In-air micro-pixe analysis of tissue samples

International Nuclear Information System (INIS)

Tanaka, A.; Ishii, K.; Komori, Y.

2002-01-01

Micro-PIXE is capable of providing spatial distributions of elements in the micro-meter scale and its application to biology is useful to elucidate the cellular metabolism. Since, in this method, a sample target is usually irradiated with proton or α-particle beams in vacuum, beam heating results in evaporation of volatile elements an shrinking of the sample. In order to avoid these side effects, we previously developed a technique of in-air micro-PIXE analysis for samples of cultured cells. In addition to these, analysis of exposed tissue samples from living subjects is highly desirable in biological and medical research. Here, we describe a technique of in-air micro-PIXE analysis of such tissue samples. The target samples of exposed tissue slices from a Donryu rat, in which a tumor had been transplanted, were analyzed with proton micro-beams of 2.6 MeV. We report that the shape of cells and the distribution of volatile elements in the tissue sample remain uncharged when using a target preparation based on a freeze-drying method. (author)

Collecting and Storing Tissue, Blood, and Bone Marrow Samples From Patients With Rhabdomyosarcoma or Other Soft Tissue Sarcoma

Science.gov (United States)

2017-12-11

Adult Rhabdomyosarcoma; Childhood Desmoplastic Small Round Cell Tumor; Chordoma; Desmoid Tumor; Metastatic Childhood Soft Tissue Sarcoma; Nonmetastatic Childhood Soft Tissue Sarcoma; Previously Treated Childhood Rhabdomyosarcoma; Previously Untreated Childhood Rhabdomyosarcoma; Recurrent Adult Soft Tissue Sarcoma; Recurrent Childhood Rhabdomyosarcoma; Recurrent Childhood Soft Tissue Sarcoma; Stage I Adult Soft Tissue Sarcoma; Stage II Adult Soft Tissue Sarcoma; Stage III Adult Soft Tissue Sarcoma; Stage IV Adult Soft Tissue Sarcoma

SEM investigation of heart tissue samples

International Nuclear Information System (INIS)

Saunders, R; Amoroso, M

2010-01-01

We used the scanning electron microscope to examine the cardiac tissue of a cow (Bos taurus), a pig (Sus scrofa), and a human (Homo sapiens). 1mm 3 blocks of left ventricular tissue were prepared for SEM scanning by fixing in 96% ethanol followed by critical point drying (cryofixation), then sputter-coating with gold. The typical ridged structure of the myofibrils was observed for all the species. In addition crystal like structures were found in one of the samples of the heart tissue of the pig. These structures were investigated further using an EDVAC x-ray analysis attachment to the SEM. Elemental x-ray analysis showed highest peaks occurred for gold, followed by carbon, oxygen, magnesium and potassium. As the samples were coated with gold for conductivity, this highest peak is expected. Much lower peaks at carbon, oxygen, magnesium and potassium suggest that a cystallized salt such as a carbonate was present in the tissue before sacrifice.

SEM investigation of heart tissue samples

Energy Technology Data Exchange (ETDEWEB)

Saunders, R; Amoroso, M [Physics Department, University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies (Trinidad and Tobago)

2010-07-01

We used the scanning electron microscope to examine the cardiac tissue of a cow (Bos taurus), a pig (Sus scrofa), and a human (Homo sapiens). 1mm{sup 3} blocks of left ventricular tissue were prepared for SEM scanning by fixing in 96% ethanol followed by critical point drying (cryofixation), then sputter-coating with gold. The typical ridged structure of the myofibrils was observed for all the species. In addition crystal like structures were found in one of the samples of the heart tissue of the pig. These structures were investigated further using an EDVAC x-ray analysis attachment to the SEM. Elemental x-ray analysis showed highest peaks occurred for gold, followed by carbon, oxygen, magnesium and potassium. As the samples were coated with gold for conductivity, this highest peak is expected. Much lower peaks at carbon, oxygen, magnesium and potassium suggest that a cystallized salt such as a carbonate was present in the tissue before sacrifice.

DNA damage in preserved specimens and tissue samples: a molecular assessment

Directory of Open Access Journals (Sweden)

Cantin Elizabeth

2008-10-01

Full Text Available Abstract The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents – such as light, oxygen or formaldehyde – on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.

Isotopic change in the tissues of Bothrops atrox in captivity collected from environments of the eastern Amazon

Science.gov (United States)

Martinez, M. G.; Chalkidis, H. D.; Amazonas, D. R.; da Silva, A. M.; De Oliveira, R., Jr.; Camargo, P. B.

2013-12-01

The Bothrops atrox is little studied because it is sympatric Amazonian animals, and very little is known about the ecology and natural history of this species. It has a generalist diet and the distribution of this species is very wide. The adult animals forage mostly on the ground, while the younger animals prefer to stay on the vegetation. They are easily find in the rainy months in areas near lakes and seasonally flooded and are difficult to find in the driest months, a period where there is less availability of preys in these environments. Due to its aggressiveness, is considered one of the most feared snakes in South America and in the eastern Amazon, being responsible for the largest number of snakebites in the region. Through stable isotope carbon-13 and nitrogen-15, is intended to characterize the variations of the feeding habits of these collected animals in different environments and also when they are kept in captivity, feeding the animal's bioterium. The serpents were collected in environments with different land uses, such as native forest, savannah, pasture and have been brought to the serpentarium Integrated College Tapajos (FIT), being retained in order to Samplings throughout the experiment with feeding mice's own bioterium. When these snakes came from different locations, samples were collected scales and blood (T0), before receiving the new supply (captive), and every time we fed the mice the vivarium, new tissue samples were collected, (T1, T2, T3) to exchange all the nature of food for the food captivity.Based on the results of δ13C and δ15N, the samples collected in the tissues of snakes of different environments (nature and captivity), it was observed that changes in food sources reflect changes in tissues (blood and scales), also reflecting the production of poison different periods of turnover of absorbed material in those tissues, contributing to the study of animal ecology and behavior in relation to habitat.

A probable risk factor of female breast cancer: study on benign and malignant breast tissue samples.

Science.gov (United States)

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 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.

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

Science.gov (United States)

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.

MARS spectral molecular imaging of lamb tissue: data collection and image analysis

CERN Document Server

Aamir, R; Bateman, C.J.; Butler, A.P.H.; Butler, P.H.; Anderson, N.G.; Bell, S.T.; Panta, R.K.; Healy, J.L.; Mohr, J.L.; Rajendran, K.; Walsh, M.F.; Ruiter, N.de; Gieseg, S.P.; Woodfield, T.; Renaud, P.F.; Brooke, L.; Abdul-Majid, S.; Clyne, M.; Glendenning, R.; Bones, P.J.; Billinghurst, M.; Bartneck, C.; Mandalika, H.; Grasset, R.; Schleich, N.; Scott, N.; Nik, S.J.; Opie, A.; Janmale, T.; Tang, D.N.; Kim, D.; Doesburg, R.M.; Zainon, R.; Ronaldson, J.P.; Cook, N.J.; Smithies, D.J.; Hodge, K.

2014-01-01

Spectral molecular imaging is a new imaging technique able to discriminate and quantify different components of tissue simultaneously at high spatial and high energy resolution. Our MARS scanner is an x-ray based small animal CT system designed to be used in the diagnostic energy range (20 to 140 keV). In this paper, we demonstrate the use of the MARS scanner, equipped with the Medipix3RX spectroscopic photon-processing detector, to discriminate fat, calcium, and water in tissue. We present data collected from a sample of lamb meat including bone as an illustrative example of human tissue imaging. The data is analyzed using our 3D Algebraic Reconstruction Algorithm (MARS-ART) and by material decomposition based on a constrained linear least squares algorithm. The results presented here clearly show the quantification of lipid-like, water-like and bone-like components of tissue. However, it is also clear to us that better algorithms could extract more information of clinical interest from our data. Because we ...

Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

Science.gov (United States)

Kalmár, Alexandra; Péterfia, Bálint; Hollósi, Péter; Wichmann, Barnabás; Bodor, András; Patai, Árpád V; Schöller, Andrea; Krenács, Tibor; Tulassay, Zsolt; Molnár, Béla

2015-09-01

We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.

Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples.

Science.gov (United States)

Elloumi, Fathi; Hu, Zhiyuan; Li, Yan; Parker, Joel S; Gulley, Margaret L; Amos, Keith D; Troester, Melissa A

2011-06-30

Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor.

Technical note: Alternatives to reduce adipose tissue sampling bias.

Science.gov (United States)

Cruz, G D; Wang, Y; Fadel, J G

2014-10-01

Understanding the mechanisms by which nutritional and pharmaceutical factors can manipulate adipose tissue growth and development in production animals has direct and indirect effects in the profitability of an enterprise. Adipocyte cellularity (number and size) is a key biological response that is commonly measured in animal science research. The variability and sampling of adipocyte cellularity within a muscle has been addressed in previous studies, but no attempt to critically investigate these issues has been proposed in the literature. The present study evaluated 2 sampling techniques (random and systematic) in an attempt to minimize sampling bias and to determine the minimum number of samples from 1 to 15 needed to represent the overall adipose tissue in the muscle. Both sampling procedures were applied on adipose tissue samples dissected from 30 longissimus muscles from cattle finished either on grass or grain. Briefly, adipose tissue samples were fixed with osmium tetroxide, and size and number of adipocytes were determined by a Coulter Counter. These results were then fit in a finite mixture model to obtain distribution parameters of each sample. To evaluate the benefits of increasing number of samples and the advantage of the new sampling technique, the concept of acceptance ratio was used; simply stated, the higher the acceptance ratio, the better the representation of the overall population. As expected, a great improvement on the estimation of the overall adipocyte cellularity parameters was observed using both sampling techniques when sample size number increased from 1 to 15 samples, considering both techniques' acceptance ratio increased from approximately 3 to 25%. When comparing sampling techniques, the systematic procedure slightly improved parameters estimation. The results suggest that more detailed research using other sampling techniques may provide better estimates for minimum sampling.

Comparison of diagnostic efficacy between CLE, tissue sampling, and CLE combined with tissue sampling for undetermined pancreaticobiliary strictures: a meta-analysis.

Science.gov (United States)

Gao, Ya-Dong; Qu, Ya-Wei; Liu, Hai-Feng

2018-04-01

The accurate diagnosis of undetermined pancreaticobiliary strictures remains challenging. Current ERCP-guided tissue sampling methods are of low sensitivity. Confocal laser endomicroscopy (CLE) is a new procedure and allows real optical biopsies that may improve the diagnosis of undetermined pancreaticobiliary strictures. The aim of this meta-analysis was to determine the diagnostic yield of CLE, tissue sampling, and CLE combined with tissue sampling for undetermined pancreaticobiliary strictures. Pubmed, Embase, and the Cochrane Library database were reviewed for relevant studies. Pooled estimates of sensitivity and specificity with 95% confidence intervals (CIs) were calculated using the random-effects meta-analysis model. The summary receiver-operating characteristic (SROC) curve was constructed, and the area under the receiver operating characteristic curve (AUC) was calculated. Twelve studies involving 591 patients were enrolled in our analysis. The overall sensitivity and the specificity estimate of CLE for discriminating benign and malignant pancreaticobiliary strictures were 87% (95%CI, 83-91%) and 76% (95%CI, 70-81%), respectively. The AUC to assess the diagnostic efficacy was 0.8705. For tissue sampling, the overall sensitivity and the specificity estimate were 64% (95%CI, 57-70%) and 94% (95%CI, 90-97%), respectively. The AUC to assess the diagnostic efficacy was 0.8040. A combination of both methods increased the sensitivity (93%; 95%CI, 88-96%) with a specificity of 82% (95%CI, 74-89%). The AUC to assess the diagnostic efficacy was 0.9377. There was no publication bias by Deeks' Funnel Plot with p = .936. Compared with tissue sampling, CLE may increase the sensitivity for the diagnosis of malignant pancreaticobiliary strictures. A combination of both can effectively diagnose malignant pancreaticobiliary strictures.

Culture methods of allograft musculoskeletal tissue samples in Australian bacteriology laboratories.

Science.gov (United States)

Varettas, Kerry

2013-12-01

Samples of allograft musculoskeletal tissue are cultured by bacteriology laboratories to determine the presence of bacteria and fungi. In Australia, this testing is performed by 6 TGA-licensed clinical bacteriology laboratories with samples received from 10 tissue banks. Culture methods of swab and tissue samples employ a combination of solid agar and/or broth media to enhance micro-organism growth and maximise recovery. All six Australian laboratories receive Amies transport swabs and, except for one laboratory, a corresponding biopsy sample for testing. Three of the 6 laboratories culture at least one allograft sample directly onto solid agar. Only one laboratory did not use a broth culture for any sample received. An international literature review found that a similar combination of musculoskeletal tissue samples were cultured onto solid agar and/or broth media. Although variations of allograft musculoskeletal tissue samples, culture media and methods are used in Australian and international bacteriology laboratories, validation studies and method evaluations have challenged and supported their use in recovering fungi and aerobic and anaerobic bacteria.

Ethical considerations in forensic genetics research on tissue samples collected post-mortem in Cape Town, South Africa.

Science.gov (United States)

Heathfield, Laura J; Maistry, Sairita; Martin, Lorna J; Ramesar, Raj; de Vries, Jantina

2017-11-29

The use of tissue collected at a forensic post-mortem for forensic genetics research purposes remains of ethical concern as the process involves obtaining informed consent from grieving family members. Two forensic genetics research studies using tissue collected from a forensic post-mortem were recently initiated at our institution and were the first of their kind to be conducted in Cape Town, South Africa. This article discusses some of the ethical challenges that were encountered in these research projects. Among these challenges was the adaptation of research workflows to fit in with an exceptionally busy service delivery that is operating with limited resources. Whilst seeking guidance from the literature regarding research on deceased populations, it was noted that next of kin of decedents are not formally recognised as a vulnerable group in the existing ethical and legal frameworks in South Africa. The authors recommend that research in the forensic mortuary setting is approached using guidance for vulnerable groups, and the benefit to risk standard needs to be strongly justified. Lastly, when planning forensic genetics research, consideration must be given to the potential of uncovering incidental findings, funding to validate these findings and the feedback of results to family members; the latter of which is recommended to occur through a genetic counsellor. It is hoped that these experiences will contribute towards a formal framework for conducting forensic genetic research in medico-legal mortuaries in South Africa.

Equipment for collecting samples of radioactive solutions

International Nuclear Information System (INIS)

Raggenbass, A.; Fradin, J.; Joubert, G.

1958-01-01

The authors present an equipment aimed at collecting samples of fission products to perform radio-chemical analysis. As the sample must have a total activity between 1 and 50 micro-Curie, this installation comprises a sampling system and a dilution device which aims at bringing the sample to the suitable activity. Samples are collected by means of needles. The sample reproducibility is discussed. The dilution device is described

6. Label-free selective plane illumination microscopy of tissue samples

Directory of Open Access Journals (Sweden)

Muteb Alharbi

2017-10-01

Conclusion: Overall this method meets the demands of the current needs for 3D imaging tissue samples in a label-free manner. Label-free Selective Plane Microscopy directly provides excellent information about the structure of the tissue samples. This work has highlighted the superiority of Label-free Selective Plane Microscopy to current approaches to label-free 3D imaging of tissue.

Urine sample collection protocols for bioassay samples

Energy Technology Data Exchange (ETDEWEB)

MacLellan, J.A.; McFadden, K.M.

1992-11-01

In vitro radiobioassay analyses are used to measure the amount of radioactive material excreted by personnel exposed to the potential intake of radioactive material. The analytical results are then used with various metabolic models to estimate the amount of radioactive material in the subject`s body and the original intake of radioactive material. Proper application of these metabolic models requires knowledge of the excretion period. It is normal practice to design the bioassay program based on a 24-hour excretion sample. The Hanford bioassay program simulates a total 24-hour urine excretion sample with urine collection periods lasting from one-half hour before retiring to one-half hour after rising on two consecutive days. Urine passed during the specified periods is collected in three 1-L bottles. Because the daily excretion volume given in Publication 23 of the International Commission on Radiological Protection (ICRP 1975, p. 354) for Reference Man is 1.4 L, it was proposed to use only two 1-L bottles as a cost-saving measure. This raised the broader question of what should be the design capacity of a 24-hour urine sample kit.

Urine sample collection protocols for bioassay samples

Energy Technology Data Exchange (ETDEWEB)

MacLellan, J.A.; McFadden, K.M.

1992-11-01

In vitro radiobioassay analyses are used to measure the amount of radioactive material excreted by personnel exposed to the potential intake of radioactive material. The analytical results are then used with various metabolic models to estimate the amount of radioactive material in the subject's body and the original intake of radioactive material. Proper application of these metabolic models requires knowledge of the excretion period. It is normal practice to design the bioassay program based on a 24-hour excretion sample. The Hanford bioassay program simulates a total 24-hour urine excretion sample with urine collection periods lasting from one-half hour before retiring to one-half hour after rising on two consecutive days. Urine passed during the specified periods is collected in three 1-L bottles. Because the daily excretion volume given in Publication 23 of the International Commission on Radiological Protection (ICRP 1975, p. 354) for Reference Man is 1.4 L, it was proposed to use only two 1-L bottles as a cost-saving measure. This raised the broader question of what should be the design capacity of a 24-hour urine sample kit.

Preparation of tissue samples for X-ray fluorescence microscopy

International Nuclear Information System (INIS)

Chwiej, Joanna; Szczerbowska-Boruchowska, Magdalena; Lankosz, Marek; Wojcik, Slawomir; Falkenberg, Gerald; Stegowski, Zdzislaw; Setkowicz, Zuzanna

2005-01-01

As is well-known, trace elements, especially metals, play an important role in the pathogenesis of many disorders. The topographic and quantitative elemental analysis of pathologically changed tissues may shed some new light on processes leading to the degeneration of cells in the case of selected diseases. An ideal and powerful tool for such purpose is the Synchrotron Microbeam X-ray Fluorescence technique. It enables the carrying out of investigations of the elemental composition of tissues even at the single cell level. The tissue samples for histopathological investigations are routinely fixed and embedded in paraffin. The authors try to verify the usefulness of such prepared tissue sections for elemental analysis with the use of X-ray fluorescence microscopy. Studies were performed on rat brain samples. Changes in elemental composition caused by fixation in formalin or paraformaldehyde and embedding in paraffin were examined. Measurements were carried out at the bending magnet beamline L of the Hamburger Synchrotronstrahlungslabor HASYLAB in Hamburg. The decrease in mass per unit area of K, Br and the increase in P, S, Fe, Cu and Zn in the tissue were observed as a result of the fixation. For the samples embedded in paraffin, a lower level of most elements was observed. Additionally, for these samples, changes in the composition of some elements were not uniform for different analyzed areas of rat brain

Preparation of tissue samples for X-ray fluorescence microscopy

Energy Technology Data Exchange (ETDEWEB)

Chwiej, Joanna [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland)]. E-mail: jchwiej@novell.ftj.agh.edu.pl; Szczerbowska-Boruchowska, Magdalena [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland); Lankosz, Marek [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland); Wojcik, Slawomir [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland); Falkenberg, Gerald [Hamburger Synchrotronstrahlungslabor at Deutsches Elektronen-Synchrotron, Notkestr. 85, Hamburg (Germany); Stegowski, Zdzislaw [Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland); Setkowicz, Zuzanna [Department of Neuroanatomy, Institute of Zoology, Jagiellonian University, Ingardena 6, 30-060 Cracow (Poland)

2005-12-15

As is well-known, trace elements, especially metals, play an important role in the pathogenesis of many disorders. The topographic and quantitative elemental analysis of pathologically changed tissues may shed some new light on processes leading to the degeneration of cells in the case of selected diseases. An ideal and powerful tool for such purpose is the Synchrotron Microbeam X-ray Fluorescence technique. It enables the carrying out of investigations of the elemental composition of tissues even at the single cell level. The tissue samples for histopathological investigations are routinely fixed and embedded in paraffin. The authors try to verify the usefulness of such prepared tissue sections for elemental analysis with the use of X-ray fluorescence microscopy. Studies were performed on rat brain samples. Changes in elemental composition caused by fixation in formalin or paraformaldehyde and embedding in paraffin were examined. Measurements were carried out at the bending magnet beamline L of the Hamburger Synchrotronstrahlungslabor HASYLAB in Hamburg. The decrease in mass per unit area of K, Br and the increase in P, S, Fe, Cu and Zn in the tissue were observed as a result of the fixation. For the samples embedded in paraffin, a lower level of most elements was observed. Additionally, for these samples, changes in the composition of some elements were not uniform for different analyzed areas of rat brain.

28 CFR 28.12 - Collection of DNA samples.

Science.gov (United States)

2010-07-01

... Homeland Security, collecting DNA samples from: (1) Aliens lawfully in, or being processed for lawful... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Collection of DNA samples. 28.12 Section 28.12 Judicial Administration DEPARTMENT OF JUSTICE DNA IDENTIFICATION SYSTEM DNA Sample Collection...

Tritium concentrations in environmental water and food samples collected around the vicinity of the PNPP-1

International Nuclear Information System (INIS)

Garcia, T.Y.; Enriquez, S.O.; Duran, E.B.

1986-01-01

The natural radioactivity levels of tritium in environmental samples collected around the vicinity and more distant environment of the first Philippine Nuclear Power Plant (PNPP-1) in Bataan were assessed. The samples analyzed consisted of water samples such as seawater, freshwater, drinking water, groundwater and rainwater; and food samples such as cereals, vegetables, fruits; meat, milk fish and crustaceans. Tritium concentrations in water samples were determined by distillation and liquid scintillation counting techniques. The food samples were analyzed for tissue-free water tritium by the freezing-drying method followed by liquid scintillation counting techniques. (Auth.) 13 refs

Tissue stiffening coordinates morphogenesis by triggering collective cell migration in vivo.

Science.gov (United States)

Barriga, Elias H; Franze, Kristian; Charras, Guillaume; Mayor, Roberto

2018-02-22

Collective cell migration is essential for morphogenesis, tissue remodelling and cancer invasion. In vivo, groups of cells move in an orchestrated way through tissues. This movement involves mechanical as well as molecular interactions between cells and their environment. While the role of molecular signals in collective cell migration is comparatively well understood, how tissue mechanics influence collective cell migration in vivo remains unknown. Here we investigated the importance of mechanical cues in the collective migration of the Xenopus laevis neural crest cells, an embryonic cell population whose migratory behaviour has been likened to cancer invasion. We found that, during morphogenesis, the head mesoderm underlying the cephalic neural crest stiffens. This stiffening initiates an epithelial-to-mesenchymal transition in neural crest cells and triggers their collective migration. To detect changes in their mechanical environment, neural crest cells use mechanosensation mediated by the integrin-vinculin-talin complex. By performing mechanical and molecular manipulations, we show that mesoderm stiffening is necessary and sufficient to trigger neural crest migration. Finally, we demonstrate that convergent extension of the mesoderm, which starts during gastrulation, leads to increased mesoderm stiffness by increasing the cell density underneath the neural crest. These results show that convergent extension of the mesoderm has a role as a mechanical coordinator of morphogenesis, and reveal a link between two apparently unconnected processes-gastrulation and neural crest migration-via changes in tissue mechanics. Overall, we demonstrate that changes in substrate stiffness can trigger collective cell migration by promoting epithelial-to-mesenchymal transition in vivo. More broadly, our results raise the idea that tissue mechanics combines with molecular effectors to coordinate morphogenesis.

Collecting Ground Samples for Balloon-Borne Instruments

Science.gov (United States)

Jones, Jack; Zimmerman, Wayne; Wu, Jiunn Jenq

2009-01-01

A proposed system in a gondola containing scientific instruments suspended by a balloon over the surface of the Saturn moon Titan would quickly acquire samples of rock or ice from the ground below. Prototypes of a sample-collecting device that would be a major part of the system have been tested under cryogenic and non-cryogenic conditions on Earth. Systems like this one could also be used in non-cryogenic environments on Earth to collect samples of rock, soil, ice, mud, or other ground material from such inaccessible or hazardous locations as sites of suspected chemical spills or biological contamination. The sample-collecting device would be a harpoonlike device that would be connected to the balloon-borne gondola by a tether long enough to reach the ground. The device would be dropped from the gondola to acquire a sample, then would be reeled back up to the gondola, where the sample would be analyzed by the onboard instruments. Each prototype of the sample-collecting device has a sharp front (lower) end, a hollow core for retaining a sample, a spring for holding the sample in the hollow core, and a rear (upper) annular cavity for retaining liquid sample material. Aerodynamic fins at the rear help to keep the front end pointed downward. In tests, these prototype devices were dropped from various heights and used to gather samples of dry sand, moist sand, cryogenic water ice, and warmer water ice.

Evaluation of sample preparation methods and optimization of nickel determination in vegetable tissues

Directory of Open Access Journals (Sweden)

Rodrigo Fernando dos Santos Salazar

2011-02-01

Full Text Available Nickel, although essential to plants, may be toxic to plants and animals. It is mainly assimilated by food ingestion. However, information about the average levels of elements (including Ni in edible vegetables from different regions is still scarce in Brazil. The objectives of this study were to: (a evaluate and optimize a method for preparation of vegetable tissue samples for Ni determination; (b optimize the analytical procedures for determination by Flame Atomic Absorption Spectrometry (FAAS and by Electrothermal Atomic Absorption (ETAAS in vegetable samples and (c determine the Ni concentration in vegetables consumed in the cities of Lorena and Taubaté in the Vale do Paraíba, State of São Paulo, Brazil. By means of the analytical technique for determination by ETAAS or FAAS, the results were validated by the test of analyte addition and recovery. The most viable method tested for quantification of this element was HClO4-HNO3 wet digestion. All samples but carrot tissue collected in Lorena contained Ni levels above the permitted by the Brazilian Ministry of Health. The most disturbing results, requiring more detailed studies, were the Ni concentrations measured in carrot samples from Taubaté, where levels were five times higher than permitted by Brazilian regulations.

Prevalence of antimicrobial residues in eggs, tissue and feed samples in the State of Kuwait

International Nuclear Information System (INIS)

Alomirah, H.; Al-Mazeedi, H.; Al-Zenki, S.; Al-Faili, B.; Al-Foudary, M.; Abuzid, A.; Al-Sayed, I.; Sidhu, J.

2007-01-01

A total of 238 locally produced and imported eggs, tissue (meat, poultry and aquacultured fish) and feed and feedstuffs samples were collected at different seasonal periods from different farms and retail outlets in Kuwait and screened for presence of beta-lactams, tetracyclines, sulfonamides, streptomycin, macrolides and chloramphenicol (799 tests) using Charm II system. The results indicated that all of the 222 tests performed on table egg samples were negative for the analyzed antimicrobial residues indicating adherence to the guidelines for microbial use and withdrawal. Similarly, all of the 268 tests performed on tissue samples were negative for the analyzed antimicrobial residues except for chloramphenicol. These chloramphenicol positive samples, all of the 66 tests performed were negative for beta-lactams residues. Out of the 79 feed and feedstuff samples analyzed for teracyclines residues, broiler diet and concentrate samples (5%) were above the tetracyclines MRL (100 ppb.). On the other hands, results have revealed a widespread of sulfonamide residues and to a less extent chloramphenicol in tested feed and feedstuff samples. The Charm II system was reliable for rapid screening of antimicrobial residues. In general, results obtained in our study necessitate more effective and well planned national antimicrobial residues surveillance programs focusing particularly on samples imported from highly risk sources. (author)

Vitrification of in vitro matured oocytes collected from surplus ovarian medulla tissue resulting from fertility preservation of ovarian cortex tissue

DEFF Research Database (Denmark)

Yin, Huiqun; Jiang, Hong; Kristensen, Stine Gry

2016-01-01

PURPOSE: The aim of the study was to investigate the maturation rate of immature oocytes collected from ovarian medulla tissue normally discarded during preparation of ovarian cortical tissue for fertility preservation. Further we evaluated survival of derived MII oocytes following vitrification...... and warming. METHODS: 36 patients aged from 8 to 41 years who had one ovary excised for fertility preservation were included. Oocytes were collected from the medulla tissue and matured in vitro 44-48 h followed by vitrification. Number of oocytes collected, the rates of maturation and post-warming survival...... of cortical tissue may pose a risk of relapse, but the IVM approach is currently too inefficient to be the only method used for fertility preservation....

The Apollo lunar samples collection analysis and results

CERN Document Server

Young, Anthony

2017-01-01

This book focuses on the specific mission planning for lunar sample collection, the equipment used, and the analysis and findings concerning the samples at the Lunar Receiving Laboratory in Texas. Anthony Young documents the collection of Apollo samples for the first time for readers of all backgrounds, and includes interviews with many of those involved in planning and analyzing the samples. NASA contracted with the U.S. Geologic Survey to perform classroom and field training of the Apollo astronauts. NASA’s Geology Group within the Manned Spacecraft Center in Houston, Texas, helped to establish the goals of sample collection, as well as the design of sample collection tools, bags, and storage containers. In this book, detailed descriptions are given on the design of the lunar sampling tools, the Modular Experiment Transporter used on Apollo 14, and the specific areas of the Lunar Rover vehicle used for the Apollo 15, 16, and 17 missions, which carried the sampling tools, bags, and other related equipment ...

USAXS and SAXS from cancer-bearing breast tissue samples

International Nuclear Information System (INIS)

Fernandez, M.; Suhonen, H.; Keyrilaeinen, J.; Bravin, A.; Fiedler, S.; Karjalainen-Lindsberg, M.-L.; Leidenius, M.; Smitten, K. von; Suortti, P.

2008-01-01

USAXS and SAXS patterns from cancer-bearing human breast tissue samples were recorded at beamline ID02 of the ESRF using a Bonse-Hart camera and a pinhole camera. The samples were classified as being ductal carcinoma, grade II, and ductal carcinoma in situ, partly invasive. The samples included areas of healthy collagen, invaded collagen, necrotic ducts with calcifications, and adipose tissue. The scattering patterns were analyzed in different ways to separate the scattering contribution and the direct beam from the observed rocking curve (RC) of the analyzer. It was found that USAXS from all tissues was weak, and the effects on the analyzer RC were observed only in the low-intensity tails of the patterns. The intrinsic RC was convolved with different model functions for the impulse response of the sample, and the best fit with experiment was obtained by the Pearson VII function. Significantly different distributions for the Pearson exponent m were obtained in benign and malignant regions of the samples. For a comparison with analyzer-based imaging (ABI) or diffraction enhanced imaging (DEI) a 'long-slit' integration of the patterns was performed, and this emphasized the scattering contribution in the tails of the rocking curve

Genetic Sample Inventory

Data.gov (United States)

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

Molecular analysis of infectious bursal disease virus from bursal tissues collected on FTA filter paper.

Science.gov (United States)

Moscoso, Hugo; Alvarado, Ivan; Hofacre, Charles L

2006-09-01

We investigated the feasibility of using FTA filter cards for the storage of bursas of Fabricius containing infectious bursal disease virus (IBDV) and for IBDV detection by reverse transcriptase (RT)-polymerase chain reaction (PCR), and characterization by restriction fragment length polymorphism (RFLP) or nucleotide sequencing. The FTA card is a cotton-based cellulose membrane containing lyophilized chemicals that lyses many types of bacteria and viruses. IBDV was inactivated upon contact with the FTA as shown by the inability of the virus to be propagated in embryonating chicken eggs. Viral RNA in minced bursas or stamped bursas could be amplified by RT-PCR (VP2 gene fragment, 248 base pairs) after storage on FTA for at least 15 days at room temperature or 8 mo at -20 C. Analytical sensitivity of the test was between 0.5-5 ng of RNA template or 5 x 10(1) mean tissue culture infective dose (TCID50)/FTA spot. Detection rate of IBDV in domestic clinical samples collected on FTA or collected by the non-FTA standard procedure was 36.7% and 41.7%, respectively, which represents 88% agreement. Detection of IBDV from FTA cards inoculated with bursal tissues in the laboratory or in the field was 36.7% and 37.1%, respectively. Detection of IBDV from FTA samples when the cards were inoculated with bursal tissues and sent through customs into the United States was 32.9%. Analysis of the amplified products showed that molecular characterization of IBDV by RFLP or nucleotide sequencing is feasible in bursas stored on FTA at 25 C for 1-3 mo or at -20 C for at least 8 mo. The use of FTA for the collection of bursal tissues and simultaneous inactivation of IBDV allows the movement of specimens within the United States and also from outside the United States in compliance with federal regulations and in a manner adequate for molecular characterization.

X-ray scattering for the characterization of lyophilized breast tissue samples

International Nuclear Information System (INIS)

Elshemey, Wael M.; Mohamed, Fayrouz S.; Khater, Ibrahim M.

2013-01-01

This work investigates the possibility of characterizing breast cancer by measuring the X-ray scattering profiles of lyophilized excised breast tissue samples. Since X-ray scattering from water-rich tissue is dominated by scattering from water, the removal of water by lyophilization would enhance the characterization process. In the present study, X-ray scattering profiles of 22 normal, 22 malignant and 10 benign breast tissue samples are measured. The cut-offs of scatter diagrams, sensitivity, specificity and diagnostic accuracy of three characterization parameters (full width at half maximum (FWHM) for the peak at 1.1 nm −1 , area under curve (AUC), and ratio of 1st to 2nd scattering peak intensities (I 1 /I 2 %)) are calculated and compared to the data from non-lyophilized samples. Results show increased sensitivity (up to 100%) of the present data on lyophilized breast tissue samples compared to previously reported data for non-lyophilized samples while the specificity (up to 95.4%), diagnostic accuracy (up to 95.4%) and receiver operating characteristic (ROC) curve values (up to 0.9979) for both sets of data are comparable. The present study shows significant differences between normal samples and each of malignant and benign samples. Only subtle differences exist between malignant and benign lyophilized breast tissue samples where FWHM=0.7±0.1 and 0.8±0.3, AUC=1.3±0.2 and 1.4±0.2 and I 1 /I 2 %=44.9±11.0 and 52.4±7.6 for malignant and benign samples respectively. - Highlights: • X-ray scattering profiles of breast tissue samples are acquired. • Three X-ray profile characterization parameters are calculated. • The cut-offs, sensitivity, specificity and diagnostic accuracy are calculated. • They are compared to the data from non-lyophilized samples. • Results show increased sensitivity in case of lyophilized samples

The development of a Martian atmospheric Sample collection canister

Science.gov (United States)

Kulczycki, E.; Galey, C.; Kennedy, B.; Budney, C.; Bame, D.; Van Schilfgaarde, R.; Aisen, N.; Townsend, J.; Younse, P.; Piacentine, J.

The collection of an atmospheric sample from Mars would provide significant insight to the understanding of the elemental composition and sub-surface out-gassing rates of noble gases. A team of engineers at the Jet Propulsion Laboratory (JPL), California Institute of Technology have developed an atmospheric sample collection canister for Martian application. The engineering strategy has two basic elements: first, to collect two separately sealed 50 cubic centimeter unpressurized atmospheric samples with minimal sensing and actuation in a self contained pressure vessel; and second, to package this atmospheric sample canister in such a way that it can be easily integrated into the orbiting sample capsule for collection and return to Earth. Sample collection and integrity are demonstrated by emulating the atmospheric collection portion of the Mars Sample Return mission on a compressed timeline. The test results achieved by varying the pressure inside of a thermal vacuum chamber while opening and closing the valve on the sample canister at Mars ambient pressure. A commercial off-the-shelf medical grade micro-valve is utilized in the first iteration of this design to enable rapid testing of the system. The valve has been independently leak tested at JPL to quantify and separate the leak rates associated with the canister. The results are factored in to an overall system design that quantifies mass, power, and sensing requirements for a Martian atmospheric Sample Collection (MASC) canister as outlined in the Mars Sample Return mission profile. Qualitative results include the selection of materials to minimize sample contamination, preliminary science requirements, priorities in sample composition, flight valve selection criteria, a storyboard from sample collection to loading in the orbiting sample capsule, and contributions to maintaining “ Earth” clean exterior surfaces on the orbiting sample capsule.

The U.S. Geological Survey Geologic Collections Management System (GCMS)—A master catalog and collections management plan for U.S. Geological Survey geologic samples and sample collections

Science.gov (United States)

,

2015-01-01

The U.S. Geological Survey (USGS) is widely recognized in the earth science community as possessing extensive collections of earth materials collected by research personnel over the course of its history. In 2006, a Geologic Collections Inventory was conducted within the USGS Geology Discipline to determine the extent and nature of its sample collections, and in 2008, a working group was convened by the USGS National Geologic and Geophysical Data Preservation Program to examine ways in which these collections could be coordinated, cataloged, and made available to researchers both inside and outside the USGS. The charge to this working group was to evaluate the proposition of creating a Geologic Collections Management System (GCMS), a centralized database that would (1) identify all existing USGS geologic collections, regardless of size, (2) create a virtual link among the collections, and (3) provide a way for scientists and other researchers to obtain access to the samples and data in which they are interested. Additionally, the group was instructed to develop criteria for evaluating current collections and to establish an operating plan and set of standard practices for handling, identifying, and managing future sample collections. Policies and procedures promoted by the GCMS would be based on extant best practices established by the National Science Foundation and the Smithsonian Institution. The resulting report—USGS Circular 1410, “The U.S. Geological Survey Geologic Collections Management System (GCMS): A Master Catalog and Collections Management Plan for U.S. Geological Survey Geologic Samples and Sample Collections”—has been developed for sample repositories to be a guide to establishing common practices in the collection, retention, and disposal of geologic research materials throughout the USGS.

Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

Directory of Open Access Journals (Sweden)

Paula R. Almeida

2012-08-01

Full Text Available The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC and polymerase chain reaction (PCR or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs or frozen (tissue pieces. M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

SE Marine Mammal Histology/Tissue data

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples are collected from stranded marine mammals in the Southeastern United States. These tissue samples are examined histologically and evaluated to...

Biopolymers for sample collection, protection, and preservation.

Science.gov (United States)

Sorokulova, Iryna; Olsen, Eric; Vodyanoy, Vitaly

2015-07-01

One of the principal challenges in the collection of biological samples from air, water, and soil matrices is that the target agents are not stable enough to be transferred from the collection point to the laboratory of choice without experiencing significant degradation and loss of viability. At present, there is no method to transport biological samples over considerable distances safely, efficiently, and cost-effectively without the use of ice or refrigeration. Current techniques of protection and preservation of biological materials have serious drawbacks. Many known techniques of preservation cause structural damages, so that biological materials lose their structural integrity and viability. We review applications of a novel bacterial preservation process, which is nontoxic and water soluble and allows for the storage of samples without refrigeration. The method is capable of protecting the biological sample from the effects of environment for extended periods of time and then allows for the easy release of these collected biological materials from the protective medium without structural or DNA damage. Strategies for sample collection, preservation, and shipment of bacterial, viral samples are described. The water-soluble polymer is used to immobilize the biological material by replacing the water molecules within the sample with molecules of the biopolymer. The cured polymer results in a solid protective film that is stable to many organic solvents, but quickly removed by the application of the water-based solution. The process of immobilization does not require the use of any additives, accelerators, or plastifiers and does not involve high temperature or radiation to promote polymerization.

MicroRNA Expression in Laser Micro-dissected Breast Cancer Tissue Samples - a Pilot Study.

Science.gov (United States)

Seclaman, Edward; Narita, Diana; Anghel, Andrei; Cireap, Natalia; Ilina, Razvan; Sirbu, Ioan Ovidiu; Marian, Catalin

2017-10-28

Breast cancer continues to represent a significant public health burden despite outstanding research advances regarding the molecular mechanisms of cancer biology, biomarkers for diagnostics and prognostic and therapeutic management of this disease. The studies of micro RNAs in breast cancer have underlined their potential as biomarkers and therapeutic targets; however most of these studies are still done on largely heterogeneous whole breast tissue samples. In this pilot study we have investigated the expression of four micro RNAs (miR-21, 145, 155, 92) known to be involved in breast cancer, in homogenous cell populations collected by laser capture microdissection from breast tissue section slides. Micro RNA expression was assessed by real time PCR, and associations with clinical and pathological characteristics were also explored. Our results have confirmed previous associations of miR-21 expression with poor prognosis characteristics of breast cancers such as high stage, large and highly proliferative tumors. No statistically significant associations were found with the other micro RNAs investigated, possibly due to the small sample size of our study. Our results also suggest that miR-484 could be a suitable endogenous control for data normalization in breast tissues, these results needing further confirmation by future studies. In summary, our pilot study showed the feasibility of detecting micro RNAs expression in homogenous laser captured microdissected invasive breast cancer samples, and confirmed some of the previously reported associations with poor prognostic characteristics of breast tumors.

Genetic Sample Inventory - NRDA

Data.gov (United States)

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

Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues.

Science.gov (United States)

Frickmann, Hagen; Tenner-Racz, Klara; Eggert, Petra; Schwarz, Norbert G; Poppert, Sven; Tannich, Egbert; Hagen, Ralf M

2013-12-01

We report on the reliability of polymerase chain reaction (PCR) for the detection of Entamoeba histolytica from formalin-fixed, paraffin-embedded tissue in comparison with microscopy and have determined predictors that may influence PCR results. E. histolytica-specific and Entamoeba dispar-specific real-time PCR and microscopy from adjacent histologic sections were performed using a collection of formalin-fixed, paraffin-embedded tissue specimens obtained from patients with invasive amebiasis. Specimens had been collected during the previous 4 decades. Association of sample age, parasite density, and reliability of PCR was analyzed. E. histolytica PCR was positive in 20 of 34 biopsies (58.8%); 2 of these 20 were microscopically negative for amebae in neighboring tissue sections. PCR was negative in 9 samples with visible amebae in neighboring sections and in 5 samples without visible parasites in neighboring sections. PCR was negative in all specimens that were older than 3 decades. Low parasite counts and sample ages older than 20 years were predictors for false-negative PCR results. All samples were negative for E. dispar DNA. PCR is suitable for the detection of E. histolytica in formalin-fixed, paraffin-embedded tissue samples that are younger than 2 decades and that contain intermediate to high parasite numbers. Negative results in older samples were due to progressive degradation of DNA over time as indicated by control PCRs targeting the human 18S rRNA gene. Moreover, our findings support previous suggestions that only E. histolytica but not E. dispar is responsible for invasive amebiasis.

Analysis of chemical components from plant tissue samples

Science.gov (United States)

Laseter, J. L.

1972-01-01

Information is given on the type and concentration of sterols, free fatty acids, and total fatty acids in plant tissue samples. All samples were analyzed by gas chromatography and then by gas chromatography-mass spectrometry combination. In each case the mass spectral data was accumulated as a computer printout and plot. Typical gas chromatograms are included as well as tables describing test results.

Free water {sup 3}H concentration in diet samples collected during 1969-88 in Akita, Japan

Energy Technology Data Exchange (ETDEWEB)

Hisamatsu, S. [Institute for Environmental Sciences, Rokkasho, Aomori (Japan); Inoue, Y.; Miyamoto, K. [National Inst. of Radiological Sciences, Chiba (Japan); Takizawa, Y. [National Institute for Minamata Disease, Minamata, Kumamoto (Japan)

2000-05-01

Fallout {sup 3}H concentrations in diet samples collected during 1969-88 in Akita Prefecture are reported in this paper. Since {sup 3}H is a potential nuclear fuel for fusion reactors in future, its environmental behavior is important for dose assessment of released {sup 3}H from the plants. Tritium in foods is classified into two types; free water {sup 3}H (FWT) and organically-bound {sup 3}H (OBT). The FWT is practically separated by means of freeze-drying, while the OBT is measured with water sample collected by combustion of dried sample. The OBT concentrations in foods and human tissue samples were reported for {sup 3}H originating from nuclear weapon fallout. We already published {sup 3}H concentrations in diet samples collected in Akita City during 1985-88. Although results for the samples collected in U.S.A. and European countries in the 1970s showed higher specific activity of OBT than FWT, our recent results in Japan indicate almost the same specific activity between them. Since the measurements for the samples in 1960s and 1970s are important to understand the long-term movement of {sup 3}H in the environment, we have searched old diet samples. Recently, diet samples collected in Akita Prefecture during 1969-80 were found and obtained for {sup 3}H analysis. The samples were originally gathered for nutrition survey programs and consisted of duplicate diet samples for 1 day from 10-30 persons. Food samples excluding boiled rice which is the staple food was homogenized by electric mixers after adding tap water. Then, the food and the boiled rice samples were stored in a refrigerator at -20degC. Free water in the samples was collected with lyophilization, then {sup 3}H in the water sample was measured after purification with low-level liquid scintillation counters. The free water {sup 3}H concentrations were measured for 57 diet samples (dish excluding boiled rice) and 17 boiled rice samples. The free water {sup 3}H concentrations in diet and rice samples

Controlled surface topography regulates collective 3D migration by epithelial-mesenchymal composite embryonic tissues.

Science.gov (United States)

Song, Jiho; Shawky, Joseph H; Kim, YongTae; Hazar, Melis; LeDuc, Philip R; Sitti, Metin; Davidson, Lance A

2015-07-01

Cells in tissues encounter a range of physical cues as they migrate. Probing single cell and collective migratory responses to physically defined three-dimensional (3D) microenvironments and the factors that modulate those responses are critical to understanding how tissue migration is regulated during development, regeneration, and cancer. One key physical factor that regulates cell migration is topography. Most studies on surface topography and cell mechanics have been carried out with single migratory cells, yet little is known about the spreading and motility response of 3D complex multi-cellular tissues to topographical cues. Here, we examine the response to complex topographical cues of microsurgically isolated tissue explants composed of epithelial and mesenchymal cell layers from naturally 3D organized embryos of the aquatic frog Xenopus laevis. We control topography using fabricated micropost arrays (MPAs) and investigate the collective 3D migration of these multi-cellular systems in these MPAs. We find that the topography regulates both collective and individual cell migration and that dense MPAs reduce but do not eliminate tissue spreading. By modulating cell size through the cell cycle inhibitor Mitomycin C or the spacing of the MPAs we uncover how 3D topographical cues disrupt collective cell migration. We find surface topography can direct both single cell motility and tissue spreading, altering tissue-scale processes that enable efficient conversion of single cell motility into collective movement. Copyright © 2015 Elsevier Ltd. All rights reserved.

