (according to anatomical landmarks and the surgeon's visual and tactile impressions) and a small tissue sample obtained using a navigated needle when the surgeon decided to stop the resection. This specimen was considered to be a boundary specimen, where no tumor tissue was apparent. The decision to take the second sample was not influenced by IOUS. The effect of IOUS was analyzed semi-quantitatively. All 25 samples of unequivocal tumor tissue were histopathologically classified as tumor tissue and were hyperechoic on IOUS. Of the boundary specimens, eight were hypoechoic. Only one harbored tumor tissue (P=0.150). Seventeen boundaries were moderately hyperechoic, and these samples contained all possible histological results (i.e., tumor, infiltration, or no tumor). During surgery performed on relapsed, irradiated, high-grade gliomas, IOUS provided a reliable method of navigating towards the core of the tumor. At borders, it did not reliably distinguish between remnants or tumor-free tissue, but hypoechoic areas seldom contained tumor tissue.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

A probable risk factor of female breast cancer: study on benign and malignant breast tissue samples.

PubMed

Rehman, Sohaila; Husnain, Syed M

2014-01-01

The study reports enhanced Fe, Cu, and Zn contents in breast tissues, a probable risk factor of breast cancer in females. Forty-one formalin-fixed breast tissues were analyzed using atomic absorption spectrophotometry. Twenty malignant, six adjacent to malignant and 15 benign tissues samples were investigated. The malignant tissues samples were of grade 11 and type invasive ductal carcinoma. The quantitative comparison between the elemental levels measured in the two types of specimen (benign and malignant) tissues (removed after surgery) suggests significant elevation of these metals (Fe, Cu, and Zn) in the malignant tissue. The specimens were collected just after mastectomy of women aged 19 to 59 years from the hospitals of Islamabad and Rawalpindi, Pakistan. Most of the patients belong to urban areas of Pakistan. Findings of study depict that these elements have a promising role in the initiation and development of carcinoma as consistent pattern of elevation for Fe, Cu, and Zn was observed. The results showed the excessive accumulation of Fe (229 ± 121 mg/L) in malignant breast tissue samples of patients (p < 0.05) to that in benign tissues samples (49.1 ± 11.4 mg/L). Findings indicated that excess accumulation of iron in malignant tissues can be a risk factor of breast cancer. In order to validate our method of analysis, certified reference material muscle tissue lyophilized (IAEA) MA-M-2/TM was analyzed for metal studied. Determined concentrations were quite in good agreement with certified levels. Asymmetric concentration distribution for Fe, Cu, and Zn was observed in both malignant and benign tissue samples.

SEARCHBreast: a new resource to locate and share surplus archival material from breast cancer animal models to help address the 3Rs.

PubMed

Blyth, Karen; Carter, Phil; Morrissey, Bethny; Chelala, Claude; Jones, Louise; Holen, Ingunn; Speirs, Valerie

2016-04-01

Animal models have contributed to our understanding of breast cancer, with publication of results in high-impact journals almost invariably requiring extensive in vivo experimentation. As such, many laboratories hold large collections of surplus animal material, with only a fraction being used in publications relating to the original projects. Despite being developed at considerable cost, this material is an invisible and hence an underutilised resource, which often ends up being discarded. Within the breast cancer research community there is both a need and desire to make this valuable material available for researchers. Lack of a coordinated system for visualisation and localisation of this has prevented progress. To fulfil this unmet need, we have developed a novel initiative called Sharing Experimental Animal Resources: Coordinating Holdings-Breast (SEARCHBreast) which facilitates sharing of archival tissue between researchers on a collaborative basis and, de facto will reduce overall usage of animal models in breast cancer research. A secure searchable database has been developed where researchers can find, share, or upload materials related to animal models of breast cancer, including genetic and transplant models. SEARCHBreast is a virtual compendium where the physical material remains with the original laboratory. A bioanalysis pipeline is being developed for the analysis of transcriptomics data associated with mouse models, allowing comparative study with human and cell line data. Additionally, SEARCHBreast is committed to promoting the use of humanised breast tissue models as replacement alternatives to animals. Access to this unique resource is freely available to all academic researchers following registration at https://searchbreast.org.

