Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy

PubMed Central

Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Shedden, Kerby A.; Neiswanger, Katherine; Trumble, Erika; Li, Jiean J.; McNeil, Daniel W.; Crout, Richard J.; Weyant, Robert J.; Marazita, Mary L.

2016-01-01

ABSTRACT Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition. IMPORTANCE Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work. PMID:27371581

Stability of hepatitis C virus RNA and anti-HCV antibody in air-dried and freeze-dried human plasma samples.

PubMed

Poe, Amanda; Duong, Ngocvien Thi; Bedi, Kanwar; Kodani, Maja

2018-03-01

Diagnosis of hepatitis C virus (HCV) infection is based on testing for antibodies to HCV (anti-HCV), hepatitis C core antigen (HCV cAg) and HCV RNA. To ensure quality control (QC) and quality assurance (QA), proficiency panels are provided by reference laboratories and various international organizations, requiring costly dry ice shipments to maintain specimen integrity. Alternative methods of specimen preservation and transport can save on shipping and handling and help in improving diagnostics by facilitating QA/QC of various laboratories especially in resource limited countries. Plasma samples positive for anti-HCV and HCV RNA were either dried using dried tube specimens (DTS) method or lyophilization for varying durations of time and temperature. Preservation of samples using DTS method resulted in loss of anti-HCV reactivity for low-positive samples and did not generate enough volume for HCV RNA testing. Lyophilized samples tested positive for anti-HCV even after storage at 4 °C and 25 °C for 12 weeks. Further, HCV RNA was detectable in 5 of 5 (100%) samples over the course of 12 week storage at 4, 25, 37 and 45 °C. In conclusion, lyophilization of specimens maintains integrity of plasma samples for testing for markers of HCV infection and can be a potent mode of sharing proficiency samples without incurring huge shipping costs and avoids challenges with dry ice shipments between donor and recipient laboratories. Copyright © 2017. Published by Elsevier B.V.

21 CFR 864.3250 - Specimen transport and storage container.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Specimen transport and storage container. 864.3250....3250 Specimen transport and storage container. (a) Identification. A specimen transport and storage..., or body exudate during storage and transport in order that the matter contained therein can be...

21 CFR 864.3250 - Specimen transport and storage container.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Specimen transport and storage container. 864.3250....3250 Specimen transport and storage container. (a) Identification. A specimen transport and storage..., or body exudate during storage and transport in order that the matter contained therein can be...

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

PubMed

da Cunha Santos, Gilda

2018-03-01

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

Long-Term Storage at -80°C: Effect on Rate of Recovery of Mycobacterium tuberculosis From Direct Acid-Fast Bacilli Smear-Positive Sputum Samples.

PubMed

Shinu, Pottathil; AshokKumar Singh, Varsha; Nair, Anroop; Farooq, Rumana; Ishaq, Sheikh

2016-09-01

The aim of this study was to evaluate the difference in the rate of recovery of Mycobacterium tuberculosis (MTB) from routinely cultured sputum and long-term stored sputum specimens (at -80°C) using Löwenstein-Jensen (LJ) media, Mycobacterium Growth Indicator Tube (BBL MGIT(TM) ), and Middlebrook 7H11 (MB 7H11) agar. Direct acid-fast bacilli smear-positive sputum specimens (both before and after storage [n = 136]) were studied (after culturing on LJ media, BBL MGIT(TM) , and MB 7H11 agar) and the performances were compared. For the detection of MTB, BBL MGIT(TM) and MB 7H11 agar (before storage) demonstrated a sensitivity, specificity, positive predictive value (PPV) of 98.28%, 30.77%, 92.68%, 66.67%, and negative predictive value (NPV) of 97.41%, 30.77%, 92.62%, 57.14%, respectively, when compared to LJ media (before storage). Similarly, BBL MGIT(TM) and MB 7H11 agar (after storage) demonstrated a sensitivity, specificity, PPV, and NPV of 95.5%, 38.89%, 90.6%, 58.33%, and 95.5%, 66.67 %, 94.64%, 70.59%, respectively, when compared to LJ media (after storage) for the detection of MTB. None of the culture techniques independently (both before and after storage) detected growth of MTB from all the sputum specimens studied. However, BBL MGIT(TM) system and LJ media combination (both before and after storage) effectively detected the growth of MTB from sputum specimens when compared to other culture technique combinations. © 2015 Wiley Periodicals, Inc.

Preservation of pathological tissue specimens by freeze-drying for immunohistochemical staining and various molecular biological analyses.

PubMed

Matsuo, S; Sugiyama, T; Okuyama, T; Yoshikawa, K; Honda, K; Takahashi, R; Maeda, S

1999-05-01

Conditions of preserving DNA, RNA and protein in pathological specimens are of great importance as degradation of such macromolecules would critically affect results of molecular biological analysis. The feasibility of freeze-drying as a means of preserving pathological tissue samples for molecular analysis has previously been shown. In the present study, further tests on long-term storage conditions and analyses of freeze-dried samples by polymerase chain reaction (PCR), reverse transcriptase (RT)-PCR, western blotting and immunohistochemistry are reported. Rat chromosomal DNA of freeze-dried samples stored for 4 years showed slight degradation while RNA degradation was more prominently seen at an earlier stage of storage. However, these 4 year DNA and RNA samples were still able to serve as a template for some PCR and RT-PCR analyses, respectively. Overexpression of c-erbB-2 and p53 protein was demonstrated by western blotting and immunohistochemical staining using freeze-dried human breast cancer tissues. Although macromolecules in freeze-dried samples degrade to some extent during the preservation period, they should still be of value for certain molecular biological analyses and morphological examination; hence, providing more convenient and inexpensive ways of pathological tissue storage.

Evaluation of the BD Vacutainer Plus Urine C&S Preservative Tubes compared with nonpreservative urine samples stored at 4°C and room temperature.

PubMed

Eisinger, Stephen W; Schwartz, Matthew; Dam, Lisa; Riedel, Stefan

2013-09-01

The stability of urine specimens submitted for culture remains a challenge for many laboratories because of delays in specimen transport. We evaluated the usefulness of BD Vacutainer Plus Urine C&S Preservative Tube in ensuring specimen stability. Clinical urine specimens collected in sterile collection cups (n = 110) were plated onto sheep blood and MacConkey agar following standard laboratory procedures guidelines. Thereafter, specimens were divided into 3 storage conditions: nonpreservative, refrigerated; nonpreservative, room temperature (RT); BD Vacutainer Plus Urine C&S Preservative Tube, RT. For each sample type, additional cultures were set up at 2, 4, 24, and 48 hours. Initially, 18 specimens had no growth, 32 showed mixed skin flora, and 60 yielded at least 1 uropathogen. Increased colony counts of uropathogens were observed for nonpreserved urine samples stored at RT; these changes were statistically significant. Minor differences between refrigerated urine samples and BD Vacutainer Plus Urine C&S Preservative Tube samples were seen but were not statistically significant. The use of preservative-containing collection tubes is desirable to ensure specimen stability when prompt processing or refrigeration is not feasible.

Mechanical Properties of Calcium Fluoride-Based Composite Materials

PubMed Central

Kleczewska, Joanna; Pryliński, Mariusz; Podlewska, Magdalena; Sokołowski, Jerzy; Łapińska, Barbara

2016-01-01

Aim of the study was to evaluate mechanical properties of light-curing composite materials modified with the addition of calcium fluoride. The study used one experimental light-curing composite material (ECM) and one commercially available flowable light-curing composite material (FA) that were modified with 0.5–5.0 wt% anhydrous calcium fluoride. Morphology of the samples and uniformity of CaF2 distribution were analyzed using Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS). Mechanical properties were tested after 24-hour storage of specimens in dry or wet conditions. Stored dry ECM enriched with 0.5–1.0 wt% CaF2 showed higher tensile strength values, while water storage of all modified ECM specimens decreased their tensile strength. The highest Vickers hardness tested after dry storage was observed for 2.5 wt% CaF2 content in ECM. The addition of 2.0–5.0 wt% CaF2 to FA caused significant decrease in tensile strength after dry storage and overall tensile strength decrease of modified FA specimens after water storage. The content of 2.0 wt% CaF2 in FA resulted in the highest Vickers hardness tested after wet storage. Commercially available composite material (FA), unmodified with fluoride addition, demonstrated overall significantly higher mechanical properties. PMID:28004001

Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics.

PubMed

Hosokawa-Muto, Junji; Fujinami, Yoshihito; Mizuno, Natsuko

2015-08-01

Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

The biobank of the Norwegian mother and child cohort Study: A resource for the next 100 years

PubMed Central

Rønningen, Kjersti S.; Paltiel, Liv; Meltzer, Helle M.; Nordhagen, Rannveig; Lie, Kari K.; Hovengen, Ragnhild; Haugen, Margaretha; Nystad, Wenche; Magnus, Per; Hoppin, Jane A.

2007-01-01

Introduction Long-term storage of biological materials is a critical component of any epidemiological study. In designing specimen repositories, efforts need to balance future needs for samples with logistical constraints necessary to process and store samples in a timely fashion. Objectives In the Norwegian Mother and Child Cohort Study (MoBa), the Biobank was charged with long-term storage of more than 380,000 biological samples from pregnant women, their partners and their children for up to 100 years. Methods Biological specimens include whole blood, plasma, DNA and urine; samples are collected at 50 hospitals in Norway. All samples are sent via ordinary mail to the Biobank in Oslo where the samples are registered, aliquoted and DNA extracted. DNA is stored at −20 °C while whole blood, urine and plasma are stored at − 80 °C. Results As of July 2006, over 227,000 sample sets have been collected, processed and stored at the Biobank. Currently 250–300 sets are received daily. An important part of the Biobank is the quality control program. Conclusion With the unique combination of biological specimens and questionnaire data, the MoBa Study will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental factors on pregnancy outcome and on human morbidity, mortality and health in general. PMID:17031521

40 CFR 792.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 33 2013-07-01 2013-07-01 false Specimen and data storage facilities..., for the storage and retrieval of all raw data and specimens from completed studies. ... SUBSTANCES CONTROL ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Facilities § 792.51 Specimen and data...

40 CFR 792.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 32 2014-07-01 2014-07-01 false Specimen and data storage facilities..., for the storage and retrieval of all raw data and specimens from completed studies. ... SUBSTANCES CONTROL ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Facilities § 792.51 Specimen and data...

40 CFR 792.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 32 2011-07-01 2011-07-01 false Specimen and data storage facilities..., for the storage and retrieval of all raw data and specimens from completed studies. ... SUBSTANCES CONTROL ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Facilities § 792.51 Specimen and data...

40 CFR 792.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 33 2012-07-01 2012-07-01 false Specimen and data storage facilities..., for the storage and retrieval of all raw data and specimens from completed studies. ... SUBSTANCES CONTROL ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Facilities § 792.51 Specimen and data...

About Rubella (German Measles, Three-Day Measles)

MedlinePlus

... Professionals Pregnancy and Rubella Rubella Vaccination Travelers’ Health Information on Rubella Laboratory Testing CDC Laboratory Testing & Procedures Serology RNA Detection Genetic Analysis Specimen Collection, Storage, & Shipment Sample Submission Q&A ...

Rubella (German Measles, Three-Day Measles) Photos

MedlinePlus

... Professionals Pregnancy and Rubella Rubella Vaccination Travelers’ Health Information on Rubella Laboratory Testing CDC Laboratory Testing & Procedures Serology RNA Detection Genetic Analysis Specimen Collection, Storage, & Shipment Sample Submission Q&A ...

Ethics, Human Use, and the Department of Defense Serum Repository.

PubMed

Pavlin, Julie A; Welch, Robert A

2015-10-01

The Department of Defense Serum Repository (DoDSR) contains a growing archive of sera from service members collected to perform medical surveillance, clinical diagnosis, and epidemiologic studies to identify, prevent, and control diseases associated with military service. The specimens are a mandatory collection under DoD and U.S. regulations and do not include informed consent for uses beyond force health protection. Any use of the specimens for research requires deidentification of the samples and must be approved by Institutional Review Boards. However, as expansion of the DoDSR is contemplated, ethical considerations of sample collection, storage, and use must be carefully reconsidered. Other similar programs for research use of specimens collected for public health purpose are also undergoing similar reviews. It is recommended that at a minimum, service members are informed of the potential storage and use of their specimens and are allowed to opt out of additional use, or a broad informed consent is provided. The DoDSR provides a tremendous resource to the DoD and global health community, and to ensure its continued existence and improvement, the DoD must stay consistent with all principles of research ethics. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

21 CFR 58.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 1 2012-04-01 2012-04-01 false Specimen and data storage facilities. 58.51..., for the storage and retrieval of all raw data and specimens from completed studies. ... GOOD LABORATORY PRACTICE FOR NONCLINICAL LABORATORY STUDIES Facilities § 58.51 Specimen and data...

21 CFR 58.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 1 2014-04-01 2014-04-01 false Specimen and data storage facilities. 58.51..., for the storage and retrieval of all raw data and specimens from completed studies. ... GOOD LABORATORY PRACTICE FOR NONCLINICAL LABORATORY STUDIES Facilities § 58.51 Specimen and data...

21 CFR 58.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Specimen and data storage facilities. 58.51..., for the storage and retrieval of all raw data and specimens from completed studies. ... GOOD LABORATORY PRACTICE FOR NONCLINICAL LABORATORY STUDIES Facilities § 58.51 Specimen and data...

21 CFR 58.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Specimen and data storage facilities. 58.51..., for the storage and retrieval of all raw data and specimens from completed studies. ... GOOD LABORATORY PRACTICE FOR NONCLINICAL LABORATORY STUDIES Facilities § 58.51 Specimen and data...

21 CFR 58.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Specimen and data storage facilities. 58.51..., for the storage and retrieval of all raw data and specimens from completed studies. ... GOOD LABORATORY PRACTICE FOR NONCLINICAL LABORATORY STUDIES Facilities § 58.51 Specimen and data...

Experimental evaluation of sand fly collection and storage methods for the isolation and molecular detection of Phlebotomus-borne viruses.

PubMed

Remoli, Maria Elena; Bongiorno, Gioia; Fortuna, Claudia; Marchi, Antonella; Bianchi, Riccardo; Khoury, Cristina; Ciufolini, Maria Grazia; Gramiccia, Marina

2015-11-09

Several viruses have been recently isolated from Mediterranean phlebotomine sand flies; some are known to cause human disease while some are new to science. To monitor the Phlebotomus-borne viruses spreading, field studies are in progress using different sand fly collection and storage methods. Two main sampling techniques consist of CDC light traps, an attraction method allowing collection of live insects in which the virus is presumed to be fairly preserved, and sticky traps, an interception method suitable to collect dead specimens in high numbers, with a risk for virus viability or integrity. Sand flies storage requires a "deep cold chain" or specimen preservation in ethanol. In the present study the influence of sand fly collection and storage methods on viral isolation and RNA detection performances was evaluated experimentally. Specimens of laboratory-reared Phlebotomus perniciosus were artificially fed with blood containing Toscana virus (family Bunyaviridae, genus Phlebovirus). Various collection and storage conditions of blood-fed females were evaluated to mimic field procedures using single and pool samples. Isolation on VERO cell cultures, quantitative Real time-Retro-transcriptase (RT)-PCR and Nested-RT-PCR were performed according to techniques commonly used in surveillance studies. Live engorged sand flies stored immediately at -80 °C were the most suitable sample for phlebovirus identification by both virus isolation and RNA detection. The viral isolation rate remained very high (26/28) for single dead engorged females frozen after 1 day, while it was moderate (10/30) for specimens collected by sticky traps maintained up to 3 days at room temperature and then stored frozen without ethanol. Opposed to viral isolation, molecular RNA detection kept very high on dead sand flies collected by sticky traps when left at room temperature up to 6 days post blood meal and then stored frozen in presence (88/95) or absence (87/88) of ethanol. Data were confirmed using sand fly pools. While the collection and storage methods investigated had not much impact on the ability to detect viral RNA by molecular methods, they affected the capacity to recover viable viruses. Consequently, sand fly collection and handling procedures should be established in advance depending on the goal of the surveillance studies.

Maintenance of host DNA integrity in field-preserved mosquito (Diptera: Culicidae) blood meals for identification by DNA barcoding.

PubMed

Reeves, Lawrence E; Holderman, Chris J; Gillett-Kaufman, Jennifer L; Kawahara, Akito Y; Kaufman, Phillip E

2016-09-15

Determination of the interactions between hematophagous arthropods and their hosts is a necessary component to understanding the transmission dynamics of arthropod-vectored pathogens. Current molecular methods to identify hosts of blood-fed arthropods require the preservation of host DNA to serve as an amplification template. During transportation to the laboratory and storage prior to molecular analysis, genetic samples need to be protected from nucleases, and the degradation effects of hydrolysis, oxidation and radiation. Preservation of host DNA contained in field-collected blood-fed specimens has an additional caveat: suspension of the degradative effects of arthropod digestion on host DNA. Unless effective preservation methods are implemented promptly after blood-fed specimens are collected, host DNA will continue to degrade. Preservation methods vary in their efficacy, and need to be selected based on the logistical constraints of the research program. We compared four preservation methods (cold storage at -20 °C, desiccation, ethanol storage of intact mosquito specimens and crushed specimens on filter paper) for field storage of host DNA from blood-fed mosquitoes across a range of storage and post-feeding time periods. The efficacy of these techniques in maintaining host DNA integrity was evaluated using a polymerase chain reaction (PCR) to detect the presence of a sufficient concentration of intact host DNA templates for blood meal analysis. We applied a logistic regression model to assess the effects of preservation method, storage time and post-feeding time on the binomial response variable, amplification success. Preservation method, storage time and post-feeding time all significantly impacted PCR amplification success. Filter papers and, to a lesser extent, 95 % ethanol, were the most effective methods for the maintenance of host DNA templates. Amplification success of host DNA preserved in cold storage at -20 °C and desiccation was poor. Our data suggest that, of the methods tested, host DNA template integrity was most stable when blood meals were preserved using filter papers. Filter paper preservation is effective over short- and long-term storage, while ethanol preservation is only suitable for short-term storage. Cold storage at -20 °C, and desiccation of blood meal specimens, even for short time periods, should be avoided.