Threshold-dependent sample sizes for selenium assessment with stream fish tissue

Science.gov (United States)

Hitt, Nathaniel P.; Smith, David R.

2015-01-01

Natural resource managers are developing assessments of selenium (Se) contamination in freshwater ecosystems based on fish tissue concentrations. We evaluated the effects of sample size (i.e., number of fish per site) on the probability of correctly detecting mean whole-body Se values above a range of potential management thresholds. We modeled Se concentrations as gamma distributions with shape and scale parameters fitting an empirical mean-to-variance relationship in data from southwestern West Virginia, USA (63 collections, 382 individuals). We used parametric bootstrapping techniques to calculate statistical power as the probability of detecting true mean concentrations up to 3 mg Se/kg above management thresholds ranging from 4 to 8 mg Se/kg. Sample sizes required to achieve 80% power varied as a function of management thresholds and Type I error tolerance (α). Higher thresholds required more samples than lower thresholds because populations were more heterogeneous at higher mean Se levels. For instance, to assess a management threshold of 4 mg Se/kg, a sample of eight fish could detect an increase of approximately 1 mg Se/kg with 80% power (given α = 0.05), but this sample size would be unable to detect such an increase from a management threshold of 8 mg Se/kg with more than a coin-flip probability. Increasing α decreased sample size requirements to detect above-threshold mean Se concentrations with 80% power. For instance, at an α-level of 0.05, an 8-fish sample could detect an increase of approximately 2 units above a threshold of 8 mg Se/kg with 80% power, but when α was relaxed to 0.2, this sample size was more sensitive to increasing mean Se concentrations, allowing detection of an increase of approximately 1.2 units with equivalent power. Combining individuals into 2- and 4-fish composite samples for laboratory analysis did not decrease power because the reduced number of laboratory samples was compensated for by increased

GeLC-MS: A Sample Preparation Method for Proteomics Analysis of Minimal Amount of Tissue.

Science.gov (United States)

Makridakis, Manousos; Vlahou, Antonia

2017-10-10

Application of various proteomics methodologies have been implemented for the global and targeted proteome analysis of many different types of biological samples such as tissue, urine, plasma, serum, blood, and cell lines. Among the aforementioned biological samples, tissue has an exceptional role into clinical research and practice. Disease initiation and progression is usually located at the tissue level of different organs, making the analysis of this material very important for the understanding of the disease pathophysiology. Despite the significant advances in the mass spectrometry instrumentation, tissue proteomics still faces several challenges mainly due to increased sample complexity and heterogeneity. However, the most prominent challenge is attributed to the invasive procedure of tissue sampling which restricts the availability of fresh frozen tissue to minimal amounts and limited number of samples. Application of GeLC-MS sample preparation protocol for tissue proteomics analysis can greatly facilitate making up for these difficulties. In this chapter, a step by step guide for the proteomics analysis of minute amounts of tissue samples using the GeLC-MS sample preparation protocol, as applied by our group in the analysis of multiple different types of tissues (vessels, kidney, bladder, prostate, heart) is provided.

Concordance analysis of methylation biomarkers detection in self-collected and physician-collected samples in cervical neoplasm

International Nuclear Information System (INIS)

Chang, Cheng-Chang; Huang, Rui-Lan; Liao, Yu-Ping; Su, Po-Hsuan; Hsu, Yaw-Wen; Wang, Hui-Chen; Tien, Chau-Yang; Yu, Mu-Hsien; Lin, Ya-Wen; Lai, Hung-Cheng

2015-01-01

Non-attendance at gynecological clinics is a major limitation of cervical cancer screening and self-collection of samples may improve this situation. Although HPV testing of self-collected vaginal samples is acceptable, the specificity is inadequate. The current focus is increasing self-collection of vaginal samples to minimize clinic visits. In this study, we analyzed the concordance and clinical performance of DNA methylation biomarker (PAX1, SOX1, and ZNF582) detection in self-collected vaginal samples and physician-collected cervical samples for the identification of cervical neoplasm. We enrolled 136 cases with paired methylation data identified from abnormal Pap smears (n = 126) and normal controls (n = 10) regardless of HPV status at gynecological clinics. The study group comprised 37 cervical intraepithelial neoplasm I (CIN1), 23 cervical intraepithelial neoplasm II (CIN2), 16 cervical intraepithelial neoplasm III (CIN3), 30 carcinoma in situ (CIS), 13 squamous cell carcinomas (SCCs) and seven adenocarcinomas (ACs)/adenosquamous carcinomas (ASCs). PAX1, SOX1 and ZNF582 methylation in study samples was assessed by real-time quantitative methylation-specific polymerase chain reaction analysis. We generated methylation index cutoff values for the detection of CIN3+ in physician-collected cervical samples for analysis of the self-collected group. Concordance between the physician-collected and self-collected groups was evaluated by Cohen’s Kappa. Sensitivity, specificity and area under curve (AUC) were calculated for detection of CIN3+ lesions. Finally, we produced an optimal cutoff value with the best sensitivity from the self-collected groups. We generated a methylation index cutoff value from physician-collected samples for detection of CIN3+. There were no significant differences in sensitivity, specificity of PAX1, SOX1 and ZNF582 between the self-collected and physician-collected groups. The methylation status of all three genes in the normal control

Effects of Re-heating Tissue Samples to Core Body Temperature on High-Velocity Ballistic Projectile-tissue Interactions.

Science.gov (United States)

Humphrey, Caitlin; Henneberg, Maciej; Wachsberger, Christian; Maiden, Nicholas; Kumaratilake, Jaliya

2017-11-01

Damage produced by high-speed projectiles on organic tissue will depend on the physical properties of the tissues. Conditioning organic tissue samples to human core body temperature (37°C) prior to conducting ballistic experiments enables their behavior to closely mimic that of living tissues. To minimize autolytic changes after death, the tissues are refrigerated soon after their removal from the body and re-heated to 37°C prior to testing. This research investigates whether heating 50-mm-cube samples of porcine liver, kidney, and heart to 37°C for varying durations (maximum 7 h) can affect the penetration response of a high-speed, steel sphere projectile. Longer conditioning times for heart and liver resulted in a slight loss of velocity/energy of the projectile, but the reverse effect occurred for the kidney. Possible reasons for these trends include autolytic changes causing softening (heart and liver) and dehydration causing an increase in density (kidney). © 2017 American Academy of Forensic Sciences.

Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

Energy Technology Data Exchange (ETDEWEB)

Vavpetič, P., E-mail: primoz.vavpetic@ijs.si [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Vogel-Mikuš, K. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Jeromel, L. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Ogrinc Potočnik, N. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); FOM-Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); Pongrac, P. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Department of Plant Physiology, University of Bayreuth, Universitätstr. 30, 95447 Bayreuth (Germany); Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Pelicon, P. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)

2015-04-01

The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on–off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm{sup 2} and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

Seabird tissue archival and monitoring project: Protocol for collecting and banking seabird eggs

Science.gov (United States)

Weston-York, Geoff; Porter, Barbara J.; Pugh, Rebecca S.; Roseneau, David G.; Simac, Kristin S.; Becker, Paul R.; Thorsteinson, Lyman K.; Wise, Stephen A.

2001-01-01

Archiving biological and environmental samples for retrospective analysis is a major component of systematic environmental monitoring. The long-term storage of carefully selected, representative samples in an environmental specimen bank is an important complement to the real-time monitoring of the environment. These archived samples permit:The use of subsequently developed innovative analytical technology that was not available at the time the samples were archived, for clear state-of-art identification an~ quantification of analytes of interest,The identification and quantification of analytes that are of subsequent interest but that were not of interest at the time the samples were archived, andThe comparison of present and past analytical techniques and values, providing continued credibility of past analytical values, and allowing flexibility in environmental monitoring programs.Seabirds, including albatrosses, pelicans, cormorants, terns, kittiwakes, murres, guillemots, and puffins spend most of their lives at sea and have special adaptations for feeding in the marine environment, including the ability to excrete the excess salt obtained from ingesting seawater. Many species nest in dense groups (colonies) on steep, precipitous sea-cliffs and headlands.Seabirds are long-lived and slow to mature. They occupy high positions in the marine food web and are considered sensitive indicators for the marine environment (prey includes krill, small fish, and squid). Breeding success, timing of nesting, diets, and survival rates may provide early indications of changing environmental conditions (e.g., see Hatch et aI., 1993). Chemical analysis of seabird tissues, including egg contents, can be particularly useful in determining whether contaminants (and potential biological effects) associated with human industrial activities, such as offshore petroleum and mineral exploration and development, are accumulating in marine environments. The collection and archival of seabird

How do generalized jamming transitions affect collective migration in confluent tissues?

Science.gov (United States)

Manning, M. Lisa

Recent experiments have demonstrated that tissues involved in embryonic development, lung function, wound healing, and cancer progression are close to fluid-to-solid, or ``jamming'' transitions. Theoretical models for confluent 2D tissues have also been shown to exhibit continuous rigidity transitions. However, in vivobiological systems can differ in significant ways from the simple 2D models. For example, many tissues are three-dimensional, mechanically heterogeneous, and/or composed of mechanosensitive cells interspersed with extracellular matrix. We have extended existing models for confluent tissues to capture these features, and we find interesting predictions for collective cell motion that are ultimately related to an underlying generalized jamming transition. For example, in 2D, we find that heterogeneous mixtures of cells spontaneously self-organize into rigid regions of stiffer cells interspersed with string-like groups of soft cells, reminiscent of cellular streaming seen in cancer. We also find that alignment interactions (of the sort often explored in self-propelled particle models) alter the transition and generate interesting flocked liquid and flocked solid collective migration patterns. Our model predicts that 3D tissues also exhibit a jamming transition governed by cell shape, as well as history-dependent aging, and we are currently exploring whether ECM-like interactions in 3D models might help explain compressional stiffening seen in experiments on human tissue.

Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.

Directory of Open Access Journals (Sweden)

Xi Chen

Full Text Available The prognosis of colorectal cancer (CRC stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.

Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA

Directory of Open Access Journals (Sweden)

Kevin Washetine

2018-06-01

Full Text Available Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability. The conservation of samples at room temperature (RT by duplication can facilitate their protection. We describe a security system for the collection of non-small cell lung cancers (NSCLC stored in the biobank of the Nice Hospital Center, France, by duplication and conservation of lyophilized (dried, encapsulated DNA kept at RT. Therefore, three frozen tissue collections from non-smoking, early stage and sarcomatoid carcinoma NSCLC patients were selected for this study. DNA was extracted, lyophilized and encapsulated at RT under anoxic conditions using the DNAshell technology. In total, 1974 samples from 987 patients were encapsulated. Six and two capsules from each sample were stored in the biobanks of the Nice and Grenoble (France Hospitals, respectively. In conclusion, DNA maintained at RT allows for the conservation, duplication and durability of collections of interest stored in biobanks. This is a low-cost and safe technology that requires a limited amount of space and has a low environmental impact.

Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA.

Science.gov (United States)

Washetine, Kevin; Kara-Borni, Mehdi; Heeke, Simon; Bonnetaud, Christelle; Félix, Jean-Marc; Ribeyre, Lydia; Bence, Coraline; Ilié, Marius; Bordone, Olivier; Pedro, Marine; Maitre, Priscilla; Tanga, Virginie; Gormally, Emmanuelle; Mossuz, Pascal; Lorimier, Philippe; Marquette, Charles Hugo; Mouroux, Jérôme; Cohen, Charlotte; Lassalle, Sandra; Long-Mira, Elodie; Clément, Bruno; Dagher, Georges; Hofman, Véronique; Hofman, Paul

2018-06-11

Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability. The conservation of samples at room temperature (RT) by duplication can facilitate their protection. We describe a security system for the collection of non-small cell lung cancers (NSCLC) stored in the biobank of the Nice Hospital Center, France, by duplication and conservation of lyophilized (dried), encapsulated DNA kept at RT. Therefore, three frozen tissue collections from non-smoking, early stage and sarcomatoid carcinoma NSCLC patients were selected for this study. DNA was extracted, lyophilized and encapsulated at RT under anoxic conditions using the DNAshell technology. In total, 1974 samples from 987 patients were encapsulated. Six and two capsules from each sample were stored in the biobanks of the Nice and Grenoble (France) Hospitals, respectively. In conclusion, DNA maintained at RT allows for the conservation, duplication and durability of collections of interest stored in biobanks. This is a low-cost and safe technology that requires a limited amount of space and has a low environmental impact.

Support vector machine classification and validation of cancer tissue samples using microarray expression data.

Science.gov (United States)

Furey, T S; Cristianini, N; Duffy, N; Bednarski, D W; Schummer, M; Haussler, D

2000-10-01

DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and an exploration of the data for mis-labeled or questionable tissue results. We demonstrate the method in detail on samples consisting of ovarian cancer tissues, normal ovarian tissues, and other normal tissues. The dataset consists of expression experiment results for 97,802 cDNAs for each tissue. As a result of computational analysis, a tissue sample is discovered and confirmed to be wrongly labeled. Upon correction of this mistake and the removal of an outlier, perfect classification of tissues is achieved, but not with high confidence. We identify and analyse a subset of genes from the ovarian dataset whose expression is highly differentiated between the types of tissues. To show robustness of the SVM method, two previously published datasets from other types of tissues or cells are analysed. The results are comparable to those previously obtained. We show that other machine learning methods also perform comparably to the SVM on many of those datasets. The SVM software is available at http://www.cs. columbia.edu/ approximately bgrundy/svm.

Water sample-collection and distribution system

Science.gov (United States)

Brooks, R. R.

1978-01-01

Collection and distribution system samples water from six designated stations, filtered if desired, and delivers it to various analytical sensors. System may be controlled by Water Monitoring Data Acquisition System or operated manually.

Characterization Of Core Sample Collected From The Saltstone Disposal Facility

International Nuclear Information System (INIS)

Cozzi, A.; Duncan, A.

2010-01-01

During the month of September 2008, grout core samples were collected from the Saltstone Disposal Facility, Vault 4, cell E. This grout was placed during processing campaigns in December 2007 from Deliquification, Dissolution and Adjustment Batch 2 salt solution. The 4QCY07 Waste Acceptance Criteria sample collected on 11/16/07 represents the salt solution in the core samples. Core samples were retrieved to initiate the historical database of properties of emplaced Saltstone and to demonstrate the correlation between field collected and laboratory prepared samples. Three samples were collected from three different locations. Samples were collected using a two-inch diameter concrete coring bit. In April 2009, the core samples were removed from the evacuated sample container, inspected, transferred to PVC containers, and backfilled with nitrogen. Samples furthest from the wall were the most intact cylindrically shaped cored samples. The shade of the core samples darkened as the depth of coring increased. Based on the visual inspection, sample 3-3 was selected for all subsequent analysis. The density and porosity of the Vault 4 core sample, 1.90 g/cm 3 and 59.90% respectively, were comparable to values achieved for laboratory prepared samples. X-ray diffraction analysis identified phases consistent with the expectations for hydrated Saltstone. Microscopic analysis revealed morphology features characteristic of cementitious materials with fly ash and calcium silicate hydrate gel. When taken together, the results of the density, porosity, x-ray diffraction analysis and microscopic analysis support the conclusion that the Vault 4, Cell E core sample is representative of the expected waste form.

Assessing human error during collecting a hydrocarbon sample of ...

African Journals Online (AJOL)

This paper reports the assessment method of the hydrocarbon sample collection standard operation procedure (SOP) using THERP. The Performance Shaping Factors (PSF) from THERP analyzed and assessed the human errors during collecting a hydrocarbon sample of a petrochemical refinery plant. Twenty-two ...

Scientific guidelines for preservation of samples collected from Mars

International Nuclear Information System (INIS)

Gooding, J.L.

1990-04-01

The maximum scientific value of Martian geologic and atmospheric samples is retained when the samples are preserved in the conditions that applied prior to their collection. Any sample degradation equates to loss of information. Based on detailed review of pertinent scientific literature, and advice from experts in planetary sample analysis, number values are recommended for key parameters in the environmental control of collected samples with respect to material contamination, temperature, head-space gas pressure, ionizing radiation, magnetic fields, and acceleration/shock. Parametric values recommended for the most sensitive geologic samples should also be adequate to preserve any biogenic compounds or exobiological relics

Experimental and Sampling Design for the INL-2 Sample Collection Operational Test

Energy Technology Data Exchange (ETDEWEB)

Piepel, Gregory F.; Amidan, Brett G.; Matzke, Brett D.

2009-02-16

This report describes the experimental and sampling design developed to assess sampling approaches and methods for detecting contamination in a building and clearing the building for use after decontamination. An Idaho National Laboratory (INL) building will be contaminated with BG (Bacillus globigii, renamed Bacillus atrophaeus), a simulant for Bacillus anthracis (BA). The contamination, sampling, decontamination, and re-sampling will occur per the experimental and sampling design. This INL-2 Sample Collection Operational Test is being planned by the Validated Sampling Plan Working Group (VSPWG). The primary objectives are: 1) Evaluate judgmental and probabilistic sampling for characterization as well as probabilistic and combined (judgment and probabilistic) sampling approaches for clearance, 2) Conduct these evaluations for gradient contamination (from low or moderate down to absent or undetectable) for different initial concentrations of the contaminant, 3) Explore judgment composite sampling approaches to reduce sample numbers, 4) Collect baseline data to serve as an indication of the actual levels of contamination in the tests. A combined judgmental and random (CJR) approach uses Bayesian methodology to combine judgmental and probabilistic samples to make clearance statements of the form "X% confidence that at least Y% of an area does not contain detectable contamination” (X%/Y% clearance statements). The INL-2 experimental design has five test events, which 1) vary the floor of the INL building on which the contaminant will be released, 2) provide for varying the amount of contaminant released to obtain desired concentration gradients, and 3) investigate overt as well as covert release of contaminants. Desirable contaminant gradients would have moderate to low concentrations of contaminant in rooms near the release point, with concentrations down to zero in other rooms. Such gradients would provide a range of contamination levels to challenge the sampling

Trace element contamination in feather and tissue samples from Anna’s hummingbirds

Science.gov (United States)

Mikoni, Nicole A.; Poppenga, Robert H.; Ackerman, Joshua T.; Foley, Janet E.; Hazlehurst, Jenny; Purdin, Güthrum; Aston, Linda; Hargrave, Sabine; Jelks, Karen; Tell, Lisa A.

2017-01-01

Trace element contamination (17 elements; Be, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Ba, Hg, Tl, and Pb) of live (feather samples only) and deceased (feather and tissue samples) Anna's hummingbirds (Calypte anna) was evaluated. Samples were analyzed using inductively coupled plasma-mass spectrometry (ICP-MS; 17 elements) and atomic absorption spectrophotometry (Hg only). Mean plus one standard deviation (SD) was considered the benchmark, and concentrations above the mean + 1 SD were considered elevated above normal. Contour feathers were sampled from live birds of varying age, sex, and California locations. In order to reduce thermal impacts, minimal feathers were taken from live birds, therefore a novel method was developed for preparation of low mass feather samples for ICP-MS analysis. The study found that the novel feather preparation method enabled small mass feather samples to be analyzed for trace elements using ICP-MS. For feather samples from live birds, all trace elements, with the exception of beryllium, had concentrations above the mean + 1 SD. Important risk factors for elevated trace element concentrations in feathers of live birds were age for iron, zinc, and arsenic, and location for iron, manganese, zinc, and selenium. For samples from deceased birds, ICP-MS results from body and tail feathers were correlated for Fe, Zn, and Pb, and feather concentrations were correlated with renal (Fe, Zn, Pb) or hepatic (Hg) tissue concentrations. Results for AA spectrophotometry analyzed samples from deceased birds further supported the ICP-MS findings where a strong correlation between mercury concentrations in feather and tissue (pectoral muscle) samples was found. These study results support that sampling feathers from live free-ranging hummingbirds might be a useful, non-lethal sampling method for evaluating trace element exposure and provides a sampling alternative since their small body size limits traditional sampling of blood and tissues. The

Collection and preparation of samples for gamma spectrometry

International Nuclear Information System (INIS)

Pan Jingquan

1994-01-01

The paper presents the basic principles of sample collection and preparation: setting up unified sampling program, methods and procedures, sample packing, transportation and storage, determination of sample quantity, sample pretreatment and preparation of samples to be analysed, etc. for gamma spectrometry. And the paper also describes briefly the main methods and special issues of sampling and preparation for the same environmental and biological samples, such as, air, water, grass, soil and foods

Coexistence of Epstein-Barr virus and Parvovirus B19 in tonsillar tissue samples: quantitative measurement by real-time PCR.

Science.gov (United States)

Sahiner, Fatih; Gümral, Ramazan; Yildizoğlu, Üzeyir; Babayiğit, Mustafa Alparslan; Durmaz, Abdullah; Yiğit, Nuri; Saraçli, Mehmet Ali; Kubar, Ayhan

2014-08-01

In this study, we aimed to investigate the presence and copy number of six different viruses in tonsillar tissue samples removed surgically because of chronic recurrent tonsillitis or chronic obstructive tonsillar hypertrophy. In total, 56 tissue samples (tonsillar core) collected from 44 children and 12 adults were included in this study. The presence of viruses was investigated using a new TaqMan-based quantitative real-time PCR assay. Of the 56 tissue samples, 67.9% (38/56) were positive for at least one of the six viruses. Epstein-Barr virus was the most frequently detected virus, being found in 53.6% (30/56), followed by human Parvovirus B19 21.4% (12/56), human adenovirus 12.5% (7/56), human Cytomegalovirus 5.4% (3/56), BK polyomavirus 1.8% (1/56), and Herpes simplex virus 1.8% (1/56). Precancerous or cancerous changes were not detected in the tonsillar tissue samples by pathologic examination, whereas lymphoid hyperplasia was observed in 24 patients. In contrast to other viruses, B19 virus was present in high copy number in tonsillar tissues. The rates of EBV and B19 virus with high copy number (>500.000 copies/ml) were higher in children than in adults, and a positive relationship was also found between the presence of EBV and the presence of B19 virus with high copy number (P=0.037). It is previously reported that some viral agents are associated with different chronic tonsillar pathologies. In the present study, the presence of B19 virus in tonsillar core samples was investigated quantitatively for the first time, and our data suggests that EBV infections could be associated with B19 virus infections or could facilitate B19 virus replication. However, further detailed studies are needed to clarify this observation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Fieldwork and catalogue of samples collected in Polan, September 1995

Energy Technology Data Exchange (ETDEWEB)

Poulsen, N.; Drewniak, A.; Glowniak, E.; Ineson, J.; Matyja, B.A.; Merta, T.; Wierzbowski, A.

1995-12-31

This report lists the collection of samples taken during the field work of the EFP-95 Project, named `The Polish Middle to Late Jurassic Epicratonic basin, stratigraphy, facies and basin history` (short title: Jurrasic basin study, Poland) in Poland, August 7-20, 1995. The samples were collected for palynological studies, and/or sedimentaological studies, and/or source rock studies, and/or reservoir rock characteristics. Prepared samples (slides etc.) are stored in the collections of the GEUS, and remaining rock-material at the store of the GEUS. Field work with collection of samples for palynological studies has been carried earlier in 1988 and at the Oxfordian and Kimmeridgian Joint Working Groups Meeting 1992. (au)

Locating tissue collections in tissue economies--deriving value from biomedical research

DEFF Research Database (Denmark)

Tupasela, Aaro Mikael

2006-01-01

sample collections are challenged by varying conceptions of value, as well as structural factors that relate to the combination of different public population information systems in the Finnish research system. Such challenges reflect a tension in the economic aspirations of the ideology of the knowledge...

Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review

Science.gov (United States)

Dong, Yonghui; Li, Bin; Malitsky, Sergey; Rogachev, Ilana; Aharoni, Asaph; Kaftan, Filip; Svatoš, Aleš; Franceschi, Pietro

2016-01-01

Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites. PMID:26904042

Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review.

Science.gov (United States)

Dong, Yonghui; Li, Bin; Malitsky, Sergey; Rogachev, Ilana; Aharoni, Asaph; Kaftan, Filip; Svatoš, Aleš; Franceschi, Pietro

2016-01-01

Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites.

A method for the determination of potassium concentration in organic tissue samples

International Nuclear Information System (INIS)

Maciel, A.C.A.

1976-12-01

An original method has been developed to detect small variations of potassium in several samples of organic tissue. These variations are relative to elements that are biologically representative, such as carbon, oxygen, and nitrogen. The samples are irradiated with a beam of protons from a Van de Graaff accelerator (4MV). Vacancies are created in the K-shell of potassium, and x-rays are emitted when these vacancies are filled with outer electrons. These X-rays and the protons elastically scattered by the nuclei of carbon, nitrogen and oxygen are detected and their energy spectra are analysed by computer programs especially elaborated for this purpose. A technique for routine preparation of samples in the laboratory was developed including the production of aluminum support layers, and the preparation of organic tissue samples with a low temperature microtome. The unique features of this method are that it does not destroy the tissue, permitting further analysis with the microscope, and the normalization of the amount of potassium using other elements (C,O,N) instead of the total mass of the sample. (Author) [pt

Telomere length in normal and neoplastic canine tissues.

Science.gov (United States)

Cadile, Casey D; Kitchell, Barbara E; Newman, Rebecca G; Biller, Barbara J; Hetler, Elizabeth R

2007-12-01

To determine the mean telomere restriction fragment (TRF) length in normal and neoplastic canine tissues. 57 solid-tissue tumor specimens collected from client-owned dogs, 40 samples of normal tissue collected from 12 clinically normal dogs, and blood samples collected from 4 healthy blood donor dogs. Tumor specimens were collected from client-owned dogs during diagnostic or therapeutic procedures at the University of Illinois Veterinary Medical Teaching Hospital, whereas 40 normal tissue samples were collected from 12 control dogs. Telomere restriction fragment length was determined by use of an assay kit. A histologic diagnosis was provided for each tumor by personnel at the Veterinary Diagnostic Laboratory at the University of Illinois. Mean of the mean TRF length for 44 normal samples was 19.0 kilobases (kb; range, 15.4 to 21.4 kb), and the mean of the mean TRF length for 57 malignant tumors was 19.0 kb (range, 12.9 to 23.5 kb). Although the mean of the mean TRF length for tumors and normal tissues was identical, tumor samples had more variability in TRF length. Telomerase, which represents the main mechanism by which cancer cells achieve immortality, is an attractive therapeutic target. The ability to measure telomere length is crucial to monitoring the efficacy of telomerase inhibition. In contrast to many other mammalian species, the length of canine telomeres and the rate of telomeric DNA loss are similar to those reported in humans, making dogs a compelling choice for use in the study of human anti-telomerase strategies.

Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis

Science.gov (United States)

Lunny, Carole; Taylor, Darlene; Hoang, Linda; Wong, Tom; Gilbert, Mark; Lester, Richard; Krajden, Mel; Ogilvie, Gina

2015-01-01

Background The increases in STI rates since the late 1990s in Canada have occurred despite widespread primary care and targeted public health programs and in the setting of universal health care. More innovative interventions are required that would eliminate barriers to STI testing such as internet-based or mail-in home and community service testing for patients that are hard to reach, who refuse to go for clinician-based testing, or who decline an examination. Jurisdictions such as New Zealand and some American states currently use self-collected sampling, but without the required evidence to determine whether self-collected specimens are as accurate as clinician-collected specimens in terms of chlamydia and gonorrhea diagnostic accuracy. The objective of the review is to compare self-collected vaginal, urine, pharyngeal and rectal samples to our reference standard - clinician-collected cervical, urethral, pharyngeal and rectal sampling techniques to identify a positive specimen using nucleic acid amplification test assays. Methods The hierarchical summary receiver operating characteristic and the fixed effect models were used to assess the accuracy of comparable specimens that were collected by patients compared to clinicians. Sensitivity and specificity estimates with 95% confidence intervals (CI) were reported as our main outcome measures. Findings We included 21 studies based on over 6100 paired samples. Fourteen included studies examined chlamydia only, 6 compared both gonorrhea and chlamydia separately in the same study, and one examined gonorrhea. The six chlamydia studies comparing self-collection by vaginal swab to a clinician-collected cervical swab had the highest sensitivity (92%, 95% CI 87-95) and specificity (98%, 95% CI 97-99), compared to other specimen-types (urine/urethra or urine/cervix). Six studies compared urine self-samples to urethra clinician-collected samples in males and produced a sensitivity of 88% (95% CI 83-93) and a specificity of

Acceptability of self-collected versus provider-collected sampling for HPV DNA testing among women in rural El Salvador.

Science.gov (United States)

Rosenbaum, Alan J; Gage, Julia C; Alfaro, Karla M; Ditzian, Lauren R; Maza, Mauricio; Scarinci, Isabel C; Felix, Juan C; Castle, Philip E; Villalta, Sofia; Miranda, Esmeralda; Cremer, Miriam L

2014-08-01

To determine the acceptability of self-collected versus provider-collected sampling among women participating in public sector HPV-based cervical cancer screening in El Salvador. Two thousand women aged 30-49 years underwent self-collected and provider-collected sampling with careHPV between October 2012 and March 2013 (Qiagen, Gaithersburg, MD, USA). After sample collection, a random sample of women (n=518) were asked about their experience. Participants were questioned regarding sampling method preference, previous cervical cancer screening, HPV and cervical cancer knowledge, HPV risk factors, and demographic information. All 518 women approached to participate in this questionnaire study agreed and were enrolled, 27.8% (142 of 511 responding) of whom had not received cervical cancer screening within the past 3 years and were considered under-screened. Overall, 38.8% (n=201) preferred self-collection and 31.9% (n=165) preferred provider collection. Self-collection preference was associated with prior tubal ligation, HPV knowledge, future self-sampling preference, and future home-screening preference (P<0.05). Reasons for self-collection preference included privacy/embarrassment, ease, and less pain; reasons cited for provider-collection preference were result accuracy and provider knowledge/experience. Self-sampling was found to be acceptable, therefore screening programs could consider offering this option either in the clinic or at home. Self-sampling at home may increase coverage in low-resource countries and reduce the burden that screening places upon clinical infrastructure. Copyright © 2014 International Federation of Gynecology and Obstetrics. All rights reserved.

Benign mural nodules within fluid collections at MRI after soft-tissue sarcoma resection.

Science.gov (United States)

Lantos, Joshua E; Hwang, Sinchun; Panicek, David M

2014-06-01

The purpose of this study was to determine the prevalence and clinical significance of nodules within fluid collections on MRI after surgical resection of soft-tissue sarcoma. This retrospective study included 175 patients who underwent resection of primary soft-tissue sarcoma and whose postoperative MRI reports mentioned fluid. Images were reviewed to determine the presence of fluid collections of 1 cm or greater in diameter in the surgical bed and any nodule (measuring ≥ 0.7 cm) within the collection. Signal intensity and characteristics of each collection and rim and presence of septa or blood products were recorded. Size, signal intensity, and contrast enhancement of nodules were reviewed. Nodules were classified as benign or malignant on the basis of histologic results or clinical or MRI follow-up. Fluid collections were present in 75 patients. Of those, 45 collections (60%) showed homogeneous fluid signal intensity and 30 (40%) were heterogeneous; septa were present in 45 (60%) and blood products in 12 (16%). Most collections showed a thin rim (59%) and rim enhancement (88%). Nodules were present along the inner wall of six (8%) collections. Four (66%) nodules enhanced and two (33%) were T1 hyperintense. At follow-up MRI, two nodules were stable in size, one decreased, and three resolved. Nodules in three patients were biopsied; all were benign. Two other patients had no recurrence at follow-up, and another died at 3 months. A nodule within a postoperative fluid collection at MRI after soft-tissue sarcoma resection generally does not represent tumor recurrence; short-interval follow-up MRI is recommended rather than immediate biopsy.

Evaluation of standard methods for collecting and processing fuel moisture samples

Science.gov (United States)

Sally M. Haase; José Sánchez; David R. Weise

2016-01-01

A variety of techniques for collecting and processing samples to determine moisture content of wildland fuels in support of fire management activities were evaluated. The effects of using a chainsaw or handsaw to collect samples of largediameter wood, containers for storing and transporting collected samples, and quick-response ovens for estimating moisture content...

Effect of soil and water environment on typeability of PowerPlex Y (Promega) in selected tissue samples.

Science.gov (United States)

Niemcunowicz-Janica, Anna; Pepinski, Witold; Janica, Jacek Robert; Skawronska, Malgorzata; Janica, Jerzy; Koc-Zorawska, Ewa; Stolyszewski, Ireneusz

2007-01-01

In cases of decomposed bodies Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability PowerPlex Y (Promega) loci in tissue material stored in water and soil environment. Tissue material was collected during autopsies of five persons aged 20-30 years with time of death determined within the limit of 14 hours. Heart muscle, liver and lung specimens were stored in pond water, sea water, sand and peat soil. DNA was extracted by organic method from tissue samples collected in 7-day intervals. Liver specimens were typeable in all PowerPlex Y loci within 100 days of storage in pond water with gradual decline at DYS392 in sea water. Heart muscle specimens stored in pond water exhibited allelic loss at DYS19, DYS385, DYS389II and DYS392, while all loci were typeable in sea water stored samples. For lung specimens allelic loss was noted throughout the profile. Storage of liver specimens in peat soil for more than 14 days resulted in allelic drop-out, and after 21 days no profiles were typeable. Heart muscle specimens were typeable in all PowerPlex Y systems after 35-day storage in sand, while allelic drop-out and subsequent lack of profiles were noted after 14 and 35 days respectively. Lung specimens stored in garden soil exhibited allelic drop-out and subsequent lack of profiles after 7 and 21 days, respectively. All PowerPlex Y loci were typeable in the latter material in sand up to day 35 with gradual decline of longer amplicons (DYS19, DYS385, DYS389II and DYS392).

Effect of soil and water environment on typeability of PowerPlex Y (Promega in selected tissue samples.

Directory of Open Access Journals (Sweden)

Ewa Koc-Zorawska

2008-01-01

Full Text Available In cases of decomposed bodies Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability PowerPlex Y (Promega loci in tissue material stored in water and soil environment. Tissue material was collected during autopsies of five persons aged 20-30 years with time of death determined within the limit of 14 hours. Heart muscle, liver and lung specimens were stored in pond water, sea water, sand and peat soil. DNA was extracted by organic method from tissue samples collected in 7-day intervals. Liver specimens were typeable in all PowerPlex Y loci within 100 days of storage in pond water with gradual decline at DYS392 in sea water. Heart muscle specimens stored in pond water exhibited allelic loss at DYS19, DYS385, DYS389II and DYS392, while all loci were typeable in sea water stored samples. For lung specimens allelic loss was noted throughout the profile. Storage of liver specimens in peat soil for more than 14 days resulted in allelic drop-out, and after 21 days no profiles were typeable. Heart muscle specimens were typeable in all PowerPlex Y systems after 35-day storage in sand, while allelic drop-out and subsequent lack of profiles were noted after 14 and 35 days respectively. Lung specimens stored in garden soil exhibited allelic drop-out and subsequent lack of profiles after 7 and 21 days, respectively. All PowerPlex Y loci were typeable in the latter material in sand up to day 35 with gradual decline of longer amplicons (DYS19, DYS385, DYS389II and DYS392.

Curating NASA's Past, Present, and Future Astromaterial Sample Collections

Science.gov (United States)

Zeigler, R. A.; Allton, J. H.; Evans, C. A.; Fries, M. D.; McCubbin, F. M.; Nakamura-Messenger, K.; Righter, K.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (hereafter JSC curation) is responsible for curating all of NASA's extraterrestrial samples. JSC presently curates 9 different astromaterials collections in seven different clean-room suites: (1) Apollo Samples (ISO (International Standards Organization) class 6 + 7); (2) Antarctic Meteorites (ISO 6 + 7); (3) Cosmic Dust Particles (ISO 5); (4) Microparticle Impact Collection (ISO 7; formerly called Space-Exposed Hardware); (5) Genesis Solar Wind Atoms (ISO 4); (6) Stardust Comet Particles (ISO 5); (7) Stardust Interstellar Particles (ISO 5); (8) Hayabusa Asteroid Particles (ISO 5); (9) OSIRIS-REx Spacecraft Coupons and Witness Plates (ISO 7). Additional cleanrooms are currently being planned to house samples from two new collections, Hayabusa 2 (2021) and OSIRIS-REx (2023). In addition to the labs that house the samples, we maintain a wide variety of infra-structure facilities required to support the clean rooms: HEPA-filtered air-handling systems, ultrapure dry gaseous nitrogen systems, an ultrapure water system, and cleaning facilities to provide clean tools and equipment for the labs. We also have sample preparation facilities for making thin sections, microtome sections, and even focused ion-beam sections. We routinely monitor the cleanliness of our clean rooms and infrastructure systems, including measurements of inorganic or organic contamination, weekly airborne particle counts, compositional and isotopic monitoring of liquid N2 deliveries, and daily UPW system monitoring. In addition to the physical maintenance of the samples, we track within our databases the current and ever changing characteristics (weight, location, etc.) of more than 250,000 individually numbered samples across our various collections, as well as more than 100,000 images, and countless "analog" records that record the sample processing records of each individual sample. JSC Curation is co-located with JSC

Pattern of somatostatin receptors expression in normal and bladder cancer tissue samples.

Science.gov (United States)

Karavitakis, Markos; Msaouel, Pavlos; Michalopoulos, Vassilis; Koutsilieris, Michael

2014-06-01

Known risks factors for bladder cancer progression and recurrence are limited regarding their prognostic ability. Therefore identification of molecular determinants of disease progression could provide with more specific prognostic information and could be translated into new approaches for biomarker development. In the present study we evaluated, the expression patterns of somatostatin receptors 1-5 (SSTRs) in normal and tumor bladder tissues. The expression of SSTR1-5 was characterized in 45 normal and bladder cancer tissue samples using reverse transcriptase-polymerase chain reaction (RT-PCR). SSTR1 was expressed in 24 samples, SSTR2 in 15, SSTR3 in 23, SSTR4 in 16 and SSTR5 in all but one sample. Bladder cancer tissue samples expressed lower levels of SSTR3. Co-expression of SSTRs was associated with superficial disease. Our results demonstrate, for the first time, that there is expression of SSTR in normal and bladder cancer urothelium. Further studies are required to evaluate the prognostic and therapeutic significance of these findings. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Sample information - RED | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available type C : Control sample T : Target sample treatment Keyword Treatment keyword Physiology1 Physiological con...Cultivar Tissue stage detail Details of tissue stage stage Keyword Developmental stage other stage Keyword... Other developmental stage tissue Keyword Collected organ other tissue Keyword Othe

Organic analysis of ambient samples collected near Tank 241-C-103: Results from samples collected on May 12, 1994

International Nuclear Information System (INIS)

Clauss, T.W.; Ligotke, M.W.; McVeety, B.D.; Lucke, R.B.; Young, J.S.; McCulloch, M.; Fruchter, J.S.; Goheen, S.C.

1995-06-01

This report describes organic analyses results from ambient samples collected both upwind and through the vapor sampling system (VSS) near Hanford waste storage Tank 241-C-103 (referred to as Tank C-103). The results described here were obtained to support safety and toxicological evaluations. A summary of the results for inorganic and organic analytes is listed. Quantitative results were obtained for organic compounds. Five organic tentatively identified compounds (TICS) were observed above the detection limit of (ca.) 10 ppbv, but standards for most of these were not available at the time of analysis, and the reported concentrations are semiquantitative estimates. In addition, we looked for the 40 standard TO-14 analytes. We observed 39. Of these, only one was observed above the 2-ppbv calibrated instrument detection limit. Dichloromethane was above the detection limits using both methods, but the result from the TO-14 method is traceable to a standard gas mixture and is considered more accurate. Organic analytes were found only in the sample collected through the VSS, suggesting that these compounds were residual contamination from a previous sampling job. Detailed descriptions of the results appear in the text

Measurement of the hyperelastic properties of 44 pathological ex vivo breast tissue samples

International Nuclear Information System (INIS)

O'Hagan, Joseph J; Samani, Abbas

2009-01-01

The elastic and hyperelastic properties of biological soft tissues have been of interest to the medical community. There are several biomedical applications where parameters characterizing such properties are critical for a reliable clinical outcome. These applications include surgery planning, needle biopsy and brachtherapy where tissue biomechanical modeling is involved. Another important application is interpreting nonlinear elastography images. While there has been considerable research on the measurement of the linear elastic modulus of small tissue samples, little research has been conducted for measuring parameters that characterize the nonlinear elasticity of tissues included in tissue slice specimens. This work presents hyperelastic measurement results of 44 pathological ex vivo breast tissue samples. For each sample, five hyperelastic models have been used, including the Yeoh, N = 2 polynomial, N = 1 Ogden, Arruda-Boyce, and Veronda-Westmann models. Results show that the Yeoh, polynomial and Ogden models are the most accurate in terms of fitting experimental data. The results indicate that almost all of the parameters corresponding to the pathological tissues are between two times to over two orders of magnitude larger than those of normal tissues, with C 11 showing the most significant difference. Furthermore, statistical analysis indicates that C 02 of the Yeoh model, and C 11 and C 20 of the polynomial model have very good potential for cancer classification as they show statistically significant differences for various cancer types, especially for invasive lobular carcinoma. In addition to the potential for use in cancer classification, the presented data are very important for applications such as surgery planning and virtual reality based clinician training systems where accurate nonlinear tissue response modeling is required.

Measurement of the hyperelastic properties of 44 pathological ex vivo breast tissue samples

Energy Technology Data Exchange (ETDEWEB)

O' Hagan, Joseph J; Samani, Abbas [Department of Electrical and Computer Engineering, University of Western Ontario, London, ON (Canada)], E-mail: asamani@uwo.ca

2009-04-21

The elastic and hyperelastic properties of biological soft tissues have been of interest to the medical community. There are several biomedical applications where parameters characterizing such properties are critical for a reliable clinical outcome. These applications include surgery planning, needle biopsy and brachtherapy where tissue biomechanical modeling is involved. Another important application is interpreting nonlinear elastography images. While there has been considerable research on the measurement of the linear elastic modulus of small tissue samples, little research has been conducted for measuring parameters that characterize the nonlinear elasticity of tissues included in tissue slice specimens. This work presents hyperelastic measurement results of 44 pathological ex vivo breast tissue samples. For each sample, five hyperelastic models have been used, including the Yeoh, N = 2 polynomial, N = 1 Ogden, Arruda-Boyce, and Veronda-Westmann models. Results show that the Yeoh, polynomial and Ogden models are the most accurate in terms of fitting experimental data. The results indicate that almost all of the parameters corresponding to the pathological tissues are between two times to over two orders of magnitude larger than those of normal tissues, with C{sub 11} showing the most significant difference. Furthermore, statistical analysis indicates that C{sub 02} of the Yeoh model, and C{sub 11} and C{sub 20} of the polynomial model have very good potential for cancer classification as they show statistically significant differences for various cancer types, especially for invasive lobular carcinoma. In addition to the potential for use in cancer classification, the presented data are very important for applications such as surgery planning and virtual reality based clinician training systems where accurate nonlinear tissue response modeling is required.

Measurement of the hyperelastic properties of 44 pathological ex vivo breast tissue samples

Science.gov (United States)

O'Hagan, Joseph J.; Samani, Abbas

2009-04-01

The elastic and hyperelastic properties of biological soft tissues have been of interest to the medical community. There are several biomedical applications where parameters characterizing such properties are critical for a reliable clinical outcome. These applications include surgery planning, needle biopsy and brachtherapy where tissue biomechanical modeling is involved. Another important application is interpreting nonlinear elastography images. While there has been considerable research on the measurement of the linear elastic modulus of small tissue samples, little research has been conducted for measuring parameters that characterize the nonlinear elasticity of tissues included in tissue slice specimens. This work presents hyperelastic measurement results of 44 pathological ex vivo breast tissue samples. For each sample, five hyperelastic models have been used, including the Yeoh, N = 2 polynomial, N = 1 Ogden, Arruda-Boyce, and Veronda-Westmann models. Results show that the Yeoh, polynomial and Ogden models are the most accurate in terms of fitting experimental data. The results indicate that almost all of the parameters corresponding to the pathological tissues are between two times to over two orders of magnitude larger than those of normal tissues, with C11 showing the most significant difference. Furthermore, statistical analysis indicates that C02 of the Yeoh model, and C11 and C20 of the polynomial model have very good potential for cancer classification as they show statistically significant differences for various cancer types, especially for invasive lobular carcinoma. In addition to the potential for use in cancer classification, the presented data are very important for applications such as surgery planning and virtual reality based clinician training systems where accurate nonlinear tissue response modeling is required.

Methods for the collection of subsurface samples during environmental site assessments

International Nuclear Information System (INIS)

Weinstock, E.A.

1996-01-01

This paper discusses numerous sample collection techniques that have been successfully employed during Phase 2 Assessments and presents case histories of their application. Pollutants of concern include PCE and petroleum. The collection of shallow soil samples is described using commercially available hand augers and hand-driven core samplers. These devices are modified with extensions to collect deeper samples from storm drains and leaching pools. The performance of soil gas surveys are described using both hand-driven sample probes and vehicle-mounted, hydraulically driven vapor probes. Once the soil vapor is collected at the ground surface, a sample of the media is either analyzed on-site using a field-operated detection device or delivered to a laboratory for analysis. Application and case histories of the Geoprobe(trademark)sampling system, a form of direct push technology, are described. This device uses vehicle-mounted, hydraulically-driven sample probes. The probe can be advanced to depths as great as 100 feet below grade and can retrieve soil, soil gas and groundwater samples

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

Directory of Open Access Journals (Sweden)

Laura Hewitson

2014-01-01

Full Text Available In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV. Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA, was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR was conducted. The LLMDA technology was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae, Bacteroidaceae, and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.