The Washington University Central Neuroimaging Data Archive

PubMed Central

Gurney, Jenny; Olsen, Timothy; Flavin, John; Ramaratnam, Mohana; Archie, Kevin; Ransford, James; Herrick, Rick; Wallace, Lauren; Cline, Jeanette; Horton, Will; Marcus, Daniel S

2016-01-01

Since the early 2000’s, much of the neuroimaging work at Washington University (WU) has been facilitated by the Central Neuroimaging Data Archive (CNDA), an XNAT-based imaging informatics system. The CNDA is uniquely related to XNAT, as it served as the original codebase for the XNAT open source platform. The CNDA hosts data acquired in over 1000 research studies, encompassing 36,000 subjects and more than 60,000 imaging sessions. Most imaging modalities used in modern human research are represented in the CNDA, including magnetic resonance (MR), positron emission tomography (PET), computed tomography (CT), nuclear medicine (NM), computed radiography (CR), digital radiography (DX), and ultrasound (US). However, the majority of the imaging data in the CNDA are MR and PET of the human brain. Currently, about 20% of the total imaging data in the CNDA is available by request to external researchers. CNDA’s available data includes large sets of imaging sessions and in some cases clinical, psychometric, tissue, or genetic data acquired in the study of Alzheimer’s disease, brain metabolism, cancer, HIV, sickle cell anemia, and Tourette syndrome. PMID:26439514

Imaging biological tissues with electrical conductivity contrast below 1 S m−1 by means of magnetoacoustic tomography with magnetic induction

PubMed Central

Hu, Gang; Li, Xu; He, Bin

2010-01-01

Magnetoacoustic tomography with magnetic induction (MAT-MI) is a recently introduced imaging modality for noninvasive electrical impedance imaging, with ultrasound imaging resolution and a contrast reflecting the electrical conductivity properties of tissues. However, previous MAT-MI systems can only image samples that are much more conductive than real human or animal tissues. To image real biological tissue samples, a large-current-carrying coil that can give stronger magnetic stimulations and stronger MAT-MI acoustic signals is employed in this study. The conductivity values of all the tissue samples employed in this study are also directly measured using a well calibrated four-electrode system. The experimental results demonstrated the feasibility to image biological tissues with electrical conductivity contrast below 1.0 S∕m using the MAT-MI technique with safe level of electromagnetic energy applied to tissue samples. PMID:20938494

Imaging biological tissues with electrical conductivity contrast below 1 S m-1 by means of magnetoacoustic tomography with magnetic induction

NASA Astrophysics Data System (ADS)

Hu, Gang; Li, Xu; He, Bin

2010-09-01

Magnetoacoustic tomography with magnetic induction (MAT-MI) is a recently introduced imaging modality for noninvasive electrical impedance imaging, with ultrasound imaging resolution and a contrast reflecting the electrical conductivity properties of tissues. However, previous MAT-MI systems can only image samples that are much more conductive than real human or animal tissues. To image real biological tissue samples, a large-current-carrying coil that can give stronger magnetic stimulations and stronger MAT-MI acoustic signals is employed in this study. The conductivity values of all the tissue samples employed in this study are also directly measured using a well calibrated four-electrode system. The experimental results demonstrated the feasibility to image biological tissues with electrical conductivity contrast below 1.0 S/m using the MAT-MI technique with safe level of electromagnetic energy applied to tissue samples.

Selection of Russian Plutonium Beryllium Sources for Inclusion in the Nuclear Mateirals Information Program Archive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Narlesky, Joshua E; Padilla, Dennis D; Watts, Joe

2009-01-01

Throughout the 1960s and 1970s, the former Soviet Union produced and exported Plutonium-Beryllium (PuBe) neutron sources to various Eastern European countries. The Russian sources consist of an intermetallic compound of plutonium and beryllium encapsulated in an inner welded, sealed capsule and consisting of a body and one or more covers. The amount of plutonium in the sources ranges from 0.002 g up to 15 g. A portion of the sources was originally exported to East Germany. A portion of these sources were acquired by Los Alamos National Laboratory (LANL) in the late 1990s for destruction in the Offsite Source Recoverymore » Program. When the OSRP was canceled, the remaining 88 PuBe neutron sources were packaged and stored in a 55-gal drum at T A-55. This storage configuration is no longer acceptable for PuBe sources, and the sources must either be repackaged or disposed of. Repackaging would place the sources into Hagan container, and depending on the dose rates, some sources may be packaged individually increasing the footprint and cost of storage. In addition, each source will be subject to leak-checking every six months. Leaks have already been detected in some of the sources, and due to the age of these sources, it is likely that additional leaks may be detected over time, which will increase the overall complexity of handling and storage. Therefore, it was decided that the sources would be disposed of at the Waste Isolation Pilot Plant (WIPP) due to the cost and labor associated with continued storage at TA-55. However, the plutonium in the sources is of Russian origin and needs to be preserved for research purposes. Therefore, it is important that a representative sample of the sources retained and archived for future studies. This report describes the criteria used to obtain a representative sample of the sources. Nine Russian PuBe neutron sources have been selected out of a collection of 77 sources for inclusion in the NMIP archive. Selection criteria were developed so that the largest sources that are representative of the collection are included. One representative source was chosen for every 20 sources in the collection, and effort was made to preserve sources unique to the collection. In total, four representative sources and five unique sources were selected for the archive. The archive samples contain 40 grams of plutonium with an isotopic composition similar to that of weapon grade material and three grams of plutonium with an isotopic composition similar to that of reactor grade plutonium.« less