Case study: using a nondestructive DNA extraction method to generate mtDNA sequences from historical chimpanzee specimens.

PubMed

Mohandesan, Elmira; Prost, Stefan; Hofreiter, Michael

2012-01-01

A major challenge for ancient DNA (aDNA) studies using museum specimens is that sampling procedures usually involve at least the partial destruction of each specimen used, such as the removal of skin, pieces of bone, or a tooth. Recently, a nondestructive DNA extraction method was developed for the extraction of amplifiable DNA fragments from museum specimens without appreciable damage to the specimen. Here, we examine the utility of this method by attempting DNA extractions from historic (older than 70 years) chimpanzee specimens. Using this method, we PCR-amplified part of the mitochondrial HVR-I region from 65% (56/86) of the specimens from which we attempted DNA extraction. However, we found a high incidence of multiple sequences in individual samples, suggesting substantial cross-contamination among samples, most likely originating from storage and handling in the museums. Consequently, reproducible sequences could be reconstructed from only 79% (44/56) of the successfully extracted samples, even after multiple extractions and amplifications. This resulted in an overall success rate of just over half (44/86 of samples, or 51% success), from which 39 distinct HVR-I haplotypes were recovered. We found a high incidence of C to T changes, arguing for both low concentrations of and substantial damage to the endogenous DNA. This chapter highlights both the potential and the limitations of nondestructive DNA extraction from museum specimens.

40 CFR 160.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Specimen and data storage facilities... PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Facilities § 160.51 Specimen and data storage facilities. Space shall be provided for archives, limited to access by authorized personnel only, for the storage and...

40 CFR 160.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Specimen and data storage facilities... PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Facilities § 160.51 Specimen and data storage facilities. Space shall be provided for archives, limited to access by authorized personnel only, for the storage and...

40 CFR 160.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Specimen and data storage facilities... PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Facilities § 160.51 Specimen and data storage facilities. Space shall be provided for archives, limited to access by authorized personnel only, for the storage and...

40 CFR 160.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Specimen and data storage facilities... PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Facilities § 160.51 Specimen and data storage facilities. Space shall be provided for archives, limited to access by authorized personnel only, for the storage and...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

Impact of Storage Time on Hepatitis B Virus DNA Stability in Clinical Specimens Determined by Quantitative Real-time PCR.

PubMed

Zhang, Xiaolian; Yang, Dongmei; Lu, Yu; Lao, Xianjun; Qin, Xue; Li, Shan

2016-01-01

Detecting blood levels of hepatitis B virus (HBV) DNA must be accurate and credible. Shipment and storage conditions of clinical samples affect the quality of nucleic acids and can interfere with HBV DNA analysis. The aim of our study was to compare HBV DNA stability in plasma specimens at 4 degrees C for different storage periods. Blood samples from 30 hepatitis B surface antigen (HBsAg) positive patients were collected in tubes containing EDTA-K2. Each sample was divided into eight aliquots, one of which was measured immediately for the initial viral load. The remaining aliquots were then stored at 4 degrees C and assessed after 1, 2, 3, 7, 14, 21, and 30 days of storage. Quantification of HBV DNA was performed by real-time polymerase chain reaction (RT-PCR), and the difference in HBV DNA concentrations between two different time points was analysed with a paired-samples t-test. HBV DNA was measured in a range of 2.00 - 8.00 IU/mL, with low within-run and between-run coefficients of variation (< 10%). Storing plasma for one month at 4 degrees C revealed no significant decrease in HBV DNA level (p = 0.231), and no trend was evident to indicate continued reduction over a 3-week storage period. Based on the results of this study, storing plasma for up to one month at 4 degrees C does not affect the stability of HBV DNA, regardless of the initial viral load.

Genotyping for DQA1 and PM loci in urine using PCR-based amplification: effects of sample volume, storage temperature, preservatives, and aging on DNA extraction and typing.

PubMed

Vu, N T; Chaturvedi, A K; Canfield, D V

1999-05-31

Urine is often the sample of choice for drug screening in aviation/general forensic toxicology and in workplace drug testing. In some instances, the origin of the submitted samples may be challenged because of the medicolegal and socioeconomic consequences of a positive drug test. Methods for individualization of biological samples have reached a new boundary with the application of the polymerase chain reaction (PCR) in DNA profiling, but a successful characterization of the urine specimens depends on the quantity and quality of DNA present in the samples. Therefore, the present study investigated the influence of storage conditions, sample volume, concentration modes, extraction procedures, and chemical preservations on the quantity of DNA recovered, as well as the success rate of PCR-based genotyping for DQA1 and PM loci in urine. Urine specimens from male and female volunteers were divided and stored at various temperatures for up to 30 days. The results suggested that sample purification by dialfiltration, using 3000-100,000 molecular weight cut-off filters, did not enhance DNA recovery and typing rate as compared with simple centrifugation procedures. Extraction of urinary DNA by the organic method and by the resin method gave comparable typing results. Larger sample volume yielded a higher amount of DNA, but the typing rates were not affected for sample volumes between 1 and 5 ml. The quantifiable amounts of DNA present were found to be greater in female (14-200 ng/ml) than in male (4-60 ng/ml) samples and decreased with the elapsed time under both room temperature (RT) and frozen storage. Typing of the male samples also demonstrated that RT storage samples produced significantly higher success rates than that of frozen samples, while there was only marginal difference in the DNA typing rates among the conditions tested using female samples. Successful assignment of DQA1 + PM genotype was achieved for all samples of fresh urine, independent of gender, starting sample volume, or concentration method. Preservation by 0.25% sodium azide was acceptable for sample storage at 4 degrees C during a period of 30 days. For longer storage duration, freezing at -70 degrees C may be more appropriate. Thus, the applicability of the DQA1 + PM typing was clearly demonstrated for individualization of urine samples.

Comparability of the effect of storage time and temperature on serum anti-Müllerian hormone measurement between original and modified enzyme-linked immunosorbent assay.

PubMed

Yue, Chao-Yan; Ying, Chun-Mei

2017-01-01

To explore the effect of modified enzyme-linked immunosorbent assay on the AMH results is increased or decreased, and to investigate the effect of storage time and temperature on AMH measurements with and without sample premixing assay buffer using the Kangrun ELISA method. Serum AMH concentration were measured by ELISA, consistency between two kits, and comparability between original and the modified assay under different stored conditions were analyzed by Passing-Bablok regression analysis and Bland-Altman bias evaluation. There was a strong consistency between AMH concentrations measured in Kangrun ELISA and Ansh Labs ultra-sensitive AMH ELISA. Pre-mixing serum specimens with assay buffer gave consistent results compared with original assay. Modified protocol can reduce the amplitude of increase affected by sample aged and give the most consistent results regardless of storage conditions. Pre-mixing protocol did not influence the results of fresh serum or frozen serum incubation <3days at 4°C and -80°C, but when specimens detected after collection and stored in other storage conditions, should be pre-mixed with assay buffer to insure its accuracy. Copyright © 2016 Elsevier B.V. All rights reserved.

Stability Study of Cervical Specimens Collected by Swab and Stored Dry Followed by Human Papillomavirus DNA Detection Using the cobas 4800 Test.

PubMed

Lin, Chun-Qing; Zeng, Xi; Cui, Jian-Feng; Liao, Guang-Dong; Wu, Ze-Ni; Gao, Qian-Qian; Zhang, Xun; Yu, Xiu-Zhang; Chen, Wen; Xi, Ming-Rong; Qiao, You-Lin

2017-02-01

Safer, more convenient methods for cervical sample collection and storage are necessary to facilitate human papillomavirus (HPV) DNA testing in low-resource settings. Our study aimed to evaluate the stability of cervical specimens collected with dry swabs and stored dry, compared to liquid-based cytology (LBC) samples, as detected by HPV DNA testing. Women with abnormal cytological findings or HPV-positive results at colposcopy were recruited from the West China Second University Hospital, Sichuan University, between October 2013 and March 2014. From each woman, physicians collected cervical specimens with a swab placed into a Sarstedt tube and a CytoBrush placed into LBC medium. Samples were randomly assigned to be stored at uncontrolled ambient temperature for 2, 7, 14, or 28 days and then were tested for 14 high-risk HPV (HR-HPV) types using the cobas HPV test. The rates of agreement between dry swab and LBC samples for any HR-HPV type, HPV16, HPV18, and the 12 pooled HR-HPV types were 93.8%, 97.8%, 99.4%, and 93.2%, respectively, with kappa values of 0.87 (95% confidence interval [CI], 0.83 to 0.91), 0.94 (95% CI, 0.91 to 0.97), 0.94 (95% CI, 0.87 to 1.00), and 0.86 (95% CI, 0.82 to 0.90). The performance of swab samples for detection of cervical precancerous lesions by means of cobas HPV testing was equal to that of LBC samples, even with stratification by storage time. Dry storage of swab-collected cervical samples can last for 1 month without loss of test performance by cobas HPV testing, compared to LBC samples, which may offer a simple inexpensive approach for cervical cancer screening in low-resource settings. Copyright © 2017 American Society for Microbiology.

Biobanking human endometrial tissue and blood specimens: standard operating procedure and importance to reproductive biology research and diagnostic development.

PubMed

Sheldon, Elizabeth; Vo, Kim Chi; McIntire, Ramsey A; Aghajanova, Lusine; Zelenko, Zara; Irwin, Juan C; Giudice, Linda C

2011-05-01

To develop a standard operating procedure (SOP) for collection, transport, storage of human endometrial tissue and blood samples, subject and specimen annotation, and establishing sample priorities. The SOP synthesizes sound scientific procedures, the literature on ischemia research, sample collection and gene expression profiling, good laboratory practices, and the authors' experience of workflow and sample quality. The National Institutes of Health, University of California, San Francisco, Human Endometrial Tissue and DNA Bank. Women undergoing endometrial biopsy or hysterectomy for nonmalignant indications. Collecting, processing, storing, distributing endometrial tissue and blood samples under approved institutional review board protocols and written informed consent from participating subjects. Standard operating procedure. The SOP addresses rigorous and consistent subject annotation, specimen processing and characterization, strict regulatory compliance, and a reference for researchers to track collection and storage times that may influence their research. The comprehensive and systematic approach to the procurement of human blood and endometrial tissue in this SOP ensures the high quality, reliability, and scientific usefulness of biospecimens made available to investigators by the National Institutes of Health, University of California, San Francisco, Human Endometrial Tissue and DNA Bank. The detail and perspective in this SOP also provides a blueprint for implementation of similar collection programs at other institutions. Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Use of FTA gene guard filter paper for the storage and transportation of tumor cells for molecular testing.

PubMed

Dobbs, Larry J; Madigan, Merle N; Carter, Alexis B; Earls, Lori

2002-01-01

Efficient methods of storing tumor specimens for molecular testing are needed in the modern surgical pathology laboratory. The FTA Gene Guard system is a novel method for the collection and room temperature storage of blood samples for DNA testing. The method uses index card-sized filter papers that provide an ideal medium on which to store tumor specimens for DNA testing. To determine whether FTA filter paper can be used in the surgical pathology laboratory to store tumor cells for DNA testing. Cell suspensions were prepared from 60 surgical specimens, and DNA was extracted either immediately or after storage on FTA paper. The DNA extracted by each method was tested by polymerase chain reaction (PCR) for the beta-globin and interferon gamma genes, and the results were compared. Fifteen lymph node specimens stored on FTA paper were then tested for immunoglobulin heavy chain (IgH) gene rearrangement by PCR, and these results were compared with those obtained for immediately extracted DNA. University medical center. The DNA extracted from cells stored on FTA paper performed as well in the PCR as the freshly extracted DNA in nearly all cases (>95%). The results of tests for IgH gene rearrangements showed 100% concordance between the 2 methods of DNA extraction.Conclusion.-Cells from surgical specimens can be stored on FTA paper for extended lengths of time, and DNA can be extracted from these cells for PCR-based testing. FTA filter paper is a reliable medium for the storage and/or transport of tumor cells for PCR-based DNA analysis.

Assessment of the stability of mephedrone in ante-mortem and post-mortem blood specimens.

PubMed

Busardò, Francesco Paolo; Kyriakou, Chrystalla; Tittarelli, Roberta; Mannocchi, Giulio; Pantano, Flaminia; Santurro, Alessandro; Zaami, Simona; Baglìo, Giovanni

2015-11-01

The aim of this work is to test the stability of mephedrone added to whole blood collected from alive and dead mephedrone free-users and stored at three different temperatures (-20, +4 and +20°C) with and without preservatives up to 6 months, trying to establish the best storage condition in order to reduce possible analyte loss/degradation during the storage period. Different sources of blood were obtained as follow: 10 samples of blood came from 10 alive mephedrone free-users (mean age 34±15.8 years old) (Group 1), whereas 10 post mortem blood samples were obtained from 10 cadavers, in which the post mortem interval was between 24 and 36h (Group 2). The cause of death in post mortem cases (mean age 45±14.2 years old) was not drug related. Pools of blood were spiked with mephedrone at the concentration of 1mg/L and 1mL aliquots were transferred in 2mL Eppendorf capped tubes with and without preservatives as follow: with ethylenediaminetetraacetic acid (EDTA) 3%; with sodium fluoride/potassium oxalate (NaF/KOx) 1.67%/0.2%, respectively; without preservatives. All samples were stored at three different temperatures: -20°C, 4°C and 20°C and extracted and analyzed in duplicate by GC-MS according to a previously published method by Dickson et al., every other day during the first month and then weekly up to 6 months. our study allow us to affirm that -20°C is the best storage temperature for mephedrone stability in ante-mortem and post-mortem blood samples in comparison to the other two tested temperatures (+4 and +20°C), showing higher values in both groups in samples stored with and without preservatives (p<0.0001). The comparison of Group 1 (samples coming from alive subjects) and Group 2 (post-mortem samples) highlights a better stability of mephedrone in Group 1 (p<0.001) at all tested storage conditions. Finally, the analysis of blood specimens stored with and without preservatives in both groups suggests that specimens stored with NaF/KOx maintain mephedrone stability better than those stored with EDTA (p<0.001) and those stored without preservatives (p<0.0001), therefore, we strongly recommend in order to maintain the highest mephedrone stability in blood, to store specimens at -20°C adding NaF/KOx as preservative. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Use of External Quality Control Material for HIV-1 RNA Testing To Assess the Comparability of Data Generated in Separate Laboratories and the Stability of HIV-1 RNA in Samples after Prolonged Storage.

PubMed

Jennings, Cheryl; Wager, Carrie G; Scianna, Salvatore R; Zaccaro, Daniel J; Couzens, Amy; Mellors, John W; Coombs, Robert W; Bremer, James W

2018-06-01

The National Institute of Allergy and Infectious Diseases (NIAID) AIDS Clinical Trials Group (ACTG) stores specimens from its clinical trials in a biorepository and permits the use of these specimens for nonprotocol exploratory studies, once the studies for the original protocol are concluded. We sought to assess the comparability of the data generated from real-time HIV-1 RNA testing during two clinical trials with the data generated from the retesting of different aliquots of the same samples after years of storage at -80°C. Overall, there was 92% agreement in the data generated for 1,570 paired samples (kappa statistic = 0.757; 95% confidence interval [CI], 0.716 to 0.797), where samples were tested in one laboratory using the microwell plate (MWP) version of the Roche HIV-1 Monitor test within 1 to 37 days of collection and retested in another laboratory using the Cobas version of the assay after a median of 6.7 years of storage (range, 5.7 to 8.6 years). Historical external quality control data submitted to the NIAID Virology Quality Assurance program (VQA) by client laboratories using the same two versions of the Monitor assay were used to differentiate between systematic differences in the assays to evaluate the stability of HIV-1 RNA in the stored samples. No significant loss of RNA was noted in samples containing either a low concentration (<50 copies/ml) or a high concentration (≥50 copies/ml) of HIV-1 RNA ( P = 0.10 and P = 0.90, respectively) regardless of the time in storage. These data confirm the quality of the plasma samples in the ACTG biorepository following long-term storage. Copyright © 2018 American Society for Microbiology.

40 CFR 160.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Specimen and data storage facilities. 160.51 Section 160.51 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Facilities § 160.51 Specimen and data storage facilities. Space...

Hematology and pathology devices; reclassification; restricted devices; OTC test sample collection systems for drugs of abuse testing. Food and Drug Administration, HHS. Final rule.

PubMed

2000-04-07

The Food and Drug Administration (FDA) is reclassifying over-the-counter (OTC) test sample collection systems for drugs of abuse testing from class III (premarket approval) into class I (general controls) and exempting them from premarket notification (510(k)) and current good manufacturing practice (CGMP) requirements. FDA is also designating OTC test sample collection systems for drugs of abuse testing as restricted devices under the Federal Food, Drug, and Cosmetic Act (the act) and establishing restrictions intended to assure consumers that: The underlying laboratory test(s) are accurate and reliable; the laboratory performing the test(s) has adequate expertise and competency; and the product has adequate labeling and methods of communicating test results to consumers. Finally, FDA is adding a conforming amendment to the existing classification regulation for specimen transport and storage containers to clarify that it does not apply to specimen transport and storage containers that are part of an OTC test sample collection system for the purpose of testing for the presence of drugs of abuse or their metabolites in a laboratory.

Total morphine stability in urine specimens stored under various conditions.