The presence of enterovirus, adenovirus, and parvovirus B19 in myocardial tissue samples from autopsies

DEFF Research Database (Denmark)

Nielsen, Trine Skov; Hansen, Jakob; Nielsen, Lars Peter

2014-01-01

of adenovirus, enterovirus, and parvovirus B19 (PVB) in myocardial autopsy samples from myocarditis related deaths and in non-inflamed control hearts in an effort to clarify their significance as the causes of myocarditis in a forensic material. METHODS: We collected all autopsy cases diagnosed with myocarditis...... from 1992 to 2010. Eighty-four suicidal deaths with morphologically normal hearts served as controls. Polymerase chain reaction was used for the detection of the viral genomes (adenovirus, enterovirus, and PVB) in myocardial tissue specimens. The distinction between acute and persistent PVB infection...... was made by the serological determination of PVB-specific immunoglobulins M and G. RESULTS: PVB was detected in 33 of 112 (29 %) myocarditis cases and 37 of 84 (44 %) control cases. All of the samples were negative for the presence of adenovirus and enterovirus. Serological evidence of an acute PVB...

Automated MALDI Matrix Coating System for Multiple Tissue Samples for Imaging Mass Spectrometry

Science.gov (United States)

Mounfield, William P.; Garrett, Timothy J.

2012-03-01

Uniform matrix deposition on tissue samples for matrix-assisted laser desorption/ionization (MALDI) is key for reproducible analyte ion signals. Current methods often result in nonhomogenous matrix deposition, and take time and effort to produce acceptable ion signals. Here we describe a fully-automated method for matrix deposition using an enclosed spray chamber and spray nozzle for matrix solution delivery. A commercial air-atomizing spray nozzle was modified and combined with solenoid controlled valves and a Programmable Logic Controller (PLC) to control and deliver the matrix solution. A spray chamber was employed to contain the nozzle, sample, and atomized matrix solution stream, and to prevent any interference from outside conditions as well as allow complete control of the sample environment. A gravity cup was filled with MALDI matrix solutions, including DHB in chloroform/methanol (50:50) at concentrations up to 60 mg/mL. Various samples (including rat brain tissue sections) were prepared using two deposition methods (spray chamber, inkjet). A linear ion trap equipped with an intermediate-pressure MALDI source was used for analyses. Optical microscopic examination showed a uniform coating of matrix crystals across the sample. Overall, the mass spectral images gathered from tissues coated using the spray chamber system were of better quality and more reproducible than from tissue specimens prepared by the inkjet deposition method.

Importance of sampling frequency when collecting diatoms

KAUST Repository

Wu, Naicheng; Faber, Claas; Sun, Xiuming; Qu, Yueming; Wang, Chao; Ivetic, Snjezana; Riis, Tenna; Ulrich, Uta; Fohrer, Nicola

2016-01-01

There has been increasing interest in diatom-based bio-assessment but we still lack a comprehensive understanding of how to capture diatoms’ temporal dynamics with an appropriate sampling frequency (ASF). To cover this research gap, we collected

Report of the First Community Consultation on the Responsible Collection and Use of Samples for Genetic Research, September 25-26, 2000

Energy Technology Data Exchange (ETDEWEB)

Greenberg, Judith H.

2002-05-22

The First Community Consultation on the Responsible Collection and Use of Samples for Genetic Research was held in Bethesda, Maryland, on September 25-26, 2000. The consultation was convened by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH). Approximately 120 individuals participated in the consultation, half from a broad range of communities and populations, and half from government. The participants shared their views and concerns about population- and community-based genetic research, expanding the focus of the meeting from the collection and use of blood or other tissue samples for genetic research to broader issues and concerns about the conduct of genetic research in general with populations and communities.

Protocol for collecting eDNA samples from streams [Version 2.3

Science.gov (United States)

K. J. Carim; T. Wilcox; M. K. Young; K. S. McKelvey; M. K. Schwartz

2015-01-01

Throughout the 2014 field season, we had over two dozen biologist throughout the western US collect over 300 samples for eDNA analysis with paired controls. Control samples were collected by filtering 0.5 L of distilled water. No samples had any evidence of field contamination. This method of sampling verifies the cleanliness of the field equipment, as well as the...

Proteomic analysis of tissue samples in translational breast cancer research

DEFF Research Database (Denmark)

Gromov, Pavel; Moreira, José; Gromova, Irina

2014-01-01

In the last decade, many proteomic technologies have been applied, with varying success, to the study of tissue samples of breast carcinoma for protein expression profiling in order to discover protein biomarkers/signatures suitable for: characterization and subtyping of tumors; early diagnosis...... the translation of basic discoveries into the daily breast cancer clinical practice. In particular, we address major issues in experimental design by reviewing the strengths and weaknesses of current proteomic strategies in the context of the analysis of human breast tissue specimens....

Sample collection and sample analysis plan in support of the 105-C/190-C concrete and soil sampling activities

International Nuclear Information System (INIS)

Marske, S.G.

1996-07-01

This sampling and analysis plan describes the sample collection and sample analysis in support of the 105-C water tunnels and 190-C main pumphouse concrete and soil sampling activities. These analytical data will be used to identify the radiological contamination and presence of hazardous materials to support the decontamination and disposal activities

Sample Preparation of Corn Seed Tissue to Prevent Analyte Relocations for Mass Spectrometry Imaging

Science.gov (United States)

Kim, Shin Hye; Kim, Jeongkwon; Lee, Young Jin; Lee, Tae Geol; Yoon, Sohee

2017-08-01

Corn seed tissue sections were prepared by the tape support method using an adhesive tape, and mass spectrometry imaging (MSI) was performed. The effect of heat generated during sample preparation was investigated by time-of-flight secondary mass spectrometry (TOF-SIMS) imaging of corn seed tissue prepared by the tape support and the thaw-mounted methods. Unlike thaw-mounted sample preparation, the tape support method does not cause imaging distortion because of the absence of heat, which can cause migration of the analytes on the sample. By applying the tape-support method, the corn seed tissue was prepared without structural damage and MSI with accurate spatial information of analytes was successfully performed.

Sample Preparation of Corn Seed Tissue to Prevent Analyte Relocations for Mass Spectrometry Imaging.

Science.gov (United States)

Kim, Shin Hye; Kim, Jeongkwon; Lee, Young Jin; Lee, Tae Geol; Yoon, Sohee

2017-08-01

Corn seed tissue sections were prepared by the tape support method using an adhesive tape, and mass spectrometry imaging (MSI) was performed. The effect of heat generated during sample preparation was investigated by time-of-flight secondary mass spectrometry (TOF-SIMS) imaging of corn seed tissue prepared by the tape support and the thaw-mounted methods. Unlike thaw-mounted sample preparation, the tape support method does not cause imaging distortion because of the absence of heat, which can cause migration of the analytes on the sample. By applying the tape-support method, the corn seed tissue was prepared without structural damage and MSI with accurate spatial information of analytes was successfully performed. Graphical Abstract ᅟ.

Role of differential physical properties in the collective mechanics and dynamics of tissues

Science.gov (United States)

Das, Moumita

Living cells and tissues are highly mechanically sensitive and active. Mechanical stimuli influence the shape, motility, and functions of cells, modulate the behavior of tissues, and play a key role in several diseases. In this talk I will discuss how collective biophysical properties of tissues emerge from the interplay between differential mechanical properties and statistical physics of underlying components, focusing on two complementary tissue types whose properties are primarily determined by (1) the extracellular matrix (ECM), and (2) individual and collective cell properties. I will start with the structure-mechanics-function relationships in articular cartilage (AC), a soft tissue that has very few cells, and its mechanical response is primarily due to its ECM. AC is a remarkable tissue: it can support loads exceeding ten times our body weight and bear 60+ years of daily mechanical loading despite having minimal regenerative capacity. I will discuss the biophysical principles underlying this exceptional mechanical response using the framework of rigidity percolation theory, and compare our predictions with experiments done by our collaborators. Next I will discuss ongoing theoretical work on how the differences in cell mechanics, motility, adhesion, and proliferation in a co-culture of breast cancer cells and healthy breast epithelial cells may modulate experimentally observed differential migration and segregation. Our results may provide insights into the mechanobiology of tissues with cell populations with different physical properties present together such as during the formation of embryos or the initiation of tumors. This work was partially supported by a Cottrell College Science Award.

Oxidant-antioxidant status in tissue samples of oral leukoplakia

Directory of Open Access Journals (Sweden)

Kumar Chandan Srivastava

2014-01-01

Full Text Available Background: Imbalances between the oxidant-antioxidant status have been implicated in the pathogenesis of several diseases, including oral cancer. Majority of oral cancer are preceded by a well-recognized group of pre-malignant lesions. However, only a small fraction of those lesions, undergo malignant transformation. Hence, there is a great need to identify biological markers, which will assist in identifying lesion carrying high-risk. This study aims to evaluate and compare the status of oxidative stress and antioxidant enzymes in tissue samples of patients with various clinicopathological stages of oral pre-malignancy. Materials and Methods: A case control study consisting of 20 new histopathologically proven leukoplakia patients and equal number of age, sex, and habit matched healthy subjects were recruited for this study. Their tissue samples were subjected to evaluation of lipid peroxidation product, thiobarbituric acid reactive substances and antioxidant enzymes, namely, superoxide dismutase (SOD, catalase (CAT, reduced glutathione (GSH, and glutathione peroxidase (GPx using spectrophotometric methods. The data are expressed as mean ± standard deviation. The statistical comparisons were performed by independent Student′s unpaired t-test and one-way analysis of variance. Pearson′s correlation was performed for the biochemical parameters within the group and between the groups. For statistically significant correlations, simple linear regression was performed. P- value < 0.05 was considered statistically significant. Results: Significant reduction in lipid peroxidation (P < 0.001 SOD and CAT (P < 0.001 was observed in the tissue of leukoplakia patients as compared to the healthy controls. On the other hand, GSH and GPx were significantly increased in tumor samples. Conclusion: Reduced lipid peroxidation and increased activity of GSH and GPx provides the suitable environment for the tumor growth and malignant transformation in the later

Quality standards for sample collection in coagulation testing.

Science.gov (United States)

Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Lima-Oliveira, Gabriel; Guidi, Gian Cesare; Favaloro, Emmanuel J

2012-09-01

Preanalytical activities, especially those directly connected with blood sample collection and handling, are the most vulnerable steps throughout the testing process. The receipt of unsuitable samples is commonplace in laboratory practice and represents a serious problem, given the reliability of test results can be adversely compromised following analysis of these specimens. The basic criteria for an appropriate and safe venipuncture are nearly identical to those used for collecting blood for clinical chemistry and immunochemistry testing, and entail proper patient identification, use of the correct technique, as well as appropriate devices and needles. There are, however, some peculiar aspects, which are deemed to be particularly critical when collecting quality specimens for clot-based tests, and these require clearer recognition. These include prevention of prolonged venous stasis, collection of nonhemolyzed specimens, order of draw, and appropriate filling and mixing of the primary collection tubes. All of these important preanalytical issues are discussed in this article, and evidence-based suggestions as well as recommendations on how to obtain a high-quality sample for coagulation testing are also illustrated. We have also performed an investigation aimed to identify variation of test results due to underfilling of primary blood tubes, and have identified a clinically significant bias in test results when tubes are drawn at less than 89% of total fill for activated partial thromboplastin time, less than 78% for fibrinogen, and less than 67% for coagulation factor VIII, whereas prothrombin time and activated protein C resistance remain relatively reliable even in tubes drawn at 67% of the nominal volume. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

A random sampling approach for robust estimation of tissue-to-plasma ratio from extremely sparse data.

Science.gov (United States)

Chu, Hui-May; Ette, Ene I

2005-09-02

his study was performed to develop a new nonparametric approach for the estimation of robust tissue-to-plasma ratio from extremely sparsely sampled paired data (ie, one sample each from plasma and tissue per subject). Tissue-to-plasma ratio was estimated from paired/unpaired experimental data using independent time points approach, area under the curve (AUC) values calculated with the naïve data averaging approach, and AUC values calculated using sampling based approaches (eg, the pseudoprofile-based bootstrap [PpbB] approach and the random sampling approach [our proposed approach]). The random sampling approach involves the use of a 2-phase algorithm. The convergence of the sampling/resampling approaches was investigated, as well as the robustness of the estimates produced by different approaches. To evaluate the latter, new data sets were generated by introducing outlier(s) into the real data set. One to 2 concentration values were inflated by 10% to 40% from their original values to produce the outliers. Tissue-to-plasma ratios computed using the independent time points approach varied between 0 and 50 across time points. The ratio obtained from AUC values acquired using the naive data averaging approach was not associated with any measure of uncertainty or variability. Calculating the ratio without regard to pairing yielded poorer estimates. The random sampling and pseudoprofile-based bootstrap approaches yielded tissue-to-plasma ratios with uncertainty and variability. However, the random sampling approach, because of the 2-phase nature of its algorithm, yielded more robust estimates and required fewer replications. Therefore, a 2-phase random sampling approach is proposed for the robust estimation of tissue-to-plasma ratio from extremely sparsely sampled data.

Mantle biopsy: a technique for nondestructive tissue-sampling of freshwater mussels

Science.gov (United States)

David J. Berg; Wendell R. Haag; Sheldon I. Guttman; James B. Sickel

1995-01-01

Mantle biopsy is a means of obtaining tissue samples for genetic, physiological, and contaminant studies of bivalves; but the effects of this biopsy on survival have not been determined. We describe a simple technique for obtaining such samples from unionacean bivalves and how we compared survival among biopsied and control organisms in field experiments. Survival was...

Quantitative determination of selenium and mercury, and an ICP-MS semi-quantitative scan of other elements in samples of eagle tissues collected from the Pacific Northwest--Summer 2011

Science.gov (United States)

May, Thomas; Walther, Mike; Brumbaugh, William

2013-01-01

Eagle tissues from dead eagle carcasses were collected by U.S. Fish and Wildlife Service personnel at various locations in the Pacific Northwest as part of a study to document the occurrence of metal and metalloid contaminants. A group of 182 eagle tissue samples, consisting of liver, kidney, brain, talon, feather, femur, humerus, and stomach contents, were quantitatively analyzed for concentrations of selenium and mercury by atomic absorption techniques, and for other elements by semi-quantitative scan with an inductively coupled plasma-mass spectrometer. For the various tissue matrices analyzed by an ICP-MS semiquantitative scan, some elemental concentrations (micrograms per gram dry weight) were quite variable within a particular matrix; notable observations were as follows: lead concentrations ranged from 0.2 to 31 in femurs, 0.1 to 29 in humeri, 0.1 to 54 in talons, less than (<) 0.05 to 120 in livers, <0.05 to 34 in kidneys, and 0.05 to 8 in brains; copper concentrations ranged from 5 to 9 in feathers, 8 to 47 in livers, 7 to 43 in kidneys, and 7 to 28 in brains; cadmium concentrations ranged from 0.1 to 10 in kidneys. In stomach contents, concentrations of vanadium ranged from 0.08 to 5, chromium 2 to 34, manganese 1 to 57, copper 2 to 69, arsenic <0.05 to 6, rubidium 1 to 13, and barium <0.5 to 18. Selenium concentrations from highest to lowest based on the matrix mean were as follows: kidney, liver, feather, brain, stomach content, talon, femur, and humerus. For mercury, the highest to lowest concentrations were feather, liver, talon, brain, stomach content, femur, and humerus.

Standardized Method for Measuring Collection Efficiency from Wipe-sampling of Trace Explosives.

Science.gov (United States)

Verkouteren, Jennifer R; Lawrence, Jeffrey A; Staymates, Matthew E; Sisco, Edward

2017-04-10

One of the limiting steps to detecting traces of explosives at screening venues is effective collection of the sample. Wipe-sampling is the most common procedure for collecting traces of explosives, and standardized measurements of collection efficiency are needed to evaluate and optimize sampling protocols. The approach described here is designed to provide this measurement infrastructure, and controls most of the factors known to be relevant to wipe-sampling. Three critical factors (the applied force, travel distance, and travel speed) are controlled using an automated device. Test surfaces are chosen based on similarity to the screening environment, and the wipes can be made from any material considered for use in wipe-sampling. Particle samples of the explosive 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) are applied in a fixed location on the surface using a dry-transfer technique. The particle samples, recently developed to simulate residues made after handling explosives, are produced by inkjet printing of RDX solutions onto polytetrafluoroethylene (PTFE) substrates. Collection efficiency is measured by extracting collected explosive from the wipe, and then related to critical sampling factors and the selection of wipe material and test surface. These measurements are meant to guide the development of sampling protocols at screening venues, where speed and throughput are primary considerations.

78 FR 26639 - Proposed Collection; 60-Day Comment Request: Financial Sustainability of Human Tissue Biobanking...

Science.gov (United States)

2013-05-07

... Comment Request: Financial Sustainability of Human Tissue Biobanking (NCI) Summary: In compliance with the... techniques or other forms of information technology. To Submit Comments and for Further Information: To... this publication. Proposed Collection: Financial Sustainability of Human Tissue Biobanking, 0925-NEW...

A practical tissue sampling method using ordinary paper for molecular detection of infectious bursal disease virus RNA by RT-PCR.

Science.gov (United States)

Maw, Min Thein; Yamaguchi, Tsuyoshi; Kasanga, Christopher J; Terasaki, Kaori; Fukushi, Hideto

2006-12-01

A practical sampling method for bursal tissue using ordinary paper for molecular diagnosis of infectious bursal disease (IBD) was established. IBD virus-infected bursa was directly smeared on chromatography paper, filter paper, or stationery copy paper and was then fixed with absolute ethanol, Tris-HCl-saturated phenol, or phenol:chloroform:isoamyl alcohol (25:24:1). Flinders Technology Associates (FTA) card, which is designed for the collection of biological samples for molecular detection, was also used. After storage at 37 C for up to 30 days, total RNA directly extracted from the tissue fixed on the papers and FTA card were subjected to reverse transcriptase-polymerase chain reaction (RT-PCR) for detection of IBD virus (IBDV) RNA. In addition, the ability of each chemical used in the fixation and the FTA card to inactivate IBDV was evaluated. Regardless of the paper quality, storage period, and fixation method, IBDV RNA was consistently detected in all of the samples. IBDV in the bursal tissue was inactivated with phenol but not with ethanol or the unknown chemicals in FTA card. These results show that ordinary papers sustain the viral RNA, as does FTA card, but phenol fixation is superior to FTA card in inactivating IBDV. The new sampling method using ordinary paper with phenol fixation is safe, inexpensive, simple, and easy, and is thus suitable for conducting a global survey of IBD even where laboratory resources are limited. This practical method should contribute to the control of IBD worldwide.

Sex identification of polar bears from blood and tissue samples

Science.gov (United States)

Amstrup, Steven C.; Garner, G.W.; Cronin, M.A.; Patton, J.C.

1993-01-01

Polar bears (Ursus maritimus) can be adversely affected by hunting and other human perturbations because of low population densities and low reproduction rates. The sustainable take of adult females may be as low as 1.5% of the population. Females and accompanying young are most vulnerable to hunting, and hunters have not consistently reported the sex composition of the harvest, therefore a method to confirm the sexes of polar bears harvested in Alaska is needed. Evidence of the sex of harvested animals is often not available, but blood or other tissue samples often are. We extracted DNA from tissue and blood samples, and amplified segments of zinc finger (ZFX and ZFY) genes from both X and Y chromosomes with the polymerase chain reaction. Digestion of amplified portions of the X chromosome with the restriction enzyme HaeIII resulted in subdivision of the original amplified segment into four smaller fragments. Digestion with HaeIII did not subdivide the original segment amplified from the Y chromosome. The differing fragment sizes produced patterns in gel electrophoresis that distinguished samples from male and female bears 100% of the time. This technique is applicable to the investigation of many wildlife management and research questions.

Self-collected versus clinician-collected sampling for sexually transmitted infections: a systematic review and meta-analysis protocol.

Science.gov (United States)

Taylor, Darlene; Lunny, Carole; Wong, Tom; Gilbert, Mark; Li, Neville; Lester, Richard; Krajden, Mel; Hoang, Linda; Ogilvie, Gina

2013-10-10

Three meta-analyses and one systematic review have been conducted on the question of whether self-collected specimens are as accurate as clinician-collected specimens for STI screening. However, these reviews predate 2007 and did not analyze rectal or pharyngeal collection sites. Currently, there is no consensus on which sampling method is the most effective for the diagnosis of genital chlamydia (CT), gonorrhea (GC) or human papillomavirus (HPV) infection. Our meta-analysis aims to be comprehensive in that it will examine the evidence of whether self-collected vaginal, urine, pharyngeal and rectal specimens provide as accurate a clinical diagnosis as clinician-collected samples (reference standard). Eligible studies include both randomized and non-randomized controlled trials, pre- and post-test designs, and controlled observational studies. The databases that will be searched include the Cochrane Database of Systematic Reviews, Web of Science, Database of Abstracts of Reviews of Effects (DARE), EMBASE and PubMed/Medline. Data will be abstracted independently by two reviewers using a standardized pre-tested data abstraction form. Heterogeneity will be assessed using the Q2 test. Sensitivity and specificity estimates with 95% confidence intervals as well as negative and positive likelihood ratios will be pooled and weighted using random effects meta-analysis, if appropriate. A hierarchical summary receiver operating characteristics curve for self-collected specimens will be generated. This synthesis involves a meta-analysis of self-collected samples (urine, vaginal, pharyngeal and rectal swabs) versus clinician-collected samples for the diagnosis of CT, GC and HPV, the most prevalent STIs. Our systematic review will allow patients, clinicians and researchers to determine the diagnostic accuracy of specimens collected by patients compared to those collected by clinicians in the detection of chlamydia, gonorrhea and HPV.

Phase-Contrast Hounsfield Units of Fixated and Non-Fixated Soft-Tissue Samples

Science.gov (United States)

Willner, Marian; Fior, Gabriel; Marschner, Mathias; Birnbacher, Lorenz; Schock, Jonathan; Braun, Christian; Fingerle, Alexander A.; Noël, Peter B.; Rummeny, Ernst J.; Pfeiffer, Franz; Herzen, Julia

2015-01-01

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissue specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. Furthermore, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results. PMID:26322638

Soil sample collection and analysis for the Fugitive Dust Characterization Study

Science.gov (United States)

Ashbaugh, Lowell L.; Carvacho, Omar F.; Brown, Michael S.; Chow, Judith C.; Watson, John G.; Magliano, Karen C.

A unique set of soil samples was collected as part of the Fugitive Dust Characterization Study. The study was carried out to establish whether or not source profiles could be constructed using novel analytical methods that could distinguish soil dust sources from each other. The soil sources sampled included fields planted in cotton, almond, tomato, grape, and safflower, dairy and feedlot facilities, paved and unpaved roads (both urban and rural), an agricultural staging area, disturbed land with salt buildup, and construction areas where the topsoil had been removed. The samples were collected using a systematic procedure designed to reduce sampling bias, and were stored frozen to preserve possible organic signatures. For this paper the samples were characterized by particle size (percent sand, silt, and clay), dry silt content (used in EPA-recommended fugitive dust emission factors), carbon and nitrogen content, and potential to emit both PM 10 and PM 2.5. These are not the "novel analytical methods" referred to above; rather, it was the basic characterization of the samples to use in comparing analytical methods by other scientists contracted to the California Air Resources Board. The purpose of this paper is to document the methods used to collect the samples, the collection locations, the analysis of soil type and potential to emit PM 10, and the sample variability, both within field and between fields of the same crop type.

Collection of biological samples in forensic toxicology.

Science.gov (United States)

Dinis-Oliveira, R J; Carvalho, F; Duarte, J A; Remião, F; Marques, A; Santos, A; Magalhães, T

2010-09-01

Forensic toxicology is the study and practice of the application of toxicology to the purposes of the law. The relevance of any finding is determined, in the first instance, by the nature and integrity of the specimen(s) submitted for analysis. This means that there are several specific challenges to select and collect specimens for ante-mortem and post-mortem toxicology investigation. Post-mortem specimens may be numerous and can endow some special difficulties compared to clinical specimens, namely those resulting from autolytic and putrefactive changes. Storage stability is also an important issue to be considered during the pre-analytic phase, since its consideration should facilitate the assessment of sample quality and the analytical result obtained from that sample. The knowledge on degradation mechanisms and methods to increase storage stability may enable the forensic toxicologist to circumvent possible difficulties. Therefore, advantages and limitations of specimen preservation procedures are thoroughfully discussed in this review. Presently, harmonized protocols for sampling in suspected intoxications would have obvious utility. In the present article an overview is given on sampling procedures for routinely collected specimens as well as on alternative specimens that may provide additional information on the route and timing of exposure to a specific xenobiotic. Last, but not least, a discussion on possible bias that can influence the interpretation of toxicological results is provided. This comprehensive review article is intented as a significant help for forensic toxicologists to accomplish their frequently overwhelming mission.

Detection of Flavobacterium psychrophilum from fish tissue and water samples by PCR amplification

DEFF Research Database (Denmark)

Wiklund, T.; Madsen, Lone; Bruun, Morten Sichlau

2000-01-01

investigation, the possible detection of Fl. psychrophilum from fish tissue and water samples was examined using nested PCR with DNA probes against a sequence of the 16S rRNA genes. The DNA was extracted using Chelex(R) 100 chelating resin. The primers, which were tested against strains isolated from diseased...... fish, healthy fish, fish farm environments and reference strains, proved to be specific for Fl. psychrophilum. The obtained detection limit of Fl. psychrophilum seeded into rainbow trout brain tissue was 0.4 cfu in the PCR tube, corresponding to 17 cfu mg(-1) brain tissue. The PCR-assay proved...... to be more sensitive than agar cultivation of tissue samples from the brain of rainbow trout injected with Fl. psychrophilum. In non-sterile fresh water seeded with Fl. psychrophilum the detection limit of the PCR- assay was 1.7 cfu in the PCR tube, corresponding to 110 cfu ml(-1) water. The PCR...

Simultaneous sampling of tissue oxygenation and oxygen consumption in skeletal muscle.

Science.gov (United States)

Nugent, William H; Song, Bjorn K; Pittman, Roland N; Golub, Aleksander S

2016-05-01

Under physiologic conditions, microvascular oxygen delivery appears to be well matched to oxygen consumption in respiring tissues. We present a technique to measure interstitial oxygen tension (PISFO2) and oxygen consumption (VO2) under steady-state conditions, as well as during the transitions from rest to activity and back. Phosphorescence Quenching Microscopy (PQM) was employed with pneumatic compression cycling to achieve 1 to 10 Hz sampling rates of interstitial PO2 and simultaneous recurrent sampling of VO2 (3/min) in the exteriorized rat spinotrapezius muscle. The compression pressure was optimized to 120-130 mmHg without adverse effect on the tissue preparation. A cycle of 5s compression followed by 15s recovery yielded a resting VO2 of 0.98 ± 0.03 ml O2/100 cm(3)min while preserving microvascular oxygen delivery. The measurement system was then used to assess VO2 dependence on PISFO2 at rest and further tested under conditions of isometric muscle contraction to demonstrate a robust ability to monitor the on-kinetics of tissue respiration and the compensatory changes in PISFO2 during contraction and recovery. The temporal and spatial resolution of this approach is well suited to studies seeking to characterize microvascular oxygen supply and demand in thin tissues. Copyright © 2015 Elsevier Inc. All rights reserved.

Fluid sample collection and distribution system. [qualitative analysis of aqueous samples from several points

Science.gov (United States)

Brooks, R. L. (Inventor)

1979-01-01

A multipoint fluid sample collection and distribution system is provided wherein the sample inputs are made through one or more of a number of sampling valves to a progressive cavity pump which is not susceptible to damage by large unfiltered particles. The pump output is through a filter unit that can provide a filtered multipoint sample. An unfiltered multipoint sample is also provided. An effluent sample can be taken and applied to a second progressive cavity pump for pumping to a filter unit that can provide one or more filtered effluent samples. The second pump can also provide an unfiltered effluent sample. Means are provided to periodically back flush each filter unit without shutting off the whole system.

Collection and control of tritium bioassay samples at Pantex

International Nuclear Information System (INIS)

Fairrow, N.L.; Ivie, W.E.

1992-01-01

Pantex is the final assembly/disassembly point for US nuclear weapons. The Pantex internal dosimetry section monitors radiation workers once a month for tritium exposure. In order to manage collection and control of the bioassay specimens efficiently, a bar code system for collection of samples was developed and implemented to speed up the process and decrease the number of errors probable when transferring data. In the past, all the bioassay data from samples were entered manually into a computer database. Transferring the bioassay data from the liquid scintillation counter to each individual's dosimetry record required as much as two weeks of concentrated effort

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

Science.gov (United States)

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

2014-05-01

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

Tissue banking in a regional hospital: a promising future concept? First report on fresh frozen tissue banking in a hospital without an integrated institute of pathology.

Science.gov (United States)

von Strauss und Torney, Marco; Güller, Ulrich; Rezaeian, Farid; Brosi, Philippe; Terracciano, Luigi; Zuber, Markus

2012-10-01

Vital tissue provided by fresh frozen tissue banking is often required for genetic tumor profiling and tailored therapies. However, the potential patient benefits of fresh frozen tissue banking are currently limited to university hospitals. The objective of the present pilot study--the first one in the literature--was to evaluate whether fresh frozen tissue banking is feasible in a regional hospital without an integrated institute of pathology. Patients with resectable breast and colon cancer were included in this prospective study. Both malignant and healthy tissue were sampled using isopentan-based snap-freezing 1 h after tumor resection and stored at -80 °C before transfer to the main tissue bank of a University institute of pathology. The initial costs to set up tissue banking were 35,662 US$. Furthermore, the running costs are 1,250 US$ yearly. During the first 13 months, 43 samples (nine samples of breast cancer and 34 samples of colon cancer) were collected from 41 patients. Based on the pathology reports, there was no interference with standard histopathologic analyses due to the sample collection. This is the first report in the literature providing evidence that tissue banking in a regional hospital without an integrated institute of pathology is feasible. The interesting findings of the present pilot study must be confirmed by larger investigations.

Impact Of Tissue Sampling On Accuracy Of Ki67 Immunohistochemistry Evaluation In Breast Cancer

Directory of Open Access Journals (Sweden)

Justinas Besusparis

2016-06-01

The sampling requirements were dependent on the heterogeneity of the biomarker expression. To achieve a coefficient error of 10%, 5-6 cores were needed for homogeneous cases, while 11-12 cores for heterogeneous cases. In mixed tumor population, 8 TMA cores were required. Similarly, to achieve the same accuracy, approximately 4,000 nuclei must be counted when the intra-tumor heterogeneity is mixed/unknown. Tumors at the lower scale of proliferative activity would require larger sampling (10-12 TMA cores, or 5,000 nuclei to achieve the same error measurement results as for highly proliferative tumors. Our data show that optimal tissue sampling for IHC biomarker evaluation is dependent on the heterogeneity of the tissue under study and needs to be determined on a per-use basis. We propose a method that can be applied to determine the TMA sampling strategy for specific biomarkers, tissues and study targets. In addition, our findings highlight the importance of high-capacity computer-based IHC measurement techniques to improve accuracy of the testing.

Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

Science.gov (United States)

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.

High-resolution, 2- and 3-dimensional imaging of uncut, unembedded tissue biopsy samples.

Science.gov (United States)

Torres, Richard; Vesuna, Sam; Levene, Michael J

2014-03-01

Despite continuing advances in tissue processing automation, traditional embedding, cutting, and staining methods limit our ability for rapid, comprehensive visual examination. These limitations are particularly relevant to biopsies for which immediate therapeutic decisions are most necessary, faster feedback to the patient is desired, and preservation of tissue for ancillary studies is most important. The recent development of improved tissue clearing techniques has made it possible to consider use of multiphoton microscopy (MPM) tools in clinical settings, which could address difficulties of established methods. To demonstrate the potential of MPM of cleared tissue for the evaluation of unembedded and uncut pathology samples. Human prostate, liver, breast, and kidney specimens were fixed and dehydrated by using traditional histologic techniques, with or without incorporation of nucleic acid fluorescent stains into dehydration steps. A benzyl alcohol/benzyl benzoate clearing protocol was substituted for xylene. Multiphoton microscopy was performed on a home-built system. Excellent morphologic detail was achievable with MPM at depths greater than 500 μm. Pseudocoloring produced images analogous to hematoxylin-eosin-stained images. Concurrent second-harmonic generation detection allowed mapping of collagen. Subsequent traditional section staining with hematoxylin-eosin did not reveal any detrimental morphologic effects. Sample immunostains on renal tissue showed preservation of normal reactivity. Complete reconstructions of 1-mm cubic samples elucidated 3-dimensional architectural organization. Multiphoton microscopy on cleared, unembedded, uncut biopsy specimens shows potential as a practical clinical tool with significant advantages over traditional histology while maintaining compatibility with gold standard techniques. Further investigation to address remaining implementation barriers is warranted.

Fast egg collection method greatly improves randomness of egg sampling in Drosophila melanogaster

DEFF Research Database (Denmark)

Schou, Mads Fristrup

2013-01-01

When obtaining samples for population genetic studies, it is essential that the sampling is random. For Drosophila, one of the crucial steps in sampling experimental flies is the collection of eggs. Here an egg collection method is presented, which randomizes the eggs in a water column...... and diminishes environmental variance. This method was compared with a traditional egg collection method where eggs are collected directly from the medium. Within each method the observed and expected standard deviations of egg-to-adult viability were compared, whereby the difference in the randomness...... and to obtain a representative collection of genotypes, the method presented here is strongly recommended when collecting eggs from Drosophila....

OSIRIS-REx Touch-and-Go (TAG) Mission Design for Asteroid Sample Collection

Science.gov (United States)

May, Alexander; Sutter, Brian; Linn, Timothy; Bierhaus, Beau; Berry, Kevin; Mink, Ron

2014-01-01

The Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in September 2016 to rendezvous with the near-Earth asteroid Bennu in October 2018. After several months of proximity operations to characterize the asteroid, OSIRIS-REx flies a Touch-And-Go (TAG) trajectory to the asteroid's surface to collect at least 60 g of pristine regolith sample for Earth return. This paper provides mission and flight system overviews, with more details on the TAG mission design and key events that occur to safely and successfully collect the sample. An overview of the navigation performed relative to a chosen sample site, along with the maneuvers to reach the desired site is described. Safety monitoring during descent is performed with onboard sensors providing an option to abort, troubleshoot, and try again if necessary. Sample collection occurs using a collection device at the end of an articulating robotic arm during a brief five second contact period, while a constant force spring mechanism in the arm assists to rebound the spacecraft away from the surface. Finally, the sample is measured quantitatively utilizing the law of conservation of angular momentum, along with qualitative data from imagery of the sampling device. Upon sample mass verification, the arm places the sample into the Stardust-heritage Sample Return Capsule (SRC) for return to Earth in September 2023.

Biobanking of Fresh-Frozen Cancer Tissue: RNA Is Stable Independent of Tissue Type with Less Than 1 Hour of Cold Ischemia.

Science.gov (United States)

Song, Sang Yong; Jun, Jonghyun; Park, Miyeon; Park, Seo Kyu; Choi, Wonju; Park, Kyunghee; Jang, Kee-Taek; Lee, Myoyong

2018-02-01

The effects of preanalytical variables in tissue processing and storage periods on RNA quality of tissues have been well documented in each type of cancer. However, few studies have been performed on a comparative assessment of the impacts across different cancer tissues, even though it is well known that RNase activity is highly variable in various tissue types and RNase-rich tissues have been found to yield low-quality RNA. We investigated the impacts of cold ischemia times and long-term storage on RNA integrity in various types of cancer tissue, which had been fresh-frozen and collected at the Samsung Medical Center Biobank. RNA quality was also evaluated with regard to histopathological variables. We analyzed RNA integrity number (RIN) data, which had been obtained from our quality control (QC) processes over the last 7 years. Approximately 2% of samples were randomly selected and processed to measure RIN quarterly and after 6 years of storage for QC purposes. Fresh-frozen tumor tissues yielded high-quality RNA regardless of tumor type and histopathological features. Up to 1-hour cold ischemia times and up to 6-year storage times did not adversely influence RNA integrity. Only 3 samples showed RIN of <7 out of a total of 396 analyzed tumor tissues. Tissue quality was not adversely affected by long-term storage or limited variations of cold ischemia times. The low-quality samples could be correlated with the structural composition or intratumoral heterogeneity of tissues. The strict application of standardized protocols for tissue collection is the key for high-quality biobanking.

A 'feather-trap' for collecting DNA samples from birds.

Science.gov (United States)

Maurer, Golo; Beck, Nadeena; Double, Michael C

2010-01-01

Genetic analyses of birds are usually based on DNA extracted from a blood sample. For some species, however, obtaining blood samples is difficult because they are sensitive to handling, pose a conservation or animal welfare concern, or evade capture. In such cases, feathers obtained from live birds in the wild can provide an alternative source of DNA. Here, we provide the first description and evaluation of a 'feather-trap', consisting of small strips of double-sided adhesive tape placed close to a nest with chicks, as a simple, inexpensive and minimally invasive method to collect feathers. The feather-trap was tested in tropical conditions on the Australian pheasant coucal (Centropus phasianinus). None of the 12 pairs of coucals on which the feather-trap was used abandoned the nest, and feeding rates did not differ from those of birds not exposed to a feather-trap. On average, 4.2 feathers were collected per trap over 2-5 days and, despite exposure to monsoonal rain, DNA was extracted from 71.4% of samples, albeit at low concentrations. The amount of genomic DNA extracted from each feather was sufficient to reliably genotype individuals at up to five microsatellite loci for parentage analysis. We show that a feather-trap can provide a reliable alternative for obtaining DNA in species where taking blood is difficult. It may also prove useful for collecting feather samples for other purposes, e.g. stable-isotope analysis. © 2009 Blackwell Publishing Ltd.

Clinical evaluation of a Mucorales-specific real-time PCR assay in tissue and serum samples.

Science.gov (United States)

Springer, Jan; Lackner, Michaela; Ensinger, Christian; Risslegger, Brigitte; Morton, Charles Oliver; Nachbaur, David; Lass-Flörl, Cornelia; Einsele, Hermann; Heinz, Werner J; Loeffler, Juergen

2016-12-01

Molecular diagnostic assays can accelerate the diagnosis of fungal infections and subsequently improve patient outcomes. In particular, the detection of infections due to Mucorales is still challenging for laboratories and physicians. The aim of this study was to evaluate a probe-based Mucorales-specific real-time PCR assay (Muc18S) using tissue and serum samples from patients suffering from invasive mucormycosis (IMM). This assay can detect a broad range of clinically relevant Mucorales species and can be used to complement existing diagnostic tests or to screen high-risk patients. An advantage of the Muc18S assay is that it exclusively detects Mucorales species allowing the diagnosis of Mucorales DNA without sequencing within a few hours. In paraffin-embedded tissue samples this PCR-based method allowed rapid identification of Mucorales in comparison with standard methods and showed 91 % sensitivity in the IMM tissue samples. We also evaluated serum samples, an easily accessible material, from patients at risk from IMM. Mucorales DNA was detected in all patients with probable/proven IMM (100 %) and in 29 % of the possible cases. Detection of IMM in serum could enable an earlier diagnosis (up to 21 days) than current methods including tissue samples, which were gained mainly post-mortem. A screening strategy for high-risk patients, which would enable targeted treatment to improve patient outcomes, is therefore possible.

Ground-water sample collection and analysis plan for the ground-water surveillance project

International Nuclear Information System (INIS)

Bryce, R.W.; Evans, J.C.; Olsen, K.B.

1991-12-01

The Pacific Northwest Laboratory performs ground-water sampling activities at the US Department of Energy's (DOE's) Hanford Site in support of DOE's environmental surveillance responsibilities. The purpose of this document is to translate DOE's General Environmental Protection Program (DOE Order 5400.1) into a comprehensive ground-water sample collection and analysis plan for the Hanford Site. This sample collection and analysis plan sets forth the environmental surveillance objectives applicable to ground water, identifies the strategy for selecting sample collection locations, and lists the analyses to be performed to meet those objectives

Biopolymers for Sample Collection, Protection, and Preservation

Science.gov (United States)

2015-05-19

knowledge of sample collection from various matrices is crucial. Recovery and preservation of microorganisms prior to analysis are important...Another method for encapsulating bacteria for use in biodegradation of gasoline involves a complex process using gellan gum (Moslemy et al. 2002). Many...use of acacia gum in preserving microorganisms for extended periods of time without refrigeration (Krumnow et al. 2009; Sorokulova et al. 2008, 2012

Organ or tissue doses, effective dose and collective effective dose from X-ray diagnosis, in Japan

International Nuclear Information System (INIS)

Murayama, Takashi; Nishizawa, Kanae; Noda, Yutaka; Kumamoto, Yoshikazu; Iwai, Kazuo.

1996-01-01

Effective doses and collective effective doses from X-ray diagnostic examinations were calculated on the basis of the frequency of examinations estimated by a nationwide survey and the organ or tissue doses experimentally determined. The average organ or tissue doses were determined with thermoluminescence dosimeters put at various sites of organs or tissues in an adult and a child phantom. Effective doses (effective dose equivalents) were calculated as the sum of the weighted equivalent doses in all the organs or tissues of the body. As the examples of results, the effective doses per radiographic examination were approximately 7 mGy for male, and 9 mGy for female angiocardiography, and about 3 mGy for barium meal. Annual collective effective dose from X-ray diagnostic examinations in 1986 were about 104 x 10 3 person Sv from radiography and 118 x 10 3 person Sv from fluoroscopy, with the total of 222 x 10 3 person Sv. (author)

World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: IV. Tissue collection, processing, and storage in endometriosis research

DEFF Research Database (Denmark)

Fassbender, Amelie; Rahmioglu, Nilufer; Vitonis, Allison F.

2014-01-01

ObjectiveTo harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of human tissues relevant to endometriosis.......ObjectiveTo harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of human tissues relevant to endometriosis....

Evaluation of a novel dried blood spot collection device (HemaSpot™) to test blood samples collected from dogs for antibodies to Leishmania infantum.

Science.gov (United States)

Rosypal, Alexa C; Pick, Leanne D; Hernandez, Jaime O Esquivel; Lindsay, David S

2014-09-15

Collection of blood samples from veterinary and wildlife patients is often challenging because the samples have to be collected on farm or in the wild under various environmental conditions. This poses many technical problems associated with venipuncture materials, their safe use and disposal, transportation and processing of collected samples. Dried blood spot (DBS) sample collection techniques offer a simple and practical alternative to traditional blood collection methods to obtain blood samples from animals for parasite antibody evaluation. The DBS collection devices are compact, simple to use, and are particularly useful for large number of samples. Additionally, DBS samples take up less space and they are easier to transport than traditional venipuncture-collected blood samples. Visceral leishmaniasis (VL) is a potentially fatal parasitic disease of dogs and humans and it is frequently diagnosed by antibody tests. Immunochromatographic tests (ICT) for antibodies to Leishmania infantum are commercially available for dogs and they produce qualitative results in minutes. Measurement of canine antibodies to L. infantum with the ICT using traditional venipuncture has been validated previously, but the use of DBS samples has not been evaluated using this method. The purpose of the present study was to determine the ability of DBS samples to detect antibodies to L. infantum in dogs using a commercial ICT assay. One hundred plasma samples from dogs experimentally infected with the LIVT-1 strain of L. infantum were collected by venipuncture and frozen. Individual samples were thawed, and then 80 μl plasma (2 drops) was aliquotted onto the 8-spoked disk pad on individual DBS sample collection devices (HemaSpot™, Spot-On Sciences, Austin, TX), dried, and stored in the dark at room temperature. After one month and six months, respectively, 2 spokes of the 8 spokes of the disk pad of each DBS sample were removed and eluted in 200 μl PBS. The eluate was used to test

Importance of sampling frequency when collecting diatoms

KAUST Repository

Wu, Naicheng

2016-11-14

There has been increasing interest in diatom-based bio-assessment but we still lack a comprehensive understanding of how to capture diatoms’ temporal dynamics with an appropriate sampling frequency (ASF). To cover this research gap, we collected and analyzed daily riverine diatom samples over a 1-year period (25 April 2013–30 April 2014) at the outlet of a German lowland river. The samples were classified into five clusters (1–5) by a Kohonen Self-Organizing Map (SOM) method based on similarity between species compositions over time. ASFs were determined to be 25 days at Cluster 2 (June-July 2013) and 13 days at Cluster 5 (February-April 2014), whereas no specific ASFs were found at Cluster 1 (April-May 2013), 3 (August-November 2013) (>30 days) and Cluster 4 (December 2013 - January 2014) (<1 day). ASFs showed dramatic seasonality and were negatively related to hydrological wetness conditions, suggesting that sampling interval should be reduced with increasing catchment wetness. A key implication of our findings for freshwater management is that long-term bio-monitoring protocols should be developed with the knowledge of tracking algal temporal dynamics with an appropriate sampling frequency.

On the improvement of blood sample collection at clinical laboratories.

Science.gov (United States)

Grasas, Alex; Ramalhinho, Helena; Pessoa, Luciana S; Resende, Mauricio G C; Caballé, Imma; Barba, Nuria

2014-01-09

Blood samples are usually collected daily from different collection points, such hospitals and health centers, and transported to a core laboratory for testing. This paper presents a project to improve the collection routes of two of the largest clinical laboratories in Spain. These routes must be designed in a cost-efficient manner while satisfying two important constraints: (i) two-hour time windows between collection and delivery, and (ii) vehicle capacity. A heuristic method based on a genetic algorithm has been designed to solve the problem of blood sample collection. The user enters the following information for each collection point: postal address, average collecting time, and average demand (in thermal containers). After implementing the algorithm using C programming, this is run and, in few seconds, it obtains optimal (or near-optimal) collection routes that specify the collection sequence for each vehicle. Different scenarios using various types of vehicles have been considered. Unless new collection points are added or problem parameters are changed substantially, routes need to be designed only once. The two laboratories in this study previously planned routes manually for 43 and 74 collection points, respectively. These routes were covered by an external carrier company. With the implementation of this algorithm, the number of routes could be reduced from ten to seven in one laboratory and from twelve to nine in the other, which represents significant annual savings in transportation costs. The algorithm presented can be easily implemented in other laboratories that face this type of problem, and it is particularly interesting and useful as the number of collection points increases. The method designs blood collection routes with reduced costs that meet the time and capacity constraints of the problem.