76 FR 71315 - Endangered and Threatened Species; Take of Anadromous Fish

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-17

... the fish and would then sample them for biological information (fin tissue and scale samples). They..., measured, weighed, tissue-sampled, and checked for external marks and coded-wire tags depending on the.... Then the researchers would remove and preserve fish body tissues, otoliths, and coded wire tags (from...

Age estimation based on aspartic acid racemization in human sclera.

PubMed

Klumb, Karolin; Matzenauer, Christian; Reckert, Alexandra; Lehmann, Klaus; Ritz-Timme, Stefanie

2016-01-01

Age estimation based on racemization of aspartic acid residues (AAR) in permanent proteins has been established in forensic medicine for years. While dentine is the tissue of choice for this molecular method of age estimation, teeth are not always available which leads to the need to identify other suitable tissues. We examined the suitability of total tissue samples of human sclera for the estimation of age at death. Sixty-five samples of scleral tissue were analyzed. The samples were hydrolyzed and after derivatization, the extent of aspartic acid racemization was determined by gas chromatography. The degree of AAR increased with age. In samples from younger individuals, the correlation of age and D-aspartic acid content was closer than in samples from older individuals. The age-dependent racemization in total tissue samples proves that permanent or at least long-living proteins are present in scleral tissue. The correlation of AAR in human sclera and age at death is close enough to serve as basis for age estimation. However, the precision of age estimation by this method is lower than that of age estimation based on the analysis of dentine which is due to molecular inhomogeneities of total tissue samples of sclera. Nevertheless, the approach may serve as a valuable alternative or addition in exceptional cases.

Fluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysis.

PubMed

Praveen, Bavishna B; Ashok, Praveen C; Mazilu, Michael; Riches, Andrew; Herrington, Simon; Dholakia, Kishan

2012-07-01

In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30  s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.

Organochlorine compounds in streambed sediment and in biological tissue from streams and their relations to land use, central Arizona

USGS Publications Warehouse

Gebler, Joseph B.