PubMed

Chang, B L; Huang, M K; Tsai, Y Y

2000-09-01

The stability of total morphine in urine stored under various conditions was studied using control and experimental specimens. Samples in the control group were prepared using drug-free urine spiked with morphine at three concentration levels (300, 1000, and 2500 ng/mL), each with the pH adjusted to 5.5, 6.5, and 7.5. Samples in the experimental group came from 20 alleged heroin addicts (provided by Taipei Municipal Psychiatric Hospital). Samples in both groups were divided into two categories--one with and one without the precipitate (formed at 0 degrees C) removed. Samples in each of these two categories were further divided into two sub-groups--one with and one without sodium azide (0.05%) added. Total morphine contents in these samples were first determined by gas chromatography-mass spectrometry prior to storage and at 6, 12, 18, and 24 months following storage at -20, 4, 25, and 35 degrees C. Effects of sample treatment (azide addition and precipitate removal), pH, and storage temperature and length were evaluated by examining the percentage of total morphine remaining at the four time intervals following the initial determination. Major findings were as follows: (1) total morphine decomposition was minimal when stored for 12 months at -20 degrees C, which is a common current practice; (2) samples with lower initial sample pH had slower total morphine decomposition rates; and (3) azide addition appeared to have no detectable effect, whereas precipitate removal appeared to marginally reduce the decomposition rate, especially for samples with lower pH.

RNA quality in fresh-frozen gastrointestinal tumor specimens-experiences from the tumor and healthy tissue bank TU Dresden.

PubMed

Zeugner, Silke; Mayr, Thomas; Zietz, Christian; Aust, Daniela E; Baretton, Gustavo B

2015-01-01

The term "pre-analytics" summarizes all procedures concerned with specimen collection or processing as well as logistical aspects like transport or storage of tissue specimens. All or these variables as well as tissue-specific characteristics affect sample quality. While certain parameters like warm ischemia or tissue-specific characteristics cannot be changed, other parameters can be assessed and optimized. The aim of this study was to determine RNA quality by assessing the RIN values of specimens from different organs and to assess the influence of vacuum preservation. Samples from the GI tract, in general, appear to have lower RNA quality when compared to samples from other organ sites. This may be due to the digestive enzymes or bacterial colonization. Processing time in pathology does not significantly influence RNA quality. Tissue preservation with a vacuum sealer leads to preserved RNA quality over an extended period of time and offers a feasible alternative to minimize the influence of transport time into pathology.

[Establishment and Management of Multiple Myeloma Specimen Bank Applied for Molecular Biological Researches].

PubMed

Li, Han-Qing; Mei, Jian-Gang; Cao, Hong-Qin; Shao, Liang-Jing; Zhai, Yong-Ping

2017-12-01

To establish a multiple myeloma specimen bank applied for molecular biological researches and to explore the methods of specimen collection, transportation, storage, quality control and the management of specimen bank. Bone marrow and blood samples were collected from multiple myeloma patients, plasma cell sorting were operated after the separation of mononuclear cells from bone marrow specimens. The plasma cells were divided into 2 parts, one was added with proper amount of TRIzol and then kept in -80 °C refrigerator for subsequent RNA extraction, the other was added with proper amount of calf serum cell frozen liquid and then kept in -80 °C refrigerator for subsequent cryopreservation of DNA extraction after numbered respectively. Serum and plasma were separated from peripheral blood, specimens of serum and plasma were then stored at -80 °C refrigerator after registration. Meantime, the myeloma specimen information management system was established, managed and maintained by specially-assigned persons and continuous modification and improvement in the process of use as to facilitate the rapid collection, management, query of the effective samples and clinical data. A total of 244 portions plasma cells, 564 portions of serum, and 1005 portions of plasma were collected, clinical characters were documented. A multiple myeloma specimen bank have been established initially, which can provide quality samples and related clinical information for molecular biological research on multiple myeloma.

Effect of short-term room temperature storage on the microbial community in infant fecal samples.

PubMed

Guo, Yong; Li, Sheng-Hui; Kuang, Ya-Shu; He, Jian-Rong; Lu, Jin-Hua; Luo, Bei-Jun; Jiang, Feng-Ju; Liu, Yao-Zhong; Papasian, Christopher J; Xia, Hui-Min; Deng, Hong-Wen; Qiu, Xiu

2016-05-26

Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.

Solution Preserves Nucleic Acids in Body-Fluid Specimens

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Stowe, Raymond P.

2004-01-01

A solution has been formulated to preserve deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in specimens of blood, saliva, and other bodily fluids. Specimens of this type are collected for diagnostic molecular pathology, which is becoming the method of choice for diagnosis of many diseases. The solution makes it possible to store such specimens at room temperature, without risk of decomposition, for subsequent analysis in a laboratory that could be remote from the sampling location. Thus, the solution could be a means to bring the benefits of diagnostic molecular pathology to geographic regions where refrigeration equipment and diagnostic laboratories are not available. The table lists the ingredients of the solution. The functions of the ingredients are the following: EDTA chelates divalent cations that are necessary cofactors for nuclease activity. In so doing, it functionally removes these cations and thereby retards the action of nucleases. EDTA also stabilizes the DNA helix. Tris serves as a buffering agent, which is needed because minor contaminants in an unbuffered solution can exert pronounced effects on pH and thereby cause spontaneous degradation of DNA. SDS is an ionic detergent that inhibits ribonuclease activity. SDS has been used in some lysis buffers and as a storage buffer for RNA after purification. The use of the solution is straightforward. For example, a sample of saliva is collected by placing a cotton roll around in the subject's mouth until it becomes saturated, then the cotton is placed in a collection tube. Next, 1.5 mL of the solution are injected directly into the cotton and the tube is capped for storage at room temperature. The effectiveness of the solution has been demonstrated in tests on specimens of saliva containing herpes simplex virus. In the tests, the viral DNA, as amplified by polymerase chain reaction, was detected even after storage for 120 days.

Pre-heating mitigates composite degradation

PubMed Central

da SILVA, Jessika Calixto; Rogério Vieira, REGES; REGE, Inara Carneiro Costa; CRUZ, Carlos Alberto dos Santos; VAZ, Luís Geraldo; ESTRELA, Carlos; de CASTRO, Fabrício Luscino Alves

2015-01-01

ABSTRACT Dental composites cured at high temperatures show improved properties and higher degrees of conversion; however, there is no information available about the effect of pre-heating on material degradation. Objectives This study evaluated the effect of pre-heating on the degradation of composites, based on the analysis of radiopacity and silver penetration using scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS). Material and Methods Thirty specimens were fabricated using a metallic matrix (2x8 mm) and the composites Durafill VS (Heraeus Kulzer), Z-250 (3M/ESPE), and Z-350 (3M/ESPE), cured at 25°C (no pre-heating) or 60°C (pre-heating). Specimens were stored sequentially in the following solutions: 1) water for 7 days (60°C), plus 0.1 N sodium hydroxide (NaOH) for 14 days (60°C); 2) 50% silver nitrate (AgNO3) for 10 days (60°C). Specimens were radiographed at baseline and after each storage time, and the images were evaluated in gray scale. After the storage protocol, samples were analyzed using SEM/EDS to check the depth of silver penetration. Radiopacity and silver penetration data were analyzed using ANOVA and Tukey’s tests (α=5%). Results Radiopacity levels were as follows: Durafill VSZ-350>Z-250 (p<0.05). After storage in water/NaOH, pre-heated specimens presented higher radiopacity values than non-pre-heated specimens (p<0.05). There was a lower penetration of silver in pre-heated specimens (p<0.05). Conclusions Pre-heating at 60°C mitigated the degradation of composites based on analysis of radiopacity and silver penetration depth. PMID:26814459

National survey on the pre-analytical variability in a representative cohort of Italian laboratories.

PubMed

Lippi, Giuseppe; Montagnana, Martina; Giavarina, Davide

2006-01-01

Owing to remarkable advances in automation, laboratory technology and informatics, the pre-analytical phase has become the major source of variability in laboratory testing. The present survey investigated the development of several pre-analytical processes within a representative cohort of Italian clinical laboratories. A seven-point questionnaire was designed to investigate the following issues: 1a) the mean outpatient waiting time before check-in and 1b) the mean time from check-in to sample collection; 2) the mean time from sample collection to analysis; 3) the type of specimen collected for clinical chemistry testing; 4) the degree of pre-analytical automation; 5a) the number of samples shipped to other laboratories and 5b) the availability of standardised protocols for transportation; 6) the conditions for specimen storage; and 7) the availability and type of guidelines for management of unsuitable specimens. The questionnaire was administered to 150 laboratory specialists attending the SIMEL (Italian Society of Laboratory Medicine) National Meeting in June 2006. 107 questionnaires (71.3%) were returned. Data analysis revealed a high degree of variability among laboratories for the time required for check-in, outpatient sampling, sample transportation to the referral laboratory and analysis upon the arrival. Only 31% of laboratories have automated some pre-analytical steps. Of the 87% of laboratories that ship specimens to other facilities without sample preparation, 19% have no standardised protocol for transportation. For conventional clinical chemistry testing, 74% of the laboratories use serum evacuated tubes (59% with and 15% without serum separator), whereas the remaining 26% use lithium-heparin evacuated tubes (11% with and 15% without plasma separator). The storage period and conditions for rerun/retest vary widely. Only 63% of laboratories have a codified procedure for the management of unsuitable specimens, which are recognised by visual inspection (69%) or automatic detection (29%). Only 56% of the laboratories have standardised procedures for the management of unsuitable specimens, which vary widely on a local basis. The survey highlights broad heterogeneity in several pre-analytical processes among Italian laboratories. The lack of reliable guidelines encompassing evidence-based practice is a major problem for the standardisation of this crucial part of the testing process and represents a major challenge for laboratory medicine in the 2000s.

The effect of water storage, elapsed time and contaminants on the bond strength and interfacial polymerization of a nanohybrid composite.

PubMed

Perriard, Jean; Lorente, Maria Cattani; Scherrer, Susanne; Belser, Urs C; Wiskott, H W Anselm

2009-12-01

To systematically characterize the effect of time lapse, water storage, and selected contaminants on the bond strength of a nanofilled dental composite. Half-dumbbell-shaped samples were fabricated out of light-polymerizing composite resin. To function as substrates they were aged for 30 days in water. Prior to bonding, the substrates' surfaces were subjected to the following treatments: 1) Removing a 0.2- to 0.4-mm layer using a fluted carbide bur; 2) grit blasting with 50 microm alumina particles; 3) etching with phosphoric acid gel; 4) grit blasting followed by etching; 5) blasting with tribochemical particles followed by silane application; 6) sanding with 400-grit paper, air aging of the adherent half-sample before bonding; 7) surface contamination with saliva; 8) surface contamination with blood. In each group (n = 30), freshly polymerized (except in group 6) adherent half-samples were bonded to the substrate half-samples by a layer of unfilled adhesive resin. Fifteen full dumbbell-shaped specimens were subjected to tensile testing after 1 h and 15 after 7 days water storage. In a positive control group, freshly cured half-samples were bonded shortly after fabrication. The tensile strength was analyzed using Weibull statistics and presented in terms of the material's characteristic strength and shape parameter. Fractographs of the two weakest and strongest samples of each group were produced. The surfaces were searched to locate hackle, wake hackle and the origin of the fracture. Surface roughness and time lapse increased the bond strength of the repaired specimens. All groups in which surface roughness was produced before bonding increased in repair strength. Post-bonding aging improved strength. Fractographs yielded interpretable data whenever larger surfaces of single phase bonding resin were present. 1) Roughening and etching an aged composite's surface prior to applying a coat of unfilled resin and the filled material increases repair bond strength by up to 100%. 2) The repair bond strength of a roughened aged composite is 25% to 30% inferior to the tensile strength of solid specimens. 3) After 7 days' storage in water, no detrimental effect could be seen from saliva or blood contamination if the surfaces were properly rinsed.

Long-term bonding effectiveness of simplified etch-and-rinse adhesives to dentin after different surface pre-treatments

PubMed Central

Verma, Radhika; Singh, Udai Pratap; Tyagi, Shashi Prabha; Nagpal, Rajni; Manuja, Naveen

2013-01-01

Objective: To evaluate the effect of 2% chlorhexidine (CHX) and 30% proanthocyanidin (PA) application on the immediate and long-term bond strength of simplified etch-and-rinse adhesives to dentin. Materials and Methods: One hundred twenty extracted human molar teeth were ground to expose the flat dentin surface. The teeth were equally divided into six groups according to the adhesives used, either Tetric N Bond or Solobond M and pretreatments given either none, CHX, or PA. Composite cylinder was bonded to each specimen using the respective adhesive technique. Half the samples from each group (n = 10) were then tested immediately. The remaining samples were tested after 6 month storage in distilled water. Results: The mean bond strength of samples was not significantly different upon immediate testing being in the range of 8.4(±0.7) MPa. The bond strength fell dramatically in the control specimens after 6 month storage to around 4.7(±0.33) MPa, while the bond strength was maintained in the samples treated with both CHX and PA. Conclusion: Thirty percent PA was comparable to 2% CHX with respect to preservation of the resin dentin bond over 6 months. PMID:23956543

Reduction of Photo Bleaching and Long Term Archiving of Chemically Cleared GFP-Expressing Mouse Brains

PubMed Central

Becker, Klaus; Hahn, Christian Markus; Saghafi, Saiedeh; Jährling, Nina; Wanis, Martina; Dodt, Hans-Ulrich

2014-01-01

Tissue clearing allows microscopy of large specimens as whole mouse brains or embryos. However, lipophilic tissue clearing agents as dibenzyl ether limit storage time of GFP-expressing samples to several days and do not prevent them from photobleaching during microscopy. To preserve GFP fluorescence, we developed a transparent solid resin formulation, which maintains the specimens' transparency and provides a constant signal to noise ratio even after hours of continuous laser irradiation. If required, high-power illumination or long exposure times can be applied with virtually no loss in signal quality and samples can be archived for years. PMID:25463047

[The Scope, Quality and Safety Requirements of Drug Abuse Testing].

PubMed

Küme, Tuncay; Karakükcü, Çiğdem; Pınar, Aslı; Coşkunol, Hakan

2017-01-01

The aim of this review is to inform about the scopes and requirements of drug abuse testing. Drug abuse testing is one of the tools for determination of drug use. It must fulfill the quality and safety requirements in judgmental legal and administrative decisions. Drug abuse testing must fulfill some requirements like selection of the appropriate test matrix, appropriate screening test panel, sampling in detection window, patient consent, identification of the donor, appropriate collection site, sample collection with observation, identification and control of the sample, specimen custody chain in preanalytical phase; analysis in authorized laboratories, specimen validity tests, reliable testing METHODS, strict quality control, two-step analysis in analytical phase; storage of the split specimen, confirmation of the split specimen in the objection, result custody chain, appropriate cut-off concentration, the appropriate interpretation of the result in postanalytical phase. The workflow and analytical processes of drug abuse testing are explained in last regulation of the Department of Medical Laboratory Services, Ministry of Health in Turkey. The clinical physicians have to know and apply the quality and safety requirements in drug abuse testing according to last regulations in Turkey.

40 CFR 792.51 - Specimen and data storage facilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 31 2010-07-01 2010-07-01 true Specimen and data storage facilities. 792.51 Section 792.51 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Facilities § 792.51 Specimen and data...

Validity and Reliability of Perinatal Biomarkers after Storage as Dry Blood Spots on Paper

PubMed Central

Mihalopoulos, Nicole L.; Phillips, Terry M.; Slater, Hillarie; Thomson, J. Anne; Varner, Michael W.; Moyer-Mileur, Laurie J.

2013-01-01

Ojective To validate use of chip-based immunoaffinity capillary electrophoresis on dry blood spot samples (DBSS) to measure obesity-related cytokines. Methods Chip-based immunoaffinity capillary electrophoresis was used to measure adiponectin, leptin and insulin in serum and DBSS in pregnant women, cord blood, and infant heelstick at birth and 6 weeks. Concordance of measurements was determined with Pearson's correlation. Results We report high concordance between results obtained from serum and DBSS with the exception of cord blood specimens. Conclusions Ease of sample collection and storage makes DBSS an optimal method for use in studies involving neonates and young children. PMID:21735507

DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.

PubMed

Guyard, Alice; Boyez, Alice; Pujals, Anaïs; Robe, Cyrielle; Tran Van Nhieu, Jeanne; Allory, Yves; Moroch, Julien; Georges, Odette; Fournet, Jean-Christophe; Zafrani, Elie-Serge; Leroy, Karen

2017-10-01

Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p < 0.001). Overall, remaining proportion of DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.

Comparison of Two Methods of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissue Specimens

PubMed Central

Gouveia, Gisele Rodrigues; Ferreira, Suzete Cleusa; Ferreira, Jerenice Esdras; Siqueira, Sheila Aparecida Coelho; Pereira, Juliana

2014-01-01

The present study aimed to compare two different methods of extracting RNA from formalin-fixed paraffin-embedded (FFPE) specimens of diffuse large B-cell lymphoma (DLBCL). We further aimed to identify possible influences of variables—such as tissue size, duration of paraffin block storage, fixative type, primers used for cDNA synthesis, and endogenous genes tested—on the success of amplification from the samples. Both tested protocols used the same commercial kit for RNA extraction (the RecoverAll Total Nucleic Acid Isolation Optimized for FFPE Samples from Ambion). However, the second protocol included an additional step of washing with saline buffer just after sample rehydration. Following each protocol, we compared the RNA amount and purity and the amplification success as evaluated by standard PCR and real-time PCR. The results revealed that the extra washing step added to the RNA extraction process resulted in significantly improved RNA quantity and quality and improved success of amplification from paraffin-embedded specimens. PMID:25105117

Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens

PubMed Central

Guan, YaoYao; Gravitt, Patti E.; Howard, Roslyn; Eby, Yolanda J.; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E.

2016-01-01

The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p = 0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. PMID:23370404

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

Pietrzyk, Robert; McMonigal, K. A.; Sams, C. F.; Johnson, M. A.