Implementation of immunohistochemistry on frozen ear notch tissue samples in diagnosis of bovine viral diarrhea virus in persistently infected cattle

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Bedeković Tomislav

2011-12-01

Full Text Available Abstract Background Bovine viral diarrhea is a contagious disease of domestic and wild ruminants and one of the most economically important diseases in cattle. Bovine viral diarrhea virus belongs to the genus Pestivirus, within the family Flaviviridae. The identification and elimination of the persistently infected animals from herds is the initial step in the control and eradication programs. It is therefore necessary to have reliable methods for diagnosis of bovine viral diarrhea virus. One of those methods is immunohistochemistry. Immunohistochemistry on formalin fixed, paraffin embedded tissue is a routine technique in diagnosis of persistently infected cattle from ear notch tissue samples. However, such technique is inappropriate due to complicated tissue fixation process and it requires more days for preparation. On the contrary, immunohistochemistry on frozen tissue was usually applied on organs from dead animals. In this paper, for the first time, the imunohistochemistry on frozen ear notch tissue samples was described. Findings Seventeen ear notch tissue samples were obtained during the period 2008-2009 from persistently infected cattle. Samples were fixed in liquid nitrogen and stored on -20°C until testing. Ear notch tissue samples from all persistently infected cattle showed positive results with good section quality and possibility to determinate type of infected cells. Conclusions Although the number of samples was limited, this study indicated that immunohistochemistry on formalin fixed paraffin embedded tissue can be successfully replaced with immunohistochemistry on frozen ear notch tissue samples in diagnosis of persistently infected cattle.

Active Collection of Land Cover Sample Data from Geo-Tagged Web Texts

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Dongyang Hou

2015-05-01

Full Text Available Sample data plays an important role in land cover (LC map validation. Traditionally, they are collected through field survey or image interpretation, either of which is costly, labor-intensive and time-consuming. In recent years, massive geo-tagged texts are emerging on the web and they contain valuable information for LC map validation. However, this kind of special textual data has seldom been analyzed and used for supporting LC map validation. This paper examines the potential of geo-tagged web texts as a new cost-free sample data source to assist LC map validation and proposes an active data collection approach. The proposed approach uses a customized deep web crawler to search for geo-tagged web texts based on land cover-related keywords and string-based rules matching. A data transformation based on buffer analysis is then performed to convert the collected web texts into LC sample data. Using three provinces and three municipalities directly under the Central Government in China as study areas, geo-tagged web texts were collected to validate artificial surface class of China’s 30-meter global land cover datasets (GlobeLand30-2010. A total of 6283 geo-tagged web texts were collected at a speed of 0.58 texts per second. The collected texts about built-up areas were transformed into sample data. User’s accuracy of 82.2% was achieved, which is close to that derived from formal expert validation. The preliminary results show that geo-tagged web texts are valuable ancillary data for LC map validation and the proposed approach can improve the efficiency of sample data collection.

Collection and preparation of wet and dry stream-sediment samples

International Nuclear Information System (INIS)

Puchlik, K.

1977-03-01

Lawrence Livermore Laboratory is responsible for the Hydrogeochemistry and Stream Sediment Reconnaissance (HSSR) program for uranium in the seven far western states. The work thus far has concentrated on the arid to semi-arid regions of the West and this paper discusses the collection and preparation of sediment samples in the Basin and Range province. The sample collection and preparation procedures described here may not be applicable to other parts of the far western states or other areas. These procedures also differ somewhat from those used by the other three laboratories involved in the HSSR program

Minimally invasive collection of adipose tissue facilitates the study of eco-physiology in small-bodied mammals

Science.gov (United States)

Jeff Clerc; Theodore J. Weller; Jeffrey B. Schineller; Joseph M. Szewczak; Diana Fisher

2016-01-01

Adipose tissue is the primary fuel storage for vertebrates and is an important component of energy budgets during periods of peak energetic demands. Investigating the composition of adipose tissue can provide information about energetics, migration, reproduction, and other life-history traits. Until now, most field methods for sampling the adipose tissue of...

Pediatric blood sample collection from a pre-existing peripheral intravenous (PIV) catheter.

Science.gov (United States)

Braniff, Heather; DeCarlo, Ann; Haskamp, Amy Corey; Broome, Marion E

2014-01-01

Aiming to minimize pain in a hospitalized child, the purpose of this observational study was to describe characteristics of blood samples collected from pre-existing peripheral intravenous (PIV) catheters in pediatric patients. One hundred and fifty blood samples were reviewed for number of unusable samples requiring a specimen to be re-drawn. Success of the blood draw and prevalence of the loss of the PIV following blood collection was also measured. Findings included one clotted specimen, success rate of 91.3%, and 1.3% of PIVs becoming non-functional after collection. Obtaining blood specimens from a pre-existing PIV should be considered in a pediatric patient. Copyright © 2014 Elsevier Inc. All rights reserved.

Second harmonic sound field after insertion of a biological tissue sample

Science.gov (United States)

Zhang, Dong; Gong, Xiu-Fen; Zhang, Bo

2002-01-01

Second harmonic sound field after inserting a biological tissue sample is investigated by theory and experiment. The sample is inserted perpendicular to the sound axis, whose acoustical properties are different from those of surrounding medium (distilled water). By using the superposition of Gaussian beams and the KZK equation in quasilinear and parabolic approximations, the second harmonic field after insertion of the sample can be derived analytically and expressed as a linear combination of self- and cross-interaction of the Gaussian beams. Egg white, egg yolk, porcine liver, and porcine fat are used as the samples and inserted in the sound field radiated from a 2 MHz uniformly excited focusing source. Axial normalized sound pressure curves of the second harmonic wave before and after inserting the sample are measured and compared with the theoretical results calculated with 10 items of Gaussian beam functions.

Online recovery of radiocesium from soil, tissue paper and plant samples by supercritical fluid extraction

International Nuclear Information System (INIS)

Kanekar, A.S.; Pathak, P.N.; Mohapatra, P.K.

2014-01-01

The feasibility of recovery of radio-cesium from soil, tissue papers, and plant samples has been evaluated by supercritical fluid extraction (SFE) route employing calix(4)arene-mono(crown-6) (CC) dissolved in acetonitrile. These studies showed that quantitative recovery of 137 Cs from soil samples was difficult under the conditions of these studies. However, experiments performed on tissue papers (cellulose matrix) showed quantitative recovery of 137 Cs. On the other hand, 137 Cs recovery from plant samples varied between ∼50 % (for stems) and ∼67.2 % (for leaves) employing 1x10 -3 M CC + 4 M HNO 3 dissolved in acetonitrile. (author)

Spectroscopic analysis of bladder cancer tissues using Fourier transform infrared spectroscopy

Science.gov (United States)

Al-Muslet, Nafie A.; Ali, Essam E.

2012-03-01

Bladder cancer is one of the most common cancers in Africa. It takes several days to reach a diagnosis using histological examinations of specimens obtained by endoscope, which increases the medical expense. Recently, spectroscopic analysis of bladder cancer tissues has received considerable attention as a diagnosis technique due to its sensitivity to biochemical variations in the samples. This study investigated the use of Fourier transform infrared (FTIR) spectroscopy to analyze a number of bladder cancer tissues. Twenty-two samples were collected from 11 patients diagnosed with bladder cancer from different hospitals without any pretreatment. From each patient two samples were collected, one normal and another cancerous. FTIR spectrometer was used to differentiate between normal and cancerous bladder tissues via changes in spectra of these samples. The investigations detected obvious changes in the bands of proteins (1650, 1550 cm-1), lipids (2925, 2850 cm-1), and nucleic acid (1080, 1236 cm-1). The results show that FTIR spectroscopy is promising as a rapid, accurate, nondestructive, and easy to use alternative method for identification and diagnosis of bladder cancer tissues.

A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.

Science.gov (United States)

Bonta, Maximilian; Török, Szilvia; Hegedus, Balazs; Döme, Balazs; Limbeck, Andreas

2017-03-01

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues. Graphical abstract Sample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

Bioavailability and Variability of Cd, Pb, Zn, and Cu Pollution in Soft Tissues and Shell of Saccostrea cucullata Collected from the Coast of Qeshm Island, Persian Gulf, Iran

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Ali Kazemi

2016-07-01

Full Text Available Background: Marine pollution is a global environmental problem that its monitoring by ideal biomonitors is of great importance. Marine organisms, especially mussels, have the ability to accumulate metals from the environment; they can be considered as a biomonitoring agent. Methods: In this study, concentrations of heavy metals were measured in Saccostrea cucullata collected from seven sites on Qeshm Island's Coast. To achieve a digesting sample, each soft tissue was obtained and each of the shell homogeneous powders, 0.8 g and 1 g, respectively, were mixed with 10 mL HNO3 (69% and poured into a PTFE digestion vessel. The prepared samples were evaluated for Cd, Cu, and Zn by using a flame AAS Model 67OG and for Pb by using a graphite furnace AAS. Results: The distributions of metals between soft tissues and shells were compared in each sampling site. For seven sites, Cd, Zn, and Cu levels in soft tissues were higher than in the shells, but Pb level was higher in the shells than in the soft tissues. In addition, the results indicated the coefficient of variation (CV in the soft tissues was lower than the shells for Cd, and in the shells lower than the soft tissues for Pb, whereas the CV values were different in both the soft tissues and shells for Zn and Cu. Conclusion: The results of this study support using these materials in S. cucullata for biomonitoring. Shells are appropriate for monitoring Pb contamination, and the soft tissues are more apt for monitoring Cd, Zn, and Cu contamination.

An Improved Method for Collection of Cerebrospinal Fluid from Anesthetized Mice

DEFF Research Database (Denmark)

Lim, Nastasia K-H; Moestrup, Visse Theresia Skov; Zhang, Xiao

2017-01-01

a technique that improves on current methods of collection to minimize contamination from blood and allow for the abundant collection of CSF (on average 10-15 µL can be collected). This technique can be used with other dissection methods for tissue collection from mice, as it does not impact any tissues......The cerebrospinal fluid (CSF) is a valuable body fluid for analysis in neuroscience research. It is one of the fluids in closest contact with the central nervous system and thus, can be used to analyze the diseased state of the brain or spinal cord without directly accessing these tissues. However......, in mice it is difficult to obtain from the cisterna magna due to its closeness to blood vessels, which often contaminate samples. The area for CSF collection in mice is also difficult to dissect to and often only small samples are obtained (maximum of 5-7 µL or less). This protocol describes in detail...

Genetic Characterization of Echinococcus granulosus from a Large Number of Formalin-Fixed, Paraffin-Embedded Tissue Samples of Human Isolates in Iran

Science.gov (United States)

Rostami, Sima; Torbaghan, Shams Shariat; Dabiri, Shahriar; Babaei, Zahra; Mohammadi, Mohammad Ali; Sharbatkhori, Mitra; Harandi, Majid Fasihi

2015-01-01

Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus, presents an important medical and veterinary problem globally, including that in Iran. Different genotypes of E. granulosus have been reported from human isolates worldwide. This study identifies the genotype of the parasite responsible for human hydatidosis in three provinces of Iran using formalin-fixed paraffin-embedded tissue samples. In this study, 200 formalin-fixed paraffin-embedded tissue samples from human CE cases were collected from Alborz, Tehran, and Kerman provinces. Polymerase chain reaction amplification and sequencing of the partial mitochondrial cytochrome c oxidase subunit 1 gene were performed for genetic characterization of the samples. Phylogenetic analysis of the isolates from this study and reference sequences of different genotypes was done using a maximum likelihood method. In total, 54.4%, 0.8%, 1%, and 40.8% of the samples were identified as the G1, G2, G3, and G6 genotypes, respectively. The findings of the current study confirm the G1 genotype (sheep strain) to be the most prevalent genotype involved in human CE cases in Iran and indicates the high prevalence of the G6 genotype with a high infectivity for humans. Furthermore, this study illustrates the first documented human CE case in Iran infected with the G2 genotype. PMID:25535316

IMPROVEMENT OF METHODS FOR HYDROBIOLOGICAL RESEARCH AND MODIFICATION OF STANDARD TOOLS FOR SAMPLE COLLECTION

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M. M. Aligadjiev

2015-01-01

Full Text Available Aim. The paper discusses the improvement of methods of hydrobiological studies by modifying tools for plankton and benthic samples collecting. Methods. In order to improve the standard methods of hydro-biological research, we have developed tools for sampling zooplankton and benthic environment of the Caspian Sea. Results. Long-term practice of selecting hydrobiological samples in the Caspian Sea shows that it is required to complete the modernization of the sampling tools used to collect hydrobiological material. With the introduction of Azov and Black Sea invasive comb jelly named Mnemiopsis leidyi A. Agassiz to the Caspian Sea there is a need to collect plankton samples without disturbing its integrity. Tools for collecting benthic fauna do not always give a complete picture of the state of benthic ecosystems because of the lack of visual site selection for sampling. Moreover, while sampling by dredge there is a probable loss of the samples, especially in areas with difficult terrain. Conclusion. We propose to modify a small model of Upstein net (applied in shallow water to collect zooplankton samples with an upper inverted cone that will significantly improve the catchability of the net in theCaspian Sea. Bottom sampler can be improved by installing a video camera for visual inspection of the bottom topography, and use sensors to determine tilt of the dredge and the position of the valves of the bucket. 

An integrated sample preparation to determine coccidiostats and emerging Fusarium-mycotoxins in various poultry tissues with LC-MS/MS.

Science.gov (United States)

Jestoi, Marika; Rokka, Mervi; Peltonen, Kimmo

2007-05-01

The usefulness of an existing sample preparation technique used for ionophoric coccidiostats (lasalocid, monensin, salinomycin and narasin) was applied in the analysis of emerging Fusarium-mycotoxins beauvericin (BEA) and enniatins (ENNs) in poultry tissues (liver and meat). Also, maduramicin and liver as a new sample matrix was introduced. The developed methods were validated and applied for the determination of coccidiostats and BEA/ENNs in Finnish poultry tissues in 2004-2005. The validation parameters demonstrated that the integrated sample preparation technique is applicable to the parallel determination of these contaminants in poultry tissues. Of the samples analysed (276 meat and 43 liver), only trace levels of LAS, MON, SAL, NAR and MAD were detected in 7, 3, 5, 6 and 4% of the samples, respectively. Interestingly, for the first time, traces of BEA and ENNs could also be detected in animal tissues. BEA and ENNs A, A1, B and B1 were found in 2, 0.3, 0.6, 4 and 3% of the samples, respectively. The simultaneous presence of coccidiostats and mycotoxins was detected in three turkey samples in 2004.

Attitudes towards biomedical use of tissue sample collections, consent, and biobanks among Finns

DEFF Research Database (Denmark)

Tupasela, Aaro Mikael; Sihvo, Sinikka; Snell, Karolna

2010-01-01

To ascertain the attitudes towards the use of existing diagnostic and research samples, the setting up of a national biobank, and different types of informed consent among Finns. Method: A population survey of 2,400 randomly selected Finns aged 24-65 was conducted at the beginning of 2007....

Distribution of polybrominated diphenyl ethers in Japanese autopsy tissue and body fluid samples.

Science.gov (United States)

Hirai, Tetsuya; Fujimine, Yoshinori; Watanabe, Shaw; Nakano, Takeshi

2012-09-01

Brominated flame retardants are components of many plastics and are used in products such as cars, textiles, televisions, and personal computers. Human exposure to polybrominated diphenyl ether (PBDE) flame retardants has increased exponentially during the last three decades. Our objective was to measure the body burden and distribution of PBDEs and to determine the concentrations of the predominant PBDE congeners in samples of liver, bile, adipose tissue, and blood obtained from Japanese autopsy cases. Tissues and body fluids obtained from 20 autopsy cases were analyzed. The levels of 25 PBDE congeners, ranging from tri- to hexa-BDEs, were assessed. The geometric means of the sum of the concentrations of PBDE congeners having detection frequencies >50 % (ΣPBDE) in the blood, liver, bile, and adipose tissue were 2.4, 2.6, 1.4, and 4.3 ng/g lipid, respectively. The most abundant congeners were BDE-47 and BDE-153, followed by BDE-100, BDE-99, and BDE-28+33. These concentrations of PBDE congeners were similar to other reports of human exposure in Japan but were notably lower than concentrations than those reported in the USA. Significant positive correlations were observed between the concentrations of predominant congeners and ΣPBDE among the samples analyzed. The ΣPBDE concentration was highest in the adipose tissue, but PBDEs were distributed widely among the tissues and body fluids analyzed. The PBDE levels observed in the present study are similar to those reported in previous studies in Japan and significantly lower than those reported in the USA.

Clinical application for the preservation of phospho-proteins through in-situ tissue stabilization

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Ding Wei

2010-11-01

Full Text Available Abstract Background Protein biomarkers will play a pivotal role in the future of personalized medicine for both diagnosis and treatment decision-making. While the results of several pre-clinical and small-scale clinical studies have demonstrated the value of protein biomarkers, there have been significant challenges to translating these findings into routine clinical care. Challenges to the use of protein biomarkers include inter-sample variability introduced by differences in post-collection handling and ex vivo degradation of proteins and protein modifications. Results In this report, we re-create laboratory and clinical scenarios for sample collection and test the utility of a new tissue stabilization technique in preserving proteins and protein modifications. In the laboratory setting, tissue stabilization with the Denator Stabilizor T1 resulted in a significantly higher yield of phospho-protein when compared to standard snap freeze preservation. Furthermore, in a clinical scenario, tissue stabilization at collection resulted in a higher yield of total phospho-protein, total phospho-tyrosine, pErkT202/Y204 and pAktS473 when compared to standard methods. Tissue stabilization did not have a significant effect on other post-translational modifications such as acetylation and glycosylation, which are more stable ex-vivo. Tissue stabilization did decrease total RNA quantity and quality. Conclusion Stabilization at the time of collection offers the potential to better preserve tissue protein and protein modification levels, as well as reduce the variability related to tissue processing delays that are often associated with clinical samples.

Human blood RNA stabilization in samples collected and transported for a large biobank

Science.gov (United States)

2012-01-01

Background The Norwegian Mother and Child Cohort Study (MoBa) is a nation-wide population-based pregnancy cohort initiated in 1999, comprising more than 108.000 pregnancies recruited between 1999 and 2008. In this study we evaluated the feasibility of integrating RNA analyses into existing MoBa protocols. We compared two different blood RNA collection tube systems – the PAXgene™ Blood RNA system and the Tempus™ Blood RNA system - and assessed the effects of suboptimal blood volumes in collection tubes and of transportation of blood samples by standard mail. Endpoints to characterize the samples were RNA quality and yield, and the RNA transcript stability of selected genes. Findings High-quality RNA could be extracted from blood samples stabilized with both PAXgene and Tempus tubes. The RNA yields obtained from the blood samples collected in Tempus tubes were consistently higher than from PAXgene tubes. Higher RNA yields were obtained from cord blood (3 – 4 times) compared to adult blood with both types of tubes. Transportation of samples by standard mail had moderate effects on RNA quality and RNA transcript stability; the overall RNA quality of the transported samples was high. Some unexplained changes in gene expression were noted, which seemed to correlate with suboptimal blood volumes collected in the tubes. Temperature variations during transportation may also be of some importance. Conclusions Our results strongly suggest that special collection tubes are necessary for RNA stabilization and they should be used for establishing new biobanks. We also show that the 50,000 samples collected in the MoBa biobank provide RNA of high quality and in sufficient amounts to allow gene expression analyses for studying the association of disease with altered patterns of gene expression. PMID:22988904

A single lysis solution for the analysis of tissue samples by different proteomic technologies

DEFF Research Database (Denmark)

Gromov, P.; Celis, J.E.; Gromova, I.

2008-01-01

-based proteomics (reverse-phase lysate arrays or direct antibody arrays), allowing the direct comparison of qualitative and quantitative data yielded by these technologies when applied to the same samples. The usefulness of the CLB1 solution for gel-based proteomics was further established by 2D PAGE analysis...... dissease, is driving scientists to increasingly use clinically relevant samples for biomarker and target discovery. Tissues are heterogeneous and as a result optimization of sample preparation is critical for generating accurate, representative, and highly reproducible quantitative data. Although a large...... number of protocols for preparation of tissue lysates has been published, so far no single recipe is able to provide a "one-size fits all" solubilization procedure that can be used to analyse the same lysate using different proteomics technologies. Here we present evidence showing that cell lysis buffer...

Collection and preparation of water samples for hydrogeochemical reconnaissance

International Nuclear Information System (INIS)

Baucom, E.I.; Ferguson, R.B.; Wallace, R.M.

1977-01-01

A method based on ion exchange and neutron activation analysis (NAA) was developed and field-tested to determine uranium over the range 0.02 to 10,000 ppb in natural water using a single procedure. Water samples are filtered in the field using a specially-designed one-liter filter apparatus pressurized to 40 psig with an inert gas. The filtered water is treated with a high purity, mixed cation-anion resin in the hydronium-hydroxide form. All ions are removed from solution under the strong driving force of the neutralization reaction. Anionic, cationic, and natural complexes of uranium can be concentrated with this method. Field tests showed greater than 95 percent recovery of 13 elements analyzed (including greater than 99 percent recovery of uranium) and greater than or equal to 90 percent recovery of 4 other elements. Uranium collected on the resin was quantitatively determined by NAA. Coefficient of variation for sampling plus analysis was less than 20 percent for samples containing more than 0.1 ppb uranium. Advantages of this method include: (1) wide dynamic range, (2) low detection limit for uranium (0.02 ppb), (3) high precision and accuracy, (4) relatively low cost, (5) high-yield recovery from low-level aqueous samples without risk of loss to containers, (6) decreased risk of significant sample contamination compared with other low-level methods, (7) production of stable samples suitable for retrievable storage, and(8) concentration of other ions that can be determined by NAA. This paper presents (1) background regarding development of procedures for sample collection and preparation, (2) results of development programs, (3) description of equipment and field procedures, and (4) preliminary conclusions regarding use of this technology for hydrogeochemical reconnaissance for uranium

Micro-PIXE on thin plant tissue samples in frozen hydrated state: A novel addition to JSI nuclear microprobe

International Nuclear Information System (INIS)

Vavpetič, P.; Pelicon, P.; Vogel-Mikuš, K.; Grlj, N.; Pongrac, P.; Jeromel, L.; Ogrinc, N.; Regvar, M.

2013-01-01

Recently we completed a construction of a cryostat at Jožef Stefan Institute (JSI) nuclear microprobe enabling us to analyze various types of biological samples in frozen hydrated state using micro-PIXE/STIM/RBS. Sample load-lock system was added to our existing setup to enable us to quickly insert a sample holder with frozen hydrated tissue samples onto a cold goniometer head cooled with liquid nitrogen inside the measuring chamber. Cryotome-cut slices of frozen hydrated plant samples were mounted between two thin silicon nitride foils and then attached to the sample holder. Sufficient thermal contact between silicon nitride foils and sample holder must be achieved, as well as between the sample holder and the cold goniometer head inside the measuring chamber to prevent melting of the samples. Matrix composition of frozen hydrated tissue is consisted mostly of ice. Thinning of the sample as well as water evaporation during high vacuum and proton beam exposure was inspected by the measurements with RBS and STIM method simultaneously with micro-PIXE. For first measuring attempts a standard micro-PIXE configuration for tissue mapping was used with proton beam cross section of 1.2 × 1.2 μm 2 and a beam current of 100 pA. The temperature of the cold goniometer head was kept below 130 K throughout the entire proton beam exposure. First measurements of thin plant tissue samples in frozen hydrated state show minute sample degradation during the 10 h period of micro-PIXE measurements

Is tissue CA125 expression in epithelial ovarian adenocarcinoma heterogenic?

DEFF Research Database (Denmark)

Sparholt, Morten H; Høgdall, Claus K; Nedergaard, Lotte

2013-01-01

To evaluate if heterogeneity of tissue cancer antigen 125 (CA125) expression is present in epithelial serous adenocarcinomas. Furthermore, to investigate whether there is a correlation between levels of CA125 tissue expression, serum level of CA125, stage, and grade. A total of 10 patients...... diagnosed with serous ovarian adenocarcinomas were included. Preoperative blood samples were collected to determine serum CA125 levels. Tumor tissue from primary surgery was collected and processed for immunohistochemical analyses. CA125 was expressed in varying degrees in tumor tissues from all patients....... Mean tissue CA125 expression for each patient ranged from 36% to 98%. Intrapatient variations in tissue expression ranged from 10% to 90% point. No significant correlations between levels of CA125 tissue expression, serum level of CA125, stage, and grade were found. We found that the tissue expression...

[Tissue repositories for research at Sheba Medical Center(SMC].

Science.gov (United States)

Cohen, Yehudit; Barshack, Iris; Onn, Amir

2013-06-01

Cancer is the number one cause of death in both genders. Breakthroughs in the understanding of cancer biology, the identification of prognostic factors, and the development of new treatments are increasingly dependent on access to human cancer tissues with linked clinicopathological data. Access to human tumor samples and a large investment in translational research are needed to advance this research. The SMC tissue repositories provide researchers with biological materials, which are essential tools for cancer research. SMC tissue repositories for research aim to collect, document and preserve human biospecimens from patients with cancerous diseases. This is in order to provide the highest quality and well annotated biological biospecimens, used as essential tools to achieve the growing demands of scientific research needs. Such repositories are partners in acceLerating biomedical research and medical product development through clinical resources, in order to apply best options to the patients. Following Institutional Review Board approval and signing an Informed Consent Form, the tumor and tumor-free specimens are coLLected by a designated pathologist at the operating room only when there is a sufficient amount of the tumor, in excess of the routine needs. Blood samples are collected prior to the procedure. Other types of specimens collected include ascites fluid, pleural effusion, tissues for Optimal Cutting Temperature [OCT] and primary culture etc. Demographic, clinical, pathologicaL, and follow-up data are collected in a designated database. SMC has already established several organ or disease-specific tissue repositories within different departments. The foundation of tissue repositories requires the concentrated effort of a multidisciplinary team composed of paramedical, medical and scientific professionals. Research projects using these specimens facilitate the development of 'targeted therapy', accelerate basic research aimed at clarifying molecular

Determination of Magnesium in Needle Biopsy Samples of Muscle Tissue by Means of Neutron Activation Analysis

Energy Technology Data Exchange (ETDEWEB)

Brune, D; Sjoeberg, H E

1964-07-15

Magnesium has been determined by means of neutron-activation analysis in needle biopsy samples of the order of magnitude 1 mg dry weight. The procedure applied was to extract the Mg-27 activity from irradiated muscle tissue with concentrated hydrochloric acid followed by a fast hydroxide precipitation and gamma-spectrometric measurements. The Mg activity was recovered in the muscle tissue samples to (97 {+-} 2) per cent. The sensitivity for the magnesium determination is estimated as 0.3 {mu}g.

Blood venous sample collection: Recommendations overview and a checklist to improve quality.

Science.gov (United States)

Giavarina, Davide; Lippi, Giuseppe

2017-07-01

The extra-analytical phases of the total testing process have substantial impact on managed care, as well as an inherent high risk of vulnerability to errors which is often greater than that of the analytical phase. The collection of biological samples is a crucial preanalytical activity. Problems or errors occurring shortly before, or soon after, this preanalytical step may impair sample quality and characteristics, or else modify the final results of testing. The standardization of fasting requirements, rest, patient position and psychological state of the patient are therefore crucial for mitigating the impact of preanalytical variability. Moreover, the quality of materials used for collecting specimens, along with their compatibility, can guarantee sample quality and persistence of chemical and physical characteristics of the analytes over time, so safeguarding the reliability of testing. Appropriate techniques and sampling procedures are effective to prevent problems such as hemolysis, undue clotting in the blood tube, draw of insufficient sample volume and modification of analyte concentration. An accurate identification of both patient and blood samples is a key priority as for other healthcare activities. Good laboratory practice and appropriate training of operators, by specifically targeting collection of biological samples, blood in particular, may greatly improve this issue, thus lowering the risk of errors and their adverse clinical consequences. The implementation of a simple and rapid check-list, including verification of blood collection devices, patient preparation and sampling techniques, was found to be effective for enhancing sample quality and reducing some preanalytical errors associated with these procedures. The use of this tool, along with implementation of objective and standardized systems for detecting non-conformities related to unsuitable samples, can be helpful for standardizing preanalytical activities and improving the quality of

Contaminants of emerging concern in the Great Lakes Basin: A report on sediment, water, and fish tissue chemistry collected in 2010-2012

Science.gov (United States)

Choy, Steven J.; Annis, Mandy L.; Banda, JoAnn; Bowman, Sarah R.; Brigham, Mark E.; Elliott, Sarah M.; Gefell, Daniel J.; Jankowski, Mark D.; Jorgenson, Zachary G.; Lee, Kathy E.; Moore, Jeremy N.; Tucker, William A.

2017-01-01

Despite being detected at low levels in surface waters and sediments across the United States, contaminants of emerging concern (CECs) in the Great Lakes Basin are not well characterized in terms of spatial and temporal occurrence. Additionally, although the detrimental effects of exposure to CECs on fish and wildlife have been documented for many CECs in laboratory studies, we do not adequately understand the implications of the presence of CECs in the environment. Based on limited studies using current environmentally relevant concentrations of chemicals, however, risks to fish and wildlife are evident. As a result, there is an increasing urgency to address data gaps that are vital to resource management decisions. The U.S. Fish and Wildlife Service, in collaboration with the U.S. Geological Survey, is leading a Great Lakes Basin-wide evaluation of CECs (CEC Project) with the objectives to (a) characterize the spatial and temporal distribution of CECs; (b) evaluate risks to fish and wildlife resources; and (c) develop tools to aid resource managers in detecting, averting, or minimizing the ecological consequences to fish and wildlife that are exposed to CECs. This report addresses objective (a) of the CEC Project, summarizing sediment and water chemistry data collected from 2010 to 2012 and fish liver tissue chemistry data collected in 2012; characterizes the sampling locations with respect to potential sources of CECs in the landscape; and provides an initial interpretation of the variation in CEC concentrations relative to the identified sources. Data collected during the first three years of our study, which included 12 sampling locations and analysis of 134 chemicals, indicate that contaminants were more frequently detected in sediment compared to water. Chemicals classified as alkyphenols, flavors/ fragrances, hormones, PAHs, and sterols had higher average detection frequencies in sediment compared to water, while the opposite was observed for pesticides

A vocabulary for the identification and delineation of teratoma tissue components in hematoxylin and eosin-stained samples

Directory of Open Access Journals (Sweden)

Ramamurthy Bhagavatula

2014-01-01

Full Text Available We propose a methodology for the design of features mimicking the visual cues used by pathologists when identifying tissues in hematoxylin and eosin (H&E-stained samples. Background: H&E staining is the gold standard in clinical histology; it is cheap and universally used, producing a vast number of histopathological samples. While pathologists accurately and consistently identify tissues and their pathologies, it is a time-consuming and expensive task, establishing the need for automated algorithms for improved throughput and robustness. Methods: We use an iterative feedback process to design a histopathology vocabulary (HV, a concise set of features that mimic the visual cues used by pathologists, e.g. "cytoplasm color" or "nucleus density." These features are based in histology and understood by both pathologists and engineers. We compare our HV to several generic texture-feature sets in a pixel-level classification algorithm. Results: Results on delineating and identifying tissues in teratoma tumor samples validate our expert knowledge-based approach. Conclusions: The HV can be an effective tool for identifying and delineating teratoma components from images of H&E-stained tissue samples.

Develop of omni-tritium sample preparation device

International Nuclear Information System (INIS)

Tian Junhua; Zheng Min; Zhang Dong

2008-06-01

The content of total tritium analysis is required in order to know the tritium contaminated degree of biological samples accurately. But the conversion and collection of organic tritium are difficult. A device to treat total tritium samples was developed. Plant samples were treated by combustion and catalysis. After expelling the free HTO in the samples when heated in abundant oxygen, the samples were ignited. Combustion gas passed the catalysts at 800 degree C and its oxidation was catalyzed, and then the combined tritium in tissues was converted into HTO. HTO was collected by water-cooling tube and condenser. For other samples, HTO was treated and collected by high temperature (The highest temperature is 1000 degree C)-catalysis-double condensation method. This device had solved the problem that organic tritium is difficult to gather. (authors)

Transgenic zebrafish reveal tissue-specific differences in estrogen signaling in response to environmental water samples.

Science.gov (United States)

Gorelick, Daniel A; Iwanowicz, Luke R; Hung, Alice L; Blazer, Vicki S; Halpern, Marnie E

2014-04-01

Environmental endocrine disruptors (EEDs) are exogenous chemicals that mimic endogenous hormones such as estrogens. Previous studies using a zebrafish transgenic reporter demonstrated that the EEDs bisphenol A and genistein preferentially activate estrogen receptors (ERs) in the larval heart compared with the liver. However, it was not known whether the transgenic zebrafish reporter was sensitive enough to detect estrogens from environmental samples, whether environmental estrogens would exhibit tissue-specific effects similar to those of BPA and genistein, or why some compounds preferentially target receptors in the heart. We tested surface water samples using a transgenic zebrafish reporter with tandem estrogen response elements driving green fluorescent protein expression (5xERE:GFP). Reporter activation was colocalized with tissue-specific expression of ER genes by RNA in situ hybridization. We observed selective patterns of ER activation in transgenic fish exposed to river water samples from the Mid-Atlantic United States, with several samples preferentially activating receptors in embryonic and larval heart valves. We discovered that tissue specificity in ER activation was due to differences in the expression of ER subtypes. ERα was expressed in developing heart valves but not in the liver, whereas ERβ2 had the opposite profile. Accordingly, subtype-specific ER agonists activated the reporter in either the heart valves or the liver. The use of 5xERE:GFP transgenic zebrafish revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero was associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

Technical note: The development of a methodology for ruminal and colon tissue biopsying of young Holstein dairy calves.

Science.gov (United States)

van Niekerk, J K; Middeldorp, M; Steele, M A

2018-05-09

The objectives of this study were to develop a methodology for biopsying the rumen and colon of young dairy calves and to collect suitable quality tissue samples for microscopic and gene expression analysis. Six Holstein dairy bull calves (45.0 ± 1.5 kg birth weight) were ruminally cannulated during the second week of life and weaned at the end of wk 6. Ruminal and colon tissue samples were collected at the end of wk 5, 6, 7, 8, and 12. Calves were not sedated but were restrained in a chute for sampling. The endoscope (100 cm length, 9.8 mm diameter) was introduced through the rumen cannula to harvest ruminal tissue. Endoscopic biopsies of the rumen with endoscopic biopsy forceps were unsuccessful 85% of the time because they were unable to shear the ruminal tissue. Thereafter, an Allis clamp was used to retrieve the blind sac through the rumen cannula to perform direct tissue biopsying with surgical scissors. To biopsy the colon, the lubricated distal tip of an endoscope was slowly inserted into the calf's anus. A total of 6 colon tissue samples (12.6 ± 0.74 mg) were collected per calf per time point from the distal colon 30 to 40 cm from the calf's anus using endoscopic biopsy forceps, which were inserted through the instrument channel. A new forcep was used between sites and calves. Between calves, the outside of the endoscope was washed with 4% chlorohexidine and rinsed with water and the instrument channel was washed with distilled water and 70% ethanol. Colon and ruminal samples were processed for histological measurements, and RNA was isolated and sequenced. High-quality RNA (RNA integrity number 8.8 ± 0.08) was collected from samples, and light and electron microscopy was performed on samples. In conclusion, endoscopic biopsying can be used for tissue harvest in the colon of young calves. However, it was found that collecting ruminal tissue by retracting the rumen from the cannula and taking samples with surgical scissors was more successful than an

The Autism Simplex Collection : an international, expertly phenotyped autism sample for genetic and phenotypic analyses

OpenAIRE

Buxbaum, Joseph D.; Bolshakova, Nadia; Brownfeld, Jessica M.; Anney, Richard J. L.; Bender, Patrick; Bernier, Raphael; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Freitag, Christine M.; Hallmayer, Joachim; Geschwind, Daniel H.; Klauck, Sabine M.; Nurnberger, John I.; Oliveira, Guiomar

2014-01-01

Background: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. Methods: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection ...

Comparison of ESR1 Mutations in Tumor Tissue and Matched Plasma Samples from Metastatic Breast Cancer Patients

Directory of Open Access Journals (Sweden)

Takashi Takeshita

2017-10-01

Full Text Available BACKGROUND: ESR1 mutation in circulating cell-free DNA (cfDNA is emerging as a noninvasive biomarker of acquired resistance to endocrine therapy, but there is a paucity of data comparing the status of ESR1 gene in cfDNA with that in its corresponding tumor tissue. The objective of this study is to validate the degree of concordance of ESR1 mutations between plasma and tumor tissue. METHODS: ESR1 ligand-binding domain mutations Y537S, Y537N, Y537C, and D538G were analyzed using droplet digital PCR in 35 patients with metastatic breast cancer (MBC (35 tumor tissue samples and 67 plasma samples. RESULTS: Of the 35 paired samples, 26 (74.3% were concordant: one patient had detectable ESR1 mutations both plasma (ESR1 Y537S/Y537N and tumor tissue (ESR1 Y537S/Y537C, and 25 had WT ESR1 alleles in both. Nine (25.7% had discordance between the plasma and tissue results: five had mutations detected only in their tumor tissue (two Y537S, one Y537C, one D538G, and one Y537S/Y537N/D538G, and four had mutations detected only in their plasma (one Y537S, one Y537N, and two Y537S/Y537N/D538G. Furthermore, longitudinal plasma samples from 19 patients were used to assess changes in the presence of ESR1 mutations during treatment. Eleven patients had cfDNA ESR1 mutations over the course of treatment. A total of eight of 11 patients with MBC with cfDNA ESR1 mutations (72.7% had the polyclonal mutations. CONCLUSION: We have shown the independent distribution of ESR1 mutations between plasma and tumor tissue in 35 patients with MBC.

Activity Concentration for Surface Soil Samples Collected from Arrant, Qena, Egypt

International Nuclear Information System (INIS)

Harb, S.; Salahel Din, K.; Abbady, A.; Moustafa, M.

2010-01-01

Soil samples were collected from four regions from Armant area. Qena, Upper Egypt for measure their natural radioactivity concentrations due to Ra-226, Th-232 and K-40 radionuclides. Thirty-Four surface soil samples were analyzed by using low-level gamma-spectrometric analysis. The average activity concentration for Ra-226 in (Bq/kg) in the collected soil samples were found to be 27.3 ±3.2, 11.4±1.09, 10.6±1.2, and 11.4±1.02 while the average value for Th-232 were 15.1±1.4, 11.1±0.77, 10.8 ± 0.72 and 11.1 ± 0.8 (Bq/kg) for soil samples from North, South, West and East. The corresponding average values for K-40 were 521.4±16.8, 463±14.8, 488.9±15.6 and 344.5±10.7 (Bq/kg), respectively. Based on radionuclides concentration in surface soil samples the radiological effects can be assessed

Tylosin depletion in edible tissues of turkeys.

Science.gov (United States)

Montesissa, C; De Liguoro, M; Santi, A; Capolongo, F; Biancotto, G

1999-10-01

The depletion of tylosin residues in edible turkey tissues was followed after 3 days of administration of tylosin tartrate at 500 mg l-1 in drinking water, to 30 turkeys. Immediately after the end of the treatment (day 0) and at day 1, 3, 5 and 10 of withdrawal, six turkeys (three males and three females) per time were sacrificed and samples of edible tissues were collected. Tissue homogenates were extracted, purified and analysed by HPLC according to a method previously published for the analysis of tylosin residues in pig tissues. In all tissues, tylosin residues were already below the detection limits of 50 micrograms kg-1 at time zero. However, in several samples of tissues (skin + fat, liver, kidney, muscle), from the six turkeys sacrificed at that time, one peak corresponding to an unknown tylosin equivalent was detected at measurable concentrations. The identification of this unknown compound was performed by LC-MS/MS analysis of the extracts from incurred samples. The mass fragmentation of the compound was consistent with the structure of tylosin D (the alcoholic derivative of tylosin A), the major metabolite of tylosin previously recovered and identified in tissues and/or excreta from treated chickens, cattle and pigs.

An international study of the performance of sample collection from patients

NARCIS (Netherlands)

Dzik, WH; Murphy, MF; Andreu, G; Heddle, N; Hogman, C; Kekomaki, R; Murphy, S; Shimizu, M; Smit Sibinga, C.T.

2003-01-01

Background and Objectives Collection of a blood sample from the correct patient is the first step in the process of safe transfusion. The aim of this international collaborative study was to assess the frequency of mislabelled and miscollected samples drawn for blood grouping. Materials and Methods

Wildlife specimen collection, preservation, and shipment

Science.gov (United States)

White, C. LeAnn; Dusek, Robert J.; Franson, J. Christian; Friend, Milton; Gibbs, Samantha E.J.; Wild, Margaret A.

2015-01-01

Specimens are used to provide supporting information leading to the determination of the cause of disease or death in wildlife and for disease monitoring or surveillance. Commonly used specimens for wildlife disease investigations include intact carcasses, tissues from carcasses, euthanized or moribund animals, parasites, ingested food, feces, or environmental samples. Samples from live animals or the environment (e.g., contaminated feed) in the same vicinity as a mortality event also may be helpful. The type of specimen collected is determined by availability of samples and biological objectives. Multiple fresh, intact carcasses from affected species are the most useful in establishing a cause for a mortality event. Submission of entire carcasses allows observation of gross lesions and abnormalities, as well as disease testing of multiple tissues. Samples from live animals may be more appropriate when sick animals cannot be euthanized (e.g., threatened or endangered species) or for research and monitoring projects examining disease or agents circulating in apparently healthy animals or those not exhibiting clinical signs. Samples from live animals may include collections of blood, hair, feathers, feces, or ectoparasites, or samples obtained by swabbing lesions or orifices. Photographs and videos are useful additions for recording field and clinical signs and conveying conditions at the site. Collection of environmental samples (e.g., feces, water, feed, or soil) may be appropriate when animals cannot be captured for sampling or the disease agent may persist in the environment. If lethal collection is considered necessary, biologists should refer to the policies, procedures, and permit requirements of their institution/facility and the agency responsible for species management (U.S. Fish and Wildlife Service or State natural resource agency) prior to use in the field. If threatened or endangered species are found dead, or there is evidence of illegal take, field

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

Science.gov (United States)

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

Equipment for collecting samples of radioactive solutions; Installation de prelevements d'echantillons de solutions radioactives

Energy Technology Data Exchange (ETDEWEB)

Raggenbass, A.; Fradin, J.; Joubert, G.

1958-12-03

The authors present an equipment aimed at collecting samples of fission products to perform radio-chemical analysis. As the sample must have a total activity between 1 and 50 micro-Curie, this installation comprises a sampling system and a dilution device which aims at bringing the sample to the suitable activity. Samples are collected by means of needles. The sample reproducibility is discussed. The dilution device is described.

Assessing the Functional Limitations of Lipids and Fatty Acids for Diet Determination: The Importance of Tissue Type, Quantity, and Quality

Directory of Open Access Journals (Sweden)

Lauren Meyer

2017-11-01

Full Text Available Lipid and fatty acid (FA analysis is commonly used to describe the trophic ecology of an increasing number of taxa. However, the applicability of these analyses is contingent upon the collection and storage of sufficient high quality tissue, the limitations of which are previously unexplored in elasmobranchs. Using samples from 110 white sharks, Carcharodon carcharias, collected throughout Australia, we investigated the importance of tissue type, sample quantity, and quality for reliable lipid class and FA analysis. We determined that muscle and sub-dermal tissue contain distinct lipid class and FA profiles, and were not directly comparable. Muscle samples as small as 12 mg dry weight (49 mg wet weight, provided reliable and consistent FA profiles, while sub-dermal tissue samples of 40 mg dry weight (186 mg wet weight or greater were required to yield consistent profiles. This validates the suitability of minimally invasive sampling methods such as punch biopsies. The integrity of FA profiles in muscle was compromised after 24 h at ambient temperature (~20°C, making these degraded samples unreliable for accurate determination of dietary sources, yet sub-dermal tissue retained stable FA profiles under the same conditions, suggesting it may be a more robust tissue for trophic ecology work with potentially degraded samples. However, muscle samples archived for up to 16 years in −20°C retain their FA profiles, highlighting that tissue from museum or private collections can yield valid insights into the trophic ecology of marine elasmobranchs.

A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

Science.gov (United States)

Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

2017-01-01

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

PIXE Analysis of Aerosol and Soil Samples Collected in the Adirondack Mountains

Science.gov (United States)

Yoskowitz, Joshua; Ali, Salina; Nadareski, Benjamin; Labrake, Scott; Vineyard, Michael

2014-09-01

We have performed an elemental analysis of aerosol and soil samples collected at Piseco Lake in Upstate New York using proton induced X-ray emission spectroscopy (PIXE). This work is part of a systematic study of airborne pollution in the Adirondack Mountains. Of particular interest is the sulfur content that can contribute to acid rain, a well-documented problem in the Adirondacks. We used a nine-stage cascade impactor to collect the aerosol samples near Piseco Lake and distribute the particulate matter onto Kapton foils by particle size. The soil samples were also collected at Piseco Lake and pressed into cylindrical pellets for experimentation. PIXE analysis of the aerosol and soil samples were performed with 2.2-MeV proton beams from the 1.1-MV Pelletron accelerator in the Union College Ion-Beam Analysis Laboratory. There are higher concentrations of sulfur at smaller particle sizes (0.25-1 μm), suggesting that it could be suspended in the air for days and originate from sources very far away. Other elements with significant concentrations peak at larger particle sizes (1-4 μm) and are found in the soil samples, suggesting that these elements could originate in the soil. The PIXE analysis will be described and the resulting data will be presented.

Advanced Curation Activities at NASA: Implications for Astrobiological Studies of Future Sample Collections

Science.gov (United States)

McCubbin, F. M.; Evans, C. A.; Fries, M. D.; Harrington, A. D.; Regberg, A. B.; Snead, C. J.; Zeigler, R. A.

2017-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10F JSC is charged with curation of all extraterrestrial material under NASA control, including future NASA missions. The Directive goes on to define Curation as including documentation, preservation, preparation, and distribution of samples for re-search, education, and public outreach. Here we briefly describe NASA's astromaterials collections and our ongoing efforts related to enhancing the utility of our current collections as well as our efforts to prepare for future sample return missions. We collectively refer to these efforts as advanced curation.