2000-01-01

Streambed-sediment samples from 13 sites and biological-tissue samples from 11 sites in the Gila River Basin in central Arizona were analyzed for 32 organochlorine compounds in streambed sediment and 28 compounds in biological tissue during 1996 as part of the U.S. Geological Survey's National Water-Quality Assessment program. The objectives of the study were to determine the occurrence and distribution of organochlorine compounds and their relation to land use. Sampling sites were categorized on the basis of major land uses in the basin or the source of water in the stream. Because land uses were mixed or had changed over time, some land-use categories were combined. Sites were categorized as forest/rangeland (6), forest/urban (1), urban (4), or agricultural/urban (2). Thirteen organochlorine compounds were detected in streambed-sediment samples, and 10 were detected in tissue samples. The number of compounds found in streambed-sediment samples from individual sites ranged from 0 to 10, and the range for individual tissue samples was 0 to 7. Comparison of the number of detections in streambed-sediment samples to the number of detections in tissue samples from particular sites where both were sampled yielded five instances where more compounds were detected in streambed sediment, six instances where more compounds were detected in tissue, and five instances where the number of detections in streambed sediment and tissue were equal. The frequency of detection of particular compounds for sites where both streambed sediment and tissue were sampled resulted in five compounds being detected more frequently in streambed sediment, five more frequently in tissue, and three compounds that were equally frequent in streambed sediment and in tissue. Few contaminants were detected in samples from the forest/rangeland sites; greater numbers of compounds were detected at the urban sites and at the forest/urban site. The greatest number of compounds and the highest concentrations of many contaminants were detected at agriculture/urban sites. The compound detected most frequently in streambed-sediment and tissue samples was p,p'-DDE. Streambed-sediment guideline values for the protection of aquatic life for p,p'-DDE and total DDT were exceeded at both agricultural/urban sites, The streambed-sediment guideline value for the protection of aquatic life for total chlordane was exceeded at one agricultural/urban site, one urban site, and the forest/urban site. The streambed-sediment guideline value for the protection of aquatic life for total PCB’s was exceeded at one agricultural/urban site. Guideline values for the protection of fish-eating wildlife for total DDT and for toxaphene were exceeded only in samples from the two agricultural/urban sites. The guideline value for the protection of fish-eating wildlife for total PCB’s was equaled or exceeded in samples from two sites—one urban and one agricultural/urban site. Screening values established by the U.S. Environmental Protection Agency for the protection of human health for edible portions of fish were exceeded by total DDT and by toxaphene in fish-tissue samples from both agricultural/urban sites. The human-health criterion for total PCB’s was exceeded in two fish-tissue samples from an agricultural site and from an urban site. Tissue samples analyzed in this study were for whole fish, and thus, concentration data are not entirely comparable to the screening values of the U.S. Environmental Protection Agency. Because these exceedences were an order of magnitude above the criteria, however, it is possible that concentrations in the edible portions of fish from these locations could present a human- health risk. Analyses of samples of edible portions of fish from these locations would be needed to adequately assess the presence or absence of a human-health risk. The similarity of the results of this study to the results of other studies of organochlorine compounds in the environment suggests that there is a correlation between contaminants in sediment and biological-tissue samples and land uses. As with other studies of the occurrence and distribution of organochlorine contaminants in streambed sediments and biological tissue, this study shows that many organochlorine compounds continue to persist in the environment and thus could pose a threat to aquatic life, fish-eating wildlife, and possibly to humans who consume contaminated fish.

An efficient field and laboratory workflow for plant phylotranscriptomic projects1

PubMed Central

Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Timoneda, Alfonso; Feng, Tao; Marx, Hannah E.; Walker, Joseph F.; Smith, Stephen A.

2017-01-01

Premise of the study: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. Methods and Results: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms. These included difficult mucilaginous tissues such as those of Cactaceae and Droseraceae. Conclusions: Our workflow is not only cost effective (ca. $270 per sample, as of August 2016, from tissue to reads) and time efficient (less than 50 h for 10–12 samples including all laboratory work and sample curation), but also has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds. PMID:28337391

Evaluation of sample holders designed for long-lasting X-ray micro-tomographic scans of ex-vivo soft tissue samples

NASA Astrophysics Data System (ADS)

Dudak, J.; Zemlicka, J.; Krejci, F.; Karch, J.; Patzelt, M.; Zach, P.; Sykora, V.; Mrzilkova, J.

2016-03-01

X-ray microradiography and microtomography are imaging techniques with increasing applicability in the field of biomedical and preclinical research. Application of hybrid pixel detector Timepix enables to obtain very high contrast of low attenuating materials such as soft biological tissue. However X-ray imaging of ex-vivo soft tissue samples is a difficult task due to its structural instability. Ex-vivo biological tissue is prone to fast drying-out which is connected with undesired changes of sample size and shape producing later on artefacts within the tomographic reconstruction. In this work we present the optimization of our Timepix equipped micro-CT system aiming to maintain soft tissue sample in stable condition. Thanks to the suggested approach higher contrast of tomographic reconstructions can be achieved while also large samples that require detector scanning can be easily measured.

Maximizing RNA yield from archival renal tumors and optimizing gene expression analysis.

PubMed

Glenn, Sean T; Head, Karen L; Teh, Bin T; Gross, Kenneth W; Kim, Hyung L

2010-01-01

Formalin-fixed, paraffin-embedded tissues are widely available for gene expression analysis using TaqMan PCR. Five methods, including 4 commercial kits, for recovering RNA from paraffin-embedded renal tumor tissue were compared. The MasterPure kit from Epicentre produced the highest RNA yield. However, the difference in RNA yield between the kit from Epicenter and Invitrogen's TRIzol method was not significant. Using the top 3 RNA isolation methods, the manufacturers' protocols were modified to include an overnight Proteinase K digestion. Overnight protein digestion resulted in a significant increase in RNA yield. To optimize the reverse transcription reaction, conventional reverse transcription with random oligonucleotide primers was compared to reverse transcription using primers specific for genes of interest. Reverse transcription using gene-specific primers significantly increased the quantity of cDNA detectable by TaqMan PCR. Therefore, expression profiling of formalin-fixed, paraffin-embedded tissue using TaqMan qPCR can be optimized by using the MasterPure RNA isolation kit modified to include an overnight Proteinase K digestion and gene-specific primers during the reverse transcription.