2009-01-01

The NASA Biological Specimen Repository (NBSR) has been established to collect, process, annotate, store, and distribute specimens under the authority of the NASA/JSC Committee for the Protection of Human Subjects. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The NBSR is a secure controlled storage facility that is used to maintain biological specimens over extended periods of time, under well-controlled conditions, for future use in approved human spaceflight-related research protocols. The repository supports the Human Research Program, which is charged with identifying and investigating physiological changes that occur during human spaceflight, and developing and implementing effective countermeasures when necessary. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can validate clinical hypotheses, study space-flight related changes, and investigate physiological markers All samples collected require written informed consent from each long duration crewmember. The NBSR collects blood and urine samples from all participating long duration ISS crewmembers. These biological samples are collected pre-flight at approximately 45 days prior to launch, during flight on flight days 15, 30, 60 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days following landing. The number of inflight sessions is dependent on the duration of the mission. Operations began in 2007 and as of October 2009, 23 USOS crewmembers have completed or agreed to participate in this project. As currently planned, these human biological samples will be collected from crewmembers covering multiple ISS missions until the end of U.S. presence on the ISS or 2017. The NBSR will establish guidelines for sample distribution that are consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. A NBSR Advisory Board composed of representatives of all participating agencies will be established to evaluate each request by an investigator for use of the samples to ensure the request reflects the mission of the NBSR.

Effect of simulated pulpal pressure on all-in-one adhesive bond strengths to dentine.

PubMed

Hosaka, Keiichi; Nakajima, Masatoshi; Yamauti, Monica; Aksornmuang, Juthatip; Ikeda, Masaomi; Foxton, Richard M; Pashley, David H; Tagami, Junji

2007-03-01

To evaluate the durability of all-in-one adhesive systems bonded to dentine with and without simulated hydrostatic pulpal pressure (PP). Flat dentine surfaces of extracted human molars were prepared. Two all-in-one adhesive systems, One-Up Bond F (OBF) (Tokuyama Corp., Tokyo, Japan), and Fluoro Bond Shake One (FBS) (Shofu Co., Kyoto, Japan) were applied to the dentine surfaces under either a PP of 0 or 15cm H(2)O. Then, resin composite build-ups were made. The specimens bonded under pressure were stored in 37 degrees C water for 24h, 1 and 3 months under 15cm H(2)O PP. Specimens not bonded under pressure were stored under zero PP. After storage, the specimens were sectioned into slabs that were trimmed to hourglass shapes and subjected to micro-tensile bond testing (muTBS). The data were analysed using two-way ANOVA and Holm-Sidak HSD multiple comparison tests (alpha=0.05). The muTBS of OBF fell significantly (p<0.05) when PP was applied during bonding and storage, regardless of storage time. In contrast, although the muTBS of OBF specimens bonded and stored without hydrostatic pressure storage fell significantly over the 3 months period, the decrease was less than half as much as specimens stored under PP. In FBS bonded specimens, although there was no significant difference between the muTBS with and without hydrostatic pulpal pressure at 24h, by 1 and 3 months of storage under PP, significant reductions were seen compared with the control group without PP. The muTBS of OBF bonded specimens was lowered more by simulated PP than by storage time; specimens bonded with FBS were not sensitive to storage time in the absence of PP, but showed lower bond strengths at 1 and 3 months in the presence of PP.

Standard Specimen Reference Set: Pancreatic — EDRN Public Portal

Cancer.gov

The primary objective of the EDRN Pancreatic Cancer Working Group Proposal is to create a reference set consisting of well-characterized serum/plasma specimens to use as a resource for the development of biomarkers for the early detection of pancreatic adenocarcinoma. The testing of biomarkers on the same sample set permits direct comparison among them; thereby, allowing the development of a biomarker panel that can be evaluated in a future validation study. Additionally, the establishment of an infrastructure with core data elements and standardized operating procedures for specimen collection, processing and storage, will provide the necessary preparatory platform for larger validation studies when the appropriate marker/panel for pancreatic adenocarcinoma has been identified.

Stability of selected serum proteins after long-term storage in the Janus Serum Bank.

PubMed

Gislefoss, Randi E; Grimsrud, Tom K; Mørkrid, Lars

2009-01-01

Human serum from biobanks is frequently used in prospective epidemiological studies. Long-term storage may modify its composition. A better understanding of the stability of the serum components may improve the interpretation of future studies. The concentrations of selected proteins; immunoglobulins, carrier proteins and enzymes in samples stored at -25 degrees C for 25 years and 2 years were compared with 1-month-old samples. For each length of storage time, 130 specimens were randomly selected from apparently healthy male blood donors aged 40-49 years. We examined the distribution of values, compared dispersion and localization of central tendency, and established reference intervals for each component. The study demonstrated non-significant or numerically small group differences in the concentrations of albumin, aspartate amino transferase, cystatin C, immunoglobulin E, immunoglobulin G, and sex hormone binding globulin. Mean values between fresh and 25-year-old samples suggested larger differences during storage for alanine amino transferase (-73.4%), creatinine kinase (-96.1%), insulin C-peptide (-98.7%), ferritin (-18.5%) and transferrin (+8.2%). The findings showed that long-term storage can introduce a considerable bias for vulnerable components.

An allowable cladding peak temperature for spent nuclear fuels in interim dry storage

NASA Astrophysics Data System (ADS)

Cha, Hyun-Jin; Jang, Ki-Nam; Kim, Kyu-Tae

2018-01-01

Allowable cladding peak temperatures for spent fuel cladding integrity in interim dry storage were investigated, considering hydride reorientation and mechanical property degradation behaviors of unirradiated and neutron irradiated Zr-Nb cladding tubes. Cladding tube specimens were heated up to various temperatures and then cooled down under tensile hoop stresses. Cool-down specimens indicate that higher heat-up temperature and larger tensile hoop stress generated larger radial hydride precipitation and smaller tensile strength and plastic hoop strain. Unirradiated specimens generated relatively larger radial hydride precipitation and plastic strain than did neutron irradiated specimens. Assuming a minimum plastic strain requirement of 5% for cladding integrity maintenance in interim dry storage, it is proposed that a cladding peak temperature during the interim dry storage is to keep below 250 °C if cladding tubes are cooled down to room temperature.

76 FR 4431 - Privacy Act of 1974; Report of Modified or Altered System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

..., records on biological specimens (e.g. blood, urine, etc.), and related documents such as [[Page 4433... Disease Control and Prevention (CDC), for laboratory analysis of samples and for collaborative efforts (i... PRACTICES FOR STORING, RETRIEVING, ACCESSING, RETAINING, AND DISPOSING OF RECORDS IN THE SYSTEM: STORAGE...

Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

NASA Astrophysics Data System (ADS)

Gaither, M. R.; Szabó, Z.; Crepeau, M. W.; Bird, C. E.; Toonen, R. J.

2011-06-01

Specimen collection is time consuming and expensive, yet few laboratories test preservation methods before setting out on field expeditions. The most common preservation buffer used for coral specimens is >70% EtOH. However, alternatives exist that are less flammable, easier to ship, and are widely used in other taxa. Here, we compare the effects of salt-saturated DMSO (SSD) and EtOH preservation buffers on post-extraction DNA quantity and quality. We found that soft tissue integrity was better maintained and higher quantities of DNA were extracted from EtOH-preserved specimens; however, by all other measures, SSD was a superior preservative to EtOH. Extractions of SSD-preserved specimens resulted in higher molecular weight DNA, higher PCR success, and more efficient amplification than specimens preserved in EtOH. Our results show that SSD is generally a superior preservative to EtOH for specimens destined for PCR studies, but species-specific differences indicate that preservation comparisons should be undertaken before collection and storage of samples.

Influence of investment, disinfection, and storage on the microhardness of ocular resins.

PubMed

Goiato, Marcelo Coelho; dos Santos, Daniela Micheline; Gennari-Filho, Humberto; Zavanelli, Adriana Cristina; Dekon, Stefan Fiuza de Carvalho; Mancuso, Daniela Nardi

2009-01-01

The longevity of an ocular prosthesis is directly related to the resistance to erosion of its material. The purpose of this study was to evaluate the effects of chemical disinfection and the method of investment on the microhardness of ocular prosthesis acrylic resin. Thirty-two test specimen investments were obtained in two silicones. A segment was cut in each test specimen, and each specimen was fixed in an acrylic disk. The specimens were then polished and submitted to the first microhardness test before immersion in distilled water and incubation for 2 months. During this 2-month period, the specimens were immersed in a water bath at 37 degrees C and were disinfected daily; half were disinfected with neutral soap and the other half were disinfected with 4% chlorhexidine gluconate. After the storage phase and disinfection, a second microhardness test was performed. The surface microhardness values for the acrylic resins were submitted to ANOVA, followed by the Tukey test. The disinfection and the period of storage did not statistically influence the surface microhardness of the acrylic resin, independent of the method of investment of the specimens (Zetalabor or Vipi Sil). The investment of specimens with Zetalabor silicone presented a greater surface hardness, independent of the type of disinfection and the period of storage. Based on these results, we suggest that the microhardness of the resin evaluated was not influenced by the method of disinfection or the time of storage used and was affected only by the investment material.

Collection, transport and general processing of clinical specimens in Microbiology laboratory.

PubMed

Sánchez-Romero, M Isabel; García-Lechuz Moya, Juan Manuel; González López, Juan José; Orta Mira, Nieves

2018-02-06

The interpretation and the accuracy of the microbiological results still depend to a great extent on the quality of the samples and their processing within the Microbiology laboratory. The type of specimen, the appropriate time to obtain the sample, the way of sampling, the storage and transport are critical points in the diagnostic process. The availability of new laboratory techniques for unusual pathogens, makes necessary the review and update of all the steps involved in the processing of the samples. Nowadays, the laboratory automation and the availability of rapid techniques allow the precision and turn-around time necessary to help the clinicians in the decision making. In order to be efficient, it is very important to obtain clinical information to use the best diagnostic tools. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens.

PubMed

Guan, Yaoyao; Gravitt, Patti E; Howard, Roslyn; Eby, Yolanda J; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E

2013-04-01

The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p=0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. Copyright © 2012 Elsevier B.V. All rights reserved.

Space Station Biological Research Project (SSBRP) Cell Culture Unit (CCU) and incubator for International Space Station (ISS) cell culture experiments

NASA Technical Reports Server (NTRS)

Vandendriesche, Donald; Parrish, Joseph; Kirven-Brooks, Melissa; Fahlen, Thomas; Larenas, Patricia; Havens, Cindy; Nakamura, Gail; Sun, Liping; Krebs, Chris; de Luis, Javier;

X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens

PubMed Central

de Jonge, Martin D.; Ryan, Christopher G.; Jacobsen, Chris J.

2014-01-01

X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer. PMID:25177992

Comparative analysis of storage conditions and homogenization methods for tick and flea species for identification by MALDI-TOF MS.

PubMed

Nebbak, A; El Hamzaoui, B; Berenger, J-M; Bitam, I; Raoult, D; Almeras, L; Parola, P

2017-12-01

Ticks and fleas are vectors for numerous human and animal pathogens. Controlling them, which is important in combating such diseases, requires accurate identification, to distinguish between vector and non-vector species. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was applied to the rapid identification of arthropods. The growth of this promising tool, however, requires guidelines to be established. To this end, standardization protocols were applied to species of Rhipicephalus sanguineus (Ixodida: Ixodidae) Latreille and Ctenocephalides felis felis (Siphonaptera: Pulicidae) Bouché, including the automation of sample homogenization using two homogenizer devices, and varied sample preservation modes for a period of 1-6 months. The MS spectra were then compared with those obtained from manual pestle grinding, the standard homogenization method. Both automated methods generated intense, reproducible MS spectra from fresh specimens. Frozen storage methods appeared to represent the best preservation mode, for up to 6 months, while storage in ethanol is also possible, with some caveats for tick specimens. Carnoy's buffer, however, was shown to be less compatible with MS analysis for the purpose of identifying ticks or fleas. These standard protocols for MALDI-TOF MS arthropod identification should be complemented by additional MS spectrum quality controls, to generalize their use in monitoring arthropods of medical interest. © 2017 The Royal Entomological Society.

Tumoural specimens for forensic purposes: comparison of genetic alterations in frozen and formalin-fixed paraffin-embedded tissues.

PubMed

Ananian, Viviana; Tozzo, Pamela; Ponzano, Elena; Nitti, Donato; Rodriguez, Daniele; Caenazzo, Luciana

2011-05-01

In certain circumstances, tumour tissue specimens are the only DNA resource available for forensic DNA analysis. However, cancer tissues can show microsatellite instability and loss of heterozygosity which, if concerning the short tandem repeats (STRs) used in the forensic field, can cause misinterpretation of the results. Moreover, though formalin-fixed paraffin-embedded tissues (FFPET) represent a large resource for these analyses, the quality of the DNA obtained from this kind of specimen can be an important limit. In this study, we evaluated the use of tumoural tissue as biological material for the determination of genetic profiles in the forensic field, highlighting which STR polymorphisms are more susceptible to tumour genetic alterations and which of the analysed tumours show a higher genetic variability. The analyses were conducted on samples of the same tissues conserved in different storage conditions, to compare genetic profiles obtained by frozen tissues and formalin-fixed paraffin-embedded tissues. The importance of this study is due to the large number of specimens analysed (122), the large number of polymorphisms analysed for each specimen (39), and the possibility to compare, many years after storage, the same tissue frozen and formalin-fixed paraffin-embedded. In the comparison between the genetic profiles of frozen tumour tissues and FFPET, the same genetic alterations have been reported in both kinds of specimens. However, FFPET showed new alterations. We conclude that the use of FFPET requires greater attention than frozen tissues in the results interpretation and great care in both pre-extraction and extraction processes.

Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards.

PubMed

McGuire, Jimmy A; Cotoras, Darko D; O'Connell, Brendan; Lawalata, Shobi Z S; Wang-Claypool, Cynthia Y; Stubbs, Alexander; Huang, Xiaoting; Wogan, Guinevere O U; Hykin, Sarah M; Reilly, Sean B; Bi, Ke; Riyanto, Awal; Arida, Evy; Smith, Lydia L; Milne, Heather; Streicher, Jeffrey W; Iskandar, Djoko T

2018-01-01

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus . Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

Impact of 6-month frozen storage of cervical specimens in alkaline buffer conditions on human papillomavirus genotyping.

PubMed

LaMere, Brandon J; Howell, Renee; Fetterman, Barbara; Shieh, Jen; Castle, Philip E

2008-08-01

The impact of 6-month storage of cervical specimens under alkaline conditions that occurs as the result of Hybrid Capture 2 testing on human papillomavirus (HPV) genotyping is not well documented. To examine this issue, 143 frozen hc2-positive specimens in specimen transport medium were selected at random from each of the following groups: specimens stored for 6 months, 4 months, and 2.5 months under alkaline pH (pH 12-13) and specimens stored 1 month at neutral pH (pH 6-7) as controls. Specimens were tested in a masked fashion for 20 HPV genotypes (HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, and 82) using a prototype, research-use-only GP5+/6+ L1 consensus PCR method and multiplex hybridization using Luminex xMAP for detection of specific HPV genotypes One control specimen had missing test results. There were no statistical differences in the number of HPV genotypes detected, number of carcinogenic HPV genotypes detected, or in the signal strength among HPV-positive results across groups. Six-month frozen storage of cervical specimens at alkaline pH had little impact on testing for HPV genotypes among hc2-positive women using this HPV genotyping method.

Maintaining respect and fairness in the usage of stored shared specimens

PubMed Central

2013-01-01

Background Every year, research specimens are shipped from one institution to another as well as across national boundaries. A significant proportion of specimens move from poor to rich countries. Concerns are always raised on the future usage of the stored specimens shipped to research insitutions from developing countries. Creating awareness of the processes is required in all sectors involved in biomedical research. To maintain fairness and respect in sharing biomedical specimens and reserch products requires safeguarding by Ethics Review Committees in both provider and recepient institutions. Training in basic ethical principles in research is required to all sectors involved in biomedical research so as to level up the research playing field. Discussion By agreeing to provide specimens, individuals and communities from whom samples are collected would have placed their trust and all ensuing up-keep of the specimens to the researchers. In most collaborative set-up, laid down material transfer agreements are negotiated and signed before the shipment of specimens. Researchers, research ethics committees (RECs) and institutions in the countries of origin are supposed to serve as overseers of the specimens. There is need to advocate for honesty in sample handling and sharing, and also need to oversee any written commitments by researchers, RECs and institutions at source as well as in recipient institution. Commitments from source RECs and Institutional Review Boards (IRBs) and in the receiving institution on overseeing the future usage of stored specimens are required; including the ultimate confirmation abiding by the agreement. Training in ethical issues pertaining to sample handling and biomedical research in general is essential at all levels of academic pursuit. While sharing of biological specimens and research data demands honesty and oversight by ethical regulatory agents from both institutions in developing country and recepient institutions in developed countries. Concluding summary Archiving of biological specimens requires reconsideration for the future of biomedical findings and scientific break-throughs. Biomedical ethical regulations still need to established clear viable regulations that have vision for the future of science through shared and archived samples. This discussion covers and proposes essential points that need to be considered in view of future generations and scientific break-throughs. The discussion is based on the experience of working in resource-limited settings, the local regulatory laws and the need to refine research regulations governing sharing and storage of specimens for the future of science. PMID:24565022

Maintaining respect and fairness in the usage of stored shared specimens.