Selection of reference genes for tissue/organ samples on day 3 fifth-instar larvae in silkworm, Bombyx mori.

Science.gov (United States)

Wang, Genhong; Chen, Yanfei; Zhang, Xiaoying; Bai, Bingchuan; Yan, Hao; Qin, Daoyuan; Xia, Qingyou

2018-06-01

The silkworm, Bombyx mori, is one of the world's most economically important insect. Surveying variations in gene expression among multiple tissue/organ samples will provide clues for gene function assignments and will be helpful for identifying genes related to economic traits or specific cellular processes. To ensure their accuracy, commonly used gene expression quantification methods require a set of stable reference genes for data normalization. In this study, 24 candidate reference genes were assessed in 10 tissue/organ samples of day 3 fifth-instar B. mori larvae using geNorm and NormFinder. The results revealed that, using the combination of the expression of BGIBMGA003186 and BGIBMGA008209 was the optimum choice for normalizing the expression data of the B. mori tissue/organ samples. The most stable gene, BGIBMGA003186, is recommended if just one reference gene is used. Moreover, the commonly used reference gene encoding cytoplasmic actin was the least appropriate reference gene of the samples investigated. The reliability of the selected reference genes was further confirmed by evaluating the expression profiles of two cathepsin genes. Our results may be useful for future studies involving the quantification of relative gene expression levels of different tissue/organ samples in B. mori. © 2018 Wiley Periodicals, Inc.

77 FR 38323 - Proposed Extension of Existing Information Collection; Respirable Coal Mine Dust Sampling

Science.gov (United States)

2012-06-27

... Information Collection; Respirable Coal Mine Dust Sampling AGENCY: Mine Safety and Health Administration... Sampling'' to more accurately reflect the type of information that is collected. Chronic exposure to... dust levels since 1970 and, consequently, the prevalence rate of black lung among coal miners, severe...

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

Science.gov (United States)

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

Acceptability of self-collected vaginal samples for HPV testing in an ...

African Journals Online (AJOL)

Objective: To evaluate the acceptability of self-collected vaginal samples for HPV testing in women living in rural and urban areas of ... Conclusion: Acceptability of self-sampling for HPV testing was similarly excellent in both groups despite their difference in terms ... cancer is the leading cause of death caused by cancer in.

Equilibrium Passive Sampling of POP in Lipid-Rich and Lean Fish Tissue: Quality Control Using Performance Reference Compounds.

Science.gov (United States)

Rusina, Tatsiana P; Carlsson, Pernilla; Vrana, Branislav; Smedes, Foppe

2017-10-03

Passive sampling is widely used to measure levels of contaminants in various environmental matrices, including fish tissue. Equilibrium passive sampling (EPS) of persistent organic pollutants (POP) in fish tissue has been hitherto limited to application in lipid-rich tissue. We tested several exposure methods to extend EPS applicability to lean tissue. Thin-film polydimethylsiloxane (PDMS) passive samplers were exposed statically to intact fillet and fish homogenate and dynamically by rolling with cut fillet cubes. The release of performance reference compounds (PRC) dosed to passive samplers prior to exposure was used to monitor the exchange process. The sampler-tissue exchange was isotropic, and PRC were shown to be good indicators of sampler-tissue equilibration status. The dynamic exposures demonstrated equilibrium attainment in less than 2 days for all three tested fish species, including lean fish containing 1% lipid. Lipid-based concentrations derived from EPS were in good agreement with lipid-normalized concentrations obtained using conventional solvent extraction. The developed in-tissue EPS method is robust and has potential for application in chemical monitoring of biota and bioaccumulation studies.

A novel method for single sample multi-axial nanoindentation of hydrated heterogeneous tissues based on testing great white shark jaws.

Science.gov (United States)

Ferrara, Toni L; Boughton, Philip; Slavich, Eve; Wroe, Stephen

2013-01-01

Nanomechanical testing methods that are suitable for a range of hydrated tissues are crucial for understanding biological systems. Nanoindentation of tissues can provide valuable insights into biology, tissue engineering and biomimetic design. However, testing hydrated biological samples still remains a significant challenge. Shark jaw cartilage is an ideal substrate for developing a method to test hydrated tissues because it is a unique heterogeneous composite of both mineralized (hard) and non-mineralized (soft) layers and possesses a jaw geometry that is challenging to test mechanically. The aim of this study is to develop a novel method for obtaining multidirectional nanomechanical properties for both layers of jaw cartilage from a single sample, taken from the great white shark (Carcharodon carcharias). A method for obtaining multidirectional data from a single sample is necessary for examining tissue mechanics in this shark because it is a protected species and hence samples may be difficult to obtain. Results show that this method maintains hydration of samples that would otherwise rapidly dehydrate. Our study is the first analysis of nanomechanical properties of great white shark jaw cartilage. Variation in nanomechanical properties were detected in different orthogonal directions for both layers of jaw cartilage in this species. The data further suggest that the mineralized layer of shark jaw cartilage is less stiff than previously posited. Our method allows multidirectional nanomechanical properties to be obtained from a single, small, hydrated heterogeneous sample. Our technique is therefore suitable for use when specimens are rare, valuable or limited in quantity, such as samples obtained from endangered species or pathological tissues. We also outline a method for tip-to-optic calibration that facilitates nanoindentation of soft biological tissues. Our technique may help address the critical need for a nanomechanical testing method that is applicable

A novel method for single sample multi-axial nanoindentation of hydrated heterogeneous tissues based on testing great white shark jaws.

Directory of Open Access Journals (Sweden)

Toni L Ferrara

Full Text Available Nanomechanical testing methods that are suitable for a range of hydrated tissues are crucial for understanding biological systems. Nanoindentation of tissues can provide valuable insights into biology, tissue engineering and biomimetic design. However, testing hydrated biological samples still remains a significant challenge. Shark jaw cartilage is an ideal substrate for developing a method to test hydrated tissues because it is a unique heterogeneous composite of both mineralized (hard and non-mineralized (soft layers and possesses a jaw geometry that is challenging to test mechanically. The aim of this study is to develop a novel method for obtaining multidirectional nanomechanical properties for both layers of jaw cartilage from a single sample, taken from the great white shark (Carcharodon carcharias. A method for obtaining multidirectional data from a single sample is necessary for examining tissue mechanics in this shark because it is a protected species and hence samples may be difficult to obtain. Results show that this method maintains hydration of samples that would otherwise rapidly dehydrate. Our study is the first analysis of nanomechanical properties of great white shark jaw cartilage. Variation in nanomechanical properties were detected in different orthogonal directions for both layers of jaw cartilage in this species. The data further suggest that the mineralized layer of shark jaw cartilage is less stiff than previously posited. Our method allows multidirectional nanomechanical properties to be obtained from a single, small, hydrated heterogeneous sample. Our technique is therefore suitable for use when specimens are rare, valuable or limited in quantity, such as samples obtained from endangered species or pathological tissues. We also outline a method for tip-to-optic calibration that facilitates nanoindentation of soft biological tissues. Our technique may help address the critical need for a nanomechanical testing method

Extraction of methylmercury from tissue and plant samples by acid leaching

Energy Technology Data Exchange (ETDEWEB)

Hintelmann, Holger; Nguyen, Hong T. [Trent University, Chemistry Department, Peterborough, ON (Canada)

2005-01-01

A simple and efficient extraction method based on acidic leaching has been developed for measurement of methylmercury (MeHg) in benthic organisms and plant material. Methylmercury was measured by speciated isotope-dilution mass spectrometry (SIDMS), using gas chromatography interfaced with inductively coupled plasma mass spectrometry (GC-ICP-MS). Reagent concentration and digestion temperature were optimized for several alkaline and acidic extractants. Recovery was evaluated by addition of MeHg enriched with CH{sub 3}{sup 201}Hg{sup +}. Certified reference materials (CRM) were used to evaluate the efficiency of the procedure. The final digestion method used 5 mL of 4 mol L{sup -1} HNO{sub 3} at 55 C to leach MeHg from tissue and plant material. The digest was further processed by aqueous phase ethylation, without interference with the ethylation step, resulting in 96{+-}7% recovery of CH{sub 3}{sup 201}Hg{sup +} from oyster tissue and 93{+-}7% from pine needles. Methylmercury was stable in this solution for at least 1 week and measured concentrations of MeHg in CRM were statistically not different from certified values. The method was applied to real samples of benthic invertebrates and inter-laboratory comparisons were conducted using lyophilized zooplankton, chironomidae, and notonectidae samples. (orig.)

Continuous wave terahertz reflection imaging of human colorectal tissue

Science.gov (United States)

Doradla, Pallavi; Alavi, Karim; Joseph, Cecil S.; Giles, Robert H.

2013-03-01

Continuous wave terahertz (THz) imaging has the potential to offer a safe, non-ionizing, and nondestructive medical imaging modality for delineating colorectal cancer. Fresh excisions of normal colon tissue were obtained from surgeries performed at the University of Massachusetts Medical School, Worcester. Reflection measurements of thick sections of colorectal tissues, mounted in an aluminum sample holder, were obtained for both fresh and formalin fixed tissues. The two-dimensional reflection images were acquired by using an optically pumped far-infrared molecular gas laser operating at 584 GHz with liquid Helium cooled silicon bolometer detector. Using polarizers in the experiment both co-polarized and cross-polarized remittance form the samples was collected. Analysis of the images showed the importance of understanding the effects of formalin fixation while determining reflectance level of tissue response. The resulting co- and cross-polarized images of both normal and formalin fixed tissues showed uniform terahertz response over the entire sample area. Initial measurements indicated a co-polarized reflectance of 16%, and a cross-polarized reflectance of 0.55% from fresh excisions of normal colonic tissues.

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

Directory of Open Access Journals (Sweden)

Anna Esteve-Codina

Full Text Available The molecular classification of glioblastoma (GBM based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.

Portable Automation of Static Chamber Sample Collection for Quantifying Soil Gas Flux

Energy Technology Data Exchange (ETDEWEB)

Davis, Morgan P.; Groh, Tyler A.; Parkin, Timothy B.; Williams, Ryan J.; Isenhart, Thomas M.; Hofmockel, Kirsten S.

2018-01-01

Quantification of soil gas flux using the static chamber method is labor intensive. The number of chambers that can be sampled is limited by the spacing between chambers and the availability of trained research technicians. An automated system for collecting gas samples from chambers in the field would eliminate the need for personnel to return to the chamber during a flux measurement period and would allow a single technician to sample multiple chambers simultaneously. This study describes Chamber Automated Sampling Equipment (FluxCASE) to collect and store chamber headspace gas samples at assigned time points for the measurement of soil gas flux. The FluxCASE design and operation is described, and the accuracy and precision of the FluxCASE system is evaluated. In laboratory measurements of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) concentrations of a standardized gas mixture, coefficients of variation associated with automated and manual sample collection were comparable, indicating no loss of precision. In the field, soil gas fluxes measured from FluxCASEs were in agreement with manual sampling for both N2O and CO2. Slopes of regression equations were 1.01 for CO2 and 0.97 for N2O. The 95% confidence limits of the slopes of the regression lines included the value of one, indicating no bias. Additionally, an expense analysis found a cost recovery ranging from 0.6 to 2.2 yr. Implementing the FluxCASE system is an alternative to improve the efficiency of the static chamber method for measuring soil gas flux while maintaining the accuracy and precision of manual sampling.

Trace Elements Analysis of Archeological Brick Samples Collected from Different Historical Placs in Rajshahi Division

International Nuclear Information System (INIS)

Begum, Bilkis A.; Biswas, Shapan K.; Matin, Mohammed A.; Hoque, Mohammed M.; Hopke, Philip K.

2007-01-01

Twenty-nine brick samples were collected from different temples and palaces, namely Paharpur, Kumarpur, Gaurbari, Puthia and Natore in Rajshahi Division in Bangladesh. The samples were analyzed by X-ray Fluorescence (XRF) method. The elemental data sets have been analyzed in order to find out the general characteristics and any significant differences among the collected samples and identify the origin of these brick samples. Most of the crustal elements have enrichment factor (EF) values close to unity. Only Cu and Pb have high values that may come from painting as these have been collected from temples and palaces.(author)

A comparison of human papillomavirus testing of clinician-collected and self-collected samples during follow-up after screen-and-treat.

Science.gov (United States)

Taylor, Sylvia; Wang, Chunhui; Wright, Thomas C; Denny, Lynette; Kuhn, Louise

2011-08-15

Screen-and-treat cervical cancer prevention programs based on high-risk human papillomavirus (HPV) testing and cryotherapy have been shown to be effective in resource-limited settings. However, because cryotherapy is not 100% effective, follow-up is needed after treatment to detect post-treatment failures. We compared the test performances of high-risk HPV testing (Hybrid Capture 2) using self-collected and clinician-collected samples as well as cervical cytology for identifying cervical intraepithelial neoplasia grades 2 or 3 or invasive cervical cancer (CIN2+) among women who did (n=812) and did not (n=1858) undergo cryotherapy in a South African screen-and-treat trial. At 6 months after enrolment (and after cryotherapy, if performed), women were tested using all three screening methods and then underwent colposcopy/biopsy. A predefined subset of women (n=1,455) had extended follow-up with colposcopy/biopsy at 12 months. A total of 33 and 91 cases of CIN2+ were detected among treated and untreated women, respectively. The sensitivity of HPV testing using clinician-collected samples and cervical cytology did not differ by treatment status. HPV testing of clinician-collected samples detected the most cases of CIN2+ among both treated (85%) and untreated (91%) women (p=0.31). Cytology (at a cutoff of atypical squamous cells of undetermined significance or greater) detected 76% of cases among both treated and untreated women. However, the sensitivity of HPV testing using self-collected samples was significantly lower among treated versus untreated women (55% vs. 78%, p=0.01). HPV testing using self-collected vaginal specimens may be useful in primary screening but performs poorly for detecting post-treatment failures. Copyright © 2010 UICC.

Chlorophenol and alkylphenol concentrations in sediment and mussel tissues collected from selected locations in Kentucky Lake, USA

Energy Technology Data Exchange (ETDEWEB)

Loganathan, B.; Brown, B.; Owen, D. [Murray State Univ., Murray, KY (United States); Sajwan, K. [Savannah State Univ., Savannah, GA (United States)

2004-09-15

Kentucky (KY) Lake is one the major human-constructed lakes in the US. It serves as an ultimate repository of substances entering this watershed from portions of seven southeastern states, which include a sizeable fraction of the U.S. chemical processing, agricultural chemical products and electronics manufacturing industries. Although a few studies have examined the levels of chlorinated organics in the KY Lake and the lowermost Tennessee River, there have been no reports on the distribution on the levels of chlorophenols and alkylphenols in sediment and/or biological tissues from this region. In this study, sediment, and freshwater mussels were collected from selected locations in KY Lake and Lake Barkley and analyzed for CPs and APs. Furthermore, wood samples from abandoned docks, navigational towers and wood found in the lake bottom were also analyzed to examine the sources of CPs to the lakes.

Telomerase activity as a marker for malignancy in feline tissues.

Science.gov (United States)

Cadile, C D; Kitchell, B E; Biller, B J; Hetler, E R; Balkin, R G

2001-10-01

To establish the diagnostic significance of the telomeric repeat amplification protocol (TRAP) assay in detecting feline malignancies. Solid tissue specimens collected from 33 client-owned cats undergoing diagnostic or therapeutic procedures at the University of Illinois Veterinary Medical Teaching Hospital between July 1997 and September 1999 and an additional 20 tissue samples were collected from 3 clinically normal control cats euthanatized at the conclusion of an unrelated study. The TRAP assay was used for detection of telomerase activity. Each result was compared to its respective histopathologic diagnosis. Twenty-nine of 31 malignant and 1 of 22 benign or normal tissue samples had telomerase activity, indicating 94% sensitivity and 95% specificity of the TRAP assay in our laboratory. The diagnostic significance of telomerase activity has been demonstrated in humans and recently in dogs by our laboratory. We tested feline samples to determine whether similar patterns of telomerase activity exist. On the basis of our results, the TRAP assay may be clinically useful in providing a rapid diagnosis of malignancy in cats. The telomerase enzyme may also serve as a therapeutic target in feline tumors.

Impact of anesthesia and euthanasia on metabolomics of mammalian tissues: studies in a C57BL/6J mouse model.

Directory of Open Access Journals (Sweden)

Katherine A Overmyer

Full Text Available A critical application of metabolomics is the evaluation of tissues, which are often the primary sites of metabolic dysregulation in disease. Laboratory rodents have been widely used for metabolomics studies involving tissues due to their facile handing, genetic manipulability and similarity to most aspects of human metabolism. However, the necessary step of administration of anesthesia in preparation for tissue sampling is not often given careful consideration, in spite of its potential for causing alterations in the metabolome. We examined, for the first time using untargeted and targeted metabolomics, the effect of several commonly used methods of anesthesia and euthanasia for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J mice. The data revealed dramatic, tissue-specific impacts of tissue collection strategy. Among many differences observed, post-euthanasia samples showed elevated levels of glucose 6-phosphate and other glycolytic intermediates in skeletal muscle. In heart and liver, multiple nucleotide and purine degradation metabolites accumulated in tissues of euthanized compared to anesthetized animals. Adipose tissue was comparatively less affected by collection strategy, although accumulation of lactate and succinate in euthanized animals was observed in all tissues. Among methods of tissue collection performed pre-euthanasia, ketamine showed more variability compared to isoflurane and pentobarbital. Isoflurane induced elevated liver aspartate but allowed more rapid initiation of tissue collection. Based on these findings, we present a more optimal collection strategy mammalian tissues and recommend that rodent tissues intended for metabolomics studies be collected under anesthesia rather than post-euthanasia.

Impact of anesthesia and euthanasia on metabolomics of mammalian tissues: studies in a C57BL/6J mouse model.

Science.gov (United States)

Overmyer, Katherine A; Thonusin, Chanisa; Qi, Nathan R; Burant, Charles F; Evans, Charles R

2015-01-01

A critical application of metabolomics is the evaluation of tissues, which are often the primary sites of metabolic dysregulation in disease. Laboratory rodents have been widely used for metabolomics studies involving tissues due to their facile handing, genetic manipulability and similarity to most aspects of human metabolism. However, the necessary step of administration of anesthesia in preparation for tissue sampling is not often given careful consideration, in spite of its potential for causing alterations in the metabolome. We examined, for the first time using untargeted and targeted metabolomics, the effect of several commonly used methods of anesthesia and euthanasia for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J mice. The data revealed dramatic, tissue-specific impacts of tissue collection strategy. Among many differences observed, post-euthanasia samples showed elevated levels of glucose 6-phosphate and other glycolytic intermediates in skeletal muscle. In heart and liver, multiple nucleotide and purine degradation metabolites accumulated in tissues of euthanized compared to anesthetized animals. Adipose tissue was comparatively less affected by collection strategy, although accumulation of lactate and succinate in euthanized animals was observed in all tissues. Among methods of tissue collection performed pre-euthanasia, ketamine showed more variability compared to isoflurane and pentobarbital. Isoflurane induced elevated liver aspartate but allowed more rapid initiation of tissue collection. Based on these findings, we present a more optimal collection strategy mammalian tissues and recommend that rodent tissues intended for metabolomics studies be collected under anesthesia rather than post-euthanasia.

Impact of Anesthesia and Euthanasia on Metabolomics of Mammalian Tissues: Studies in a C57BL/6J Mouse Model

Science.gov (United States)

Overmyer, Katherine A.; Thonusin, Chanisa; Qi, Nathan R.; Burant, Charles F.; Evans, Charles R.

2015-01-01

A critical application of metabolomics is the evaluation of tissues, which are often the primary sites of metabolic dysregulation in disease. Laboratory rodents have been widely used for metabolomics studies involving tissues due to their facile handing, genetic manipulability and similarity to most aspects of human metabolism. However, the necessary step of administration of anesthesia in preparation for tissue sampling is not often given careful consideration, in spite of its potential for causing alterations in the metabolome. We examined, for the first time using untargeted and targeted metabolomics, the effect of several commonly used methods of anesthesia and euthanasia for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J mice. The data revealed dramatic, tissue-specific impacts of tissue collection strategy. Among many differences observed, post-euthanasia samples showed elevated levels of glucose 6-phosphate and other glycolytic intermediates in skeletal muscle. In heart and liver, multiple nucleotide and purine degradation metabolites accumulated in tissues of euthanized compared to anesthetized animals. Adipose tissue was comparatively less affected by collection strategy, although accumulation of lactate and succinate in euthanized animals was observed in all tissues. Among methods of tissue collection performed pre-euthanasia, ketamine showed more variability compared to isoflurane and pentobarbital. Isoflurane induced elevated liver aspartate but allowed more rapid initiation of tissue collection. Based on these findings, we present a more optimal collection strategy mammalian tissues and recommend that rodent tissues intended for metabolomics studies be collected under anesthesia rather than post-euthanasia. PMID:25658945

Methods for collecting algal samples as part of the National Water-Quality Assessment Program

Science.gov (United States)

Porter, Stephen D.; Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic algae (periphyton) and phytoplankton communities are characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. This multidisciplinary approach provides multiple lines of evidence for evaluating water-quality status and trends, and for refining an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. Water quality can be characterized by evaluating the results of qualitative and quantitative measurements of the algal community. Qualitative periphyton samples are collected to develop of list of taxa present in the sampling reach. Quantitative periphyton samples are collected to measure algal community structure within selected habitats. These samples of benthic algal communities are collected from natural substrates, using the sampling methods that are most appropriate for the habitat conditions. Phytoplankton samples may be collected in large nonwadeable streams and rivers to meet specific program objectives. Estimates of algal biomass (chlorophyll content and ash-free dry mass) also are optional measures that may be useful for interpreting water-quality conditions. A nationally consistent approach provides guidance on site, reach, and habitat selection, as well as information on methods and equipment for qualitative and quantitative sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data locally, regionally, and nationally.

Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

2016-01-01

Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.Human colon mucosal biopsies were extracted from the sigmoideum...

Simultaneous PIXE and PIGE analyses of aerosol samples collected in urban areas

International Nuclear Information System (INIS)

Boni, C.; Caruso, E.; Cereda, E.; Marcazzan, G.M.; Redaelli, P.; Bacci, P.

1988-01-01

The paper concerns the simultaneous PIXE (Particle Induced X-ray Emission) and PIGE (Proton Induced Gamma-ray Emission) analyses of aerosol samples collected in urban areas. The results show that PIGE can detect Li, F, Na, Al, and Si in fly ashes and F, Na, Al and Si in atmospheric aerosol. The PIXE-PIGE technique has also been applied to 80 samples of atmospheric particular matter collected above Milan during the winter and summer months of 1986/7, and the average values of concentrations and enrichment factors are given for the detected elements. (U.K.)

Assembly for collecting samples for purposes of identification or analysis and method of use

Science.gov (United States)

Thompson, Cyril V [Knoxville, TN; Smith, Rob R [Knoxville, TN

2010-02-02

An assembly and an associated method for collecting a sample of material desired to be characterized with diagnostic equipment includes or utilizes an elongated member having a proximal end with which the assembly is manipulated by a user and a distal end. In addition, a collection tip which is capable of being placed into contact with the material to be characterized is supported upon the distal end. The collection tip includes a body of chemically-inert porous material for binding a sample of material when the tip is placed into contact with the material and thereby holds the sample of material for subsequent introduction to the diagnostic equipment.

Comparative multielement analyses of airborne particulate samples collected in various areas

International Nuclear Information System (INIS)

Mamuro, Tetsuo; Matsuda, Yatsuka; Mizohata, Akira

1973-01-01

In order to grasp the characteristic features of the air pollution by particulates in various areas in Japan, multielement analyses by instrumental neutron activation analysis and radioisotope energy dispersive X-ray fluorescence analysis were applied to 31 airborne particulate samples collected in 15 different areas, and the analytical results obtained were compared with one another. All the samples were collected by so-called ''10 micron cut'' samplers, the collection efficiency of which is considered to be 50% at 8μ and nearly zero beyond 10μ. Among the areas in question there are clean seaside areas, heavily industrialized areas, small cities along the Inland Sea or the Pacific Ocean around which industrialization is progressing, a small city having only a big iron work, an area famous for its ceramic industry and so on. The atmospheres over them were found to be quite different not only in pollution extent but also in pollution pattern. (auth.)

Tissue distribution of enrofloxacin in African clawed frogs (Xenopus laevis) after intramuscular and subcutaneous administration.

Science.gov (United States)

Felt, Stephen; Papich, Mark G; Howard, Antwain; Long, Tyler; McKeon, Gabriel; Torreilles, Stéphanie; Green, Sherril

2013-03-01

As part of an enrofloxacin pharmacokinetic study, concentrations of enrofloxacin and ciprofloxacin (metabolite) were measured in various tissues (brain, heart, kidney, liver, lung, and spleen) collected from treated (subcutaneous delivery, n = 3; intramuscular delivery, n = 3; untreated controls, n = 2) adult female Xenopus laevis by using HPLC. Enrofloxacin was rapidly absorbed after administration by either route and readily diffused into all sampled tissues. Enrofloxacin and ciprofloxacin were present in the tissue samples collected at 8 h. The highest average tissue concentrations for enrofloxacin were found in kidney, with the lowest concentrations in liver. Ciprofloxacin tissue concentrations paralleled but were always lower than those of enrofloxacin for all time points and tissues except brain and kidney. These results, together with previously published pharmacokinetic data and known minimal inhibitory concentrations of common pathogenic bacteria, provide a strong evidence-based rationale for choosing enrofloxacin to treat infectious diseases in X. laevis.

Characteristics of the samples in the FNG fission deposit collection

Energy Technology Data Exchange (ETDEWEB)

Meadows, J.W.

1990-12-01

Information concerning the samples in the Fast Neutron Generator (FNG) Group's fission deposit collection has been assembled. This includes the physical dimensions, isotopic analyses, half-lives, alpha emission rates specific activities and deposit weights. 10 refs., 9 figs., 5 tabs.

Molecular diagnosis of rhino-orbito-cerebral mucormycosis from fresh tissue samples.

Science.gov (United States)

Zaman, Kamran; Rudramurthy, Shivaprakash Mandya; Das, Ashim; Panda, Naresh; Honnavar, Prasanna; Kaur, Harsimran; Chakrabarti, Arunaloke

2017-08-01

We aimed to evaluate a PCR-based technique for the diagnosis of mucormycosis and the identification of fungi from fresh tissue specimens in patients with rhino-orbito-cerebral-mucormycosis (ROCM). Fifty cases of ROCM were included in the study. Conventional identification was performed using microscopy and culture. Molecular diagnosis was performed by amplifying the ribosomal DNA using pan-fungal ITS primers and semi-nested Mucorales-specific primers of the 18S region. The amplified products were sequenced to identify the agents. The utility of PCR-RFLP of the 18S region of rDNA was evaluated to identify the Mucorales. The ROCM cases were diagnosed by the demonstration of aseptate ribbon-like hyphae in biopsy specimens collected from the patients. Isolation was possible in 24 (48 %) samples. The ITS2 PCR confirmed mucormycosis in 27 cases (54 %; CI 59.4-68.2). By comparison, Mucorales-specific PCR was able to amplify DNA and the sequence enabled the identification of Mucorales speciesin all the patients. PCR-RFLP of the 18S region of rDNA could only identify the agent to genus level. The molecular technique was able to identify Mucorales species in 26 (42 %) cases that were negative by culture. Mucorales-specific semi-nested PCR targeting the 18S region is a better technique than ITS2 PCR for diagnosis. PCR-RFLP of the 18S region helps in identification to genus level.

A comparison of results for samples collected with bailers constructed of different materials

International Nuclear Information System (INIS)

Thomey, N.; Ogle, R.; Jackson, J.

1992-01-01

A bailer is one of the most common sampling devices used to collect ground water samples. Bailers constructed from various materials are available; teflon, polyvinyl chloride (PVC), polyethylene, and stainless steel are all commonly used. It is widely recognized that sample results can be affected by the material from which the bailer is constructed. Teflon and stainless steel are usually recommended based upon their inert properties. The cost of these bailers is significantly higher than other types. For the purposes of petroleum storage tank investigations, sampling devices that would not compromise sample quality but be more economical than teflon or stainless steel would be especially desirable. Water samples were collected using the different types of bailers; teflon, stainless steel, PVC, and polyethylene. Split samples were analyzed for benzene, toluene, ethylbenzene, total xylenes, and Total Petroleum Hydrocarbons. The analytical results were compared to determine if differences were due to normal analytical variances or due to interaction of the sample with the sampling device. No difference was noted in the results which were obtained

Risk for molecular contamination of tissue samples evaluated for targeted anti-cancer therapy.

Directory of Open Access Journals (Sweden)

Eyal Asor

Full Text Available With the increasing usage of sensitive PCR technology for pharmacogenetics, cross contamination becomes a significant concern. Researchers employed techniques which basically include replacing laboratory equipment after each sample preparation; however, there are no recommended guidelines. In the present work we wanted to evaluate the risk of cross contamination during tissue processing using the routine precaution measures. Twenty-one surgical samples of lung adenocarcinoma were used, of which 7 contained EGFR exon 19 mutation, 7 contained EGFR exon 21 mutation (p.L858R and 7 were EGFR wild-type. The samples were ordered by alternating the mutation group to maximize the potential for cross contamination and underwent tissue sectioning and de-paraffinization. The entire process was performed using the same tools. Following DNA extraction all samples underwent PCR amplification and were scrutinized for small fractions of EGFR mutation using deep sequencing with the Ion torrent PGM technology. Twenty samples yielded results. The fraction of mutated copies was 41 ± 23% (range 11-66 for the cases with known exon 19 mutation and 48±24% (range 0-65 for the cases with known exon 21 mutations. No in-frame exon 19 deletion mutations were identified in the wild-type (WT and exon 21 groups. The fraction of EGFR exon 21 (codon 858 mutations was 0.018±0.014% (range 0-0.05% in the WT and exon 19 groups, which was not statistically different than the background sequencing artifact noise for the same base-pair alteration (p = 0.21. Our results suggest that standard precautions are sufficient for molecular pathology diagnosis of surgical samples and are not associated with increased risk of cross contamination.

Application of bar codes to the automation of analytical sample data collection

International Nuclear Information System (INIS)

Jurgensen, H.A.

1986-01-01

The Health Protection Department at the Savannah River Plant collects 500 urine samples per day for tritium analyses. Prior to automation, all sample information was compiled manually. Bar code technology was chosen for automating this program because it provides a more accurate, efficient, and inexpensive method for data entry. The system has three major functions: sample labeling is accomplished at remote bar code label stations composed of an Intermec 8220 (Intermec Corp.) interfaced to an IBM-PC, data collection is done on a central VAX 11/730 (Digital Equipment Corp.). Bar code readers are used to log-in samples to be analyzed on liquid scintillation counters. The VAX 11/730 processes the data and generates reports, data storage is on the VAX 11/730 and backed up on the plant's central computer. A brief description of several other bar code applications at the Savannah River Plant is also presented

Sample collection: an overview of the Hydrogeochemical and Stream Sediment Reconnaissance Program

International Nuclear Information System (INIS)

Bolivar, S.L.

1979-01-01

A Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) for uranium is currently being conducted throughout the conterminous United States and Alaska. The HSSR is part of the National Uranium Resource Evaluation sponsored by the US Department of Energy. This ambitious geochemical reconnaissance program is conducted by four national laboratories: Los Alamos Scientific Laboratory, Lawrence Livermore Laboratory, Oak Ridge Gaseous Diffusion Plant, and Savannah River Laboratory. The program is based on an extensive review of world literature, reconnaissance work done in other countries, and pilot studies conducted by each laboratory. Sample-collection methods and sample density are determined to optimize the probability of detecting potential uranium mineralization. To achieve this aim, each laboratory has developed independent standardized field collection procedures that are designed for its section of the country. Field parameters such as pH, conductivity, climate, geography, and geology are recorded at each site. Most samples are collected at densities of one sample site per 10 to 23 km 2 . The HSSR program has helped to improve existing hydrogeochemical reconnaissance exploration techniques. In addition to providing industry with data that may help to identify potential uranium districts and to extend known uranium provinces, the HSSR also provides multi-element analytical data, which can be used in water quality, soil, sediment, environmental, and base-metal exploration studies

The Importance of Meteorite Collections to Sample Return Missions: Past, Present, and Future Considerations

Science.gov (United States)

Welzenbach, L. C.; McCoy, T. J.; Glavin, D. P.; Dworkin, J. P.; Abell, P. A.

2012-01-01

While much of the scientific community s current attention is drawn to sample return missions, it is the existing meteorite and cosmic dust collections that both provide the paradigms to be tested by these missions and the context for interpreting the results. Recent sample returns from the Stardust and Hayabusa missions provided us with new materials and insights about our Solar System history and processes. As an example, Stardust sampled CAIs among the population of cometary grains, requiring extensive and unexpected radial mixing in the early solar nebula. This finding would not have been possible, however, without extensive studies of meteoritic CAIs that established their high-temperature, inner Solar System formation. Samples returned by Stardust also revealed the first evidence of a cometary amino acid, a discovery that would not have been possible with current in situ flight instrument technology. The Hayabusa mission provided the final evidence linking ordinary chondrites and S asteroids, a hypothesis that developed from centuries of collection and laboratory and ground-based telescopic studies. In addition to these scientific findings, studies of existing meteorite collections have defined and refined the analytical techniques essential to studying returned samples. As an example, the fortuitous fall of the Allende CV3 and Murchison CM2 chondrites within months before the return of Apollo samples allowed testing of new state-of-the-art analytical facilities. The results of those studies not only prepared us to better study lunar materials, but unanticipated discoveries changed many of our concepts about the earliest history and processes of the solar nebula. This synergy between existing collections and future space exploration is certainly not limited to sample return missions. Laboratory studies confirmed the existence of meteorites from Mars and raised the provocative possibility of preservation of ancient microbial life. The laboratory studies in

A practical guideline to remote biopsy darting of wildebeests for genetic sampling

Directory of Open Access Journals (Sweden)

Domnic Mijele

2016-12-01

Full Text Available The use of biopsy darts for remote collection of tissue samples from free-ranging terrestrial and aquatic animal species has gained popularity in the recent past. The success of darting is very important since scientists may not have many chances to re-dart the same animal, especially with the free-ranging elusive wildlife species. We used wildebeest (Connochaetes taurinus as a model to estimate the optimum shooting distance, pressure and the shot part of the body through which a researcher can optimize the success and amount of tissue collected from similar wild land mammalian species. Wildebeests were darted at six categories of distances ranging between 10 and 45 m and dart gun pressures of 5–14 millibar. The number of failed darts increased by increasing the darting distance: 0% (10 m, 0% (20 m, 6% (30 m, 20% (35 m, 71% (40 m, and 67% (45 m. There was a notable effect of the distances on the amount of tissue collected 20 m offered the best results. Dart gun pressure had no effect on the amount of tissue samples obtained. The amount of tissue obtained from successful darts was the same whether the animal was darted on the shoulder or thigh. In this paper, we present a practical guideline for remote biopsy darting of wildebeest to obtain optimum amount of tissue samples, which could be generalized for similar wild land mammalian species.

Collection and preparation of bottom sediment samples for analysis of radionuclides and trace elements

International Nuclear Information System (INIS)

2003-07-01

The publication is the first in a series of TECDOCs on sampling and sample handling as part of the IAEA support to improve reliability of nuclear analytical techniques (NATs) in Member State laboratories. The purpose of the document is to provide information on the methods for collecting sediments, the equipment used, and the sample preparation techniques for radionuclide and elemental analysis. The most appropriate procedures for defining the strategies and criteria for selecting sampling locations, for sample storage and transportation are also given. Elements of QA/QC and documentation needs for sampling and sediment analysis are discussed. Collection and preparation of stream and river bottom sediments, lake bottom sediments, estuary bottom sediments, and marine (shallow) bottom sediments are covered. The document is intended to be a comprehensive manual for the collection and preparation of bottom sediments as a prerequisite to obtain representative and meaningful results using NATs. Quality assurance and quality control (QA/QC) is emphasized as an important aspect to ensure proper collection, transportation, preservation, and analysis since it forms the basis for interpretation and legislation. Although there are many approaches and methods available for sediment analyses, the scope of the report is limited to sample preparation for (1) analysis of radionuclides (including sediment dating using radionuclides such as Pb-210 and Cs-137) and (2) analysis of trace, minor and major elements using nuclear and related analytical techniques such as NAA, XRF and PIXE

Collection and preparation of bottom sediment samples for analysis of radionuclides and trace elements

Energy Technology Data Exchange (ETDEWEB)

NONE

2003-07-01

The publication is the first in a series of TECDOCs on sampling and sample handling as part of the IAEA support to improve reliability of nuclear analytical techniques (NATs) in Member State laboratories. The purpose of the document is to provide information on the methods for collecting sediments, the equipment used, and the sample preparation techniques for radionuclide and elemental analysis. The most appropriate procedures for defining the strategies and criteria for selecting sampling locations, for sample storage and transportation are also given. Elements of QA/QC and documentation needs for sampling and sediment analysis are discussed. Collection and preparation of stream and river bottom sediments, lake bottom sediments, estuary bottom sediments, and marine (shallow) bottom sediments are covered. The document is intended to be a comprehensive manual for the collection and preparation of bottom sediments as a prerequisite to obtain representative and meaningful results using NATs. Quality assurance and quality control (QA/QC) is emphasized as an important aspect to ensure proper collection, transportation, preservation, and analysis since it forms the basis for interpretation and legislation. Although there are many approaches and methods available for sediment analyses, the scope of the report is limited to sample preparation for (1) analysis of radionuclides (including sediment dating using radionuclides such as Pb-210 and Cs-137) and (2) analysis of trace, minor and major elements using nuclear and related analytical techniques such as NAA, XRF and PIXE.

Direct detection of the AR-E211 G > A gene polymorphism from blood and tissue samples without DNA isolation.

Science.gov (United States)

Reptova, Silvie; Trtkova, Katerina Smesny; Kolar, Zdenek

2014-04-01

The pathogenesis of prostate cancer (CaP) involves alterations in a gene structure of the androgen receptor (AR). The single nucleotide polymorphism AR-E211 G > A localized in exon 1 of the AR gene (G1733A) was detected using direct polymerase chain reaction and restriction digestion (PCR-RFLP) method on blood and tissue samples without prior DNA isolation. We used blood samples of patients with a diagnosis of benign prostatic hyperplasia (BPH) or CaP. From monitored group of CaP patients were selected specimen in formalin-fixed paraffin-embedded tissue blocks with morphology of BPH and CaP. The main objective of our study was to develop a method based the direct PCR-RFLP analysis from blood and tissue without prior DNA isolation for faster genotyping analysis of a large number of samples. We found no statistically significant differences in allelic % of the AR-E211 G > A polymorphism between BPH and CaP patients (p ≤ 0.8462). Genotyping of the AR-E211 G > A variant in blood was not identical with tumor tissue genotyping analysis. Significant agreement between blood and tissue AR-E211 G > A polymorphism only in non-tumor tissue focus was confirmed. Although we analyzed a limited number of the tissue samples, we suppose that a presence of the minor allele A may be associated with cancer transformation-induced changes of the modified AR gene.

Sources of variability in collection and preparation of paint and lead-coating samples.

Science.gov (United States)

Harper, S L; Gutknecht, W F

2001-06-01

Chronic exposure of children to lead (Pb) can result in permanent physiological impairment. Since surfaces coated with lead-containing paints and varnishes are potential sources of exposure, it is extremely important that reliable methods for sampling and analysis be available. The sources of variability in the collection and preparation of samples were investigated to improve the performance and comparability of methods and to ensure that data generated will be adequate for its intended use. Paint samples of varying sizes (areas and masses) were collected at different locations across a variety of surfaces including metal, plaster, concrete, and wood. A variety of grinding techniques were compared. Manual mortar and pestle grinding for at least 1.5 min and mechanized grinding techniques were found to generate similar homogenous particle size distributions required for aliquots as small as 0.10 g. When 342 samples were evaluated for sample weight loss during mortar and pestle grinding, 4% had 20% or greater loss with a high of 41%. Homogenization and sub-sampling steps were found to be the principal sources of variability related to the size of the sample collected. Analysis of samples from different locations on apparently identical surfaces were found to vary by more than a factor of two both in Pb concentration (mg cm-2 or %) and areal coating density (g cm-2). Analyses of substrates were performed to determine the Pb remaining after coating removal. Levels as high as 1% Pb were found in some substrate samples, corresponding to more than 35 mg cm-2 Pb. In conclusion, these sources of variability must be considered in development and/or application of any sampling and analysis methodologies.

Optical coherence tomography detection of shear wave propagation in inhomogeneous tissue equivalent phantoms and ex-vivo carotid artery samples

Science.gov (United States)

Razani, Marjan; Luk, Timothy W.H.; Mariampillai, Adrian; Siegler, Peter; Kiehl, Tim-Rasmus; Kolios, Michael C.; Yang, Victor X.D.

2014-01-01

In this work, we explored the potential of measuring shear wave propagation using optical coherence elastography (OCE) in an inhomogeneous phantom and carotid artery samples based on a swept-source optical coherence tomography (OCT) system. Shear waves were generated using a piezoelectric transducer transmitting sine-wave bursts of 400 μs duration, applying acoustic radiation force (ARF) to inhomogeneous phantoms and carotid artery samples, synchronized with a swept-source OCT (SS-OCT) imaging system. The phantoms were composed of gelatin and titanium dioxide whereas the carotid artery samples were embedded in gel. Differential OCT phase maps, measured with and without the ARF, detected the microscopic displacement generated by shear wave propagation in these phantoms and samples of different stiffness. We present the technique for calculating tissue mechanical properties by propagating shear waves in inhomogeneous tissue equivalent phantoms and carotid artery samples using the ARF of an ultrasound transducer, and measuring the shear wave speed and its associated properties in the different layers with OCT phase maps. This method lays the foundation for future in-vitro and in-vivo studies of mechanical property measurements of biological tissues such as vascular tissues, where normal and pathological structures may exhibit significant contrast in the shear modulus. PMID:24688822

Curating NASA's future extraterrestrial sample collections: How do we achieve maximum proficiency?

Science.gov (United States)

McCubbin, Francis; Evans, Cynthia; Allton, Judith; Fries, Marc; Righter, Kevin; Zolensky, Michael; Zeigler, Ryan

2016-07-01

Introduction: The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "The curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "…documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the ongoing efforts to ensure that the future activities of the NASA Curation Office are working to-wards a state of maximum proficiency. Founding Principle: Curatorial activities began at JSC (Manned Spacecraft Center before 1973) as soon as design and construction planning for the Lunar Receiving Laboratory (LRL) began in 1964 [1], not with the return of the Apollo samples in 1969, nor with the completion of the LRL in 1967. This practice has since proven that curation begins as soon as a sample return mission is conceived, and this founding principle continues to return dividends today [e.g., 2]. The Next Decade: Part of the curation process is planning for the future, and we refer to these planning efforts as "advanced curation" [3]. Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envisioned by NASA exploration goals. We are (and have been) planning for future curation, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, curation of organically- and biologically-sensitive samples, and the use of minimally invasive analytical techniques (e.g., micro-CT, [4]) to characterize samples. These efforts will be useful for Mars Sample Return

Planning for the Collection and Analysis of Samples of Martian Granular Materials Potentially to be Returned by Mars Sample Return

Science.gov (United States)

Carrier, B. L.; Beaty, D. W.

2017-12-01

NASA's Mars 2020 rover is scheduled to land on Mars in 2021 and will be equipped with a sampling system capable of collecting rock cores, as well as a specialized drill bit for collecting unconsolidated granular material. A key mission objective is to collect a set of samples that have enough scientific merit to justify returning to Earth. In the case of granular materials, we would like to catalyze community discussion on what we would do with these samples if they arrived in our laboratories, as input to decision-making related to sampling the regolith. Numerous scientific objectives have been identified which could be achieved or significantly advanced via the analysis of martian rocks, "regolith," and gas samples. The term "regolith" has more than one definition, including one that is general and one that is much more specific. For the purpose of this analysis we use the term "granular materials" to encompass the most general meaning and restrict "regolith" to a subset of that. Our working taxonomy includes the following: 1) globally sourced airfall dust (dust); 2) saltation-sized particles (sand); 3) locally sourced decomposed rock (regolith); 4) crater ejecta (ejecta); and, 5) other. Analysis of martian granular materials could serve to advance our understanding areas including habitability and astrobiology, surface-atmosphere interactions, chemistry, mineralogy, geology and environmental processes. Results of these analyses would also provide input into planning for future human exploration of Mars, elucidating possible health and mechanical hazards caused by the martian surface material, as well as providing valuable information regarding available resources for ISRU and civil engineering purposes. Results would also be relevant to matters of planetary protection and ground-truthing orbital observations. We will present a preliminary analysis of the following, in order to generate community discussion and feedback on all issues relating to: What are the

Analysis Of Transcriptomes In A Porcine Tissue Collection Using RNA-Seq And Genome Assembly 10

DEFF Research Database (Denmark)

Hornshøj, Henrik; Thomsen, Bo; Hedegaard, Jakob

2011-01-01

The release of Sus scrofa genome assembly 10 supports improvement of the pig genome annotation and in depth transcriptome analyses using next-generation sequencing technologies. In this study we analyze RNA-seq reads from a tissue collection, including 10 separate tissues from Duroc boars and 10...... short read alignment software we mapped the reads to the genome assembly 10. We extracted contig sequences of gene transcripts using the Cufflinks software. Based on this information we identified expressed genes that are present in the genome assembly. The portion of these genes being previously known...... was roughly estimated by sequence comparison to known genes. Similarly, we searched for genes that are expressed in the tissues but not present in the genome assembly by aligning the non-genome-mapped reads to known gene transcripts. For the genes predicted to have alternative transcript variants by Cufflinks...

Differentiated embryonic chondrocytes 1 expression of periodontal ligament tissue and gingival tissue in the patients with chronic periodontitis.