Fibrinogen Demonstration in Oral Lichen Planus: An Immunofluorescence Study on Archival Tissues.

PubMed

Shirol, Pallavi D; Naik, Veena; Kale, Alka

2015-10-01

Lichen planus is a premalignant condition with minimal diagnostic aids. This study is an attempt to use paraffin embedded sections of lichen planus with immunofluorescein stain and to evaluate the immunofluorescent sections to establish pattern of fibrinogen deposition. Thirty-five paraffin embedded sections of old and new cases of oral lichen planus (study group) and five normal oral mucosa (control group) were chosen. Two sections of each (H & E) case were taken, one was stained with hematoxylin and eosin and another with fluorescein isothiocynate conjugate (FITC) polyclonal rabbit antibody against fibrinogen. Fluorescent findings were examined with a fluorescent microscope. A high statistical significant correlation was found in respect to fluorescence positivity, intensity of fluorescence and distribution of fluorescence each with p < 0.0001 and fluorescence at blood vessel walls (p = 0.0003). This study suggested that paraffin embedded sections can be successfully used in direct immunofluorescence staining in routine set up where only formalin fixed tissues are received. Paraffin embedded sections can be successfully used in direct immunofluorescence staining when only formalin fixed tissues are received.

Assessment of tissue-specific cortisol activity with regard to degeneration of the suspensory ligaments in horses with pituitary pars intermedia dysfunction.

PubMed

Hofberger, Sina C; Gauff, Felicia; Thaller, Denise; Morgan, Ruth; Keen, John A; Licka, Theresia F

2018-02-01

OBJECTIVE To identify signs of tissue-specific cortisol activity in samples of suspensory ligament (SL) and neck skin tissue from horses with and without pituitary pars intermedia dysfunction (PPID). SAMPLE Suspensory ligament and neck skin tissue samples obtained from 26 euthanized horses with and without PPID. PROCEDURES Tissue samples were collected from 12 horses with and 14 horses without PPID (controls). Two control horses had received treatment with dexamethasone; data from those horses were not used in statistical analyses. The other 12 control horses were classified as old horses (≥ 14 years old) and young horses (≤ 9 years old). Standard histologic staining, staining for proteoglycan accumulation, and immunostaining of SL and neck skin tissue sections for glucocorticoid receptors, insulin, 11β hydroxysteroid dehydrogenase type 1, and 11β hydroxysteroid dehydrogenase type 2 were performed. Findings for horses with PPID were compared with findings for young and old horses without PPID. RESULTS Compared with findings for old and young control horses, there were significantly more cells stained for glucocorticoid receptors in SL samples and for 11 β hydroxysteroid dehydrogenase type 1 in SL and skin tissue samples from horses with PPID. Insulin could not be detected in any of the SL or skin tissue samples. Horses with PPID had evidence of SL degeneration with significantly increased proteoglycan accumulation. Neck skin tissue was found to be significantly thinner in PPID-affected horses than in young control horses. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that tissue-specific dysregulation of cortisol metabolism may contribute to the SL degeneration associated with PPID in horses.

Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

PubMed

Bernsen, M R; Dijkman, H B; de Vries, E; Figdor, C G; Ruiter, D J; Adema, G J; van Muijen, G N

1998-10-01

Molecular analysis of small tissue samples has become increasingly important in biomedical studies. Using a laser dissection microscope and modified nucleic acid isolation protocols, we demonstrate that multiple mRNA as well as DNA sequences can be identified from a single-cell sample. In addition, we show that the specificity of procurement of tissue samples is not compromised by smear contamination resulting from scraping of the microtome knife during sectioning of lesions. The procedures described herein thus allow for efficient RT-PCR or PCR analysis of multiple nucleic acid sequences from small tissue samples obtained by laser-assisted microdissection.