PubMed

Mduluza, Takafira; Midzi, Nicholas; Duruza, Donold; Ndebele, Paul

2013-01-01

Every year, research specimens are shipped from one institution to another as well as across national boundaries. A significant proportion of specimens move from poor to rich countries. Concerns are always raised on the future usage of the stored specimens shipped to research institutions from developing countries. Creating awareness of the processes is required in all sectors involved in biomedical research. To maintain fairness and respect in sharing biomedical specimens and research products requires safeguarding by Ethics Review Committees in both provider and recipient institutions. Training in basic ethical principles in research is required to all sectors involved in biomedical research so as to level up the research playing field. By agreeing to provide specimens, individuals and communities from whom samples are collected would have placed their trust and all ensuing up-keep of the specimens to the researchers. In most collaborative set-up, laid down material transfer agreements are negotiated and signed before the shipment of specimens. Researchers, research ethics committees (RECs) and institutions in the countries of origin are supposed to serve as overseers of the specimens. There is need to advocate for honesty in sample handling and sharing, and also need to oversee any written commitments by researchers, RECs and institutions at source as well as in recipient institution. Commitments from source RECs and Institutional Review Boards (IRBs) and in the receiving institution on overseeing the future usage of stored specimens are required; including the ultimate confirmation abiding by the agreement. Training in ethical issues pertaining to sample handling and biomedical research in general is essential at all levels of academic pursuit. While sharing of biological specimens and research data demands honesty and oversight by ethical regulatory agents from both institutions in developing country and recipient institutions in developed countries. Archiving of biological specimens requires reconsideration for the future of biomedical findings and scientific break-throughs. Biomedical ethical regulations still need to established clear viable regulations that have vision for the future of science through shared and archived samples. This discussion covers and proposes essential points that need to be considered in view of future generations and scientific break-throughs. The discussion is based on the experience of working in resource-limited settings, the local regulatory laws and the need to refine research regulations governing sharing and storage of specimens for the future of science.

The effects of frozen tissue storage conditions on the integrity of RNA and protein.

PubMed

Auer, H; Mobley, J A; Ayers, L W; Bowen, J; Chuaqui, R F; Johnson, L A; Livolsi, V A; Lubensky, I A; McGarvey, D; Monovich, L C; Moskaluk, C A; Rumpel, C A; Sexton, K C; Washington, M K; Wiles, K R; Grizzle, W E; Ramirez, N C

2014-10-01

Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

Recovery and Stability of Δ9-Tetrahydrocannabinol Using the Oral-Eze® Oral Fluid Collection System and Intercept® Oral Specimen Collection Device.

PubMed

Samano, Kimberly L; Anne, Lakshmi; Johnson, Ted; Tang, Kenneth; Sample, R H Barry

2015-10-01

Oral fluid (OF) is increasingly used for clinical, forensic and workplace drug testing as an alternative to urine. Uncertainties surrounding OF collection device performance, drug stability and testing reproducibility may be partially responsible for delays in the implementation of OF testing in regulated drug testing programs. Stability of Δ(9)-tetrahydrocannabinol (THC) fortified and authentic specimens was examined after routine collection, transport and laboratory testing. Acceptable recovery and stability were observed when THC-fortified OF (1.5 and 4.5 ng/mL) was applied to Oral-Eze devices. Neat OF samples collected with Oral-Eze, processed per the package insert, and fortified with THC (3 and 6 ng/mL) were stable (±20%) at room temperature (21-25°C), refrigerated (2-8°C) and frozen (-25 to -15°C) conditions up to 1 month, while samples collected with Intercept devices showed decreases at refrigerated and room temperatures. After long-term refrigerated or frozen storage, maximum reductions in THC concentrations were 42% for Oral-Eze and 69% for Intercept. After ≥1 year frozen storage, 80.7% of laboratory specimens positive for THC (3 ng/mL cut-off) by GC-MS were reconfirmed positive (within 25%), with an average THC decrease of 4.2%. Specimens (n = 47) processed with Oral-Eze (diluted) and tested via enzyme immunoassay were concordant with LC-MS-MS results and showed 100% sensitivity and 95% specificity. Paired specimens collected with Oral-Eze and Intercept exhibited 98% overall agreement between the immunoassay test systems. Collectively, these data demonstrate consistent and reproducible recovery and stability of THC in OF after collection, transport and laboratory testing using the Oral-Eze OF Collection System. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

FT Raman microscopy of untreated natural plant fibres

NASA Astrophysics Data System (ADS)

Edwards, H. G. M.; Farwell, D. W.; Webster, D.

1997-11-01

The application of FT-Raman microscopy to the non-destructive analysis of natural plant fibres is demonstrated with samples of flax, jute, ramie, cotton, kapok, sisal and coconut fibre. Vibrational assignments are proposed and characteristic features of each material are presented. Samples were not pre-treated chemically before analysis and were used directly from their respective storage collection; the adaptation of the Raman microscopic technique to the identification of specimens of natural fibres in archaeological burial sites is explored for its forensic potential.

Proposed BioRepository platform solution for the ALS research community.

PubMed

Sherman, Alex; Bowser, Robert; Grasso, Daniela; Power, Breen; Milligan, Carol; Jaffa, Matthew; Cudkowicz, Merit

2011-01-01

ALS is a rare disorder whose cause and pathogenesis is largely unknown ( 1 ). There is a recognized need to develop biomarkers for ALS to better understand the disease, expedite diagnosis and to facilitate therapy development. Collaboration is essential to obtain a sufficient number of samples to allow statistically meaningful studies. The availability of high quality biological specimens for research purposes requires the development of standardized methods for collection, long-term storage, retrieval and distribution of specimens. The value of biological samples to scientists and clinicians correlates with the completeness and relevance of phenotypical and clinical information associated with the samples ( 2 , 3 ). While developing a secure Web-based system to manage an inventory of multi-site BioRepositories, algorithms were implemented to facilitate ad hoc parametric searches across heterogeneous data sources that contain data from clinical trials and research studies. A flexible schema for a barcode label was introduced to allow association of samples to these data. The ALSBank™ BioRepository platform solution for managing biological samples and associated data is currently deployed by the Northeast ALS Consortium (NEALS). The NEALS Consortium and the Massachusetts General Hospital (MGH) Neurology Clinical Trials Unit (NCTU) support a network of multiple BioBanks, thus allowing researchers to take advantage of a larger specimen collection than they might have at an individual institution. Standard operating procedures are utilized at all collection sites to promote common practices for biological sample integrity, quality control and associated clinical data. Utilizing this platform, we have created one of the largest virtual collections of ALS-related specimens available to investigators studying ALS.

The Center for HIV/AIDS Vaccine Immunology (CHAVI) Multi-site Quality Assurance Program for Cryopreserved Human Peripheral Blood Mononuclear Cells

PubMed Central

Sarzotti-Kelsoe, Marcella; Needham, Leila K.; Rountree, Wes; Bainbridge, John; Gray, Clive M.; Fiscus, Susan A.; Ferrari, Guido; Stevens, Wendy S.; Stager, Susan L.; Binz, Whitney; Louzao, Raul; Long, Kristy O.; Mokgotho, Pauline; Moodley, Niranjini; Mackay, Melanie; Kerkau, Melissa; McMillion, Takesha; Kirchherr, Jennifer; Soderberg, Kelly A.; Haynes, Barton F.; Denny, Thomas N.

2014-01-01

The Center for HIV/AIDS Vaccine Immunology (CHAVI) consortium was established to determine the host and virus factors associated with HIV transmission, infection and containment of virus replication, with the goal of advancing the development of an HIV protective vaccine. Studies to meet this goal required the use of cryopreserved Peripheral Blood Mononuclear Cell (PBMC) specimens, and therefore it was imperative that a quality assurance (QA) oversight program be developed to monitor PBMC samples obtained from study participants at multiple international sites. Nine site-affiliated laboratories in Africa and the USA collected and processed PBMCs, and cryopreserved PBMC were shipped to CHAVI repositories in Africa and the USA for long-term storage. A three-stage program was designed, based on Good Clinical Laboratory Practices (GCLP), to monitor PBMC integrity at each step of this process. The first stage evaluated the integrity of fresh PBMCs for initial viability, overall yield, and processing time at the site-affiliated laboratories (Stage 1); for the second stage, the repositories determined post-thaw viability and cell recovery of cryopreserved PBMC, received from the site-affiliated laboratories (Stage 2); the third stage assessed the long-term specimen storage at each repository (Stage 3). Overall, the CHAVI PBMC QA oversight program results highlight the relative importance of each of these stages to the ultimate goal of preserving specimen integrity from peripheral blood collection to long-term repository storage. PMID:24910414

Release of ICTP and CTX telopeptides from demineralized dentin matrices: Effect of time, mass and surface area.

PubMed

Turco, Gianluca; Cadenaro, Milena; Maravić, Tatjana; Frassetto, Andrea; Marsich, Eleonora; Mazzoni, Annalisa; Di Lenarda, Roberto; Tay, Franklin R; Pashley, David H; Breschi, Lorenzo

2018-03-01

The present study evaluated the influence of time, mass and surface area of demineralized dentin collagen matrices on telopeptides release. The hypotheses tested were that the rates of ICTP and CTX release by matrix bound endogenous proteases are 1) not time-dependent, 2) unrelated to specimen mass, 3) unrelated to specimen surface area. Non-carious human molars (N=24) were collected and randomly assigned to three groups. Dentin slabs with three different thicknesses: 0.37mm, 0.75mm, and 1.50mm were completely demineralized and stored in artificial saliva for one week. Collagen degradation was evaluated by sampling storage media for ICTP and CTX telopeptidases. Activity of MMPs in the aging medium was evaluated using fluorometric activity assay kit. A statistically significant (p<0.05) decrease in the release of both ICTP and CTX fragments over time was observed irrespective of the specimen thickness. When data were normalized by the specimen mass, no significant differences were observed. Releases of ICTP and CTX were significantly related to the aging time as a function of surface area for the first 12h. Total MMP activity, mainly related to MMP-2 and -9, decreased with time (p<0.05). Because the release of collagen fragments was influenced by specimen storage time and surface area, it is likely that cleaved collagen fragments closer to the specimen surface diffuse into the incubation medium; those further away from the exposed surface are still entrapped within the demineralized dentin matrix. Bound MMPs can only degrade the substrate within the limited zone of their molecular mobility. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

40 CFR 792.190 - Storage and retrieval of records and data.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 31 2010-07-01 2010-07-01 true Storage and retrieval of records and data. 792.190 Section 792.190 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... mutagenicity tests, specimens of soil, water, and plants, and wet specimens of blood, urine, feces, and...

21 CFR 864.3250 - Specimen transport and storage container.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Specimen transport and storage container. 864.3250 Section 864.3250 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Pathology Instrumentation and Accessories § 864...

21 CFR 864.3250 - Specimen transport and storage container.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Specimen transport and storage container. 864.3250 Section 864.3250 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Pathology Instrumentation and Accessories § 864...

21 CFR 864.3250 - Specimen transport and storage container.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Specimen transport and storage container. 864.3250 Section 864.3250 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Pathology Instrumentation and Accessories § 864...

Membrane materials for storing biological samples intended for comparative nanotoxicological testing

NASA Astrophysics Data System (ADS)

Metelkin, A.; Kuznetsov, D.; Kolesnikov, E.; Chuprunov, K.; Kondakov, S.; Osipov, A.; Samsonova, J.

2015-11-01

The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems.

Storage Medium Affects the Surface Porosity of Dental Cements.

PubMed

Saghiri, M Ali; Shabani, Asal; Asatourian, Armen; Sheibani, Nader

2017-08-01

Calcium silicate-based cements physical properties is influenced by environmental changes. Here, we intended to evaluate the effect of storage medium on surface porosity of root Mineral Trioxide Aggregate (MTA) and Biodentine cement. A total of 40 polyethylene tubes were selected and divided into two groups: Group A (MTA) and Group B (Biodentine). Each group was subdivided into two subgroups (n=10). In subgroups A1 and B1, tubes were transferred to Distilled Water (DW), while samples of subgroup A2 and B2 were transferred to Synthetic Tissue Fluid (STF) as storage medium and samples were stored for three days. All specimens were then placed in a desiccator for 24 hours and then subject to surface porosity evaluation by Scanning Electron Microscopy (SEM) at ×500, ×1000, ×2000 and ×5000 magnifications. The number and the surface porosities were determined by Image J analysis. Data were analyzed by ANOVA at level of significance of p<0.05. The lowest surface porosity was observed in MTA samples stored in STF and the highest was in Biodentine samples stored in DW. Significant differences were noted between groups and subgroups of each group (p< 0.05). MTA samples stored in DW and STF showed significantly lower surface porosities compared to Biodentine samples (p < 0.05). Storage medium can drastically affect the surface porosity of tested calcium silicate-based cements. However, MTA showed lower surface porosity compared to Biodentine cement, which can result in lower microleakage in applied area.

Effect of extraoral aging conditions on mechanical properties of maxillofacial silicone elastomer.

PubMed

Hatamleh, Muhanad M; Polyzois, Gregory L; Silikas, Nick; Watts, David C

2011-08-01

The purpose of this study was to investigate the effect of extraoral human and environmental conditions on the mechanical properties (tensile strength and modulus, elongation, tear strength hardness) of maxillofacial silicone elastomer. Specimens were fabricated using TechSil-S25 silicone elastomer (Technovent Ltd, Leeds, UK). Eight groups were prepared (21 specimens in each group; eight tensile, eight tear, five hardness) and conditioned differently as follows (groups 1 through 8): Dry storage for 24 hours; dry storage in dark for 6 months; storage in simulated sebum solution for 6 months; storage in simulated acidic perspiration for 6 months; accelerated artificial daylight aging under controlled moisture for 360 hours; outdoor weathering for 6 months; storage in antimicrobial silicone-cleaning solution for 30 hours; and mixed conditioning of sebum storage and light aging for 360 hours. The conditioning period selected simulated a prosthesis being in service for up to 12 months. Tensile and tear test specimens were fabricated and tested according to the International Standards Organization (ISO) standards no. 37 and 34, respectively. Shore A hardness test specimens were fabricated and tested according to the American Standards for Testing and Materials (ASTM) D 2240. Data were analyzed with one-way ANOVA, Bonferroni, and Dunnett's T3 post hoc tests (p < 0.05). Weibull analysis was also used for tensile strength and tear strength. Statistically significant differences were evident among all properties tested. Mixed conditioning of simulated sebum storage under accelerated artificial daylight aging significantly degraded mechanical properties of the silicone (p < 0.05). Mechanical properties of maxillofacial elastomers are adversely affected by human and environmental factors. Mixed aging of storage in simulated sebum under accelerated daylight aging was the most degrading regime. Accelerated aging of silicone specimens in simulated sebum under artificial daylight for 12 months of simulated clinical service greatly affected functional properties of silicone elastomer; however, in real practice, the effect is modest, since sebum concentration is lower, and daylight is less concentrated. © 2011 by The American College of Prosthodontists.

Evaluation of different sources of DNA for use in genome wide studies and forensic application.

PubMed

Al Safar, Habiba S; Abidi, Fatima H; Khazanehdari, Kamal A; Dadour, Ian R; Tay, Guan K

2011-02-01

In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

Ebola Preparedness: Diagnosis Improvement Using Rapid Approaches for Proficiency Testing

PubMed Central

Lau, Katherine A.; Theis, Torsten; Gray, Joanna

2016-01-01

ABSTRACT The unprecedented 2015 Ebolavirus (EBOV) outbreak in West Africa was declared a public health emergency, making diagnosis and quality of testing a global issue. The accuracy of laboratory diagnostic capacity for EBOV was assessed in 2014 to 2016 using a proficiency testing (PT) strategy developed by the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) in Biosecurity. Following a literature search, EBOV-specific gene targets were ranked according to the frequency of their use in published methods. The most commonly used gene regions (nucleoprotein [NP], glycoprotein [GP], and RNA-dependent RNA polymerase [L]) were selected for the design of in vitro RNA transcripts to be included in the simulated EBOV specimens used for EBOV detection with PCR-based assays. Specimens were tested for stability and found to be stable on long-term storage (1 year) at −80°C and on shorter-term storage in lyophilized form (1 week at ambient temperature and a subsequent week at −80°C). These specimens were used in three EBOV PTs offered from April 2014 to March 2016. In the first and third PTs, all laboratories (3/3 and 9/9, respectively) correctly identified specimens containing EBOV RNA transcripts, while in the second PT, all but one laboratory (5/6) correctly confirmed the presence of EBOV. The EBOV PT panel was useful for ensuring the competency of laboratories in detecting EBOV in the absence of readily available clinical samples. The simulated EBOV specimen was safe, stable, and reliable and can be used in lyophilized form for future EBOV PT programs, allowing simplicity of transport. PMID:27974537

Digital Management and Curation of the National Rock and Ore Collections at NMNH, Smithsonian

NASA Astrophysics Data System (ADS)

Cottrell, E.; Andrews, B.; Sorensen, S. S.; Hale, L. J.

2011-12-01

The National Museum of Natural History, Smithsonian Institution, is home to the world's largest curated rock collection. The collection houses 160,680 physical rock and ore specimen lots ("samples"), all of which already have a digital record that can be accessed by the public through a searchable web interface (http://collections.mnh.si.edu/search/ms/). In addition, there are 66 accessions pending that when catalogued will add approximately 60,000 specimen lots. NMNH's collections are digitally managed on the KE EMu° platform which has emerged as the premier system for managing collections in natural history museums worldwide. In 2010 the Smithsonian released an ambitious 5 year Digitization Strategic Plan. In Mineral Sciences, new digitization efforts in the next five years will focus on integrating various digital resources for volcanic specimens. EMu sample records will link to the corresponding records for physical eruption information housed within the database of Smithsonian's Global Volcanism Program (GVP). Linkages are also planned between our digital records and geochemical databases (like EarthChem or PetDB) maintained by third parties. We anticipate that these linkages will increase the use of NMNH collections as well as engender new scholarly directions for research. Another large project the museum is currently undertaking involves the integration of the functionality of in-house designed Transaction Management software with the EMu database. This will allow access to the details (borrower, quantity, date, and purpose) of all loans of a given specimen through its catalogue record. We hope this will enable cross-referencing and fertilization of research ideas while avoiding duplicate efforts. While these digitization efforts are critical, we propose that the greatest challenge to sample curation is not posed by digitization and that a global sample registry alone will not ensure that samples are available for reuse. We suggest instead that the ability of the Earth science community to identify and preserve important collections and make them available for future study is limited by personnel and space resources from the level of the individual PI to the level of national facilities. Moreover, when it comes to specimen "estate planning," the cultural attitudes of scientists, institutions, and funding agencies are often inadequate to provide for long-term specimen curation - even if specimen discovery is enabled by digital registry. Timely access to curated samples requires that adequate resources be devoted to the physical care of specimens (facilities) and to the personnel costs associated with curation - from the conservation, storage, and inventory management of specimens, to the dispersal of samples for research, education, and exhibition.