Science.gov (United States)

Hu, Shenlin; Shang, Wei; Yue, Haitao; Chen, Ruini; Dong, Zheng; Hu, Jinhua; Mao, Zhao; Yang, Jian

2015-04-01

To evaluate the DEC1 expression of periodontal ligament tissue and gingival tissue in the patients with chronic periodontitis. 20 non-smoking patients with chronic periodontitis and 20 healthy individuals were enrolled. Periodontal ligament tissue and gingival tissue samples from healthy subjects were collected during teeth extraction for orthodontic reason or the third molar extraction. The parallel samples from patients with chronic periodontitis were obtained during periodontal flap operations or teeth extraction as part of periodontal treatment. The DEC1 expression and the alkaline phosphatase (ALP) activity of both the periodontal ligament tissue and gingival tissue were determined by Western blot, Immunohistochemistry and ALP Detection Kit. The DEC1 expression of periodontal ligament tissue in the patients with chronic periodontitis decreased significantly along with the decreased ALP activity. On the contrary, the DEC1 expression of gingival tissue in the patients with chronic periodontitis increased significantly. Further study found that the DEC1 expression of gingival tissue increased mainly in the suprabasal layer of gingival epithelial cells but decreased in the gingival connective tissue of the patients with chronic periodontitis. The DEC1 expression decreases in the periodontal ligament tissue which is related to the osteogenic capacity, whereas the DEC1 expression increases in the suprabasal layer of gingival epithelial cells which are involved in immune inflammatory response in the patients with chronic periodontitis. The findings provide a new target to explore the pathology and the therapy of periodontitis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

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Lei Wei

2016-10-01

Full Text Available Abstract Background The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent to the excised neoplasm is often used for this purpose as it is simultaneously collected and generally contains the same tissue type as the neoplasm. Following NGS analysis, we and others have frequently observed low-level somatic mutations in these non-neoplastic tissues, which may impose additional challenges to somatic mutation detection as it complicates germline variant filtering. Methods We hypothesized that the low-level somatic mutation observed in non-neoplastic tissues may be entirely or partially caused by inadvertent contamination by neoplastic cells during the surgical pathology gross assessment or tissue procurement process. To test this hypothesis, we applied a systematic protocol designed to collect multiple grossly non-neoplastic tissues using different methods surrounding each single neoplasm. The procedure was applied in two breast cancer lumpectomy specimens. In each case, all samples were first sequenced by whole-exome sequencing to identify somatic mutations in the neoplasm and determine their presence in the adjacent non-neoplastic tissues. We then generated ultra-deep coverage using targeted sequencing to assess the levels of contamination in non-neoplastic tissue samples collected under different conditions. Results Contamination levels in non-neoplastic tissues ranged up to 3.5 and 20.9 % respectively in the two cases tested, with consistent pattern correlated with the manner of grossing and procurement. By carefully controlling the conditions of various steps during this process, we were able to eliminate any detectable contamination in both patients. Conclusion The results demonstrated that the

Use of alkaline or enzymatic sample pretreatment prior to characterization of gold nanoparticles in animal tissue by single-particle ICPMS

DEFF Research Database (Denmark)

Löschner, Katrin; Brabrand, Myung Suk Jung; Sloth, Jens Jørgen

2014-01-01

, not much is known about the applicability of spICPMS for determination of NPs in complex matrices such as biological tissues. In the present study, alkaline and enzymatic treatments were applied to solubilize spleen samples from rats, which had been administered 60-nm gold nanoparticles (Au......NPs) intravenously. The results showed that similar size distributions of AuNPs were obtained independent of the sample preparation method used. Furthermore, the quantitative results for AuNP mass concentration obtained with spICPMS following alkaline sample pretreatment coincided with results for total gold...... concentration obtained by conventional ICPMS analysis of acid-digested tissue. The recovery of AuNPs from enzymatically digested tissue, however, was approximately four times lower. Spiking experiments of blank spleen samples with AuNPs showed that the lower recovery was caused by an inferior transport...

Survey of elemental concentrations in lichen samples collected from Sao Paulo State

International Nuclear Information System (INIS)

Saiki, M.; Horimoto, L.K.; Vasconcellos, M.B.A.; Coccaro, D.M.B.; Marcelli, M.P.

2001-01-01

Samples of the lichen Canoparmelia texana collected in seven different sites of Sao Paulo State and one site of the Parana State were analysed by neutron activation analysis in order to obtain information on the air quality in these regions and also to select a region of interest for the evaluation of baseline level of elements in lichen species. Concentrations of the elements Al, As, Br, Ca, Cd, Cl, Co, Cs, Fe, Hf, K, Mg, Mn, Na, Rb, Sb, Sc, Se, Ti, Th, U, V, Zn and lanthanides were determined and a preliminary comparisons was made between the results obtained for samples collected in different sites. (author)

DNA methylation age is elevated in breast tissue of healthy women.

Science.gov (United States)

Sehl, Mary E; Henry, Jill E; Storniolo, Anna Maria; Ganz, Patricia A; Horvath, Steve

2017-07-01

Limited evidence suggests that female breast tissue ages faster than other parts of the body according to an epigenetic biomarker of aging known as the "epigenetic clock." However, it is unknown whether breast tissue samples from healthy women show a similar accelerated aging effect relative to other tissues, and what could drive this acceleration. The goal of this study is to validate our initial finding of advanced DNA methylation (DNAm) age in breast tissue, by directly comparing it to that of peripheral blood tissue from the same individuals, and to do a preliminary assessment of hormonal factors that could explain the difference. We utilized n = 80 breast and 80 matching blood tissue samples collected from 40 healthy female participants of the Susan G. Komen Tissue Bank at the Indiana University Simon Cancer Center who donated these samples at two time points spaced at least a year apart. DNA methylation levels (Illumina 450K platform) were used to estimate the DNAm age. DNAm age was highly correlated with chronological age in both peripheral blood (r = 0.94, p < 0.0001) and breast tissues (r = 0.86, p < 0.0001). A measure of epigenetic age acceleration (age-adjusted DNAm Age) was substantially increased in breast relative to peripheral blood tissue (p = 1.6 × 10 -11 ). The difference between DNAm age of breast and blood decreased with advancing chronologic age (r = -0.53, p = 4.4 × 10 -4 ). Our data clearly demonstrate that female breast tissue has a higher epigenetic age than blood collected from the same subject. We also observe that the degree of elevation in breast diminishes with advancing age. Future larger studies will be needed to examine associations between epigenetic age acceleration and cumulative hormone exposure.

Acceptability of self-collection sampling for HPV-DNA testing in low-resource settings: a mixed methods approach.

Science.gov (United States)

Bansil, Pooja; Wittet, Scott; Lim, Jeanette L; Winkler, Jennifer L; Paul, Proma; Jeronimo, Jose

2014-06-12

Vaginal self-sampling with HPV-DNA tests is a promising primary screening method for cervical cancer. However, women's experiences, concerns and the acceptability of such tests in low-resource settings remain unknown. In India, Nicaragua, and Uganda, a mixed-method design was used to collect data from surveys (N = 3,863), qualitative interviews (N = 72; 20 providers and 52 women) and focus groups (N = 30 women) on women's and providers' experiences with self-sampling, women's opinions of sampling at home, and their future needs. Among surveyed women, 90% provided a self- collected sample. Of these, 75% reported it was easy, although 52% were initially concerned about hurting themselves and 24% were worried about not getting a good sample. Most surveyed women preferred self-sampling (78%). However it was not clear if they responded to the privacy of self-sampling or the convenience of avoiding a pelvic examination, or both. In follow-up interviews, most women reported that they didn't mind self-sampling, but many preferred to have a provider collect the vaginal sample. Most women also preferred clinic-based screening (as opposed to home-based self-sampling), because the sample could be collected by a provider, women could receive treatment if needed, and the clinic was sanitary and provided privacy. Self-sampling acceptability was higher when providers prepared women through education, allowed women to examine the collection brush, and were present during the self-collection process. Among survey respondents, aids that would facilitate self-sampling in the future were: staff help (53%), additional images in the illustrated instructions (31%), and a chance to practice beforehand with a doll/model (26%). Self-and vaginal-sampling are widely acceptable among women in low-resource settings. Providers have a unique opportunity to educate and prepare women for self-sampling and be flexible in accommodating women's preference for self-sampling.

Radionuclides in animal tissue samples from various regions of Austria

International Nuclear Information System (INIS)

Tatzber, F.

1981-06-01

An investigation of the concentration of radioactive substances in animal species from various regions of Austria has been carried out. For bone and liver of deer, radionuclide concentrations typical for central Europe were found. The content of 90 Sr were higher in gasteropod shells than in deer bone. Similar concentrations of 90 Sr were found in isopods as in snail shells related to fresh weight, but related to Ca content the values in isopods were higher than in all other animals. Based on these results, a study of snail shells and of isopods as bioindicators for 90 Sr content in environmental control is indicated. In tissue samples of the same species, but from different regions of Austria, the fallout radionuclide concentrations were found to be related to altitude ( 90 Sr) and to the amount of precipitation ( 137 Cs). These correlation differences could point to a different deposition behaviours of 90 Sr and 137 Cs, the former being deposited mainly with solid precipitation. This seems plausible since aerosols carried over continental distances show a high sulfate content and alkaline earth metal sulfates are less soluble than alkali sulfates. Examination of absolute concentration values related to fresh tissue weight show high fallout radionuclide concentrations, as compared to natural radionuclide concentration, especially in hard tissues. These fallout levels constitute a significant radioactive load on the biosphere. Due to the long physical half-life of 90 Sr and 137 Cs, this situation will remain virtually unchanged during the next decades, even if no further nuclear weapons tests are carried out. (G.G.)

Quality control in diagnostic molecular pathology in the Netherlands; proficiency testing for patient identification in tissue samples

NARCIS (Netherlands)

Thunnissen, F. B. J. M.; Tilanus, M. G. J.; Ligtenberg, M. J. L.; Nederlof, P. M.; Dinjens, W. N. M.; Meulemans, E.; van den Brule, A. J. C.; van Noesel, C. J. M.; de Leeuw, W. J. F.; Schuuring, E.

2004-01-01

Aims: To describe the evolution of proficiency testing for molecular diagnostic pathology with respect to determining unambiguously the patient identity of tissue samples by microsatellite analysis. Method: Four rounds of quality control exchanges of samples from different patients were sent with

Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments.

Science.gov (United States)

Choi, Sungshin; Ray, Hami E; Lai, San-Huei; Alwood, Joshua S; Globus, Ruth K

2016-01-01

Even with recent scientific advancements, challenges posed by limited resources and capabilities at the time of sample dissection continue to limit the collection of high quality tissues from experiments that can be conducted only infrequently and at high cost, such as in space. The resources and time it takes to harvest tissues post-euthanasia, and the methods and duration of long duration storage, potentially have negative impacts on sample quantity and quality, thereby limiting the scientific outcome that can be achieved. The goals of this study were to optimize methods for both sample recovery and science return from rodent experiments, with possible relevance to both ground based and spaceflight studies. The first objective was to determine the impacts of tissue harvest time post-euthanasia, preservation methods, and storage duration, focusing on RNA quality and enzyme activities in liver and spleen as indices of sample quality. The second objective was to develop methods that will maximize science return by dissecting multiple tissues after long duration storage in situ at -80°C. Tissues of C57Bl/6J mice were dissected and preserved at various time points post-euthanasia and stored at -80°C for up to 11 months. In some experiments, tissues were recovered from frozen carcasses which had been stored at -80°C up to 7 months. RNA quantity and quality was assessed by measuring RNA Integrity Number (RIN) values using an Agilent Bioanalyzer. Additionally, the quality of tissues was assessed by measuring activities of hepatic enzymes (catalase, glutathione reductase and GAPDH). Fresh tissues were collected up to one hour post-euthanasia, and stored up to 11 months at -80°C, with minimal adverse effects on the RNA quality of either livers or RNAlater-preserved spleens. Liver enzyme activities were similar to those of positive controls, with no significant effect observed at any time point. Tissues dissected from frozen carcasses that had been stored for up to 7

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

Directory of Open Access Journals (Sweden)

Parida Shreemanta K

2010-01-01

Full Text Available Abstract Background For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or in-silico deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues. Results Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach. Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available. Conclusions The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in

Chemical pollutants in field-collected canvasback tissues, eggs, and food materials

Science.gov (United States)

White, D.H.; Dieter, M.P.; Stendell, R.C.

1976-01-01

In 1972 studies began on the levels of environmental pollutants in canvasback tissues, eggs, and food items. The purpose of the studies were to determine if the levels of toxic chemicals found in canvasbacks were of the magnitude to cause problems affecting reproduction and survival. Overall, levels of organochlorine pesticides and PCB's were low in canvasbacks and their eggs. Some individual birds, however, laid eggs with elevated residues of DDE (12.1 ppm) or PCB's (28.6 ppm). There was no significant difference between eggshell thicknesses of 1972-73 and pre-1946 collections. About 12% of the canvasbacks analyzed had elevated levels of blood lead with reduced ALAD enzyme activity. Adult canvasbacks collected from the Chesapeake Bay in 1975 had moderate to high levels of cadmium in their kidneys. Cadmium, in excessive amounts is very toxic and can curtail spermatogenesis in male birds. Although no single toxic chemical found in wild canvasbacks appears to be a major factor in population declines, the cumulative effects of sublethal levels of all the pollutants may render birds susceptible to disease, hunting pressure or predation.

Validation of freezing tissues and cells for analysis of DNA strand break levels by comet assay

Science.gov (United States)

Jackson, Petra

2013-01-01

The comet analysis of DNA strand break levels in tissues and cells has become a common method of screening for genotoxicity. The large majority of published studies have used fresh tissues and cells processed immediately after collection. However, we have used frozen tissues and cells for more than 10 years, and we believe that freezing samples improve efficiency of the method. We compared DNA strand break levels measured in fresh and frozen bronchoalveolar cells, and lung and liver tissues from mice exposed to the known mutagen methyl methanesulphonate (0, 25, 75, 112.5mg/kg). We used a high-throughput comet protocol with fully automated scoring of DNA strand break levels. The overall results from fresh and frozen samples were in agreement [R 2 = 0.93 for %DNA in tail (%TDNA) and R 2 = 0.78 for tail length (TL)]. A slightly increased %TDNA was observed in lung and liver tissue from vehicle controls; and TL was slightly reduced in bronchoalveolar lavage cells from the high-dose group. In our comet protocol, a small block of tissue designated for comet analysis is frozen immediately at tissue collection and kept deep frozen until rapidly homogenised and embedded in agarose. To demonstrate the feasibility of long-term freezing of samples, we analysed the day-to-day variation of our internal historical negative and positive comet assay controls collected over a 10-year period (1128 observations, 11 batches of frozen untreated and H2O2-treated A549 lung epithelial cells). The H2O2 treatment explained most of the variation 57–77% and the day-to-day variation was only 2–12%. The presented protocol allows analysis of samples collected over longer time span, at different locations, with reduced variation by reducing number of electrophoreses and is suitable for both toxicological and epidemiological studies. The use of frozen tissues; however, requires great care during preparation before analysis, with handling as a major risk factor. PMID:24136994

Evaluation of a new simple collection device for sampling of microparticles in exhaled breath.

Science.gov (United States)

Seferaj, Sabina; Ullah, Shahid; Tinglev, Åsa; Carlsson, Sten; Winberg, Jesper; Stambeck, Peter; Beck, Olof

2018-03-12

The microparticle fraction of exhaled breath is of interest for developing clinical biomarkers. Exhaled particles may contain non-volatile components from all parts of the airway system, formed during normal breathing. This study aimed to evaluate a new, simple sampling device, based on impaction, for collecting microparticles from exhaled breath. Performance of the new device was compared with that of the existing SensAbues membrane filter device. The analytical work used liquid chromatography-tandem mass spectrometry methods. The new device collected three subsamples and these were separately analysed from eight individuals. No difference was observed between the centre position (0.91 ng/sample) and the side positions (1.01 ng/sample) using major phosphatidylcholine (PC) 16:0/16:0 as the analyte. Exhaled breath was collected from eight patients on methadone maintenance treatment. The intra-individual variability in measured methadone concentration between the three collectors was 8.7%. In another experiment using patients on methadone maintenance treatment, the sampling efficiency was compared with an established filter device. Compared to the existing device, the efficiency of the new device was 121% greater for methadone and 1450% greater for DPPC. The data from lipid analysis also indicated that a larger fraction of the collected material was from the distal parts. Finally, a study using an optical particle counter indicated that the device preferentially collects the larger particle fraction. In conclusion, this study demonstrates the usefulness of the new device for collecting non-volatile components from exhaled breath. The performance of the device was superior to the filter device in several aspects.

[Establishment and Management of Multicentral Collection Bio-sample Banks of Malignant Tumors from Digestive System].

Science.gov (United States)

Shen, Si; Shen, Junwei; Zhu, Liang; Wu, Chaoqun; Li, Dongliang; Yu, Hongyu; Qiu, Yuanyuan; Zhou, Yi

2015-11-01

To establish and manage of multicentral collection bio-sample banks of malignant tumors from digestive system, the paper designed a multicentral management system, established the standard operation procedures (SOPs) and leaded ten hospitals nationwide to collect tumor samples. The biobank has been established for half a year, and has collected 695 samples from patients with digestive system malignant tumor. The clinical data is full and complete, labeled in a unified way and classified to be managed. The clinical and molecular biology researches were based on the biobank, and obtained achievements. The biobank provides a research platform for malignant tumor of digestive system from different regions and of different types.

Sample collection and preparation of biofluids and extracts for gas chromatography-mass spectrometry.

Science.gov (United States)

Emwas, Abdul-Hamid M; Al-Talla, Zeyad A; Kharbatia, Najeh M

2015-01-01

To maximize the utility of gas chromatography-mass spectrometry (GC-MS) in metabonomics research, all stages of the experimental design should be standardized, including sample collection, storage, preparation, and sample separation. Moreover, the prerequisite for any GC-MS analysis is that a compound must be volatile and thermally stable if it is to be analyzed using this technique. Since many metabolites are nonvolatile and polar in nature, they are not readily amenable to analysis by GC-MS and require initial chemical derivatization of the polar functional groups in order to reduce the polarity and to increase the thermal stability and volatility of the analytes. In this chapter, an overview is presented of the optimum approach to sample collection, storage, and preparation for gas chromatography-mass spectrometry-based metabonomics with particular focus on urine samples as example of biofluids.

Dietary intake and burden of lanthanide in main organs and tissues for Chinese man

International Nuclear Information System (INIS)

Zhu Hongda; Liu Qingfeng; Ouyang Li; Liu Husheng; Wang Naifen; Liu Yaqiong; Zhang Yongbao; Wang Ke; Chen Rusong

2004-01-01

Objective: To determine lanthanide concentrations in dietary foods and main organs or tissues for Chinese adult man and to estimate their daily intakes by ingestion and organ or tissue burdens. Methods: Ten kinds of organ or tissue samples collected in autopsy from 21 supplemental subjects of 4 areas with different dietary types in China who died suddenly, and had been healthy and normal before death. The concentrations of 11 lanthanide in foods and 14 lanthanide in these organ or tissue samples, including those collected from 31 subjects in the past, were analyzed by using ICP-MS or INAA technique as well as necessary QC measures. With uses of the local diet composition and relevant organ or tissue weights for Chinese Reference Man, their daily intakes and organ or tissue burdens were estimated. Results: The concentrations of 14 lanthanide in 12 categories of foods and 10 kinds of organ or tissue samples, their dietary daily intakes and organ or tissue burdens for Chinese adult men were obtained. Conclusion: Besides updating the relevant data of La, Ce and Eu in 5 kinds of organ or tissue and diet, this research obtained data on concentrations of other 11 lanthanide in Chinese foods and 10 kinds of organ or tissue, their daily intakes and burdens for the first time in China. The results provide more systematic bases for developing the parameters of Chinese Reference Man than before. This study provides also comparative data for different kinds of lanthanide, foods, organs or tissues and also the background values of Chinese soil

FRD tissue archive

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The fishery genetics tissue collection has over 80,000 tissues stored in 95% ethanol representing fishes and invertebrates collected globally but with a focus on the...

Performance of a hydrostatic sampler for collecting samples at the water-sediment interface in lakes

Directory of Open Access Journals (Sweden)

Fernando PEDROZO

2008-02-01

Full Text Available The water-sediment interface plays a significant role in the determination of the trophic degree of a waterbody. Numerous redox reactions take place there, resulting in the release of contaminants from the sediments to the water column. The aim of the present work was to develop an equipment for collecting samples from the water-sediment interface. Such equipment was to have a simple design, low construction cost, no depth limitations, and high levels of personal safety and to be reliable in the collection of samples. The performance of the hydrostatic sampler thus developed was tested against samples collected either remotely with a corer or directly with syringes by autonomous divers. The hydrostatic sampler permits access to depths where the costs of the traditional diving methodology are expensive, and where working conditions are dangerous for the diver. The hydrostatic sampler provides an additional means of collecting samples from the water-sediment interface, which together with pore-water samples, facilitates the investigation and understanding of chemical mechanisms in lakes, for instance, those that control the P release from sediment to the water column.

Variability and reliability of POP concentrations in multiple breast milk samples collected from the same mothers.

Science.gov (United States)

Kakimoto, Risa; Ichiba, Masayoshi; Matsumoto, Akiko; Nakai, Kunihiko; Tatsuta, Nozomi; Iwai-Shimada, Miyuki; Ishiyama, Momoko; Ryuda, Noriko; Someya, Takashi; Tokumoto, Ieyasu; Ueno, Daisuke

2018-01-13

Risk assessment of infant using a realistic persistent organic pollutant (POP) exposure through breast milk is essential to devise future regulation of POPs. However, recent investigations have demonstrated that POP levels in breast milk collected from the same mother showed a wide range of variation daily and monthly. To estimate the appropriate sample size of breast milk from the same mother to obtain reliable POP concentrations, breast milk samples were collected from five mothers living in Japan from 2006 to 2012. Milk samples from each mother were collected 3 to 6 times a day through 3 to 7 days consecutively. Food samples as the duplicated method were collected from two mothers during the period of breast milk sample collection. Those were employed for POP (PCBs, DDTs, chlordanes, and HCB) analysis. PCB concentrations detected in breast milk samples showed a wide range of variation which was maximum 63 and 60% of relative standard deviation (RSD) in lipid and wet weight basis, respectively. The time course trend of those variations among the mothers did not show any typical pattern. A larger amount of PCB intake through food seemed to affect 10 h after those concentrations in breast milk in lipid weight basis. Intraclass correlation coefficient (ICC) analyses indicated that the appropriate sample size for good reproducibility of POP concentrations in breast milk required at least two samples for lipid and wet weight basis.

Browning of Subcutaneous White Adipose Tissue in Humans

OpenAIRE

Sidossis, Labros S.; Porter, Craig; Saraf, Manish K.; Børsheim, Elisabet; Radhakrishnan, Ravi S.; Chao, Tony; Ali, Arham; Chondronikola, Maria; Mlcak, Ronald; Finnerty, Celeste C.; Hawkins, Hal K.; Toliver-Kinsky, Tracy; Herndon, David N.

2015-01-01

Since the presence of brown adipose tissue (BAT) was confirmed in adult humans, BAT has become a therapeutic target for obesity and insulin resistance. We examined whether human subcutaneous white adipose tissue (sWAT) can adopt a BAT-like phenotype using a clinical model of prolonged and severe adrenergic stress. sWAT samples were collected from severely burned and healthy individuals. A subset of burn victims were prospectively followed during their acute hospitalization. Browning of sWAT w...

Virus characterization and discovery in formalin-fixed paraffin-embedded tissues.

Science.gov (United States)

Bodewes, Rogier; van Run, Peter R W A; Schürch, Anita C; Koopmans, Marion P G; Osterhaus, Albert D M E; Baumgärtner, Wolfgang; Kuiken, Thijs; Smits, Saskia L

2015-03-01

Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

Buczkowski, Brian J.; Kelsey, Sarah A.

2007-01-01

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

The value of banked samples for oncology drug discovery and development.

Science.gov (United States)

Shaw, Peter M; Patterson, Scott D

2011-01-01

To gain insights into human biology and pathobiology, ready access to banked human tissue samples that encompass a representative cross section of the population is required. For optimal use, the banked human tissue needs to be appropriately consented, collected, annotated, and stored. If any of these elements are missing, the studies using these samples are compromised. These elements are critical whether the research is for academic or pharmaceutical industry purposes. An additional temporal element that adds enormous value to such banked samples is treatment and outcome information from the people who donated the tissue. To achieve these aims, many different groups have to work effectively together, not least of which are the individuals who donate their tissue with appropriate consent. Such research is unlikely to benefit the donors but others who succumb to the same disease. The development of a large accessible human tissue bank resource (National Cancer Institute's Cancer HUman Biobank [caHUB]) that provides an ongoing supply of human tissue for all working toward the common goal of understanding human health and disease has a number of advantages. These include, but are not limited to, access to a broad cross section of healthy and diseased populations beyond what individual collections may achieve for understanding disease pathobiology, therapeutic target discovery, as well as a source of material for diagnostic assay validation. Models will need to be developed to enable fair access to caHUB under terms that enable appropriate intellectual property protection and ultimate data sharing to ensure that the biobank successfully distributes samples to a broad range of researchers.

JSC Advanced Curation: Research and Development for Current Collections and Future Sample Return Mission Demands

Science.gov (United States)

Fries, M. D.; Allen, C. C.; Calaway, M. J.; Evans, C. A.; Stansbery, E. K.

2015-01-01

Curation of NASA's astromaterials sample collections is a demanding and evolving activity that supports valuable science from NASA missions for generations, long after the samples are returned to Earth. For example, NASA continues to loan hundreds of Apollo program samples to investigators every year and those samples are often analyzed using instruments that did not exist at the time of the Apollo missions themselves. The samples are curated in a manner that minimizes overall contamination, enabling clean, new high-sensitivity measurements and new science results over 40 years after their return to Earth. As our exploration of the Solar System progresses, upcoming and future NASA sample return missions will return new samples with stringent contamination control, sample environmental control, and Planetary Protection requirements. Therefore, an essential element of a healthy astromaterials curation program is a research and development (R&D) effort that characterizes and employs new technologies to maintain current collections and enable new missions - an Advanced Curation effort. JSC's Astromaterials Acquisition & Curation Office is continually performing Advanced Curation research, identifying and defining knowledge gaps about research, development, and validation/verification topics that are critical to support current and future NASA astromaterials sample collections. The following are highlighted knowledge gaps and research opportunities.

Effect of soil and water environment on typeability of PowerPlex Y (Promega) in selected tissue samples.

OpenAIRE

Ewa Koc-Zorawska; Jerzy Janica; Malgorzata Skawronska; Jacek Robert Janica; Witold Pepinski; Anna Niemcunowicz-Janica; Ireneusz Stolyszewski

2008-01-01

In cases of decomposed bodies Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability PowerPlex Y (Promega) loci in tissue material stored in water and soil environment. Tissue material was collected during autopsies of five persons aged 20-30 years with time of death determined within the limit of 14 hours. Heart muscle, liver and lung specimens were stored in pond water, sea water, sand and peat soil. DNA was extracted by organic method...

Theory of sampling and its application in tissue based diagnosis

Directory of Open Access Journals (Sweden)

Kayser Gian

2009-02-01

Full Text Available Abstract Background A general theory of sampling and its application in tissue based diagnosis is presented. Sampling is defined as extraction of information from certain limited spaces and its transformation into a statement or measure that is valid for the entire (reference space. The procedure should be reproducible in time and space, i.e. give the same results when applied under similar circumstances. Sampling includes two different aspects, the procedure of sample selection and the efficiency of its performance. The practical performance of sample selection focuses on search for localization of specific compartments within the basic space, and search for presence of specific compartments. Methods When a sampling procedure is applied in diagnostic processes two different procedures can be distinguished: I the evaluation of a diagnostic significance of a certain object, which is the probability that the object can be grouped into a certain diagnosis, and II the probability to detect these basic units. Sampling can be performed without or with external knowledge, such as size of searched objects, neighbourhood conditions, spatial distribution of objects, etc. If the sample size is much larger than the object size, the application of a translation invariant transformation results in Kriege's formula, which is widely used in search for ores. Usually, sampling is performed in a series of area (space selections of identical size. The size can be defined in relation to the reference space or according to interspatial relationship. The first method is called random sampling, the second stratified sampling. Results Random sampling does not require knowledge about the reference space, and is used to estimate the number and size of objects. Estimated features include area (volume fraction, numerical, boundary and surface densities. Stratified sampling requires the knowledge of objects (and their features and evaluates spatial features in relation to

Validation of Marek's disease diagnosis and monitoring of Marek's disease vaccines from samples collected in FTA cards.

Science.gov (United States)

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 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.

The decrease in silicon concentration of the connective tissues with age in rats is a marker of connective tissue turnover.

Science.gov (United States)

Jugdaohsingh, Ravin; Watson, Abigail I E; Pedro, Liliana D; Powell, Jonathan J

2015-06-01

Silicon may be important for bone and connective tissue health. Higher concentrations of silicon are suggested to be associated with bone and the connective tissues, compared with the non-connective soft tissues. Moreover, in connective tissues it has been suggested that silicon levels may decrease with age based upon analyses of human aorta. These claims, however, have not been tested under controlled conditions. Here connective and non-connective tissues were collected and analysed for silicon levels from female Sprague-Dawley rats of different ages (namely, 3, 5, 8, 12, 26 and 43 weeks; n=8-10 per age group), all maintained on the same feed source and drinking water, and kept in the same environment from weaning to adulthood. Tissues (696 samples) were digested in nitric acid and analysed by inductively coupled plasma optical emission spectrometry for total silicon content. Fasting serum samples were also collected, diluted and analysed for silicon. Higher concentrations of silicon (up to 50-fold) were found associated with bone and the connective tissues compared with the non-connective tissues. Although total silicon content increased with age in all tissues, the highest connective tissue silicon concentrations (up to 9.98 μg/g wet weight) were found in young weanling rats, decreasing thereafter with age (by 2-6 fold). Fasting serum silicon concentrations reflected the pattern of connective tissue silicon concentrations and, both measures, when compared to collagen data from a prior experiment in Sprague-Dawley rats, mirrored type I collagen turnover with age. Our findings confirm the link between silicon and connective tissues and would imply that young growing rats have proportionally higher requirements for dietary silicon than mature adults, for bone and connective tissue development, although this was not formally investigated here. However, estimation of total body silicon content suggested that actual Si requirements may be substantially lower than

The decrease in silicon concentration of the connective tissues with age in rats is a marker of connective tissue turnover☆

Science.gov (United States)

Jugdaohsingh, Ravin; Watson, Abigail I.E.; Pedro, Liliana D.; Powell, Jonathan J.

2015-01-01

Silicon may be important for bone and connective tissue health. Higher concentrations of silicon are suggested to be associated with bone and the connective tissues, compared with the non-connective soft tissues. Moreover, in connective tissues it has been suggested that silicon levels may decrease with age based upon analyses of human aorta. These claims, however, have not been tested under controlled conditions. Here connective and non-connective tissues were collected and analysed for silicon levels from female Sprague–Dawley rats of different ages (namely, 3, 5, 8, 12, 26 and 43 weeks; n = 8–10 per age group), all maintained on the same feed source and drinking water, and kept in the same environment from weaning to adulthood. Tissues (696 samples) were digested in nitric acid and analysed by inductively coupled plasma optical emission spectrometry for total silicon content. Fasting serum samples were also collected, diluted and analysed for silicon. Higher concentrations of silicon (up to 50-fold) were found associated with bone and the connective tissues compared with the non-connective tissues. Although total silicon content increased with age in all tissues, the highest connective tissue silicon concentrations (up to 9.98 μg/g wet weight) were found in young weanling rats, decreasing thereafter with age (by 2–6 fold). Fasting serum silicon concentrations reflected the pattern of connective tissue silicon concentrations and, both measures, when compared to collagen data from a prior experiment in Sprague–Dawley rats, mirrored type I collagen turnover with age. Our findings confirm the link between silicon and connective tissues and would imply that young growing rats have proportionally higher requirements for dietary silicon than mature adults, for bone and connective tissue development, although this was not formally investigated here. However, estimation of total body silicon content suggested that actual Si requirements may be substantially

PAH data in tissues of subsistence harvested marine mammal - Determination of PAH baseline values in tissues from subsistence-harvested marine mammals on the North Slope

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Over the past 15 years, high quality marine mammal tissue and fluid samples collected by subsistence hunters in the North Slope region of Alaska have been archived...

Radioisotopic method for the measurement of lipolysis in small samples of human adipose tissue

International Nuclear Information System (INIS)

Leibel, R.L.; Hirsch, J.; Berry, E.M.; Gruen, R.K.

1984-01-01

To facilitate the study of adrenoreceptor response in small needle biopsy samples of human subcutaneous adipose tissue, we developed a dual radioisotopic technique for measuring lipolysis rate. Aliquots (20-75 mg) of adipose tissue fragments were incubated in a buffered albumin medium containing [ 3 H]palmitate and [ 14 C]glucose, each of high specific activity. In neutral glycerides synthesized in this system, [ 14 C]glucose is incorporated exclusively into the glyceride-glycerol moiety and 3 H appears solely in the esterified fatty acid. Alpha-2 and beta-1 adrenoreceptor activation of tissue incubated in this system does not alter rates of 14 C-labeled glyceride accumulation, but does produce a respective increase or decrease in the specific activity of fatty acids esterified into newly synthesized glycerides. This alteration in esterified fatty acid specific activity is reflected in the ratio of 14 C: 3 H in newly synthesized triglycerides extracted from the incubated adipose tissue. There is a high correlation (r . 0.90) between the 14 C: 3 H ratio in triglycerides and the rate of lipolysis as reflected in glycerol release into the incubation medium. The degree of adrenoreceptor activation by various concentrations of lipolytic and anti-lipolytic substances can be assessed by comparing this ratio in stimulated tissue to that characterizing unstimulated tissue or the incubation medium. This technique permits the study of very small, unweighed tissue biopsy fragments, the only limitation on sensitivity being the specific activity of the medium glucose and palmitate. It is, therefore, useful for serial examinations of adipose tissue adrenoreceptor dose-response characteristics under a variety of clinical circumstances

Electron probe microanalysis for clinical investigations: Microdrop and soft tissue analysis

International Nuclear Information System (INIS)

Ingram, M.J.; Ingram, F.D.

1984-01-01

The most important advantage offered by electron probe microanalysis (EPA) for clinical investigations is the ability to analyze smaller volumes of tissue than is possible with conventional techniques. The sample can be a biological soft tissue specimen, which involves subcellular localization, or a picoliter fluid droplet. In either case, the analysis can be nondestructive and permit multiple analyses for a number of elements in a given sample. The most highly developed electron microprobe analytical technique is fluid drop analysis, popularly referred to as microdrop analysis. This method provides the investigator with an analytic capability that has an accuracy of measurement often 1% or better on 20 to 30 picoliter fluid droplets. Electron microprobe techniques have been used for studies of animal hard tissue and for studies that involve insoluble inclusions. However, the development of techniques for studies of labile constituents in animal soft tissue has been much slower. It has been necessary not only to develop appropriate methods of tissue preparation, but also to establish sound techniques for tissue collection. Although there are adequate methods for collection of most types of tissue from laboratory animals, many of these methods are not suitable for human subjects. In order to provide the reader with a better understanding of the capabilities and potential for the application of electron microprobe methodology to problems in clinical medicine, the authors discuss some of their experiences with liquid droplet analysis and quantitative electrolyte distribution measurements in animal soft tissue

Impact of collection container material and holding times on sample integrity for mercury and methylmercury in water

Energy Technology Data Exchange (ETDEWEB)

Riscassi, Ami L [ORNL; Miller, Carrie L [ORNL; Brooks, Scott C [ORNL

2014-01-01

Mercury (Hg) and methylmercury (MeHg) concentrations in streamwater can vary on short timescales (hourly or less) during storm flow and on a diel cycle; the frequency and timing of sampling required to accurately characterize these dynamics may be difficult to accomplish manually. Automated sampling can assist in sample collection; however use has been limited for Hg and MeHg analysis due to stability concerns of trace concentrations during extended storage times. We examined the viability of using automated samplers with disposable low-density polyethylene (LDPE) sample bags to collect industrially contaminated streamwater for unfiltered and filtered Hg and MeHg analysis. Specifically we investigated the effect of holding times ranging from hours to days on streamwater collected during baseflow and storm flow. Unfiltered and filtered Hg and MeHg concentrations decreased with increases in time prior to sample processing; holding times of 24 hours or less resulted in concentration changes (mean 11 7% different) similar to variability in duplicates collected manually during analogous field conditions (mean 7 10% different). Comparisons of samples collected with manual and automated techniques throughout a year for a wide range of stream conditions were also found to be similar to differences observed between duplicate grab samples. These results demonstrate automated sampling into LDPE bags with holding times of 24 hours or less can be effectively used to collect streamwater for Hg and MeHg analysis, and encourage the testing of these materials and methods for implementation in other aqueous systems where high-frequency sampling is warranted.

78 FR 79009 - Proposed Information Collection; Radiation Sampling and Exposure Records (Pertains to Underground...

Science.gov (United States)

2013-12-27

... soliciting comments concerning the proposed information collection for updating Radiation Sampling and... exposed with no adverse effects have been established and are expressed as working levels (WL). The... mandatory samplings. Records must include the sample date, location, and results, and must be retained at...

Chemical and ancillary data associated with bed sediment, young of year Bluefish (Pomatomus saltatrix) tissue, and mussel (Mytilus edulis and Geukensia demissa) tissue collected after Hurricane Sandy in bays and estuaries of New Jersey and New York, 2013–14

Science.gov (United States)

Smalling, Kelly L.; Deshpande, Ashok D.; Blazer, Vicki; Galbraith, Heather S.; Dockum, Bruce W.; Romanok, Kristin M.; Colella, Kaitlyn; Deetz, Anna C.; Fisher, Irene J.; Imbrigiotta, Thomas E.; Sharack, Beth; Summer, Lisa; Timmons, DeMond; Trainor, John J.; Wieczorek, Daniel; Samson, Jennifer; Reilly, Timothy J.; Focazio, Michael J.

2015-09-09

This report describes the methods and data associated with a reconnaissance study of young of year bluefish and mussel tissue samples as well as bed sediment collected as bluefish habitat indicators during August 2013–April 2014 in New Jersey and New York following Hurricane Sandy in October 2012. This study was funded by the Disaster Relief Appropriations Act of 2013 (PL 113-2) and was conducted by the U.S. Geological Survey (USGS) in cooperation with the National Oceanic and Atmospheric Administration (NOAA).

Sample preparation procedure for PIXE elemental analysis on soft tissues

International Nuclear Information System (INIS)

Kubica, B.; Kwiatek, W.M.; Dutkiewicz, E.M.; Lekka, M.

1997-01-01

Trace element analysis is one of the most important field in analytical chemistry. There are several instrumental techniques which are applied for determinations of microscopic elemental content. The PIXE (Proton Induced X-ray Emission) technique is one of the nuclear techniques that is commonly applied for such purpose due to its multielemental analysis possibilities. The aim of this study was to establish the optimal conditions for target preparation procedure. In this paper two different approaches to the topic are presented and widely discussed. The first approach was the traditional pellet technique and the second one was mineralization procedure. For the analysis soft tissue such as liver was used. Some results are also presented on water samples. (author)

Identification of immune cell infiltration in hematoxylin-eosin stained breast cancer samples: texture-based classification of tissue morphologies

Science.gov (United States)

Turkki, Riku; Linder, Nina; Kovanen, Panu E.; Pellinen, Teijo; Lundin, Johan

2016-03-01

The characteristics of immune cells in the tumor microenvironment of breast cancer capture clinically important information. Despite the heterogeneity of tumor-infiltrating immune cells, it has been shown that the degree of infiltration assessed by visual evaluation of hematoxylin-eosin (H and E) stained samples has prognostic and possibly predictive value. However, quantification of the infiltration in H and E-stained tissue samples is currently dependent on visual scoring by an expert. Computer vision enables automated characterization of the components of the tumor microenvironment, and texture-based methods have successfully been used to discriminate between different tissue morphologies and cell phenotypes. In this study, we evaluate whether local binary pattern texture features with superpixel segmentation and classification with support vector machine can be utilized to identify immune cell infiltration in H and E-stained breast cancer samples. Guided with the pan-leukocyte CD45 marker, we annotated training and test sets from 20 primary breast cancer samples. In the training set of arbitrary sized image regions (n=1,116) a 3-fold cross-validation resulted in 98% accuracy and an area under the receiver-operating characteristic curve (AUC) of 0.98 to discriminate between immune cell -rich and - poor areas. In the test set (n=204), we achieved an accuracy of 96% and AUC of 0.99 to label cropped tissue regions correctly into immune cell -rich and -poor categories. The obtained results demonstrate strong discrimination between immune cell -rich and -poor tissue morphologies. The proposed method can provide a quantitative measurement of the degree of immune cell infiltration and applied to digitally scanned H and E-stained breast cancer samples for diagnostic purposes.

Concentrations of buparvaquone in milk and tissue of dairy cows.

Science.gov (United States)

McDougall, S; Hillerton, J E; Pegram, D

2016-11-01

To determine the concentration of the anti-theilerial drug buparvaquone in the milk and tissue of dairy cattle following treatment with two different formulations, and to assess the effect of clinical theileriosis on the concentration of buparvaquone in milk. Healthy lactating dairy cows (n=25) were injected once (Day 0) I/M with 2.5 mg/kg of one of two formulations of buparvaquone (Butalex; n=12 or Bupaject; n=13). Milk samples were collected from all cows daily until Day 35. Five cows were slaughtered on each of Days 56, 119, 147, 203 and 328, and samples of liver, muscle and injection site tissue collected. Milk samples were also collected from cows (n=14) clinically affected with theileriosis for up to 21 days after treatment with buparvaquone. Milk and tissue samples were analysed by liquid chromatography-mass spectrometry; limits of detection (LOD) were 0.00018 mg/kg for muscle and 0.00023 mg/L for milk. Concentrations of buparvaquone in milk and tissues were log10-transformed for analysis using multivariate models. In healthy cows, concentrations of buparvaquone in milk declined with time post-treatment (pcows at Day 35. Concentration in milk was higher one day after treatment in cows treated with Butalex than in cows treated with Bupaject, but not different thereafter (p=0.007). Concentrations of buparvaquone in muscle were below the LOD for four of five animals at Day 119 and for all animals by Day 147, but were above the LOD at the injection site of one cow, and in the liver of three cows at Day 328. Tissue concentrations did not differ with formulation nor was there a formulation by time interaction (p>0.3). Concentrations of buparvaquone in the milk of clinically affected animals were not different from those of healthy animals at 1 and 21 days post-treatment (p=0.72). Between 21 and 25 days post-treatment concentrations were below the LOD in 9/14 milk samples from clinically affected cows. Detectable concentrations of buparvaquone were found in

Biased visualization of hypoperfused tissue by computed tomography due to short imaging duration: improved classification by image down-sampling and vascular models

Energy Technology Data Exchange (ETDEWEB)

Mikkelsen, Irene Klaerke; Ribe, Lars Riisgaard; Bekke, Susanne Lise; Tietze, Anna; Oestergaard, Leif; Mouridsen, Kim [Aarhus University Hospital, Center of Functionally Integrative Neuroscience, Aarhus C (Denmark); Jones, P.S.; Alawneh, Josef [University of Cambridge, Department of Clinical Neurosciences, Cambridge (United Kingdom); Puig, Josep; Pedraza, Salva [Dr. Josep Trueta Girona University Hospitals, Department of Radiology, Girona Biomedical Research Institute, Girona (Spain); Gillard, Jonathan H. [University of Cambridge, Department of Radiology, Cambridge (United Kingdom); Warburton, Elisabeth A. [Cambrigde University Hospitals, Addenbrooke, Stroke Unit, Cambridge (United Kingdom); Baron, Jean-Claude [University of Cambridge, Department of Clinical Neurosciences, Cambridge (United Kingdom); Centre Hospitalier Sainte Anne, INSERM U894, Paris (France)

2015-07-15

Lesion detection in acute stroke by computed-tomography perfusion (CTP) can be affected by incomplete bolus coverage in veins and hypoperfused tissue, so-called bolus truncation (BT), and low contrast-to-noise ratio (CNR). We examined the BT-frequency and hypothesized that image down-sampling and a vascular model (VM) for perfusion calculation would improve normo- and hypoperfused tissue classification. CTP datasets from 40 acute stroke patients were retrospectively analysed for BT. In 16 patients with hypoperfused tissue but no BT, repeated 2-by-2 image down-sampling and uniform filtering was performed, comparing CNR to perfusion-MRI levels and tissue classification to that of unprocessed data. By simulating reduced scan duration, the minimum scan-duration at which estimated lesion volumes came within 10 % of their true volume was compared for VM and state-of-the-art algorithms. BT in veins and hypoperfused tissue was observed in 9/40 (22.5 %) and 17/40 patients (42.5 %), respectively. Down-sampling to 128 x 128 resolution yielded CNR comparable to MR data and improved tissue classification (p = 0.0069). VM reduced minimum scan duration, providing reliable maps of cerebral blood flow and mean transit time: 5 s (p = 0.03) and 7 s (p < 0.0001), respectively. BT is not uncommon in stroke CTP with 40-s scan duration. Applying image down-sampling and VM improve tissue classification. (orig.)