Organic compounds and trace elements in fish tissue and bed sediment from streams in the Yellowstone River basin, Montana and Wyoming, 1998

USGS Publications Warehouse

Peterson, David A.; Boughton, Gregory K.

2000-01-01

A comprehensive water-quality investigation of the Yellowstone River Basin began in 1997, under the National Water-Quality Assessment (NAWQA) Program. Twenty-four sampling sites were selected for sampling of fish tissue and bed sediment during 1998. Organic compounds analyzed included organochlorine insecticides and their metabolites and total polychlorinated biphenyls (PCBs) from fish-tissue and bed-sediment samples, and semivolatile organic compounds from bed-sediment samples. A broad suite of trace elements was analyzed from both fish-tissue and bed-sediment samples, and a special study related to mercury also was conducted. Of the 12 organochlorine insecticides and metabolites detected in the fish-tissue samples, the most compounds per site were detected in samples from integrator sites which represent a mixture of land uses. The presence of DDT, and its metabolites DDD and DDE, in fish collected in the Yellowstone Park area likely reflects long-term residual effects from historical DDT-spraying programs for spruce budworm. Dieldrin, chlordane, and other organic compounds also were detected in the fish-tissue samples. The compound p, p'-DDE was detected at 71 percent of the sampling sites, more than any other compound. The concentrations of total DDT in fish samples were low, however, compared to concentrations from historical data from the study area, other NAWQA studies in the Rocky Mountains, and national baseline concentrations. Only 2 of the 27 organochlorine insecticides and metabolites and total PCBs analyzed in bed sediment were detected. Given that 12 of the compounds were detected in fish-tissue samples, fish appeared to be more sensitive indicators of contamination than bed sediment.Concentrations of some trace elements in fish and bed sediment were higher at sites in mineralized areas than at other sites. Concentrations of selenium in fish tissue from some sites were above background levels. Concentrations of arsenic, chromium, copper, and lead in some of the bed-sediment samples potentially exceeded criteria for the protection of aquatic life.

Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

PubMed Central

2014-01-01

Background A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means. Results Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains. Conclusions These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts. PMID:24384040

Quality control of human tissues--experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank.

PubMed

Sandusky, George E; Teheny, Katie Heinz; Esterman, Mike; Hanson, Jeff; Williams, Stephen D

2007-01-01

The success of molecular research and its applications in both the clinical and basic research arenas is strongly dependent on the collection, handling, storage, and quality control of fresh human tissue samples. This tissue bank was set up to bank fresh surgically obtained human tissue using a Clinical Annotated Tissue Database (CATD) in order to capture the associated patient clinical data and demographics using a one way patient encryption scheme to protect patient identification. In this study, we determined that high quality of tissue samples is imperative for both genomic and proteomic molecular research. This paper also contains a brief compilation of the literature involved in the patient ethics, patient informed consent, patient de-identification, tissue collection, processing, and storage as well as basic molecular research generated from the tissue bank using good clinical practices. The current applicable rules, regulations, and guidelines for handling human tissues are briefly discussed. More than 6,610 cancer patients have been consented (97% of those that were contacted by the consenter) and 16,800 tissue specimens have been banked from these patients in 9 years. All samples collected in the bank were QC'd by a pathologist. Approximately 1,550 tissue samples have been requested for use in basic, clinical, and/or biomarker cancer research studies. Each tissue aliquot removed from the bank for a research study were evaluated by a second H&E, if the samples passed the QC, they were submitted for genomic and proteomic molecular analysis/study. Approximately 75% of samples evaluated were of high histologic quality and used for research studies. Since 2003, we changed the patient informed consent to allow the tissue bank to gather more patient clinical follow-up information. Ninety two percent of the patients (1,865 patients) signed the new informed consent form and agreed to be re-contacted for follow-up information on their disease state. In addition, eighty five percent of patients (1,584) agreed to be re-contacted to provide a biological fluid sample to be used for biomarker research.

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Fei; Maslov, Sergei; Yoo, Shinjae

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

DOE PAGES

He, Fei; Maslov, Sergei; Yoo, Shinjae; ...

2016-05-25

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

30 CFR 780.21 - Hydrologic information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Hydrologic information. 780.21 Section 780.21... Hydrologic information. (a) Sampling and analysis methodology. All water-quality analyses performed to meet... information on the availability of this material at NARA, call 202-741-6030, or go to: http://www.archives.gov...