Evaluation of Nucleic Acid Stabilization Products for Ambient Temperature Shipping and Storage of Viral RNA and Antibody in a Dried Whole Blood Format

PubMed Central

Dauner, Allison L.; Gilliland, Theron C.; Mitra, Indrani; Pal, Subhamoy; Morrison, Amy C.; Hontz, Robert D.; Wu, Shuenn-Jue L.

2015-01-01

Loss of sample integrity during specimen transport can lead to false-negative diagnostic results. In an effort to improve upon the status quo, we used dengue as a model RNA virus to evaluate the stabilization of RNA and antibodies in three commercially available sample stabilization products: Whatman FTA Micro Cards (GE Healthcare Life Sciences, Pittsburgh, PA), DNAstāble Blood tubes (Biomātrica, San Diego, CA), and ViveST tubes (ViveBio, Alpharetta, GA). Both contrived and clinical dengue-positive specimens were stored on these products at ambient temperature or 37°C for up to 1 month. Antibody and viral RNA levels were measured by enzyme-linked immunosorbent assay (ELISA) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays, respectively, and compared with frozen unloaded controls. We observed reduced RNA and antibody levels between stabilized contrived samples and frozen controls at our earliest time point, and this was particularly pronounced for the FTA cards. However, despite some time and temperature dependent loss, a 94.6–97.3% agreement was observed between stabilized clinical specimens and their frozen controls for all products. Additional considerations such as cost, sample volume, matrix, and ease of use should inform any decision to incorporate sample stabilization products into a diagnostic testing workflow. We conclude that DNAstāble Blood and ViveST tubes are useful alternatives to traditional filter paper for ambient temperature shipment of clinical specimens for downstream molecular and serological testing. PMID:25940193

The effect of fiber reinforcement type and water storage on strength properties of a provisional fixed partial denture resin.

PubMed

Uzun, Gülay; Keyf, Filiz

2003-04-01

Fracture resistance of provisional restorations is an important clinical concern. This property is directly related to transverse strength. Strengthening of provisional fixed partial dentures may result from reinforcement with various fiber types. This study evaluated the effect of fiber type and water storage on the transverse strength of a commercially available provisional resin under two different conditions. The denture resin was reinforced with either glass or aramid fiber or no reinforcement was used. Uniform samples were made from a commercially available autopolymerizing provisional fixed partial denture resin. Sixteen bar-shaped specimens (60 x 10 x 4 mm) were reinforced with pre-treated epoxy resin-coated glass fibers, with aramid fibers, or with no fibers. Eight specimens of each group, with and without fibers, were tested after 24 h of fabrication (immediate group), and after 30-day water storage. A three-point loading test was used to measure the transverse strength, the maximal deflection, and the modulus of elasticity. The Kruskal-Wallis Analysis of Variance was used to examine differences among the three groups, and then the Mann-Whitney U Test and Wilcoxon Signed Ranks Test were applied to determine pair-wise differences. The transverse strength and the maximal deflection values in the immediate group and in the 30-day water storage group were not statistically significant. In the group tested immediately, the elasticity modulus was found to be significant (P = 0.042). In the 30-day water storage group, all the values were statistically insignificant. The highest transverse strength was displayed by the glass-reinforced resin (66.25MPa) in the immediate group. The transverse strength value was 62.04MPa for the unreinforced samples in the immediate group. All the specimens exhibited lower transverse strength with an increase in water immersion time. The transverse strength value was 61.13 MPa for the glass-reinforced resin and was 61.24 MPa for the unreinforced resin. The aramid-reinforced resin decreased from 62.29 to 58.77 MPa. The addition of fiber reinforcement enhanced the physical properties (the transverse strength, the maximal deflection, the modulus of elasticity) of the processed material over that seen with no addition of fiber. Water storage did not statistically affect the transverse strength of the provisional denture resin compared to that of the unreinforced resin. The transverse strength was lowered at water storage but it was not statistically significant. The transverse strength was enhanced by fiber addition compared to the unreinforced resin. The glass fiber was superior to the other fiber. Also the modulus of elasticity was enhanced by fiber addition compared to the unreinforced resin.

Microfluidic "Pouch" Chips for Immunoassays and Nucleic Acid Amplification Tests.

PubMed

Mauk, Michael G; Liu, Changchun; Qiu, Xianbo; Chen, Dafeng; Song, Jinzhao; Bau, Haim H

2017-01-01

Microfluidic cassettes ("chips") for processing and analysis of clinical specimens and other sample types facilitate point-of-care (POC) immunoassays and nucleic acid based amplification tests. These single-use test chips can be self-contained and made amenable to autonomous operation-reducing or eliminating supporting instrumentation-by incorporating laminated, pliable "pouch" and membrane structures for fluid storage, pumping, mixing, and flow control. Materials and methods for integrating flexible pouch compartments and diaphragm valves into hard plastic (e.g., acrylic and polycarbonate) microfluidic "chips" for reagent storage, fluid actuation, and flow control are described. We review several versions of these pouch chips for immunoassay and nucleic acid amplification tests, and describe related fabrication techniques. These protocols thus offer a "toolbox" of methods for storage, pumping, and flow control functions in microfluidic devices.

Views of female breast cancer patients who donated biologic samples regarding storage and use of samples for genetic research.

PubMed

Kaphingst, K A; Janoff, J M; Harris, L N; Emmons, K M

2006-05-01

Although social and ethical issues related to the storage and use of biologic specimens for genetic research have been discussed extensively in the medical literature, few empiric data exist describing patients' views. This qualitative study explored the views of 26 female breast cancer patients who had consented to donate blood or tissue samples for breast cancer research. Participants generally did not expect personal benefits from research and had few unprompted concerns. Few participants had concerns about use of samples for studies not planned at the time of consent. Some participants did express concerns about insurance or employment discrimination, while others believed that current privacy protections might actually slow breast cancer research. Participants were generally more interested in receiving individual genetic test results from research studies than aggregate results. Most participants did not want individual results of uncertain clinical significance, although others believed that they should be able to receive such information. These data examined the range of participants' views regarding the storage and use of biologic samples. Further research with different and diverse patient populations is critical to establishing an appropriate balance between protecting the rights of human subjects in genetic research and allowing research to progress.

Is it possible to detect PEth 16:0/18:1 and PEth 18:1/18:1 in red blood cells after 20 years of storage in liquid nitrogen?

PubMed

Boll, Robert; Johnson, Theron; Kaaks, Rudolf; Kühn, Tilman; Skopp, Gisela

2017-09-01

Phosphatidylethanol (PEth), as measured in freshly drawn blood samples, could be a promising new biomarker for habitual alcohol consumption, but it is still unknown whether PEth can also be determined from blood samples having been stored frozen for a longer period. PEth 16:0/18:1 and PEth 18:1/18:1 were determined by LC-MS/MS from red blood cells (RBC) derived from blood samples of (I) 20 healthy volunteers (after 1 month of storage at -80 °C) and (II) 232 participants of the population-based European Prospective Investigation into Cancer and Nutrition (EPIC)-Heidelberg study (after 20 years of storage at -196 °C). Analyses involved liquid-liquid extraction from 100 μl aliquots with phosphatidylpropanol (PProp 18:1/18:1) as the internal standard. Extracts were subjected to a 10-min LC gradient separation, using multiple reaction monitoring of deprotonated molecules for quantification. After 1 month of storage at -80 °C, PEth was detectable in all samples at mean concentrations of 393.6 ± 12.4 ng/ml (PEth 16:0/18:1) and 43.3 ± 1.1 ng/ml (PEth 18:1/18:1). In samples stored for 20 years at -196 °C, PEth was detectable in 23.7% of all samples at mean concentrations of 412.2 ± 655.5 ng/ml (PEth 16:0/18:1) and 38.0 ± 74.8 ng/ml (PEth 18:1/18:1). PEth can be determined reliably from samples of moderate habitual alcohol consumers after 1 month of storage at -80 °C. Our data suggest that PEth is generally also detectable in samples after 20 years of storage at -196 °C. Further studies are needed to assess the still unknown impact of storage duration and temperature on different PEth specimen concentrations.

The preservation of urine samples for determination of renal stone risk factors

NASA Technical Reports Server (NTRS)

Nicar, M. J.; Hsu, M. C.; Johnson, T.; Pak, C. Y.

1987-01-01

A preservation technique for urine specimens before determination of stone risk factors was evaluated. The purpose of these experiments was to prove the effectiveness of the preservatives used to prevent changes in the concentrations of those constituents measured. Measured concentrations in fresh specimens were compared with those in the same specimens after storage with the preservatives. Refrigeration at 4 degrees C up to five days was appropriate in a laboratory setting, as no significant changes in urinary concentrations occurred. Refrigeration, however, did not offer a convenient method for shipping. Chemical preservation was found to be an effective alternative to refrigeration. Thymol prevented changes in concentration of pH, citrate, uric acid, sulfate, sodium, potassium, and cyclic AMP, while a mixture of hydrochloric (HCl) acid and boric acid prevented changes in calcium, magnesium, phosphorus, oxalate, ammonium, and creatinine. Thus, the addition of thymol or HCl/boric acid to urine specimens will prevent significant changes in the concentrations of stone risk factors.

Effect of storage duration/solution on microshear bond strength of composite to enamel.

PubMed

Tosun, Gul; Sener, Yagmur; Sengun, Abdulkadir

2007-01-01

The aim of this study was to determine the effect of three storage solutions and two storage durations on microshear bond strength (microSBS) of a resin composite. Sixty non-carious human permanent molars were stored in three storage solutions (0.1% thymol, 10% formalin, and distilled water). Each tooth was separated mesio-distally into two parts. Specimens of the first part were stored for 24 hours, while specimens of the second part were stored for two months in the solutions. After each storage period, the enamel surface was covered with a composite resin in combination with an etch-rinse adhesive system. Specimens were then serially sectioned into sticks of 1 mm' bond area and subjected to microSBS test. There were no statistically significant differences between the two storage periods for each solution (p>0.05). The thymol solution group showed lower microSBS values than those of distilled water for both storage periods (p<0.05). As for the formalin group, its microSBS values were not statistically different from those of distilled water and thymol groups at each storage period (p>0.05). In conclusion, the thymol solution caused the microSBS of the resin composite to decrease when compared to both formalin and distilled water after 24 hours and two months. However, the microSBS of the resin composite was not affected by storage duration.

Preparation of viral samples within biocontainment for ultrastructural analysis: Utilization of an innovative processing capsule for negative staining.

PubMed

Monninger, Mitchell K; Nguessan, Chrystal A; Blancett, Candace D; Kuehl, Kathleen A; Rossi, Cynthia A; Olschner, Scott P; Williams, Priscilla L; Goodman, Steven L; Sun, Mei G

2016-12-01

Transmission electron microscopy can be used to observe the ultrastructure of viruses and other microbial pathogens with nanometer resolution. In a transmission electron microscope (TEM), the image is created by passing an electron beam through a specimen with contrast generated by electron scattering from dense elements in the specimen. Viruses do not normally contain dense elements, so a negative stain that places dense heavy metal salts around the sample is added to create a dark border. To prepare a virus sample for a negative stain transmission electron microscopy, a virus suspension is applied to a TEM grid specimen support, which is a 3mm diameter fragile specimen screen coated with a few nanometers of plastic film. Then, deionized (dI) water rinses and a negative stain solution are applied to the grid. All infectious viruses must be handled in a biosafety cabinet (BSC) and many require a biocontainment laboratory environment. Staining viruses in biosafety levels (BSL) 3 and 4 is especially challenging because the support grids are small, fragile, and easily moved by air currents. In this study we evaluated a new device for negative staining viruses called mPrep/g capsule. It is a capsule that holds up to two TEM grids during all processing steps and for storage after staining is complete. This study reports that the mPrep/g capsule method is valid and effective to negative stain virus specimens, especially in high containment laboratory environments. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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

PubMed Central

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

2015-01-01

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

Sample handling for mass spectrometric proteomic investigations of human urine.

PubMed

Petri, Anette Lykke; Høgdall, Claus; Christensen, Ib Jarle; Simonsen, Anja Hviid; T'jampens, Davy; Hellmann, Marja-Leena; Kjaer, Susanne Krüger; Fung, Eric T; Høgdall, Estrid

2008-09-01

Because of its non-invasive sample collection method, human urine is an attractive biological material both for discovering biomarkers and for use in future screening trials for different diseases. Before urine can be used for these applications, standardized protocols for sample handling that optimize protein stability are required. In this explorative study, we examine the influence of different urine collection methods, storage temperatures, storage times, and repetitive freeze-thaw procedures on the protein profiles obtained by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Prospectively collected urine samples from 11 women were collected as either morning or midday specimens. The effects of storage temperature, time to freezing, and freeze-thaw cycles were assessed by calculating the number, intensity, and reproducibility of peaks visualized by SELDI-TOF-MS. On the CM10 array, 122 peaks were detected and 28 peaks were found to be significantly different between urine types, storage temperature and time to freezing. On the IMAC-Cu array, 65 peaks were detected and 1 peak was found to be significantly different according to time to freezing. No significant differences were demonstrated for freeze-thaw cycles. Optimal handling and storage conditions are necessary in clinical urine proteomic investigations. Collection of urine with a single and consistently performed protocol is needed to reduce analytical bias. Collecting only one urine type, which is stored for a limited period at 4°C until freezing at -80°C prior to analysis will provide the most stable profiles. Copyright © 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Storage Medium Affects the Surface Porosity of Dental Cements

PubMed Central

Shabani, Asal; Asatourian, Armen; Sheibani, Nader

2017-01-01

Introduction Calcium silicate-based cements physical properties is influenced by environmental changes. Aim Here, we intended to evaluate the effect of storage medium on surface porosity of root Mineral Trioxide Aggregate (MTA) and Biodentine cement. Materials and Methods A total of 40 polyethylene tubes were selected and divided into two groups: Group A (MTA) and Group B (Biodentine). Each group was subdivided into two subgroups (n=10). In subgroups A1 and B1, tubes were transferred to Distilled Water (DW), while samples of subgroup A2 and B2 were transferred to Synthetic Tissue Fluid (STF) as storage medium and samples were stored for three days. All specimens were then placed in a desiccator for 24 hours and then subject to surface porosity evaluation by Scanning Electron Microscopy (SEM) at ×500, ×1000, ×2000 and ×5000 magnifications. The number and the surface porosities were determined by Image J analysis. Data were analyzed by ANOVA at level of significance of p<0.05. Results The lowest surface porosity was observed in MTA samples stored in STF and the highest was in Biodentine samples stored in DW. Significant differences were noted between groups and subgroups of each group (p< 0.05). MTA samples stored in DW and STF showed significantly lower surface porosities compared to Biodentine samples (p < 0.05). Conclusion Storage medium can drastically affect the surface porosity of tested calcium silicate-based cements. However, MTA showed lower surface porosity compared to Biodentine cement, which can result in lower microleakage in applied area. PMID:28969288

Ebola Preparedness: Diagnosis Improvement Using Rapid Approaches for Proficiency Testing.

PubMed

Lau, Katherine A; Theis, Torsten; Gray, Joanna; Rawlinson, William D

2017-03-01

The unprecedented 2015 Ebolavirus (EBOV) outbreak in West Africa was declared a public health emergency, making diagnosis and quality of testing a global issue. The accuracy of laboratory diagnostic capacity for EBOV was assessed in 2014 to 2016 using a proficiency testing (PT) strategy developed by the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) in Biosecurity. Following a literature search, EBOV-specific gene targets were ranked according to the frequency of their use in published methods. The most commonly used gene regions (nucleoprotein [NP], glycoprotein [GP], and RNA-dependent RNA polymerase [L]) were selected for the design of in vitro RNA transcripts to be included in the simulated EBOV specimens used for EBOV detection with PCR-based assays. Specimens were tested for stability and found to be stable on long-term storage (1 year) at -80°C and on shorter-term storage in lyophilized form (1 week at ambient temperature and a subsequent week at -80°C). These specimens were used in three EBOV PTs offered from April 2014 to March 2016. In the first and third PTs, all laboratories (3/3 and 9/9, respectively) correctly identified specimens containing EBOV RNA transcripts, while in the second PT, all but one laboratory (5/6) correctly confirmed the presence of EBOV. The EBOV PT panel was useful for ensuring the competency of laboratories in detecting EBOV in the absence of readily available clinical samples. The simulated EBOV specimen was safe, stable, and reliable and can be used in lyophilized form for future EBOV PT programs, allowing simplicity of transport. Copyright © 2017 American Society for Microbiology.

Contributions of intrinsic and extrinsic polarization species to energy storage properties of Ba0.95Ca0.05Zr0.2Ti0.8O3 ceramics

NASA Astrophysics Data System (ADS)

Zhan, Di; Xu, Qing; Huang, Duan-Ping; Liu, Han-Xing; Chen, Wen; Zhang, Feng

2018-03-01

Ba0.95Ca0.05Zr0.2Ti0.8O3 ceramics were prepared at different sintering temperatures by citrate precursor and solid-state reaction methods, respectively. The crystal structure and microstructure of the specimens were characterized. In view of energy storage capacitor utilizations, the dielectric properties of the specimens were investigated at room temperature as a function of frequency and applied electric field. Moreover, the nature of mobile charge carriers in the specimens was diagnosed by complex impedance spectroscopy at elevated temperatures. While the dielectric constants of the specimens prepared by different methods are quite different (4.4 × 103-2.2 × 104 at 10 kHz) at zero electric field, the energy storage densities at an identical strong electric field are similar (e.g. 0.32-0.41 J/cm3 at 120 kV/cm). The dielectric constants under bias electric field were fitted to a multipolarization mechanism model to resolve the contributions of intrinsic and extrinsic polarization mechanisms. It turned out that the extrinsic contributions fade out within low electric field range (<20 kV/cm) and thereby the intrinsic lattice polarization governs the overall dielectric responses at higher fields. Based on the fitting result, the energy storage properties of the specimens were interpreted.