Biased visualization of hypoperfused tissue by computed tomography due to short imaging duration: improved classification by image down-sampling and vascular models

International Nuclear Information System (INIS)

Mikkelsen, Irene Klaerke; Ribe, Lars Riisgaard; Bekke, Susanne Lise; Tietze, Anna; Oestergaard, Leif; Mouridsen, Kim; Jones, P.S.; Alawneh, Josef; Puig, Josep; Pedraza, Salva; Gillard, Jonathan H.; Warburton, Elisabeth A.; Baron, Jean-Claude

2015-01-01

Lesion detection in acute stroke by computed-tomography perfusion (CTP) can be affected by incomplete bolus coverage in veins and hypoperfused tissue, so-called bolus truncation (BT), and low contrast-to-noise ratio (CNR). We examined the BT-frequency and hypothesized that image down-sampling and a vascular model (VM) for perfusion calculation would improve normo- and hypoperfused tissue classification. CTP datasets from 40 acute stroke patients were retrospectively analysed for BT. In 16 patients with hypoperfused tissue but no BT, repeated 2-by-2 image down-sampling and uniform filtering was performed, comparing CNR to perfusion-MRI levels and tissue classification to that of unprocessed data. By simulating reduced scan duration, the minimum scan-duration at which estimated lesion volumes came within 10 % of their true volume was compared for VM and state-of-the-art algorithms. BT in veins and hypoperfused tissue was observed in 9/40 (22.5 %) and 17/40 patients (42.5 %), respectively. Down-sampling to 128 x 128 resolution yielded CNR comparable to MR data and improved tissue classification (p = 0.0069). VM reduced minimum scan duration, providing reliable maps of cerebral blood flow and mean transit time: 5 s (p = 0.03) and 7 s (p < 0.0001), respectively. BT is not uncommon in stroke CTP with 40-s scan duration. Applying image down-sampling and VM improve tissue classification. (orig.)

Comparison of semen parameters in samples collected by masturbation at a clinic and at home.

Science.gov (United States)

Elzanaty, Saad; Malm, Johan

2008-06-01

To investigate differences in semen quality between samples collected by masturbation at a clinic and at home. Cross-sectional study. Fertility center. Three hundred seventy-nine men assessed for infertility. None. Semen was analyzed according to World Health Organization guidelines. Seminal markers of epididymal (neutral alpha-glucosidase), prostatic (prostate-specific antigen and zinc), and seminal vesicle (fructose) function were measured. Two patient groups were defined according to sample collection location: at a clinic (n = 273) or at home (n = 106). Compared with clinic-collected semen, home-collected samples had statistically significantly higher values for sperm concentration, total sperm count, rapid progressive motility, and total count of progressive motility. Semen volume, proportion of normal sperm morphology, neutral alpha-glucosidase, prostate-specific antigen, zinc, and fructose did not differ significantly between groups. An abnormal sperm concentration (masturbation at home compared with at a clinic. This should be taken into consideration in infertility investigations.

Measurement of characteristic prompt gamma rays emitted from oxygen and carbon in tissue-equivalent samples during proton beam irradiation.

Science.gov (United States)

Polf, Jerimy C; Panthi, Rajesh; Mackin, Dennis S; McCleskey, Matt; Saastamoinen, Antti; Roeder, Brian T; Beddar, Sam

2013-09-07

The purpose of this work was to characterize how prompt gamma (PG) emission from tissue changes as a function of carbon and oxygen concentration, and to assess the feasibility of determining elemental concentration in tissues irradiated with proton beams. For this study, four tissue-equivalent water-sucrose samples with differing densities and concentrations of carbon, hydrogen, and oxygen were irradiated with a 48 MeV proton pencil beam. The PG spectrum emitted from each sample was measured using a high-purity germanium detector, and the absolute detection efficiency of the detector, average beam current, and delivered dose distribution were also measured. Changes to the total PG emission from (12)C (4.44 MeV) and (16)O (6.13 MeV) per incident proton and per Gray of absorbed dose were characterized as a function of carbon and oxygen concentration in the sample. The intensity of the 4.44 MeV PG emission per incident proton was found to be nearly constant for all samples regardless of their carbon concentration. However, we found that the 6.13 MeV PG emission increased linearly with the total amount (in grams) of oxygen irradiated in the sample. From the measured PG data, we determined that 1.64 × 10(7) oxygen PGs were emitted per gram of oxygen irradiated per Gray of absorbed dose delivered with a 48 MeV proton beam. These results indicate that the 6.13 MeV PG emission from (16)O is proportional to the concentration of oxygen in tissue irradiated with proton beams, showing that it is possible to determine the concentration of oxygen within tissues irradiated with proton beams by measuring (16)O PG emission.

The national DBS brain tissue network pilot study: need for more tissue and more standardization.

Science.gov (United States)

Vedam-Mai, V; Krock, N; Ullman, M; Foote, K D; Shain, W; Smith, K; Yachnis, A T; Steindler, D; Reynolds, B; Merritt, S; Pagan, F; Marjama-Lyons, J; Hogarth, P; Resnick, A S; Zeilman, P; Okun, M S

2011-08-01

Over 70,000 DBS devices have been implanted worldwide; however, there remains a paucity of well-characterized post-mortem DBS brains available to researchers. We propose that the overall understanding of DBS can be improved through the establishment of a Deep Brain Stimulation-Brain Tissue Network (DBS-BTN), which will further our understanding of DBS and brain function. The objectives of the tissue bank are twofold: (a) to provide a complete (clinical, imaging and pathological) database for DBS brain tissue samples, and (b) to make available DBS tissue samples to researchers, which will help our understanding of disease and underlying brain circuitry. Standard operating procedures for processing DBS brains were developed as part of the pilot project. Complete data files were created for individual patients and included demographic information, clinical information, imaging data, pathology, and DBS lead locations/settings. 19 DBS brains were collected from 11 geographically dispersed centers from across the U.S. The average age at the time of death was 69.3 years (51-92, with a standard deviation or SD of 10.13). The male:female ratio was almost 3:1. Average post-mortem interval from death to brain collection was 10.6 h (SD of 7.17). The DBS targets included: subthalamic nucleus, globus pallidus interna, and ventralis intermedius nucleus of the thalamus. In 16.7% of cases the clinical diagnosis failed to match the pathological diagnosis. We provide neuropathological findings from the cohort, and perilead responses to DBS. One of the most important observations made in this pilot study was the missing data, which was approximately 25% of all available data fields. Preliminary results demonstrated the feasibility and utility of creating a National DBS-BTN resource for the scientific community. We plan to improve our techniques to remedy omitted clinical/research data, and expand the Network to include a larger donor pool. We will enhance sample preparation to

Office-based narrow band imaging-guided flexible laryngoscopy tissue sampling: A cost-effectiveness analysis evaluating its impact on Taiwanese health insurance program.

Science.gov (United States)

Fang, Tuan-Jen; Li, Hsueh-Yu; Liao, Chun-Ta; Chiang, Hui-Chen; Chen, I-How

2015-07-01

Narrow band imaging (NBI)-guided flexible laryngoscopy tissue sampling for laryngopharyngeal lesions is a novel technique. Patients underwent the procedure in an office-based setting without being sedated, which is different from the conventional technique performed using direct laryngoscopy. Although the feasibility and effects of this procedure were established, its financial impact on the institution and Taiwanese National Health Insurance program was not determined. This is a retrospective case-control study. From May 2010 to April 2011, 20 consecutive patients who underwent NBI flexible laryngoscopy tissue sampling were recruited. During the same period, another 20 age-, sex-, and lesion-matched cases were enrolled in the control group. The courses for procedures and financial status were analyzed and compared between groups. Office-based NBI flexible laryngoscopy tissue sampling procedure took 27 minutes to be completed, while 191 minutes were required for the conventional technique. Average reimbursement for each case was New Taiwan Dollar (NT$)1264 for patients undergoing office-based NBI flexible laryngoscopy tissue sampling, while NT$10,913 for those undergoing conventional direct laryngoscopy in the operation room (p institution suffered a loss of at least NT$690 when performing NBI flexible laryngoscopy tissue sampling. Office-based NBI flexible laryngoscopy tissue sampling is a cost-saving procedure for patients and the Taiwanese National Health Insurance program. It also saves the procedure time. However, the net financial loss for the institution and physician would limit its popularization unless reimbursement patterns are changed. Copyright © 2013. Published by Elsevier B.V.

Simultaneous Determination of 30 Trace Elements in Cancerous and Noncancerous Human Tissue Samples with Gamma-ray Spectrometry

Energy Technology Data Exchange (ETDEWEB)

Samsahl, K; Brune, D; Wester, P O

1963-10-15

The following trace elements were quantitatively determined by gamma-ray spectrometry in T samples of non-cancerous and 5 samples of cancerous human tissue: P, Ca, Cr, Fe, Co, Cu, Zn, As, Se, Br, Rb, Mo, Ag, Cd, Sb, Cs, La, Au, and Hg. In some of the samples the following elements were qualitatively determined: Ti+Sc, Ga, Sr, In, Ba, Ce, Hf, Os, Pt, and U. Most of the trace elements were found to be present in much higher concentrations in the non-cancerous than in the corresponding cancerous liver samples. In a typical run one sample each of cancerous and non-cancerous tissue was irradiated together with standards of the elements to be determined in a thermal flux of 2.10{sup 13} n/cm{sup 2}/sec. for 24 hours. The radioactive trace elements were separated into 16, and in some cases 18, groups by means of a chemical group separation method. Subsequently, the gamma spectrometric measurements were performed. Two persons can manage the chemical separations and measure the different activities from a run in 1,5 days. A new method of comparing unknown samples with standards was developed.

Use of self-collected capillary blood samples for islet autoantibody screening in relatives: a feasibility and acceptability study.

Science.gov (United States)

Liu, Y; Rafkin, L E; Matheson, D; Henderson, C; Boulware, D; Besser, R E J; Ferrara, C; Yu, L; Steck, A K; Bingley, P J

2017-07-01

To evaluate the feasibility of using self-collected capillary blood samples for islet autoantibody testing to identify risk in relatives of people with Type 1 diabetes. Participants were recruited via the observational TrialNet Pathway to Prevention study, which screens and monitors relatives of people with Type 1 diabetes for islet autoantibodies. Relatives were sent kits for capillary blood collection, with written instructions, an online instructional video link and a questionnaire. Sera from capillary blood samples were tested for autoantibodies to glutamic acid decarboxylase, islet antigen-2, insulin and zinc transporter 8. 'Successful' sample collection was defined as obtaining sufficient volume and quality to provide definitive autoantibody results, including confirmation of positive results by repeat assay. In 240 relatives who returned samples, the median (range) age was 15.5 (1-49) years and 51% were male. Of these samples, 98% were sufficient for glutamic acid decarboxylase, islet antigen-2 and zinc transporter 8 autoantibody testing and 84% for insulin autoantibody testing and complete autoantibody screen. The upper 90% confidence bound for unsuccessful collection was 4.4% for glutamic acid decarboxylase, islet antigen-2 and/or zinc transporter 8 autoantibody assays, and 19.3% for insulin autoantibodies. Despite 43% of 220 questionnaire respondents finding capillary blood collection uncomfortable or painful, 82% preferred home self-collection of capillary blood samples compared with outpatient venepuncture (90% of those aged 18 years). The perceived difficulty of collecting capillary blood samples did not affect success rate. Self-collected capillary blood sampling offers a feasible alternative to venous sampling, with the potential to facilitate autoantibody screening for Type 1 diabetes risk. © 2017 Diabetes UK.

New Zealand guidelines for the collection of groundwater samples for chemical and isotopic analyses

International Nuclear Information System (INIS)

Rosen, M.R.; Cameron, S.G.; Reeves, R.R.; Taylor, C.B.

1999-01-01

Chemical and isotopic analyses of groundwater are important tools for differentiating between the natural composition and human-induced contaminants of groundwater. A comprehensive suite of inorganic water chemical analyses is necessary to characterise waters. The geology of New Zealand is diverse, so it is impractical to characterise a ''typical'' groundwater chemical composition. Each aquifer system should be evaluated individually because the major dissolved species contain useful information about the pathways of water through the soil zone into the aquifer. Analyses of major ions such as chloride, nitrate, potassium and sulphate often give indication of septic systems and agricultural contamination. The minor ions, while most are not considered contaminants, are often indicators of human activity. Iron and manganese are good indicators of Eh potential, which is an important control on the mobility of many heavy metals. The inexpensive inorganic chemical analytical suite should be used as a guide to advisability of more expensive contaminant testing. The purpose of this manual is to provide consistent groundwater sampling guidelines for use throughout New Zealand. Sinton's (1998) guide to groundwater sampling techniques provided a sound basis for the accurate collection of groundwater samples. However Sinton did not address sampling materials and techniques for the collection of samples for ultra trace component analysis or the collection of environmental isotope samples. These important aspects of groundwater sampling have been included in this updated manual. (author). 30 refs., 12 figs., 5 tabs., 1 appendix

Elastic moduli of normal and pathological human breast tissues: an inversion-technique-based investigation of 169 samples

Science.gov (United States)

Samani, Abbas; Zubovits, Judit; Plewes, Donald

2007-03-01

Understanding and quantifying the mechanical properties of breast tissues has been a subject of interest for the past two decades. This has been motivated in part by interest in modelling soft tissue response for surgery planning and virtual-reality-based surgical training. Interpreting elastography images for diagnostic purposes also requires a sound understanding of normal and pathological tissue mechanical properties. Reliable data on tissue elastic properties are very limited and those which are available tend to be inconsistent, in part as a result of measurement methodology. We have developed specialized techniques to measure tissue elasticity of breast normal tissues and tumour specimens and applied them to 169 fresh ex vivo breast tissue samples including fat and fibroglandular tissue as well as a range of benign and malignant breast tumour types. Results show that, under small deformation conditions, the elastic modulus of normal breast fat and fibroglandular tissues are similar while fibroadenomas were approximately twice the stiffness. Fibrocystic disease and malignant tumours exhibited a 3-6-fold increased stiffness with high-grade invasive ductal carcinoma exhibiting up to a 13-fold increase in stiffness compared to fibrogalndular tissue. A statistical analysis showed that differences between the elastic modulus of the majority of those tissues were statistically significant. Implications for the specificity advantages of elastography are reviewed.

Elastic moduli of normal and pathological human breast tissues: an inversion-technique-based investigation of 169 samples

International Nuclear Information System (INIS)

Samani, Abbas; Zubovits, Judit; Plewes, Donald

2007-01-01

Understanding and quantifying the mechanical properties of breast tissues has been a subject of interest for the past two decades. This has been motivated in part by interest in modelling soft tissue response for surgery planning and virtual-reality-based surgical training. Interpreting elastography images for diagnostic purposes also requires a sound understanding of normal and pathological tissue mechanical properties. Reliable data on tissue elastic properties are very limited and those which are available tend to be inconsistent, in part as a result of measurement methodology. We have developed specialized techniques to measure tissue elasticity of breast normal tissues and tumour specimens and applied them to 169 fresh ex vivo breast tissue samples including fat and fibroglandular tissue as well as a range of benign and malignant breast tumour types. Results show that, under small deformation conditions, the elastic modulus of normal breast fat and fibroglandular tissues are similar while fibroadenomas were approximately twice the stiffness. Fibrocystic disease and malignant tumours exhibited a 3-6-fold increased stiffness with high-grade invasive ductal carcinoma exhibiting up to a 13-fold increase in stiffness compared to fibrogalndular tissue. A statistical analysis showed that differences between the elastic modulus of the majority of those tissues were statistically significant. Implications for the specificity advantages of elastography are reviewed

Elastic moduli of normal and pathological human breast tissues: an inversion-technique-based investigation of 169 samples

Energy Technology Data Exchange (ETDEWEB)

Samani, Abbas [Department of Medical Biophysics/Electrical and Computer Engineering, University of Western Ontario, Medical Sciences Building, London, Ontario, N6A 5C1 (Canada); Zubovits, Judit [Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5 (Canada); Plewes, Donald [Department of Medical Biophysics, University of Toronto, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5 (Canada)

2007-03-21

Understanding and quantifying the mechanical properties of breast tissues has been a subject of interest for the past two decades. This has been motivated in part by interest in modelling soft tissue response for surgery planning and virtual-reality-based surgical training. Interpreting elastography images for diagnostic purposes also requires a sound understanding of normal and pathological tissue mechanical properties. Reliable data on tissue elastic properties are very limited and those which are available tend to be inconsistent, in part as a result of measurement methodology. We have developed specialized techniques to measure tissue elasticity of breast normal tissues and tumour specimens and applied them to 169 fresh ex vivo breast tissue samples including fat and fibroglandular tissue as well as a range of benign and malignant breast tumour types. Results show that, under small deformation conditions, the elastic modulus of normal breast fat and fibroglandular tissues are similar while fibroadenomas were approximately twice the stiffness. Fibrocystic disease and malignant tumours exhibited a 3-6-fold increased stiffness with high-grade invasive ductal carcinoma exhibiting up to a 13-fold increase in stiffness compared to fibrogalndular tissue. A statistical analysis showed that differences between the elastic modulus of the majority of those tissues were statistically significant. Implications for the specificity advantages of elastography are reviewed.

Dental tissue as a thermoluminescence dosimetry dosimeter

International Nuclear Information System (INIS)

Solaimani, F.; Zahmatkesh, M.H.; Akhlaghpoor, Sh.

2003-01-01

Background: Thermoluminescence dosimetry is one of the dosimetry procedures used widely as routine and personal dosimeters. In order to extend this kind of dosimeters, dental tissue has been examined and was found promising as a Thermoluminescence Dosimetry dosimeter. Materials and Methods: In this study, 70 health teeth were collected. The only criterion, wich was considered for selection of the teeth, was the healthiness of them regardless of age and gender of the donors. All collected samples were washed and cleaned and milled uniformly. The final powder had a uniform grain size between 100-300 micrometer. The sample was divided into four groups. Group A and B were used for measurement of density and investigation of variation of thermoluminescent characteristics with temperature respectively. Groups C and D were used for investigation of variation of thermoluminescent intensity with dose and fading of this intensity with time. In all cases the results obtained with dental tissue were compared to a standard LiF, thermoluminescence dosimetry dosimeter. Results: It was found that, average density of the dental tissue was 1.570 g/cm 3 , which is comparable to density of LiF, which is 1.612g/cm 3 . It was also concluded that the range of 0-300 d ig C , dental tissue has a simple curve with two specific peaks at 140 and 25 d ig C respectively. The experiment also showed that, the variation of relative intensity versus dose is linear in the range of 0.04-0.1 Gy. The fading rate of dental tissue is higher than LiF but still in the acceptable range (14% per month in compare to 5.2% per month). Conclusion: Dental tissue as a natural dosimeter is comparable with Thermoluminescence Dosimetry and can be used in accidental events with a good approximation

Extraction of DNA from plant and fungus tissues in situ

Directory of Open Access Journals (Sweden)

Abu Almakarem Amal S

2012-06-01

Full Text Available Abstract Background When samples are collected in the field and transported to the lab, degradation of the nucleic acids contained in the samples is frequently observed. Immediate extraction and precipitation of the nucleic acids reduces degradation to a minimum, thus preserving accurate sequence information. An extraction method to obtain high quality DNA in field studies is described. Findings DNA extracted immediately after sampling was compared to DNA extracted after allowing the sampled tissues to air dry at 21°C for 48 or 72 hours. While DNA extracted from fresh tissues exhibited little degradation, DNA extracted from all tissues exposed to 21°C air for 48 or 72 hours exhibited varying degrees of degradation. Yield was higher for extractions from fresh tissues in most cases. Four microcentrifuges were compared for DNA yield: one standard electric laboratory microcentrifuge (max rcf = 16,000×g, two battery-operated microcentrifuges (max rcf = 5,000 and 3,000 ×g, and one manually-operated microcentrifuge (max rcf = 120×g. Yields for all centrifuges were similar. DNA extracted under simulated field conditions was similar in yield and quality to DNA extracted in the laboratory using the same equipment. Conclusions This CTAB (cetyltrimethylammonium bromide DNA extraction method employs battery-operated and manually-operated equipment to isolate high quality DNA in the field. The method was tested on plant and fungus tissues, and may be adapted for other types of organisms. The method produced high quality DNA in laboratory tests and under simulated field conditions. The field extraction method should prove useful for working in remote sites, where ice, dry ice, and liquid nitrogen are unavailable; where degradation is likely to occur due to the long distances between the sample site and the laboratory; and in instances where other DNA preservation and transportation methods have been unsuccessful. It may be possible to adapt

Analysis of Samples Collected from the Surface of Interim Storage Canisters at Calvert Cliffs in June 2017: Revision 01.

Energy Technology Data Exchange (ETDEWEB)

Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schindelholz, Eric John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-11-01

In June 2017, dust and salt samples were collected from the surface of Spent Nuclear Fuel (SNF) dry storage canisters at the Calvert Cliffs Nuclear Power Plant. The samples were delivered to Sandia National laboratories for analysis. Two types of samples were collected: filter-backed Scotch-Brite TM pads were used to collect dry dust samples for characterization of salt and dust morphologies and distributions; and Saltsmart TM test strips were used to collect soluble salts for determining salt surface loadings per unit area. After collection, the samples were sealed into plastic sleeves for shipping. Condensation within the sleeves containing the Scotch-Brite TM samples remobilized the salts, rendering them ineffective for the intended purpose, and also led to mold growth, further compromising the samples; for these reasons, the samples were not analyzed. The SaltSmart TM samples were unaffected and were analyzed by ion chromatography for major anions and cations. The results of those analyses are presented here.

Collection and preparation of marine samples for radionuclide analysis

International Nuclear Information System (INIS)

Holm, E.

1997-01-01

The ultimate goal of research in radioecology is to be able to predict the pathways of radioactive material in the environment and hence estimate possible doses to the population in various regions. Knowledge of levels of contamination are necessary to maintain control of operations of nuclear facilities. Correct methods of sample collection, handling and preparation are among the most important parts for a correct assessment. On basis of the final results of radionuclide concentrations, scientific, medical and political decisions are taken. (author)

The Histopathologic Reliability of Tissue Taken from Cadavers within the Gross Anatomy Laboratory

Science.gov (United States)

Rae, Guenevere; Newman, William P., III; McGoey, Robin; Donthamsetty, Supriya; Karpinski, Aryn C.; Green, Jeffrey

2018-01-01

The purpose of this study was to examine the histopathologic reliability of embalmed cadaveric tissue taken from the gross anatomy laboratory. Tissue samples from hearts, livers, lungs, and kidneys were collected after the medical students' dissection course was completed. All of the cadavers were embalmed in a formalin-based fixative solution.…

A simple and novel method for retrieval of Pasteurellaceae from swab samples collected in the field

DEFF Research Database (Denmark)

Hansen, Mie J; Bertelsen, Mads F; Dietz, Rune

2013-01-01

and stored at -20°C. As a control study, 15 samples were collected from the oral cavity of a captive brown bear. One was immediately plated, while the remaining 12 swabs were stored at -20°C for 7 days and multiples of 30 days up to 330 days prior to plating. Two samples were stored without the medium for 7......Traditionally it has been difficult or impossible to collect and preserve bacterial samples of especially fastidious bacteria in mixed primary cultures, unless the samples could be transported to a laboratory within approximately 24 h. Therefore, a simple novel method for preserving swab samples...... until bacterial isolation can be completed in the laboratory was developed and evaluated. Pasteurellaceae bacteria were used as a representative for fastidious bacteria. A 7.5% glucose serum medium was used as freeze medium. Swab samples were soaked in the medium a maximum of 2 h after collection...

Procedures for the collection and preservation of groundwater and surface water samples and for the installation of monitoring wells

International Nuclear Information System (INIS)

Korte, N.; Kearl, P.

1984-01-01

Proper sampling procedures are essential for a successful water-quality monitoring program. It must be emphasized, however, that it is impossible to maintain absolutely in-situ conditions when collecting and preserving a water sample, whether from a flowing stream or an aquifer. Consequently, the most that can reasonably be expected is to collect a best possible sample with minimal disturbance. This document describes procedures for installing monitoring wells and for collecting samples of surface water and groundwater. The discussion of monitoring wells includes mention of multilevel sampling and a general overview of vadose-zone monitoring. Guidelines for well installation are presented in detail. The discussion of water-sample collection contains evaluations of sampling pumps, filtration equipment, and sample containers. Sample-preservation techniques, as published by several government and private sources, are reviewed. Finally, step-by-step procedures for collection of water samples are provided; these procedures address such considerations as necessary equipment, field operations, and written documentation. Separate procedures are also included for the collection of samples for determination of sulfide and for reactive aluminum. The report concludes with a brief discussion of adverse sampling, conditions that may significantly affect the quality of the data. Appendix A presents a rationale for the development and use of statistical considerations in water sampling to ensure a more complete water quality monitoring program. 51 references, 9 figures, 4 tables

NEW METHOD FOR DETERMINATION OF ACTINIDES AND STRONTIUM IN ANIMAL TISSUE

Energy Technology Data Exchange (ETDEWEB)

Maxwell, S; Jay Hutchison, J; Don Faison, D

2007-05-07

The analysis of actinides in animal tissue samples is very important for environmental monitoring. There is a need to measure actinide isotopes with very low detection limits in animal tissue samples, including fish, deer, hogs, beef and shellfish. A new, rapid actinide separation method has been developed and implemented that allows the measurement of plutonium, neptunium, uranium, americium, curium and strontium isotopes in large animal tissue samples (100-200 g) with high chemical recoveries and effective removal of matrix interferences. This method uses stacked TEVA Resin{reg_sign}, TRU Resin{reg_sign} and DGA-Resin{reg_sign} cartridges from Eichrom Technologies (Darien, IL, USA) that allows the rapid separation of plutonium (Pu), neptunium (Np), uranium (U), americium (Am), and curium (Cm) using a single multi-stage column combined with alpha spectrometry. Sr-90 is collected on Sr Resin{reg_sign} from Eichrom Technologies (Darien, IL, USA). After acid digestion and furnace heating of the animal tissue samples, the actinides and Sr-89/90 are separated using column extraction chromatography. This method has been shown to be effective over a wide range of animal tissue matrices. By using vacuum box cartridge technology with rapid flow rates, sample preparation time is minimized.

Multi-element composition of historical lichen collections and bark samples, indicators of changing atmospheric conditions

Science.gov (United States)

Purvis, O. W.; Chimonides, P. D. J.; Jeffries, T. E.; Jones, G. C.; Rusu, A.-M.; Read, H.

Thirty six element signatures were compared in historical Parmelia sulcata samples from the Natural History Museum herbarium collected over the period 1797-1967 with those recorded in the same species and tree bark sampled in 2000 from Burnham Beeches, lying 40 km west of London. Nineteen elements reached highest concentrations in herbarium samples, consistent with a pollution legacy and dust contamination in the herbarium. Healthy Parmelia sampled east and down-wind of London at a farm during peak SO 2 emissions in 1967 contained highest V, Ni, Zn, Cd, Se, Ge contents, supporting derivation from fuel combustion; the same sample was previously determined as having a low δ34S and high S and N contents. Lowest V, Co, Ni, Cu, Zn, Sn, Ba, Pb, Mo, Sb, Li, B, Cs, U, Th, Ga contents were recorded in a sample with a high δ34S and low S content collected in 1887 from a remote region from Ross-shire, Scotland. Se and Cd enrichment, never-the-less suggest a transboundary pollution influence. Lichen Pb concentrations from Burnham Beeches were amongst the lowest recorded in spite of lichens being collected close to roads. Herbarium samples help interpret changes in element deposition where few data exist, in spite of dust contamination.

High throughput DNA damage quantification of human tissue with home-based collection device

Science.gov (United States)

Costes, Sylvain V.; Tang, Jonathan; Yannone, Steven M.

2018-04-03

Kits, methods and systems for providing a service to provide a subject with information regarding the state of a subject's DNA damage. Collection, processing and analysis of samples are also described.

Control of the positional relationship between a sample collection instrument and a surface to be analyzed during a sampling procedure using a laser sensor

Science.gov (United States)

Van Berkel, Gary J [Clinton, TN; Kertesz, Vilmos [Knoxville, TN

2012-02-21

A system and method utilizes distance-measuring equipment including a laser sensor for controlling the collection instrument-to-surface distance during a sample collection process for use, for example, with mass spectrometric detection. The laser sensor is arranged in a fixed positional relationship with the collection instrument, and a signal is generated by way of the laser sensor which corresponds to the actual distance between the laser sensor and the surface. The actual distance between the laser sensor and the surface is compared to a target distance between the laser sensor and the surface when the collection instrument is arranged at a desired distance from the surface for sample collecting purposes, and adjustments are made, if necessary, so that the actual distance approaches the target distance.

Acceptability of self-collected vaginal samples for HPV testing in an ...

African Journals Online (AJOL)

Objective: To evaluate the acceptability of self-collected vaginal samples for HPV testing in women living in rural and urban areas of Madagascar. Materials and methods: Participants were recruited in a health care center (urban group) and smaller affiliated dispensaries (rural group). They were invited to perform ...

Measurement of phthalates in small samples of mammalian tissue

International Nuclear Information System (INIS)

Acott, P.D.; Murphy, M.G.; Ogborn, M.R.; Crocker, J.F.S.

1987-01-01

Di-(2-ethylhexyl)-phthalate (DEHP) is a phthalic acid ester that is used as a plasticizer in polyvinyl chloride products, many of which have widespread medical application. DEHP has been shown to be leached from products used for storage and delivery of blood transfusions during procedures such as plasmaphoresis, hemodialysis and open heart surgery. Results of studies in this laboratory have suggested that there is an association between the absorption and deposition of DEHP (and/or related chemicals) in the kidney and the acquired renal cystic disease (ACD) frequently seen in patients who have undergone prolonged dialysis treatment. In order to determine the relationship between the two, it has been necessary to establish a method for extracting and accurately quantitating minute amounts of these chemicals in small tissue samples. The authors have now established such a method using kidneys from normal rats and from a rat model for ACD

Combined spectroscopic imaging and chemometric approach for automatically partitioning tissue types in human prostate tissue biopsies

Science.gov (United States)

Haka, Abigail S.; Kidder, Linda H.; Lewis, E. Neil

2001-07-01

We have applied Fourier transform infrared (FTIR) spectroscopic imaging, coupling a mercury cadmium telluride (MCT) focal plane array detector (FPA) and a Michelson step scan interferometer, to the investigation of various states of malignant human prostate tissue. The MCT FPA used consists of 64x64 pixels, each 61 micrometers 2, and has a spectral range of 2-10.5 microns. Each imaging data set was collected at 16-1 resolution, resulting in 512 image planes and a total of 4096 interferograms. In this article we describe a method for separating different tissue types contained within FTIR spectroscopic imaging data sets of human prostate tissue biopsies. We present images, generated by the Fuzzy C-Means clustering algorithm, which demonstrate the successful partitioning of distinct tissue type domains. Additionally, analysis of differences in the centroid spectra corresponding to different tissue types provides an insight into their biochemical composition. Lastly, we demonstrate the ability to partition tissue type regions in a different data set using centroid spectra calculated from the original data set. This has implications for the use of the Fuzzy C-Means algorithm as an automated technique for the separation and examination of tissue domains in biopsy samples.

Increased cytotoxicity and streptolysin O activity in group G streptococcal strains causing invasive tissue infections

DEFF Research Database (Denmark)

Siemens, Nikolai; Kittang, Bård R; Chakrakodi, Bhavya

2015-01-01

Streptococcus dysgalactiae subsp. equisimilis (SDSE) has emerged as an important cause of severe skin and soft tissue infections, but little is known of the pathogenic mechanisms underlying tissue pathology. Patient samples and a collection of invasive and non-invasive group G SDSE strains (n = 6...

High throughput DNA damage quantification of human tissue with home-based collection device

Energy Technology Data Exchange (ETDEWEB)

Costes, Sylvain V.; Tang, Jonathan; Yannone, Steven M.

2018-04-03

Kits, methods and systems for providing a service to provide a subject with information regarding the state of a subject's DNA damage. Collection, processing and analysis of samples are also described.

A Tissue Retrieval and Postharvest Processing Regimen for Rodent Reproductive Tissues Compatible with Long-Term Storage on the International Space Station and Postflight Biospecimen Sharing Program

Directory of Open Access Journals (Sweden)

Vijayalaxmi Gupta

2015-01-01

Full Text Available Collection and processing of tissues to preserve space flight effects from animals after return to Earth is challenging. Specimens must be harvested with minimal time after landing to minimize postflight readaptation alterations in protein expression/translation, posttranslational modifications, and expression, as well as changes in gene expression and tissue histological degradation after euthanasia. We report the development of a widely applicable strategy for determining the window of optimal species-specific and tissue-specific posteuthanasia harvest that can be utilized to integrate into multi-investigator Biospecimen Sharing Programs. We also determined methods for ISS-compatible long-term tissue storage (10 months at −80°C that yield recovery of high quality mRNA and protein for western analysis after sample return. Our focus was reproductive tissues. The time following euthanasia where tissues could be collected and histological integrity was maintained varied with tissue and species ranging between 1 and 3 hours. RNA quality was preserved in key reproductive tissues fixed in RNAlater up to 40 min after euthanasia. Postfixation processing was also standardized for safe shipment back to our laboratory. Our strategy can be adapted for other tissues under NASA’s Biospecimen Sharing Program or similar multi-investigator tissue sharing opportunities.

CTEPP STANDARD OPERATING PROCEDURE FOR COLLECTION OF SOIL SAMPLES FOR PERSISTENT ORGANIC POLLUTANTS (SOP-2.20)

Science.gov (United States)

This SOP describes the method for collecting soil samples from the child's outdoor play area to measure for persistent organic pollutants. Soil samples are collected by scraping up the top 0.5 cm of soil in a 0.095 m2 (1 ft2) area in the middle of the child's play area.

Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California

Science.gov (United States)

Ramey, Andy M.; Schmutz, Joel A.; Fleskes, Joseph P.; Yabsley, Michael J.

2013-01-01

Information on the molecular detection of hematozoa from different tissue types and multiple years would be useful to inform sample collection efforts and interpret results of meta-analyses or investigations spanning multiple seasons. In this study, we tested blood and muscle tissue collected from northern pintails (Anas acuta) during autumn and winter of different years to evaluate prevalence and genetic diversity ofLeucocytozoon, Haemoproteus, and Plasmodium infections in this abundant waterfowl species of the Central Valley of California. We first compared results for paired blood and wing muscle samples to assess the utility of different tissue types for molecular investigations of haemosporidian parasites. Second, we explored inter-annual variability of hematozoa infection in Central Valley northern pintails and investigated possible effects of age, sex, and sub-region of sample collection on estimated parasite detection probability and prevalence. We found limited evidence for differences between tissue types in detection probability and prevalence ofLeucocytozoon, Haemoproteus, and Plasmodium parasites, which supports the utility of both sample types for obtaining information on hematozoan infections. However, we detected 11 haemosporidian mtDNA cyt bhaplotypes in blood samples vs. six in wing muscle tissue collected during the same sample year suggesting an advantage to using blood samples for investigations of genetic diversity. Estimated prevalence ofLeucocytozoon parasites was greater during 2006–2007 as compared to 2011–2012 and four unique haemosporidian mtDNA cyt b haplotypes were detected in the former sample year but not in the latter. Seven of 15 mtDNA cyt b haplotypes detected in northern pintails had 100% identity with previously reported hematozoa lineages detected in waterfowl (Haemoproteus and Leucocytozoon) or other avian taxa (Plasmodium) providing support for lack of host specificity for some parasite lineages.

Chlamydia trachomatis antibody detection in home-collected blood samples for use in epidemiological studies.

NARCIS (Netherlands)

Hoenderboom, B M; van Ess, E F; van den Broek, I V F; van Loo, I H M; Hoebe, C J P A; Ouburg, S; Morré, S A

Capillary blood collected in serum tubes was subjected to centrifugation delay while stored at room temperature. Chlamydia trachomatis (CT) IgG concentrations in aliquoted serum of these blood samples remained stable for seven days after collection. CT IgG concentrations can reliably be measured in

Improved explosive collection and detection with rationally assembled surface sampling materials

Energy Technology Data Exchange (ETDEWEB)

Chouyyok, Wilaiwan; Bays, J. Timothy; Gerasimenko, Aleksandr A.; Cinson, Anthony D.; Ewing, Robert G.; Atkinson, David A.; Addleman, R. Shane

2016-01-01

Sampling and detection of trace explosives is a key analytical process in modern transportation safety. In this work we have explored some of the fundamental analytical processes for collection and detection of trace level explosive on surfaces with the most widely utilized system, thermal desorption IMS. The performance of the standard muslin swipe material was compared with chemically modified fiberglass cloth. The fiberglass surface was modified to include phenyl functional groups. When compared to standard muslin, the phenyl functionalized fiberglass sampling material showed better analyte release from the sampling material as well as improved response and repeatability from multiple uses of the same swipe. The improved sample release of the functionalized fiberglass swipes resulted in a significant increase in sensitivity. Various physical and chemical properties were systematically explored to determine optimal performance. The results herein have relevance to improving the detection of other explosive compounds and potentially to a wide range of other chemical sampling and field detection challenges.

Tylosin depletion from edible pig tissues.

Science.gov (United States)

Prats, C; El Korchi, G; Francesch, R; Arboix, M; Pérez, B

2002-12-01

The depletion of tylosin from edible pig tissues was studied following 5 days of intramuscular (i.m.) administration of 10 mg/kg of tylosin to 16 crossbreed pigs. Animals were slaughtered at intervals after treatment and samples of muscle, kidney, liver, skin+fat, and injection site were collected and analysed by high-performance liquid chromatography (HPLC). Seven days after the completion of treatment, the concentration of tylosin in kidney, skin+fat, and at the injection site was higher than the European Union maximal residue limit (MRL) of 100 microg/kg. Tylosin residues in all tissues were below the quantification limit (50 microg/kg) at 10 and 14 days post-treatment.

Sample collection of virulent and non-virulent B. anthracis and Y. pestis for bioforensics analysis

Energy Technology Data Exchange (ETDEWEB)

Hong-geller, Elizabeth [Los Alamos National Laboratory; Valdez, Yolanda E [Los Alamos National Laboratory; Shou, Yulin [Los Alamos National Laboratory; Yoshida, Thomas M [Los Alamos National Laboratory; Marrone, Babetta L [Los Alamos National Laboratory; Dunbar, John [Los Alamos National Laboratory

2009-01-01

Validated sample collection methods are needed for recovery of microbial evidence in the event of accidental or intentional release of biological agents into the environment. To address this need, we evaluated the sample recovery efficiencies of two collection methods -- swabs and wipes -- for both non-virulent and virulent strains of B. anthracis and Y. pestis from four types of non-porous surfaces: two hydrophilic surfaces, stainless steel and glass, and two hydrophobic surfaces, vinyl and plastic. Sample recovery was quantified using Real-time qPCR to assay for intact DNA signatures. We found no consistent difference in collection efficiency between swabs or wipes. Furthermore, collection efficiency was more surface-dependent for virulent strains than non-virulent strains. For the two non-virulent strains, B. anthracis Sterne and Y. pestis A1122, collection efficiency was approximately 100% and 1 %, respectively, from all four surfaces. In contrast, recovery of B. anthracis Ames spores and Y. pestis C092 from vinyl and plastic was generally lower compared to collection from glass or stainless steel, suggesting that surface hydrophobicity may playa role in the strength of pathogen adhesion. The surface-dependent collection efficiencies observed with the virulent strains may arise from strain-specific expression of capsular material or other cell surface receptors that alter cell adhesion to specific surfaces. These findings contribute to validation of standard bioforensics procedures and emphasize the importance of specific strain and surface interactions in pathogen detection.

21 CFR 809.40 - Restrictions on the sale, distribution, and use of OTC test sample collection systems for drugs...

Science.gov (United States)

2010-04-01

... OTC test sample collection systems for drugs of abuse testing. 809.40 Section 809.40 Food and Drugs... Restrictions on the sale, distribution, and use of OTC test sample collection systems for drugs of abuse testing. (a) Over-the-counter (OTC) test sample collection systems for drugs of abuse testing (§ 864.3260...

Normalisation of spot urine samples to 24-h collection for assessment of exposure to uranium

International Nuclear Information System (INIS)

Marco, R.; Katorza, E.; Gonen, R.; German, U.; Tshuva, A.; Pelled, O.; Paz-tal, O.; Adout, A.; Karpas, Z.

2008-01-01

For dose assessment of workers at Nuclear Research Center Negev exposed to natural uranium, spot urine samples are analysed and the results are normalised to 24-h urine excretion based on 'standard' man urine volume of 1.6 l d -1 . In the present work, the urine volume, uranium level and creatinine concentration were determined in two or three 24-h urine collections from 133 male workers (319 samples) and 33 female workers (88 samples). Three volunteers provided urine spot samples from each voiding during a 24-h period and a good correlation was found between the relative level of creatinine and uranium in spot samples collected from the same individual. The results show that normalisation of uranium concentration to creatinine in a spot sample represents the 24-h content of uranium better than normalisation to the standard volume and may be used to reduce the uncertainty of dose assessment based on spot samples. (authors)

Planning Considerations Related to Collecting and Analyzing Samples of the Martian Soils

Science.gov (United States)

Liu, Yang; Mellon, Mike T.; Ming, Douglas W.; Morris, Richard V.; Noble, Sarah K.; Sullivan, Robert J.; Taylor, Lawrence A.; Beaty, David W.

2014-01-01

The Mars Sample Return (MSR) End-to-End International Science Analysis Group (E2E-iSAG [1]) established scientific objectives associ-ated with Mars returned-sample science that require the return and investigation of one or more soil samples. Soil is defined here as loose, unconsolidated materials with no implication for the presence or absence of or-ganic components. The proposed Mars 2020 (M-2020) rover is likely to collect and cache soil in addition to rock samples [2], which could be followed by future sample retrieval and return missions. Here we discuss key scientific consid-erations for sampling and caching soil samples on the proposed M-2020 rover, as well as the state in which samples would need to be preserved when received by analysts on Earth. We are seeking feedback on these draft plans as input to mission requirement formulation. A related planning exercise on rocks is reported in an accompanying abstract [3].

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

Science.gov (United States)

Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

Directory of Open Access Journals (Sweden)

Melissa R. Ingala

2018-05-01

Full Text Available The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

Validated method for the determination of perfluorinated compounds in placental tissue samples based on a simple extraction procedure followed by ultra-high performance liquid chromatography-tandem mass spectrometry analysis.

Science.gov (United States)

Martín, J; Rodríguez-Gómez, R; Zafra-Gómez, A; Alonso, E; Vílchez, J L; Navalón, A

2016-04-01

Xenobiotic exposure during pregnancy is inevitable. Determination of perfluorinated compounds (PFCs), chemicals described as environmental contaminants by Public Health Authorities due to their persistence, bioaccumulation and toxicity, is a challenge. In the present work, a method based on a simplified sample treatment involving freeze-drying, solvent extraction and dispersive clean-up of the extracts using C18 sorbents followed by an ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis was developed and validated for the determination of five perfluorinated carboxylic acids (C4-C8) and perfluorooctane sulfonate (PFOS) in placental tissue samples. The most influential parameters affecting the extraction method and clean-up were optimized using Design of Experiments (DOE). The method was validated using matrix-matched calibration. Found limits of detection (LODs) ranged from 0.03 to 2 ng g(-1) and limits of quantification (LOQs) from 0.08 to 6 ng g(-1), while inter- and intra-day variability was under 14% in all cases. Recovery rates for spiked samples ranged from 94% to 113%. The method was satisfactorily applied for the determination of compounds in human placental tissue samples collected at delivery from 25 randomly selected women. Copyright © 2015 Elsevier B.V. All rights reserved.

PIXE Analysis of Atmospheric Aerosol Samples Collected in the Adirondack Mountains

Science.gov (United States)

Yoskowitz, Josh; Ali, Salina; Nadareski, Benjamin; Safiq, Alexandrea; Smith, Jeremy; Labrake, Scott; Vineyard, Michael

2013-10-01

We have performed an elemental analysis of atmospheric aerosol samples collected at Piseco Lake in Upstate New York using proton induced x-ray emission spectroscopy (PIXE). This work is part of a systematic study of airborne pollution in the Adirondack Mountains. Of particular interest is the sulfur content that can contribute to acid rain, a well-documented problem in the Adirondacks. We used a nine-stage cascade impactor to collect the samples and distribute the particulate matter onto Kapton foils by particle size. The PIXE experiments were performed with 2.2-MeV proton beams from the 1.1-MV pelletron accelerator in the Union College Ion-Beam Analysis Laboratory. X-Ray energy spectra were measured with a silicon drift detector and analyzed with GUPIX software to determine the elemental concentrations of the aerosols. A broad range of elements from silicon to zinc were detected with significant sulfur concentrations measured for particulate matter between 0.25 and 0.5 μm in size. The PIXE analysis will be described and preliminary results will be presented.

Modulation of Cytokine mRNA Expression in Pharyngeal Epithelial Samples obtained from Cattle Infected with Foot-and-Mouth Disease Virus

DEFF Research Database (Denmark)

Stenfeldt, Anna Carolina; Heegaard, Peter M. H.; Stockmarr, Anders

2012-01-01

A novel technique of endoscopical collection of small tissue samples was used to obtain sequential tissue samples from the dorsal soft palate (DSP) of individual cattle infected with foot-and-mouth disease virus (FMDV) at different phases of the infection. Levels of mRNA encoding interferon (IFN)...

Bacteriology laboratories and musculoskeletal tissue banks in Australia.

Science.gov (United States)

Varettas, Kerry

2012-11-01

In Australia, there are six Therapeutic Goods Administration-licensed clinical bacteriology laboratories providing bacterial and fungal bioburden testing of allograft musculoskeletal samples sent from 10 tissue banks. Musculoskeletal swab and/or tissue biopsy samples are collected at the time of allograft retrieval and sent to bacteriology laboratories for bioburden testing, in some cases requiring interstate transport. Bacteria and fungi may be present within the allograft at the time of retrieval or contaminated from an external source. The type of organism recovered will determine if the allograft is rejected for transplant, which may include all allografts from the same donor. Bacteriology staff also provides unpaid support of tissue banks through meeting involvement, consultations, licence-related activities, validations and research funded by their organisation and not part of any contractual agreement. Bacteriology laboratories and tissue banks must be compliant to the Code of Good Manufacturing Practice - Human Blood and Tissues and regulated by the Therapeutic Goods Administration. Clinical bacteriology laboratories also require mandatory accreditation to Standards Australia International Organisation for Standardisation (ISO) 15189:2009 medical laboratories - particular requirements for quality and competence, and may also attain Standards Australia/New Zealand Standard ISO 9001:2000 quality management systems certification. Bacteriology laboratories and musculoskeletal tissue banks are integral partners in providing safe allograft musculoskeletal tissue for transplant. © 2012 The Author. ANZ Journal of Surgery © 2012 Royal Australasian College of Surgeons.

Heavy metals concentration in various tissues of two freshwater ...

African Journals Online (AJOL)

Heavy metals like cadmium, zinc, copper, chromium, lead and mercury were measured in the various tissues of Labeo rohita and Channa striatus and in the water samples collected from ... The values of heavy metals concentration in the present study are within the maximum permissible levels for drinking water and fish.

Series: Practical guidance to qualitative research. Part 3: Sampling, data collection and analysis.

Science.gov (United States)

Moser, Albine; Korstjens, Irene

2018-12-01

In the course of our supervisory work over the years, we have noticed that qualitative research tends to evoke a lot of questions and worries, so-called frequently asked questions (FAQs). This series of four articles intends to provide novice researchers with practical guidance for conducting high-quality qualitative research in primary care. By 'novice' we mean Master's students and junior researchers, as well as experienced quantitative researchers who are engaging in qualitative research for the first time. This series addresses their questions and provides researchers, readers, reviewers and editors with references to criteria and tools for judging the quality of qualitative research papers. The second article focused on context, research questions and designs, and referred to publications for further reading. This third article addresses FAQs about sampling, data collection and analysis. The data collection plan needs to be broadly defined and open at first, and become flexible during data collection. Sampling strategies should be chosen in such a way that they yield rich information and are consistent with the methodological approach used. Data saturation determines sample size and will be different for each study. The most commonly used data collection methods are participant observation, face-to-face in-depth interviews and focus group discussions. Analyses in ethnographic, phenomenological, grounded theory, and content analysis studies yield different narrative findings: a detailed description of a culture, the essence of the lived experience, a theory, and a descriptive summary, respectively. The fourth and final article will focus on trustworthiness and publishing qualitative research.

Series: Practical guidance to qualitative research. Part 3: Sampling, data collection and analysis

Science.gov (United States)

Moser, Albine; Korstjens, Irene

2018-01-01

Abstract In the course of our supervisory work over the years, we have noticed that qualitative research tends to evoke a lot of questions and worries, so-called frequently asked questions (FAQs). This series of four articles intends to provide novice researchers with practical guidance for conducting high-quality qualitative research in primary care. By ‘novice’ we mean Master’s students and junior researchers, as well as experienced quantitative researchers who are engaging in qualitative research for the first time. This series addresses their questions and provides researchers, readers, reviewers and editors with references to criteria and tools for judging the quality of qualitative research papers. The second article focused on context, research questions and designs, and referred to publications for further reading. This third article addresses FAQs about sampling, data collection and analysis. The data collection plan needs to be broadly defined and open at first, and become flexible during data collection. Sampling strategies should be chosen in such a way that they yield rich information and are consistent with the methodological approach used. Data saturation determines sample size and will be different for each study. The most commonly used data collection methods are participant observation, face-to-face in-depth interviews and focus group discussions. Analyses in ethnographic, phenomenological, grounded theory, and content analysis studies yield different narrative findings: a detailed description of a culture, the essence of the lived experience, a theory, and a descriptive summary, respectively. The fourth and final article will focus on trustworthiness and publishing qualitative research. PMID:29199486

Profiling quinones in ambient air samples collected from the Athabasca region (Canada).

Science.gov (United States)

Wnorowski, Andrzej; Charland, Jean-Pierre

2017-12-01

This paper presents new findings on polycyclic aromatic hydrocarbon oxidation products-quinones that were collected in ambient air samples in the proximity of oil sands exploration. Quinones were characterized for their diurnal concentration variability, phase partitioning, and molecular size distribution. Gas-phase (GP) and particle-phase (PM) ambient air samples were collected separately in the summer; a lower quinone content was observed in the PM samples from continuous 24-h sampling than from combined 12-h sampling (day and night). The daytime/nocturnal samples demonstrated that nighttime conditions led to lower concentrations and some quinones not being detected. The highest quinone levels were associated with wind directions originating from oil sands exploration sites. The statistical correlation with primary pollutants directly emitted from oil sands industrial activities indicated that the bulk of the detected quinones did not originate directly from primary emission sources and that quinone formation paralleled a reduction in primary source NO x levels. This suggests a secondary chemical transformation of primary pollutants as the origin of the determined quinones. Measurements of 19 quinones included five that have not previously been reported in ambient air or in Standard Reference Material 1649a/1649b and seven that have not been previously measured in ambient air in the underivatized form. This is the first paper to report on quinone characterization in secondary organic aerosols originating from oil sands activities, to distinguish chrysenequinone and anthraquinone positional isomers in ambient air, and to report the requirement of daylight conditions for benzo[a]pyrenequinone and naphthacenequinone to be present in ambient air. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

DNA from keratinous tissue

DEFF Research Database (Denmark)

Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted

2011-01-01

Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

Liquid scintillation alpha counting and spectrometry and its application to bone and tissue samples

International Nuclear Information System (INIS)

McDowell, W.J.; Weiss, J.F.

1976-01-01

Three methods for determination of alpha-emitting nuclides using liquid scintillation counting are compared, and the pertinent literature is reviewed. Data showing the application of each method to the measurement of plutonium concentration in tissue and bone samples are presented. Counting with a commercial beta-liquid scintillation counter and an aqueous-phase-accepting scintillator is shown to be accurate only in cases where the alpha activity is high (several hundred counts/min or more), only gross alpha counting is desired, and beta-gamma emitters are known to be absent from the sample or present at low levels compared with the alpha activity. Counting with the same equipment and an aqueous immiscible scintillator containing an extractant for the nuclide of interest (extractive scintillator) is shown to allow better control of alpha peak shift due to quenching, a significant reduction of beta-gamma interference, and, usually, a low background. The desirability of using a multichannel pulse-height analyzer in the above two counting methods is stressed. The use of equipment and procedures designed for alpha liquid scintillation counting is shown to allow alpha spectrometry with an energy resolution capability of 200 to 300 keV full-peak-width-at-half-peak-height and a background of 0.3 to 1.0 counts/min, or as low as 0.01 counts/min if pulse-shape discrimination methods are used. Methods for preparing animal bone and tissue samples for assay are described

Collection of size fractionated particulate matter sample for neutron activation analysis in Japan

International Nuclear Information System (INIS)

Otoshi, Tsunehiko; Nakamatsu, Hiroaki; Oura, Yasuji; Ebihara, Mitsuru

2004-01-01

According to the decision of the 2001 Workshop on Utilization of Research Reactor (Neutron Activation Analysis (NAA) Section), size fractionated particulate matter collection for NAA was started from 2002 at two sites in Japan. The two monitoring sites, ''Tokyo'' and ''Sakata'', were classified into ''urban'' and ''rural''. In each site, two size fractions, namely PM 2-10 '' and PM 2 '' particles (aerodynamic particle size between 2 to 10 micrometer and less than 2 micrometer, respectively) were collected every month on polycarbonate membrane filters. Average concentrations of PM 10 (sum of PM 2-10 and PM 2 samples) during the common sampling period of August to November 2002 in each site were 0.031mg/m 3 in Tokyo, and 0.022mg/m 3 in Sakata. (author)

An unsupervised MVA method to compare specific regions in human breast tumor tissue samples using ToF-SIMS.

Science.gov (United States)

Bluestein, Blake M; Morrish, Fionnuala; Graham, Daniel J; Guenthoer, Jamie; Hockenbery, David; Porter, Peggy L; Gamble, Lara J

2016-03-21

Imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal component analysis (PCA) were used to investigate two sets of pre- and post-chemotherapy human breast tumor tissue sections to characterize lipids associated with tumor metabolic flexibility and response to treatment. The micron spatial resolution imaging capability of ToF-SIMS provides a powerful approach to attain spatially-resolved molecular and cellular data from cancerous tissues not available with conventional imaging techniques. Three ca. 1 mm(2) areas per tissue section were analyzed by stitching together 200 μm × 200 μm raster area scans. A method to isolate and analyze specific tissue regions of interest by utilizing PCA of ToF-SIMS images is presented, which allowed separation of cellularized areas from stromal areas. These PCA-generated regions of interest were then used as masks to reconstruct representative spectra from specifically stromal or cellular regions. The advantage of this unsupervised selection method is a reduction in scatter in the spectral PCA results when compared to analyzing all tissue areas or analyzing areas highlighted by a pathologist. Utilizing this method, stromal and cellular regions of breast tissue biopsies taken pre- versus post-chemotherapy demonstrate chemical separation using negatively-charged ion species. In this sample set, the cellular regions were predominantly all cancer cells. Fatty acids (i.e. palmitic, oleic, and stearic), monoacylglycerols, diacylglycerols and vitamin E profiles were distinctively different between the pre- and post-therapy tissues. These results validate a new unsupervised method to isolate and interpret biochemically distinct regions in cancer tissues using imaging ToF-SIMS data. In addition, the method developed here can provide a framework to compare a variety of tissue samples using imaging ToF-SIMS, especially where there is section-to-section variability that makes it difficult to use a serial hematoxylin

Morphology of mucosa-associated lymphoid tissue in odontocetes.

Science.gov (United States)

Silva, Fernanda M O; Guimarães, Juliana P; Vergara-Parente, Jociery E; Carvalho, Vitor L; Carolina, Ana; Meirelles, O; Marmontel, Miriam; Oliveira, Bruno S S P; Santos, Silvanise M; Becegato, Estella Z; Evangelista, Janaina S A M; Miglino, Maria Angelica

2016-09-01

This study describes the mucosa-associated lymphoid tissue (MALT) in odontocetes from the Brazilian coast and freshwater systems. Seven species were evaluated and tissue samples were analyzed by light, scanning and transmission electron microscopy, and immunohistochemistry. Laryngeal tonsil was a palpable oval mass located in the larynx, composed of a lymphoepithelial complex. Dense collections of lymphocytes were found in the skin of male fetus and calf. Clusters of lymphoid tissue were found in the uterine cervix of a reproductively active juvenile female and along the pulmonary artery of an adult female. Lymphoid tissues associated with the gastrointestinal tract were characterized by diffusely arranged or organized lymphocytes. The anal tonsil was composed of an aggregate of lymphoid tissue occurring exclusively in the anal canal, being composed of squamous epithelium branches. MALT was present in different tissues and organic systems of cetaceans, providing constant protection against mucosal pathogens present in their environment. © 2016 Wiley Periodicals, Inc.

Measurement of technetium-99 in soil samples collected in Marshall Islands

Energy Technology Data Exchange (ETDEWEB)

Tagami, K.; Uchida, S. [National Inst. of Radiological Sciences, Environmental and Toxicological Sciences Research Group, Chiba (Japan)

2000-07-01

Extraction techniques for recovery of technetium-99 ({sup 99}Tc) for ICP-MS measurements were evaluated using soil samples collected from the Marshall Islands. The results of three different extraction techniques were compared: (M1) acid leaching of Tc from ashed soil; (M2) acid leaching of Tc from raw dry soil; and (M3) Tc volatilization from ashed soil using a combustion apparatus. Total Tc recoveries varied considerably between the extraction techniques but each method yielded similar analytical results for {sup 99}Tc. Applications of these extraction techniques to a series of environmental samples and ICP-MS measurements have yielded first data on the {sup 99}Tc content of Marshall Islands soil samples contaminated with close-in radioactive fallout from nuclear weapons testing. The {sup 99}Tc activity concentration in the soil samples ranged between 0.1 and 1.1 mBq/g-dw. The limit of detection for {sup 99}Tc by ICP-MS was 0.17 mBq per sample or 0.014 mBq/g-dw under standard operating conditions. (author)

Measurement of technetium-99 in soil samples collected in Marshall Islands

International Nuclear Information System (INIS)

Tagami, K.; Uchida, S.

2000-01-01

Extraction techniques for recovery of technetium-99 ( 99 Tc) for ICP-MS measurements were evaluated using soil samples collected from the Marshall Islands. The results of three different extraction techniques were compared: (M1) acid leaching of Tc from ashed soil; (M2) acid leaching of Tc from raw dry soil; and (M3) Tc volatilization from ashed soil using a combustion apparatus. Total Tc recoveries varied considerably between the extraction techniques but each method yielded similar analytical results for 99 Tc. Applications of these extraction techniques to a series of environmental samples and ICP-MS measurements have yielded first data on the 99 Tc content of Marshall Islands soil samples contaminated with close-in radioactive fallout from nuclear weapons testing. The 99 Tc activity concentration in the soil samples ranged between 0.1 and 1.1 mBq/g-dw. The limit of detection for 99 Tc by ICP-MS was 0.17 mBq per sample or 0.014 mBq/g-dw under standard operating conditions. (author)

Correlation study of trace metals in malignant and normal breast tissues by AAS technique

International Nuclear Information System (INIS)

Rahman, S.

2012-01-01

The study reports the application of atomic absorption spectrophotometry (AAS) for quantification of Fe, Cu and Zn in forty one formalin-fixed biopsy breast carcinoma tissue and adjoining fifteen normal tissue samples. These tissues samples were of category two breast carcinoma patients and of normal subjects. The qualitative comparison between the elements levels measured in the two types of specimens suggests significant elevation of these metals in the histopathological samples of carcinoma tissue. The samples were collected from women aged 19-51 years. Most of the patients belong to urban areas of Pakistan and middle to high socioeconomic status with the exception of few. Findings of study depicts that these elements have an important 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 (166.9 mg/L) in tissue samples of breast carcinoma patients (p < 0.01) than that in normal tissues samples (23.5 mg/L). In order to validate our method of analysis certified reference material Muscle Tissue Lyophilised (IAEA) MA-M-2/TM was analyzed for Fe, Cu and Zn. Determined concentrations were in good agreement with certified levels. The concentration distribution of trace elements Cu, Zn and Fe measured in the malignant tissues were found to be higher when compared to benign tissues, indicating the involvement of these metals in the breast malignancy. Results also indicate that excess iron may play a role in breast carcinogenesis. (Orig./A.B.)

Trefoil factors in saliva and gingival tissues of patients with chronic periodontitis

DEFF Research Database (Denmark)

Chaiyarit, Ponlatham; Chayasadom, Anek; Wara-Aswapati, Nawarat

2012-01-01

BACKGROUND: Trefoil factors (TFFs) are secreted molecules that are involved in cytoprotection against tissue damage and the immune response. TFFs have been detected in saliva and oral tissues, but their clinical significance has never been investigated in patients with chronic periodontitis....... The objective of this study is to determine whether TFF expression in saliva and gingival tissues is associated with periodontal pathology. METHODS: Saliva and gingival tissue samples were collected from 25 non-periodontitis individuals and 25 patients with chronic periodontitis (CP). Enzyme...... observed in patients with CP (P = 0.003 and P periodontal pathology and number of Porphyromonas gingivalis...

Sample processing, protocol, and statistical analysis of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of protein, cell, and tissue samples.

Science.gov (United States)

Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia

2014-01-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.

Detection of EWS/FLI-1 fusion in non-Ewing soft tissue tumors.

Science.gov (United States)

Trancău, I O; Huică, R; Surcel, M; Munteanu, A; Ursaciuc, C

2015-01-01

EWS/FLI-1 fusion mainly appears in Ewing's sarcoma or the primitive neuroectodermal tumors and represents a genomic marker for these tumors. However, it can appear with lower frequency in other soft tissue tumors. The paper investigates the presence of EWS/FLI-1 fusion in clinically diagnosed sarcoma belonging to different non-Ewing connective tissue tumors in order to search for a possible new biomarker valuable for investigators. 20 patients with soft tissue tumors, who underwent surgery, were tested. Intra-operative samples of normal and tumor tissue were collected for histopathological diagnosis and genetics determinations. The patients' RNA from tumor and normal peritumoral tissue was extracted and EWS/FLI-1 fusion screened by quantitative real-time PCR. The relative expression of the fusion in the tumor sample was compared to the similar expression in normal tissue. The amplification in the threshold zone was shown by 5 samples (25%): 2 clear cell sarcoma, 1 fibrosarcoma, 1 malignant tumor of nerve sheath, 1 metastatic adenocarcinoma. We differentiated between the unspecific amplification and concluded that these are weak positive results. Genomic investigation may establish the tumor malignancy and its possible affiliation earlier than histopathology. It can support the screening of EWS/FLI-1 fusion in a larger variety of clinically diagnosed soft tissue tumors.

Determination of 35S-aminoacyl-transfer ribonucleic acid specific radioactivity in small tissue samples

International Nuclear Information System (INIS)

Samarel, A.M.; Ogunro, E.A.; Ferguson, A.G.; Lesch, M.

1981-01-01

Rate determination of protein synthesis utilizing tracer amino acid incorporation requires accurate assessment of the specific radioactivity of the labeled precursor aminoacyl-tRNA pool. Previously published methods presumably useful for the measurement of any aminoacyl-tRNA were unsuccessful when applied to [ 35 S]methionine, due to the unique chemical properties of this amino acid. Herein we describe modifications of these methods necessary for the measurement of 35 S-aminoacyl-tRNA specific radioactivity from small tissue samples incubated in the presence of [ 35 S]methionine. The use of [ 35 S]methionine of high specific radioactivity enables analysis of the methionyl-tRNA from less than 100 mg of tissue. Conditions for optimal recovery of 35 S-labeled dansyl-amino acid derivatives are presented and possible applications of this method are discussed

Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues

Science.gov (United States)

Ndunguru, Joseph; Taylor, Nigel J; Yadav, Jitender; Aly, Haytham; Legg, James P; Aveling, Terry; Thompson, Graham; Fauquet, Claude M

2005-01-01

Background Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. Results DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA® Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. Conclusion Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants. PMID:15904535

Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues.

Science.gov (United States)

Ndunguru, Joseph; Taylor, Nigel J; Yadav, Jitender; Aly, Haytham; Legg, James P; Aveling, Terry; Thompson, Graham; Fauquet, Claude M

2005-05-18

Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants.

Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues

Directory of Open Access Journals (Sweden)

Aveling Terry

2005-05-01

Full Text Available Abstract Background Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. Results DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA® Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. Conclusion Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants.

Application of neutron activation analysis to trace elements determinations in lung samples

International Nuclear Information System (INIS)

Rogero, S.O.

1991-01-01

The purpose of this work was to apply the instrumental neutron activation analysis method to determine trace elements in lung samples from smokers and non smokers. Samples of lung tissues and lymph nodes from pulmonary hilum analyzed were collected from autopsies by researchers from Faculdade de Medicina da USP. (author)

Impact of collection season and storage of semen on methylation activity in swine placental and fetal tissues derived from summer or winter breedings

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DNA methylation patterns in extra-embryonic tissues have been linked to irregular fetal growth and early pregnancy loss. The objective of the current study was to evaluate methylation profiles of placental and fetal tissue collected from pregnancies derived using cooled-extended (ExT) or cryopreserv...

Multispectral fluorescence imaging of human ovarian and Fallopian tube tissue for early stage cancer detection

Science.gov (United States)

Tate, Tyler; Baggett, Brenda; Rice, Photini; Watson, Jennifer; Orsinger, Gabe; Nymeyer, Ariel C.; Welge, Weston A.; Keenan, Molly; Saboda, Kathylynn; Roe, Denise J.; Hatch, Kenneth; Chambers, Setsuko; Black, John; Utzinger, Urs; Barton, Jennifer

2015-03-01

With early detection, five year survival rates for ovarian cancer are over 90%, yet no effective early screening method exists. Emerging consensus suggests that perhaps over 50% of the most lethal form of the disease, high grade serous ovarian cancer, originates in the Fallopian tube. Cancer changes molecular concentrations of various endogenous fluorophores. Using specific excitation wavelengths and emissions bands on a Multispectral Fluorescence Imaging (MFI) system, spatial and spectral data over a wide field of view can be collected from endogenous fluorophores. Wavelength specific reflectance images provide additional information to normalize for tissue geometry and blood absorption. Ratiometric combination of the images may create high contrast between neighboring normal and abnormal tissue. Twenty-six women undergoing oophorectomy or debulking surgery consented the use of surgical discard tissue samples for MFI imaging. Forty-nine pieces of ovarian tissue and thirty-two pieces of Fallopian tube tissue were collected and imaged with excitation wavelengths between 280 nm and 550 nm. After imaging, each tissue sample was fixed, sectioned and HE stained for pathological evaluation. Comparison of mean intensity values between normal, benign, and cancerous tissue demonstrate a general trend of increased fluorescence of benign tissue and decreased fluorescence of cancerous tissue when compared to normal tissue. The predictive capabilities of the mean intensity measurements are tested using multinomial logistic regression and quadratic discriminant analysis. Adaption of the system for in vivo Fallopian tube and ovary endoscopic imaging is possible and is briefly described.

Spiked natural matrix materials as quality assessment samples

International Nuclear Information System (INIS)

Feiner, M.S.; Sanderson, C.G.

1988-01-01

The Environmental Measurements Laboratory has conducted the Quality Assessment Program since 1976 to evaluate the quality of the environmental radioactivity data, which is reported to the Department of Energy by as many as 42 commercial contractors involved in nuclear work. In this program, matrix materials of known radionuclide concentrations are distributed routinely to the contractors and the reported results are compared. The five matrices used are: soil, vegetation, animal tissue, water and filter paper. Environmental soil, vegetation and animal tissue are used, but the water and filter paper samples are prepared by spiking with known amounts of standard solutions traceable to the National Bureau of Standards. A summary of results is given to illustrate the successful operation of the program. Because of the difficulty and high cost of collecting large samples of natural matrix material and to increase the versatility of the program, an attempt was recently made to prepare the soil, vegetation and animal tissue samples with spiked solutions. A description of the preparation of these reference samples and the results of analyses are presented along with a discussion of the pitfalls and advantages of this approach. 19 refs.; 6 tabs

A portrait of tissue phosphoprotein stability in the clinical tissue procurement process.

Science.gov (United States)

Espina, Virginia; Edmiston, Kirsten H; Heiby, Michael; Pierobon, Mariaelena; Sciro, Manuela; Merritt, Barbara; Banks, Stacey; Deng, Jianghong; VanMeter, Amy J; Geho, David H; Pastore, Lucia; Sennesh, Joel; Petricoin, Emanuel F; Liotta, Lance A

2008-10-01

Little is known about the preanalytical fluctuations of phosphoproteins during tissue procurement for molecular profiling. This information is crucial to establish guidelines for the reliable measurement of these analytes. To develop phosphoprotein profiles of tissue subjected to the trauma of excision, we measured the fidelity of 53 signal pathway phosphoproteins over time in tissue specimens procured in a community clinical practice. This information provides strategies for potential surrogate markers of stability and the design of phosphoprotein preservative/fixation solutions. Eleven different specimen collection time course experiments revealed augmentation (+/-20% from the time 0 sample) of signal pathway phosphoprotein levels as well as decreases over time independent of tissue type, post-translational modification, and protein subcellular location (tissues included breast, colon, lung, ovary, and uterus (endometrium/myometrium) and metastatic melanoma). Comparison across tissue specimens showed an >20% decrease of protein kinase B (AKT) Ser-473 (p 20% increases within 90-min postprocurement. Endothelial nitric-oxide synthase Ser-1177 did not change over the time period evaluated with breast or leiomyoma tissue. Treatment with phosphatase or kinase inhibitors alone revealed that tissue kinase pathways are active ex vivo. Combinations of kinase and phosphatase inhibitors appeared to stabilize proteins that exhibited increases in the presence of phosphatase inhibitors alone (ATF-2 Thr-71, SAPK/JNK Thr-183/Tyr-185, STAT1 Tyr-701, JAK1 Tyr-1022/1023, and PAK1/PAK2 Ser-199/204/192/197). This time course study 1) establishes the dynamic nature of specific phosphoproteins in excised tissue, 2) demonstrates augmented phosphorylation in the presence of phosphatase inhibitors, 3) shows that kinase inhibitors block the upsurge in phosphorylation of phosphoproteins, 4) provides a rational strategy for room temperature preservation of proteins, and 5) constitutes a

Real time monitoring of pulsatile change in hemoglobin concentrations of cerebral tissue by a portable tissue oximeter with a 10-Hz sampling rate

Science.gov (United States)

Shiga, Toshikazu; Chihara, Eiichi; Tanabe, Kazuhisa; Tanaka, Yoshifumi; Yamamoto, Katsuyuki

1998-01-01

A portable CW tissue oximeter of a 10-Hz sampling rate was developed for examination of pulsatile components of the output signals as a mean of checking the signal reliability during long-term monitoring. Feasible studies were performed on a healthy subject. Changes in Hb and HbO2 signals of cerebral tissue were continuously measured by placing a photoprobe on the forehead during 6-hour sleep. Pulsatile changes in Hb and HbO2 were steadily observed over a whole period of the recording. The phase relation of pulsation in Hb and HbO2 was almost inverse. Not only information for reliable monitoring but also physiological parameters with respect to cerebral circulation and metabolism could be obtained by measuring the pulsatile components.

Radon exhalation rates from soil and sand samples collected from the vicinity of Yamuna river

International Nuclear Information System (INIS)

Garg, A.K.; Sushil Kumar; Chauhan, Pooja; Chauhan, R.P.

2011-01-01

Soil, sand and stones are the most popular building materials for Indian dwellings. Radon is released into ambient air from these materials due to ubiquitous uranium and radium in them, thus increasing the airborne radon concentration. The radioactivity in sand and soils is related to radioactivity in the rocks from which they are formed. These materials contain varying amount of uranium. In the present investigation, the radon emanated from soil and sand samples from different locations in the vicinity of Yamuna river has been estimated. The samples have been collected from different locations near the Yamuna river. The samples collecting sites are from Yamunanagar in Haryana to Delhi. The radon concentration in different samples has been calculated, based upon the data, the mass and the surface exhalation rates of radon emanated from them have also been calculated

Application of inductively coupled plasma mass spectrometry for multielement analysis in small sample amounts of thyroid tissue from Chernobyl area

International Nuclear Information System (INIS)

Becker, J.S.; Dietze, H.J.; Boulyga, S.F.; Bazhanova, N.N.; Kanash, N.V.; Malenchenko, A.F.

2000-01-01

As a result of the Chernobyl nuclear power plant accident in 1986, thyroid pathologies occurred among children in some regions of belarus. Besides the irradiation of children's thyroids by radioactive iodine and caesium nuclides, toxic elements from fallout are a direct risk to health. Inductively coupled plasma quadrupole-based mass spectrometry (Icp-Ms) and instrumental neutron activation analysis (IAA) were used for multielement determination in small amounts (I-10 mg) of human thyroid tissue samples. The accuracy of the applied analytical technique for small biological sample amounts was checked using NIST standard reference material oyster tissue (SRM 1566 b). Almost all essential elements as well as a number of toxic elements such as Cd, Pb, Hg, U etc. Were determined in a multitude of human thyroid tissues by quadrupole-based Icp-Ms using micro nebulization. In general, the thyroid tissue affected by pathology is characterized by higher calcium content. Some other elements, among them Sr, Zn, Fe, Mn, V, As, Cr, Ni, Pb, U, Ba, Sb, were also Accumulated in such tissue. The results obtained will be used as initial material for further specific studies of the role of particular elements in thyroid pathology development

Portable automation of static chamber sample collection for quantifying soil gas flux

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The collection of soil gas flux using the static chamber method is labor intensive. The number of chambers that can be sampled in a given time period is limited by the spacing between chambers and the availability of trained research technicians. However, the static chamber method can limit spatial ...

Progression of thanatophagy in cadaver brain and heart tissues

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Gulnaz T. Javan

2016-03-01

Full Text Available Autophagy is an evolutionarily conserved catabolic process for maintaining cellular homeostasis during both normal and stress conditions. Metabolic reprogramming in tissues of dead bodies is inevitable due to chronic ischemia and nutrient deprivation, which are well-known features that stimulate autophagy. Currently, it is not fully elucidated whether postmortem autophagy, also known as thanatophagy, occurs in dead bodies is a function of the time of death. In this study, we tested the hypothesis that thanatophagy would increase in proportion to time elapsed since death for tissues collected from cadavers. Brain and heart tissue from corpses at different time intervals after death were analyzed by Western blot. Densitometry analysis demonstrated that thanatophagy occurred in a manner that was dependent on the time of death. The autophagy-associated proteins, LC3 II, p62, Beclin-1 and Atg7, increased in a time-dependent manner in heart tissues. A potent inducer of autophagy, BNIP3, decreased in the heart tissues as time of death increased, whereas the protein levels increased in brain tissues. However, there was no expression of BNIP3 at extended postmortem intervals in both brain and heart samples. Collectively, the present study demonstrates for the first time that thanatophagy occurs in brain and heart tissues of cadavers in a time-dependent manner. Further, our data suggest that cerebral thanatophagy may occur in a Beclin-1- independent manner. This unprecedented study provides potential insight into thanatophagy as a novel method for the estimation of the time of death in criminal investigationsAbstract: Autophagy is an evolutionarily conserved catabolic process for maintaining cellular homeostasis during both normal and stress conditions. Metabolic reprogramming in tissues of dead bodies is inevitable due to chronic ischemia and nutrient deprivation, which are well-known features that stimulate autophagy. Currently, it is not fully

Matrix-comparative genomic hybridization from multicenter formalin-fixed paraffin-embedded colorectal cancer tissue blocks

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Köhne Claus-Henning

2007-04-01

Full Text Available Abstract Background The identification of genomic signatures of colorectal cancer for risk stratification requires the study of large series of cancer patients with an extensive clinical follow-up. Multicentric clinical studies represent an ideal source of well documented archived material for this type of analyses. Methods To verify if this material is technically suitable to perform matrix-CGH, we performed a pilot study using macrodissected 29 formalin-fixed, paraffin-embedded tissue samples collected within the framework of the EORTC-GI/PETACC-2 trial for colorectal cancer. The scientific aim was to identify prognostic genomic signatures differentiating locally restricted (UICC stages II-III from systemically advanced (UICC stage IV colorectal tumours. Results The majority of archived tissue samples collected in the different centers was suitable to perform matrix-CGH. 5/7 advanced tumours displayed 13q-gain and 18q-loss. In locally restricted tumours, only 6/12 tumours showed a gain on 13q and 7/12 tumours showed a loss on 18q. Interphase-FISH and high-resolution array-mapping of the gain on 13q confirmed the validity of the array-data and narrowed the chromosomal interval containing potential oncogenes. Conclusion Archival, paraffin-embedded tissue samples collected in multicentric clinical trials are suitable for matrix-CGH analyses and allow the identification of prognostic signatures and aberrations harbouring potential new oncogenes.

Mobile sources of polycyclic aromatic hydrocarbons (PAH) and nitro-PAH: Results of samples collected in a roadway tunnel

International Nuclear Information System (INIS)

Benner, B.A. Jr.; Gordon, G.E.; Wise, S.A.

1987-01-01

A recent review article emphasized the need for further characterizations of the carbonaceous fraction of mobile source emissions, particularly with the impending removal of lead alkyl octane boosters and bromine-containing lead scavengers from regular leaded gasolines. The lead and bromine emitted from the combustion of these fuels have been used as tracers of mobile source emissions for a number of years. Single vehicle emission studies have shed light on the relationship between engine operating parameters and the chemical characteristics of the emissions but they are not suitable for use in source apportionment studies which require emission data from a large number of different vehicles. Air particulate samples collected near a busy highway or in a roadway tunnel would be more appropriate for use in estimating the mobile source contribution of organic compounds to a region. Suspended particle samples collected in a heavily-travelled roadway tunnel (Baltimore Harbor Tunnel, Baltimore, Maryland) were characterized for polycyclic aromatic hydrocarbons (PAH) and some nitro-PAH by gas and liquid chromatographic techniques. These samples included those collected on Teflon filters and on glass fiber filters for investigating any differences in samples collected on an inert (Teflon) and more reactive (glass-fiber) medium. All samples collected on Teflon were backed-up with polyurethane foam plugs (PUF) which trapped any inherent vapor-phase PAH as well as any compounds ''blown-off'' the particles during collection

Measurement of tissue free water tritium in biological samples by liquid scintillation counter

International Nuclear Information System (INIS)

Wu Zongmei; Zheng Xiaomin

1993-01-01

The authors introduced a method of extracting tissue free water tritium (TFWT) by the azeotropic distribution with toluene and of measuring the activity of the TFWT in biological samples by liquid scintillation counter. The TFWT recovery ratio of pine needles (fresh), green vegetables, radish, rice, pork (muscle) and milk is 0.90, 0.95, 0.96, 0.90, 0.52 and 0.85, and TFWT activity is 1.8, 3.2, 1.8, 2.7, 3.3 and 4.0 Bq/L-H 2 O, respectively

Polychlorinated naphthalenes in human adipose tissue from New York, USA

International Nuclear Information System (INIS)

Kunisue, Tatsuya; Johnson-Restrepo, Boris; Hilker, David R.; Aldous, Kenneth M.; Kannan, Kurunthachalam

2009-01-01

Polychlorinated naphthalenes (PCNs) are persistent, bioaccumulative, and toxic contaminants. Prior to this study, the occurrence of PCNs in human adipose tissues from the USA has not been analyzed. Here, we have measured concentrations of PCNs in human adipose tissue samples collected in New York City during 2003-2005. Concentrations of PCNs were in the range of 61-2500 pg/g lipid wt. in males and 21-910 pg/g lipid wt. in females. PCN congeners 52/60 (1,2,3,5,7/1,2,4,6,7) and 66/67 (1,2,3,4,6,7/1,2,3,5,6,7) were predominant, collectively accounting for 66% of the total PCN concentrations. Concentrations of PCNs in human adipose tissues were 2-3 orders of magnitude lower than the previously reported concentrations of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). Concentrations of PCNs were not correlated with PCB concentrations. The contribution of PCNs to dioxin-like toxic equivalents (TEQs) in human adipose tissues was estimated to be <1% of the polychlorinated dibenzo-p-dioxin/dibenzofuran (PCDD/F)-TEQs. - Polychlorinated naphthalenes have been measured in human adipose tissues from the USA for the first time

Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

Science.gov (United States)

Donczo, Boglarka; Szarka, Mate; Tovari, Jozsef; Ostoros, Gyorgyi; Csanky, Eszter; Guttman, Andras

2017-06-01

Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endoductal tissue sampling of biliary strictures through endoscopic retrograde cholangiopan creatography (ERCP).

Science.gov (United States)

Pugliese, V; Antonelli, G; Vincenti, M; Gatteschi, B

1997-01-01

Pathological proof of malignant in biliary strictures is useful in the preoperative setting as it helps define therapeutic planning and prognosis, and reduces the length of the subsequent surgical intervention. However, it is difficult to obtain. The aim of this study was to evaluate the yield of histological and cytological examination of endobiliary samples obtained during endoscopic retrograde cholangiopancreatography (ERCP). Endobiliary forceps biopsy and brush cytology were performed during ERCP examination in 52 consecutive patients, 36 with malignant and 16 with benign strictures. Histology and cytology turned out to have the same sensitivity (53%). The gain in sensitivity achieved by combining the two techniques was limited, reaching a value of 61%. The specificity, however, was 100% for both methods. Most of the few complications observed were due to sphincterotomy and subsided spontaneously or with medical treatment. However, one patient experienced a serous complication and chose to be treated by surgical intervention. The complication was caused by forceps biopsy. This study shows that 1) sampling of biliary strictures during ERCP is the primary approach to tissue diagnosis; 2) brush cytology alone is sufficient in clinical practice; 3) forceps biopsy must always be used to sample intra-ampullary strictures but should be considered as a secondary step to sample strictures located more proximally, in the bile ducta, if previous cytology was negative.

Random lasing in human tissues

International Nuclear Information System (INIS)

Polson, Randal C.; Vardeny, Z. Valy

2004-01-01

A random collection of scatterers in a gain medium can produce coherent laser emission lines dubbed 'random lasing'. We show that biological tissues, including human tissues, can support coherent random lasing when infiltrated with a concentrated laser dye solution. To extract a typical random resonator size within the tissue we average the power Fourier transform of random laser spectra collected from many excitation locations in the tissue; we verified this procedure by a computer simulation. Surprisingly, we found that malignant tissues show many more laser lines compared to healthy tissues taken from the same organ. Consequently, the obtained typical random resonator was found to be different for healthy and cancerous tissues, and this may lead to a technique for separating malignant from healthy tissues for diagnostic imaging

Versatile electrochemial sensor for tissue culturing and sample handling

DEFF Research Database (Denmark)

Bakmand, Tanya; Kwasny, Dorota; Al Atraktchi, Fatima Al-Zahraa

2014-01-01

Culturing of organtypic brain tissues is a routine procedure in neural research. The visual inspection of the medium is the only way of determining the state of the tissue. At the end of culturing, post-processing techniques such as HPLC can be used to measure the concentration of the secreted...

Evaluation of Two Enzyme-Linked Immunosorbent Assay Kits for Chikungunya Virus IgM Using Samples from Deceased Organ and Tissue Donors

Science.gov (United States)

Altrich, Michelle L.; Nowicki, Marek J.

2016-01-01

The identification of nearly 3,500 cases of chikungunya virus (CHIKV) infection in U.S. residents returning in 2014 and 2015 from areas in which it is endemic has raised concerns within the transplant community that, should recently infected individuals become organ and/or tissue donors, CHIKV would be transmitted to transplant recipients. Thus, tests designed to detect recent CHIKV infection among U.S. organ and tissue donors may become necessary in the future. Accordingly, we evaluated 2 enzyme-linked immunosorbent assays (ELISAs) for CHIKV IgM readily available in the United States using 1,000 deidentified serum or plasma specimens collected from donors between November 2014 and March 2015. The Euroimmun indirect ELISA identified 38 reactive specimens; however, all 38 were negative for CHIKV IgG and IgM in immunofluorescence assays (IFAs) conducted at a reference laboratory and, thus, were falsely reactive in the Euroimmun CHIKV IgM assay. The InBios IgM-capture ELISA identified 26 reactive samples, and one was still reactive (index ≥ 1.00) when retested using the InBios kit with a background subtraction modification to identify false reactivity. This reactive specimen was CHIKV IgM negative but IgG positive by IFAs at two reference laboratories; plaque reduction neutralization testing (PRNT) demonstrated CHIKV-specific reactivity. The IgG and PRNT findings strongly suggest that the InBios CHIKV IgM-reactive result represents true reactivity, even though the IgM IFA result was negative. If testing organ/tissue donors for CHIKV IgM becomes necessary, the limitations of the currently available CHIKV IgM ELISAs and options for their optimization must be understood to avoid organ/tissue wastage due to falsely reactive results. PMID:27535838

Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

Science.gov (United States)

Thompson, Seonaid M; Craven, Rachel A; Nirmalan, Niroshini J; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

2013-04-01

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How to store plant tissues in the absence of liquid nitrogen? Ethanol preserves the RNA integrity of Cannabis sativa stem tissues

Directory of Open Access Journals (Sweden)

Lauralie Mangeot-Peter

2016-09-01

Full Text Available The preservation of intact RNA is a limiting step when gene expression profiling is performed using field-collected plant material. The use of liquid nitrogen ensures the optimal preservation of RNA, however it is not always practical, especially if the plant material has to be sampled in remote locations. Ethanol is known to preserve DNA in plant tissues even after a long storage period and here its suitability to preserve the RNA of textile hemp cortical tissues was tested. Hemp (Cannabis sativa L. is an economically important fibre crop because it supplies cellulosic bast fibres used in different industrial sectors. In this study we demonstrate the suitability of ethanol for RNA preservation by analyzing tissues stored at 4 °C for 1, 2, 4 and 8 days. We show that in all the cases the extracted RNA is intact. We finally analyze hemp stem tissues stored in ethanol for 1 month and demonstrate the preservation of the tissue structure, particularly of bast fibres.

Procedure of trace element analysis in oyster tissues by using X-ray fluorescence

International Nuclear Information System (INIS)

Vo Thi Tuong Hanh; Dinh Thi Bich Lieu; Dinh Thien Lam and Nguyen Manh Hung

2004-01-01

The procedure of trace element analysis such as Ca, Mn, Fe, Zn, Cu, Pb in molluscs (oyster tissues) was established by using X-ray fluorescence techniques. The procedure was investigated from the sample collection, drying, ashing ratio to the analytical techniques by using Cd-109, detector Si (Li) and the peak processing MCAPLUS program was applied for this study. The procedure is based on direct comparison with certified concentrations of international standard reference SRM 1566b Oyster Tissue of National Institute of Standards and Technology, Department of commerce, United States of America for Ca, Mn, Fe, Zn, Cu and the Standard Addition Methods for Pb. The accuracy of the Standard Addition Methods was estimated by CRM281 Rye Grass of Community Bureau of Reference-BCR, European Commission. The results of 10 samples which were collected from several markets in Hanoi are shown. (author)

Utilizing Raman Spectroscopy and Surface-Enhanced Raman Spectroscopy to investigate healthy and cancerous colon samples

International Nuclear Information System (INIS)

Barzegar, A.; Rezaei, H.; Malekfar, R.

2012-01-01

In this study, spontaneous Raman scattering and surface-enhanced Raman scattering, Surface-Enhanced Raman Spectroscopy spectra have been investigated. The samples which were kept in the formalin solution selected from the human's healthy and cancerous colon tissues. The Surface-Enhanced Raman Spectroscopy spectra were collected by adding colloidal solution contained silver nanoparticles to the top of the samples. The recorded spectra were compared for the spontaneous Raman spectra of healthy and cancerous colon samples. The spontaneous and surface enhanced Raman scattering data were also collected and compared for both healthy and damaged samples.

Miniature Blimps for Surveillance and Collection of Samples

Science.gov (United States)

Jones, Jack

2004-01-01

Miniature blimps are under development as robots for use in exploring the thick, cold, nitrogen atmosphere of Saturn's moon, Titan. Similar blimps can also be used for surveillance and collection of biochemical samples in buildings, caves, subways, and other, similar structures on Earth. The widely perceived need for means to thwart attacks on buildings and to mitigate the effects of such attacks has prompted consideration of the use of robots. Relative to rover-type (wheeled) robots that have been considered for such uses, miniature blimps offer the advantage of ability to move through the air in any direction and, hence, to perform tasks that are difficult or impossible for wheeled robots, including climbing stairs and looking through windows. In addition, miniature blimps are expected to have greater range and to cost less, relative to wheeled robots.

An examination of the genetic control of Douglas-fir vascular tissue phytochemicals: implications for black bear foraging.

Science.gov (United States)

Bruce A. Kimball; G.R. Johnson; Dale L. Nolte; Doreen L. Griffin

1999-01-01

Silvicultural practices can influence black bear (Ursus americanus) foraging preferences for Douglas-fir (Pseudotsuga menziesii) cambial-zone vascular tissues, but little is known about the role of genetics. To study the impact of genetic selection, vascular tissue samples were collected from Douglas-fir trees in six half-sib families from five...

Technical report: serial collections of placentomes during parturition in cattle and subsequent reproductive performance.

Science.gov (United States)

McNeel, Anthony K; Ondrak, Jeff D; Cushman, Robert A

2013-05-01

Placental separation is a complex physiological event in reproductive physiology and the underlying molecular mechanisms remain unclear. When comparing different experiments the timing of tissue collections is a significant consideration due to the variability in time between fetal expulsion and expulsion of the placenta (30 min to >24 h). This makes comparison of tissues samples across animals difficult and supports the need for serial tissue collections within animal. Additionally, the instrument most commonly used, a modified Richter-Resinsinger effeminator, for placentome collections is difficult to obtain and there are no data in the literature record regarding subsequent reproductive performance of animals subjected placentome collections. To facilitate continued research into the physiology behind placental separation, we designed an instrument from readily available components and performed serial transvaginal placentome collections in cattle. Three placentomes at 2-h intervals were collected after expulsion of the calf in 18 multiparous cows. There was no incidence of mortality and all cows resumed estrous after the procedure. Neither time from placentome collection nor age had a significant effect on pregnancy status at diagnosis (P > 0.05). These results demonstrate the viability of and utility of this device for collecting multiple placentomes in cattle.

DNA Sampling Hook

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

Comparison of three media for transport and storage of the samples collected for detection of avian influenza virus.

Science.gov (United States)

Zhang, Xiao-Chun; Liu, Shuo; Hou, Guang-Yu; Zhuang, Qing-Ye; Wang, Kai-Cheng; Jiang, Wen-Ming; Wang, Su-Chun; Li, Jin-Ping; Yu, Jian-Min; Du, Xiang; Huang, Bao-Xu; Chen, Ji-Ming

2015-09-15

Detection of avian influenza viruses (AIVs) is important for diagnosis, surveillance and control of avian influenza which is of great economic and public health significance. Proper transport and storage of samples is critical for the detection when the samples cannot be detected immediately. As recommended by some international or national authoritative entities and some publications, phosphate buffered saline (PBS), PBS-glycerol and brain heart infusion broth (BHIB) are frequently used for transport and storage of the samples collected for detection of AIVs worldwide. In this study, we compared these three media for transport and storage of simulated and authentic swab and feces samples collected for detection of AIVs using virus isolation and reverse transcription-PCR. The results suggest that PBS-glycerol is superior to PBS and BHIB as the sample transport and storage media. The results also suggest that the samples collected for detection of AIVs should be detected as soon as possible because the virus concentration of the samples may decline rapidly during storage within days at 4 or -20°C. Copyright © 2015 Elsevier B.V. All rights reserved.

A Systematic Review of Published Respondent-Driven Sampling Surveys Collecting Behavioral and Biologic Data.

Science.gov (United States)

Johnston, Lisa G; Hakim, Avi J; Dittrich, Samantha; Burnett, Janet; Kim, Evelyn; White, Richard G

2016-08-01

Reporting key details of respondent-driven sampling (RDS) survey implementation and analysis is essential for assessing the quality of RDS surveys. RDS is both a recruitment and analytic method and, as such, it is important to adequately describe both aspects in publications. We extracted data from peer-reviewed literature published through September, 2013 that reported collected biological specimens using RDS. We identified 151 eligible peer-reviewed articles describing 222 surveys conducted in seven regions throughout the world. Most published surveys reported basic implementation information such as survey city, country, year, population sampled, interview method, and final sample size. However, many surveys did not report essential methodological and analytical information for assessing RDS survey quality, including number of recruitment sites, seeds at start and end, maximum number of waves, and whether data were adjusted for network size. Understanding the quality of data collection and analysis in RDS is useful for effectively planning public health service delivery and funding priorities.