Vascular plants of waste storage sites in the 200 areas of the Hanford reservation

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

Price, K.R.; Rickard, W.H.

1973-12-01

A brief accounting of terrestrial, riparian and semi-aquatic plants known to be associated with radioactive waste storage sites in the 200 Areas of the Hanford Reservation is given. In most cases the species are characteristic of those which generally inhabit the reservation, but some plants are restricted to specialized habitats provided by particular waste storage sites. It is impractical to list all species growing at each waste storage site because of seasonal variation and changes brought about by environmental management practices. An alpbabetical listing has been prepared with an example of where each species is known to occur. The listmore » will be updated as needed and expanded to include other waste storage areas. Plant specimens were collected during spring and fall when flowering material was available. Herbarium mounts were prepared of many specimens and have been retained as part of the Hanford Reservation herbarium collection. Identification to species level was made whenever possible. Color photographs of the specimen mounts are used as training aids and demonstration material by ARHCO Radiation Monitoring personnel. (auth)« less

Efficiently Maintaining a National Resource of Historical and Contemporary Biological Collections: The NHLBI Biorepository Model.

PubMed

Shea, Katheryn E; Wagner, Elizabeth L; Marchesani, Leah; Meagher, Kevin; Giffen, Carol

2017-02-01

Reducing costs by improving storage efficiency has been a focus of the National Heart, Lung, and Blood Institute (NHLBI) Biologic Specimen Repository (Biorepository) and Biologic Specimen and Data Repositories Information Coordinating Center (BioLINCC) programs for several years. Study specimen profiles were compiled using the BioLINCC collection catalog. Cost assessments and calculations on the return on investments to consolidate or reduce a collection, were developed and implemented. Over the course of 8 months, the NHLBI Biorepository evaluated 35 collections that consisted of 1.8 million biospecimens. A total of 23 collections were selected for consolidation, with a total of 1.2 million specimens located in 21,355 storage boxes. The consolidation resulted in a savings of 4055 boxes of various sizes and 10.2 mechanical freezers (∼275 cubic feet) worth of space. As storage costs in a biorepository increase over time, the development and use of information technology tools to assess the potential advantage and feasiblity of vial consolidation can reduce maintenance expenses.

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

2010-01-01

The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

10 CFR 26.165 - Testing split specimens and retesting single specimens.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Testing split specimens and retesting single specimens. 26.165 Section 26.165 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Laboratories... laboratory or maintained in secure storage at the licensee testing facility, as required by § 26.135(a) and...

Life Sciences Research in the Centrifuge Accommodation Module of the International Space Station

NASA Technical Reports Server (NTRS)

Dalton, Bonnie P.; Plaut, Karen; Meeker, Gabrielle B.; Sun, Sid (Technical Monitor)

2000-01-01

The Centrifuge Accommodation Module (CAM) will be the home of the fundamental biology research facilities on the International Space Station (ISS). These facilities are being built by the Biological Research Project (BRP), whose goal is to oversee development of a wide variety of habitats and host systems to support life sciences research on the ISS. The habitats and host systems are designed to provide life support for a variety of specimens including cells, bacteria, yeast, plants, fish, rodents, eggs (e.g., quail), and insects. Each habitat contains specimen chambers that allow for easy manipulation of specimens and alteration of sample numbers. All habitats are capable of sustaining life support for 90 days and have automated as well as full telescience capabilities for sending habitat parameters data to investigator homesite laboratories. The habitats provide all basic life support capabilities including temperature control, humidity monitoring and control, waste management, food, media and water delivery as well as adjustable lighting. All habitats will have either an internal centrifuge or are fitted to the 2.5-meter diameter centrifuge allowing for variable centrifugation up to 2 g. Specimen chambers are removable so that the specimens can be handled in the life sciences glovebox. Laboratory support equipment is provided for handling the specimens. This includes a compound and dissecting microscope with advanced video imaging, mass measuring devices, refrigerated centrifuge for processing biological samples, pH meter, fixation and complete cryogenic storage capabilities. The research capabilities provided by the fundamental biology facilities will allow for flexibility and efficiency for long term research on the International Space Station.

Storage Effects on Sample Integrity of Environmental Surface Sampling Specimens with Bacillus anthracis Spores

PubMed Central

Perry, K. Allison; O’Connell, Heather A.; Rose, Laura J.; Noble-Wang, Judith A.; Arduino, Matthew J.

2016-01-01

The effect of packaging, shipping temperatures and storage times on recovery of Bacillus anthracis. Sterne spores from swabs was investigated. Macrofoam swabs were pre-moistened, inoculated with Bacillus anthracis spores, and packaged in primary containment or secondary containment before storage at −15°C, 5°C, 21°C, or 35°C for 0–7 days. Swabs were processed according to validated Centers for Disease Control/Laboratory Response Network culture protocols, and the percent recovery relative to a reference sample (T0) was determined for each variable. No differences were observed in recovery between swabs held at −15° and 5°C, (p ≥ 0.23). These two temperatures provided significantly better recovery than swabs held at 21°C or 35°C (all 7 days pooled, p ≤ 0.04). The percent recovery at 5°C was not significantly different if processed on days 1, 2 or 4, but was significantly lower on day 7 (day 2 vs. 7, 5°C, 102, p=0.03). Secondary containment provided significantly better percent recovery than primary containment, regardless of storage time (5°C data, p ≤ 0.008). The integrity of environmental swab samples containing Bacillus anthracis spores shipped in secondary containment was maintained when stored at −15°C or 5°C and processed within 4 days to yield the optimum percent recovery of spores. PMID:27213119

Storage Effects on Sample Integrity of Environmental Surface Sampling Specimens with Bacillus anthracis Spores.

PubMed

Perry, K Allison; O'Connell, Heather A; Rose, Laura J; Noble-Wang, Judith A; Arduino, Matthew J

The effect of packaging, shipping temperatures and storage times on recovery of Bacillus anthracis . Sterne spores from swabs was investigated. Macrofoam swabs were pre-moistened, inoculated with Bacillus anthracis spores, and packaged in primary containment or secondary containment before storage at -15°C, 5°C, 21°C, or 35°C for 0-7 days. Swabs were processed according to validated Centers for Disease Control/Laboratory Response Network culture protocols, and the percent recovery relative to a reference sample (T 0 ) was determined for each variable. No differences were observed in recovery between swabs held at -15° and 5°C, (p ≥ 0.23). These two temperatures provided significantly better recovery than swabs held at 21°C or 35°C (all 7 days pooled, p ≤ 0.04). The percent recovery at 5°C was not significantly different if processed on days 1, 2 or 4, but was significantly lower on day 7 (day 2 vs. 7, 5°C, 10 2 , p=0.03). Secondary containment provided significantly better percent recovery than primary containment, regardless of storage time (5°C data, p ≤ 0.008). The integrity of environmental swab samples containing Bacillus anthracis spores shipped in secondary containment was maintained when stored at -15°C or 5°C and processed within 4 days to yield the optimum percent recovery of spores.

Maternal–Child Microbiome: Specimen Collection, Storage and Implications for Research and Practice

PubMed Central

Jordan, Sheila; Baker, Brenda; Dunn, Alexis; Edwards, Sara; Ferranti, Erin; Mutic, Abby D.; Yang, Irene; Rodriguez, Jeannie

2017-01-01

Background The maternal microbiome is a key contributor to the development and outcomes of pregnancy and the health status of both mother and infant. Significant advances are occurring in the science of the maternal and child microbiome and hold promise in improving outcomes related to pregnancy complications, child development, and chronic health conditions of mother and child. Objectives The purpose of the paper is to review site-specific considerations in the collection and storage of maternal and child microbiome samples and its implications for nursing research and practice. Approach Microbiome sampling protocols were reviewed and synthesized. Precautions across sampling protocols were also noted. Results Oral, vaginal, gut, placental, and breastmilk are viable sources for sampling the maternal and/or child microbiome. Prior to sampling special considerations need to be addressed related to various factors including current medications, health status, and hygiene practices. Proper storage of samples will avoid degradation of cellular and DNA structures vital for analysis. Discussion Changes in the microbiome throughout the perinatal, postpartum and childhood periods are dramatic and significant to outcomes of the pregnancy and the long-term health of mother and child. Proper sampling techniques are required to produce reliable results from which evidence-based practice recommendations will be built. Ethical and practical issues surrounding study design and protocol development must also be considered when researching vulnerable groups such as pregnant women and infants. Nurses hold the responsibility to both perform the research and to translate findings from microbiome investigations for clinical use. PMID:28252577

Influence of artificial accelerated aging on dimensional stability of acrylic resins submitted to different storage protocols.

PubMed

Garcia, Lucas da Fonseca Roberti; Roselino, Lourenço de Moraes Rego; Mundim, Fabrício Mariano; Pires-de-Souza, Fernanda de Carvalho Panzeri; Consani, Simonides

2010-08-01

The aim of this study was to evaluate the influence of artificial accelerated aging on dimensional stability of two types of acrylic resins (thermally and chemically activated) submitted to different protocols of storage. One hundred specimens were made using a Teflon matrix (1.5 cm x 0.5 mm) with four imprint marks, following the lost-wax casting method. The specimens were divided into ten groups, according to the type of acrylic resin, aging procedure, and storage protocol (30 days). GI: acrylic resins thermally activated, aging, storage in artificial saliva for 16 hours, distilled water for 8 hours; GII: thermal, aging, artificial saliva for 16 hours, dry for 8 hours; GIII: thermal, no aging, artificial saliva for 16 hours, distilled water for 8 hours, GIV: thermal, no aging, artificial saliva for 16 hours, dry for 8 hours; GV: acrylic resins chemically activated, aging, artificial saliva for 16 hours, distilled water for 8 hours; GVI: chemical, aging, artificial saliva for 16 hours, dry for 8 hours; GVII: chemical, no aging, artificial saliva for 16 hours, distilled water for 8 hours; GVIII: chemical, no aging, artificial saliva for 16 hours, dry for 8 hours GIX: thermal, dry for 24 hours; and GX: chemical, dry for 24 hours. All specimens were photographed before and after treatment, and the images were evaluated by software (UTHSCSA - Image Tool) that made distance measurements between the marks in the specimens (mm), calculating the dimensional stability. Data were submitted to statistical analysis (two-way ANOVA, Tukey test, p= 0.05). Statistical analysis showed that the specimens submitted to storage in water presented the largest distance between both axes (major and minor), statistically different (p < 0.05) from control groups. All acrylic resins presented dimensional changes, and the artificial accelerated aging and storage period influenced these alterations.

Life Science Research Facility materials management requirements and concepts

NASA Technical Reports Server (NTRS)

Johnson, Catherine C.

1986-01-01

The Advanced Programs Office at NASA Ames Research Center has defined hypothetical experiments for a 90-day mission on Space Station to allow analysis of the materials necessary to conduct the experiments and to assess the impact on waste processing of recyclable materials and storage requirements of samples to be returned to earth for analysis as well as of nonrecyclable materials. The materials include the specimens themselves, the food, water, and gases necessary to maintain them, the expendables necessary to conduct the experiments, and the metabolic products of the specimens. This study defines the volumes, flow rates, and states of these materials. Process concepts for materials handling will include a cage cleaner, trash compactor, biological stabilizer, and various recycling devices.

Salt drying: a low-cost, simple and efficient method for storing plants in the field and preserving biological repositories for DNA diversity research.

PubMed

Carrió, Elena; Rosselló, Josep A

2014-03-01

Although a variety of methods have been optimized for the collection and storage of plant specimens, most of these are not suited for field expeditions for a variety of logistic reasons. Drying specimens with silica gel in polyethylene bags is currently the standard for field-sampling methods that are suitable for subsequent DNA extraction. However, silica-gel repositories are not readily available in remote areas, and its use is not very cost-effective for the long-term storage of collections or in developing countries with limited research budgets. Salting is an ancient and traditional drying process that preserves food samples by dehydrating tissues and inhibiting water-dependent cellular metabolism. We compared salt and silica-gel drying methods with respect to dehydration rates overtime, DNA quality and polymerase chain reaction(PCR) success to assess whether dry salting can be used as an effective plant preservation method for DNA analysis. Specimens from eleven plant species covering a variety of leaf structures, leaf thicknesses and water contents were analysed. Experimental work indicated that (i) levels of dehydration in sodium chloride were usually comparable to those obtained when silica gel was used, (ii) no spoilage, fungal or bacterial growth was observed for any of the species with all drying treatments and (iii) good yields of quality genomic DNA suitable for PCR applications were obtained in the salt-drying treatments. The preservation of plant tissues in commercial table salt appears to be a satisfactory, and versatile method that may be suitable in remote areas where cryogenic resources and silica repositories are not available. © 2013 John Wiley & Sons Ltd.

Influence of storage methods on the surface roughness of tissue conditioners.

PubMed

Hong, Guan; Li, YingAi; Maeda, Takeshi; Mizumachi, Wataru; Sadamori, Shinsuke; Hamada, Taizo; Murata, Hiroshi

2008-03-01

The purpose of this study was to compare the influence of three kinds of storage methods on surface roughness of tissue conditioners. Four commercial tissue conditioners (GC Soft Liner, Softone, Fictioner, and Hydro-Cast) were used in this study. Five samples of each material were stored in distilled water, air, and a denture cleanser (Polident). Mean surface roughness (R(a)) values of dental stone casts made from the tissue conditioners were measured after 0, 1, 3, 7, and 14 days of immersion using a profilometer. Significant differences in the R(a) values of the specimens were found among the three storage methods. The values of R(a) significantly increased with increase in immersion time for each storage method, except for the materials stored in air. It was found that the materials stored in air showed the most stable and lowest values of R(a). Results obtained suggested that a tissue conditioner exhibited smooth and minimal change in surface roughness with time when stored in air than in distilled water and denture cleanser.

Investigations of the microbial transformation of cortisol to prednisolone in urine samples.

PubMed

Bredehöft, Michael; Baginski, Rainer; Parr, Maria-Kristina; Thevis, Mario; Schänzer, Wilhelm

2012-03-01

Doping control samples are normally collected under non-sterile conditions and sometimes, storage and transportation are influenced by parameters such as the temperature. Therefore, microbial contamination and subsequent alteration of a sample's composition are possible. Studies regarding sample collection in cattle breeding have already shown enzymatic transformation of endogenous testosterone to boldenone causing false-positive findings. The aim of the present study was to investigate whether positive doping cases with the synthetic corticosteroids prednisolone and prednisone may result from microbial transformation of the endogenous corticosteroids cortisol and cortisone, respectively. A method comprising parameters such as pH values and screening results for synthetic glucocorticosteroids as well as incubation experiments followed by liquid chromatographic and mass spectrometric analysis was employed to test for contaminating germs with Δ(1)-dehydrogenase activity. Over 700 urine samples comprising inpatient and doping control specimens were investigated. In none of them, 1,2-dehydrogenating activity was confirmed. These findings are in accordance with other studies. However, the problem of microbial alteration of doping control specimens with special respect to 1,2-dehydrogenation must not be underestimated. Article from a special issue on steroids and microorganisms. Copyright © 2010 Elsevier Ltd. All rights reserved.

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

DOE PAGES

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

2015-07-03

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

Conceptual design of a biological specimen holding facility. [Life Science Laboratory for Space Shuttle

NASA Technical Reports Server (NTRS)

Jackson, J. K.; Yakut, M. M.

1976-01-01

An all-important first step in the development of the Spacelab Life Science Laboratory is the design of the Biological Specimen Holding Facility (BSHF) which will provide accommodation for living specimens for life science research in orbit. As a useful tool in the understanding of physiological and biomedical changes produced in the weightless environment, the BSHF will enable biomedical researchers to conduct in-orbit investigations utilizing techniques that may be impossible to perform on human subjects. The results of a comprehensive study for defining the BSHF, description of its experiment support capabilities, and the planning required for its development are presented. Conceptual designs of the facility, its subsystems and interfaces with the Orbiter and Spacelab are included. Environmental control, life support and data management systems are provided. Interface and support equipment required for specimen transfer, surgical research, and food, water and waste storage is defined. New and optimized concepts are presented for waste collection, feces and urine separation and sampling, environmental control, feeding and watering, lighting, data management and other support subsystems.

Multiplex PCR detection of Cryptosporidium sp, Giardia lamblia and Entamoeba histolytica directly from dried stool samples from Guinea-Bissauan children with diarrhoea.

PubMed

Mero, Sointu; Kirveskari, Juha; Antikainen, Jenni; Ursing, Johan; Rombo, Lars; Kofoed, Poul-Erik; Kantele, Anu

2017-09-01

In developing countries, diarrhoea is the most common cause of death for children under five years of age, with Giardia lamblia, Cryptosporidium and Entamoeba histolytica as the most frequent pathogenic parasites. Traditional microscopy for stool parasites has poor sensitivity and specificity, while new molecular methods may provide more accurate diagnostics. In poor regions with sample storage hampered by uncertain electricity supply, research would benefit from a method capable of analysing dried stools. A real-time multiplex PCR method with internal inhibition control was developed for detecting Giardia lamblia, Cryptosporidium hominis/parvum and Entamoeba histolytica directly from stool specimens. Applicability to dried samples was checked by comparing with fresh ones in a small test material. Finally, the assay was applied to dried specimens collected from Guinea-Bissauan children with diarrhoea. The PCR's analytical sensitivity limit was 0.1 ng/ml for G. lamblia DNA, 0.01 ng/ml for E. histolytica DNA and 0.1 ng/ml for Cryptosporidium sp. In the test material, the assay performed similarly with fresh and dried stools. Of the 52 Guinea-Bissauan samples, local microscopy revealed a parasite in 15%, while PCR detected 62% positive for at least one parasite: 44% of the dried samples had Giardia, 23% Cryptosporidium and 0% E. histolytica. Our new multiplex real-time PCR for protozoa presents a sensitive method applicable to dried samples. As proof of concept, it worked well on stools collected from Guinea-Bissauan children with diarrhoea. It provides an epidemiological tool for analysing dried specimens from regions poor in resources.

The Gulf Long-Term Follow-Up Study (GuLF STUDY): Biospecimen collection at enrollment.

PubMed

Engel, Lawrence S; Kwok, Richard K; Miller, Aubrey K; Blair, Aaron; Curry, Matthew D; McGrath, John A; Sandler, Dale P

2017-01-01

The 2010 Deepwater Horizon (DWH) explosion in the Gulf of Mexico led to the largest ever marine oil spill by volume. The GuLF STUDY is investigating possible adverse human health effects associated with oil spill activities. One objective of the study was to utilize biological specimens from study participants to examine spill-related adverse health effects. This study describes the methods for collecting, processing, shipping, and storing specimens during the enrollment phase of the study. GuLF STUDY participants living in Gulf States (Alabama, Florida, Louisiana, Mississippi, and eastern Texas) were eligible to complete a home visit at enrollment, one to three years after the DWH explosion. During this visit, blood, urine, toenail and hair clippings, and house dust samples were collected. Specimens were shipped overnight to a central processing laboratory in containers with cold and ambient temperature compartments. Most blood and urine specimens were then aliquoted and stored in liquid nitrogen vapor or at -80°C, with some samples stored at -20°C. A total of 11,193 participants completed a home visit, and over 99% provided at least one biospecimen. Most participants provided blood (93%), urine (99%), and toenail clippings (89%), and 40% provided hair. Nearly all participants (95%) provided house-dust samples. Most samples were received by the laboratory one (58%) or two (25%) days after collection. These biospecimens enable investigation of a range of biomarkers of spill-related adverse health effects, and possibly some biomarkers of spill-related exposures. The biospecimen collection, handling, and storage protocols were designed to maximize current and future scientific value within logistical and budgetary constraints and might serve as a template for future studies conducted in similar time-critical and geographically dispersed settings.

Use of Occult Blood Detection Cards for Real-Time PCR-Based Diagnosis of Schistosoma Mansoni Infection

PubMed Central

Schunk, Mirjam; Kebede Mekonnen, Seleshi; Wondafrash, Beyene; Mengele, Carolin; Fleischmann, Erna; Herbinger, Karl-Heinz; Verweij, Jaco J.; Geldmacher, Christof; Bretzel, Gisela; Löscher, Thomas; Zeynudin, Ahmed

2015-01-01

Background In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study. Methodology Stool specimens were collected in a highly endemic area for S. mansoni in Ethiopia and submitted in an investigator-blinded fashion to microscopic examination by Kato-Katz thick smear as well as to real-time PCR using either fresh frozen stool samples or stool smears on fecal cards which have been stored at ambient temperature for up to ten months. Principal Findings Out of 55 stool samples, 35 were positive by microscopy, 33 and 32 were positive by PCR of frozen samples and of fecal card samples, respectively. When microscopy was used as diagnostic “gold standard”, the sensitivity of PCR on fresh stool was 94.3% (95%-CI: 86.6; 100) and on fecal cards 91.4% (95%-CI: 82.2; 100). Conclusions The use of fecal cards proved to be a simple and useful method for stool collection and prolonged storage prior to PCR based diagnosis of S. mansoni infection. This technique may be a valuable approach for large scale surveillance and post treatment assessments PMID:26360049

Use of Occult Blood Detection Cards for Real-Time PCR-Based Diagnosis of Schistosoma Mansoni Infection.

PubMed

Schunk, Mirjam; Kebede Mekonnen, Seleshi; Wondafrash, Beyene; Mengele, Carolin; Fleischmann, Erna; Herbinger, Karl-Heinz; Verweij, Jaco J; Geldmacher, Christof; Bretzel, Gisela; Löscher, Thomas; Zeynudin, Ahmed

2015-01-01

In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study. Stool specimens were collected in a highly endemic area for S. mansoni in Ethiopia and submitted in an investigator-blinded fashion to microscopic examination by Kato-Katz thick smear as well as to real-time PCR using either fresh frozen stool samples or stool smears on fecal cards which have been stored at ambient temperature for up to ten months. Out of 55 stool samples, 35 were positive by microscopy, 33 and 32 were positive by PCR of frozen samples and of fecal card samples, respectively. When microscopy was used as diagnostic "gold standard", the sensitivity of PCR on fresh stool was 94.3% (95%-CI: 86.6; 100) and on fecal cards 91.4% (95%-CI: 82.2; 100). The use of fecal cards proved to be a simple and useful method for stool collection and prolonged storage prior to PCR based diagnosis of S. mansoni infection. This technique may be a valuable approach for large scale surveillance and post treatment assessments.

Adhesion of multimode adhesives to enamel and dentin after one year of water storage.

PubMed

Vermelho, Paulo Moreira; Reis, André Figueiredo; Ambrosano, Glaucia Maria Bovi; Giannini, Marcelo

2017-06-01

This study aimed to evaluate the ultramorphological characteristics of tooth-resin interfaces and the bond strength (BS) of multimode adhesive systems to enamel and dentin. Multimode adhesives (Scotchbond Universal (SBU) and All-Bond Universal) were tested in both self-etch and etch-and-rinse modes and compared to control groups (Optibond FL and Clearfil SE Bond (CSB)). Adhesives were applied to human molars and composite blocks were incrementally built up. Teeth were sectioned to obtain specimens for microtensile BS and TEM analysis. Specimens were tested after storage for either 24 h or 1 year. SEM analyses were performed to classify the failure pattern of beam specimens after BS testing. Etching increased the enamel BS of multimode adhesives; however, BS decreased after storage for 1 year. No significant differences in dentin BS were noted between multimode and control in either evaluation period. Storage for 1 year only reduced the dentin BS for SBU in self-etch mode. TEM analysis identified hybridization and interaction zones in dentin and enamel for all adhesives. Silver impregnation was detected on dentin-resin interfaces after storage of specimens for 1 year only with the SBU and CSB. Storage for 1 year reduced enamel BS when adhesives are applied on etched surface; however, BS of multimode adhesives did not differ from those of the control group. In dentin, no significant difference was noted between the multimode and control group adhesives, regardless of etching mode. In general, multimode adhesives showed similar behavior when compared to traditional adhesive techniques. Multimode adhesives are one-step self-etching adhesives that can also be used after enamel/dentin phosphoric acid etching, but each product may work better in specific conditions.

Development of optimum process for electron beam cross-linking of high density polyethylene thermal energy storage pellets, process scale-up and production of application qualities of material

NASA Technical Reports Server (NTRS)

Salyer, I. O.

1980-01-01

The electron irradiation conditions required to prepare thermally from stable high density polyethylene (HDPE) were defined. The conditions were defined by evaluating the heat of fusion and the melting temperature of several HDPE specimens. The performance tests conducted on the specimens, including the thermal cycling tests in the thermal energy storage unit are described. The electron beam irradiation tests performed on the specimens, in which the total radiation dose received by the pellets, the electron beam current, the accelerating potential, and the atmospheres were varied, are discussed.

Effects of Agitation and Storage Temperature on Measurements of Hydration Status.

PubMed

Adams, Heather M; Eberman, Lindsey E; Yeargin, Susan W; Niemann, Andrew J; Mata, Heather L; Dziedzicki, David J

2015-12-01

Hypohydration can have significant implications on normal physiological functions of the body. This study aimed to determine the impact of agitation, storage temperature, and storage time on urine osmolality compared to the criterion control. We used a descriptive diagnostic validity test design. To investigate agitation, we recruited 75 healthy individuals (males = 41, females = 34; mean age = 22 ± 5 years; mean self-reported height = 172 ± 23 cm and mass = 77 ± 17 kg) who provided one or more samples (total = 81). The independent variables were agitation (vortex, hand shaken, no agitation) and temperature (room temperature, freezer, and refrigerator) type. Participants completed informed consent, a health questionnaire and were asked to provide a urine sample, which was split and labeled according to agitation type or storage temperature. Urine osmolality was used to determine hydration status at two time points (within 2 hours [control], 48 hours). We used t-tests to determine the difference between each condition and the control and calculated percent error for each condition. No significant differences for no agitation (t79 = -0.079, P = 0.937), hand shaken (t79 = 1.395, P = 0.167) or vortex mixed (t79 = -0.753, P = 0.453) were identified when compared to the criterion control. No significant differences for room temperature (t82 = -0.720, P = 0.474), refrigerator (t82 = -2.697, P = 0.008) or freezer (t82 = 2.576, P = 0.012) were identified when compared to the criterion control. Our findings suggest agitation of urine specimen is not necessary and samples do not require refrigeration or freezing if assessed within 48 hours. Analysis within two hours of collection is not necessary and samples can be stored for up to 48 hours without impacting the hydration status of the sample.

Filter Paper-based Nucleic Acid Storage in High-throughput Solid Tumor Genotyping.

PubMed

Stachler, Matthew; Jia, Yonghui; Sharaf, Nematullah; Wade, Jacqueline; Longtine, Janina; Garcia, Elizabeth; Sholl, Lynette M

2015-01-01

Molecular testing of tumors from formalin-fixed paraffin-embedded (FFPE) tissue blocks is central to clinical practice; however, it requires histology support and increases test turnaround time. Prospective fresh frozen tissue collection requires special handling, additional storage space, and may not be feasible for small specimens. Filter paper-based collection of tumor DNA reduces the need for histology support, requires little storage space, and preserves high-quality nucleic acid. We investigated the performance of tumor smears on filter paper in solid tumor genotyping, as compared with paired FFPE samples. Whatman FTA Micro Card (FTA preps) smears were prepared from 21 fresh tumor samples. A corresponding cytology smear was used to assess tumor cellularity and necrosis. DNA was isolated from FTA preps and FFPE core samples using automated methods and quantified using SYBR green dsDNA detection. Samples were genotyped for 471 mutations on a mass spectrophotometry-based platform (Sequenom). DNA concentrations from FTA preps and FFPE correlated for untreated carcinomas but not for mesenchymal tumors (Spearman σ=0.39 and σ=-0.1, respectively). Average DNA concentrations were lower from FTA preps as compared with FFPE, but DNA quality was higher with less fragmentation. Seventy-six percent of FTA preps and 86% of FFPE samples generated adequate DNA for genotyping. FTA preps tended to perform poorly for collection of DNA from pretreated carcinomas and mesenchymal neoplasms. Of the 16 paired DNA samples that were genotyped, 15 (94%) gave entirely concordant results. Filter paper-based sample preservation is a feasible alternative to FFPE for use in automated, high-throughput genotyping of carcinomas.

Corrosion on prehistoric Cu-Sn-alloys: the influence of artificial environment and storage

NASA Astrophysics Data System (ADS)

Mödlinger, Marianne; Piccardo, Paolo

2013-12-01

The paper contributes to the identification of different corrosion products detected on the cross-section specimens sampled from Bronze Age swords and one helmet found between 60-160 years ago. The objects are kept in 1889 built oak showcases at the Natural History Museum Vienna, having suffered unknown restoration treatments. The identified corrosion products not only affect further eventual treatment in conservation science of copper base objects but also contribute to identify the often unknown find context, which is meant to facilitate archaeological interpretation of the Bronze Age weapons. The analyses of the samples were carried out using SEM-EDXS-EBSD and optical microscopy.

Method for acquiring, storing and analyzing crystal images

NASA Technical Reports Server (NTRS)

Gester, Thomas E. (Inventor); Rosenblum, William M. (Inventor); Christopher, Gayle K. (Inventor); Hamrick, David T. (Inventor); Delucas, Lawrence J. (Inventor); Tillotson, Brian (Inventor)

2003-01-01

A system utilizing a digital computer for acquiring, storing and evaluating crystal images. The system includes a video camera (12) which produces a digital output signal representative of a crystal specimen positioned within its focal window (16). The digitized output from the camera (12) is then stored on data storage media (32) together with other parameters inputted by a technician and relevant to the crystal specimen. Preferably, the digitized images are stored on removable media (32) while the parameters for different crystal specimens are maintained in a database (40) with indices to the digitized optical images on the other data storage media (32). Computer software is then utilized to identify not only the presence and number of crystals and the edges of the crystal specimens from the optical image, but to also rate the crystal specimens by various parameters, such as edge straightness, polygon formation, aspect ratio, surface clarity, crystal cracks and other defects or lack thereof, and other parameters relevant to the quality of the crystals.

US-Canada Great Lakes Regional Specimen Bank Feasibility Study.

PubMed

Kerry, A; Edmonds, C J; Landon, L; Yonker, T L

1993-11-01

A study to examine the feasibility of establishing a Regional Specimen Bank in the Great Lakes area of the United States and Canada has recently been initiated by the Michigan Audubon Society. There are several existing formal and informal specimen banking facilities active in the region but their combined adequacy has not been evaluated. This feasibility study will establish the need and use of a regional bank and the institution(s) necessary to satisfy this need will be recommended. The study will address the scope required to meet present and future needs including the types of specimens to be represented in the bank, geographic coverage and protocols for collection, shipping, processing, analysis and storage. A management policy of the bank will be developed encompassing business operation, costs, governing structure and personnel requirements. The legal requirements of the bank will be determined with regards to the acquisition of samples, transport across national boundaries, access to specimens and information, and liability during operation. An effective information dissemination network will be recommended that is compatible with national and international partners, will facilitate technology and information transfer and support the quality and status of the bank. Determination of secure, long-term funding sources will be one of the key elements to ensuring a safe repository. This feasibility study is funded by the Great Lakes Protection Fund.

Microshear Bond Strength of OptiBond All-in-One Self-adhesive Agent to Er:YAG Laser Treated Enamel After Thermocycling and Water Storage.

PubMed

Kasraei, Shahin; Yarmohammadi, Ebrahim; Ghazizadeh, Mohammad Vahid

2016-01-01

Introduction: This study aimed to compare the microshear bond strength of composite to enamel treated with Erbium-Doped Yttrium Aluminum Garnet (Er:YAG) laser using a self-etch one step bonding agent. Methods: Seventy-six enamel surfaces were prepared from 38 sound human third molar teeth. Specimens were randomly divided into four groups of 18. The enamel surface in half the specimens was irradiated with Er:YAG laser. One extra specimen from each group was evaluated under a scanning electron microscope (SEM). Composite micro-cylinders were bonded to the specimen surfaces using OptiBond All-In-One (OB) adhesive agent and stored in distilled water for 24 hours. Half the specimens were thermocycled (2000 cycles) and stored in distilled water at 37°C for three months (TW). The microshear bond strength of composite to enamel was measured using a universal testing machine at a crosshead speed of 1 mm/min. The fractured surfaces were evaluated under a stereomicroscope at ×40 magnification to determine the mode of failure. Data were analyzed using repeated measures analysis of variance (ANOVA) and t test. Results: The mean values (±standard deviation) were 17.96 ± 2.92 MPa in OB group, 22.29 ± 4.25 MPa in laser + OB group, 18.11 ± 3.52 MPa in laser + OB + TW group and 9.42 ± 2.47 MPa in OB + TW group. Repeated measures ANOVA showed that laser irradiation increased the microshear bond strength ( P < 0.001). Bond strength decreased when the samples were thermocycled and stored for three months ( P < 0.001). The interaction effect of water storage and laser treatment on bond strength was significant ( P < 0.05). Conclusion: Enamel surface preparation with Er:YAG laser is recommended to enhance the durability of the bond of self-etch bonding systems to enamel.

Microshear Bond Strength of OptiBond All-in-One Self-adhesive Agent to Er:YAG Laser Treated Enamel After Thermocycling and Water Storage

PubMed Central

Kasraei, Shahin; Yarmohammadi, Ebrahim; Ghazizadeh, Mohammad Vahid

2016-01-01

Introduction: This study aimed to compare the microshear bond strength of composite to enamel treated with Erbium-Doped Yttrium Aluminum Garnet (Er:YAG) laser using a self-etch one step bonding agent. Methods: Seventy-six enamel surfaces were prepared from 38 sound human third molar teeth. Specimens were randomly divided into four groups of 18. The enamel surface in half the specimens was irradiated with Er:YAG laser. One extra specimen from each group was evaluated under a scanning electron microscope (SEM). Composite micro-cylinders were bonded to the specimen surfaces using OptiBond All-In-One (OB) adhesive agent and stored in distilled water for 24 hours. Half the specimens were thermocycled (2000 cycles) and stored in distilled water at 37°C for three months (TW). The microshear bond strength of composite to enamel was measured using a universal testing machine at a crosshead speed of 1 mm/min. The fractured surfaces were evaluated under a stereomicroscope at ×40 magnification to determine the mode of failure. Data were analyzed using repeated measures analysis of variance (ANOVA) and t test. Results: The mean values (±standard deviation) were 17.96 ± 2.92 MPa in OB group, 22.29 ± 4.25 MPa in laser + OB group, 18.11 ± 3.52 MPa in laser + OB + TW group and 9.42 ± 2.47 MPa in OB + TW group. Repeated measures ANOVA showed that laser irradiation increased the microshear bond strength (P < 0.001). Bond strength decreased when the samples were thermocycled and stored for three months (P < 0.001). The interaction effect of water storage and laser treatment on bond strength was significant (P < 0.05). Conclusion: Enamel surface preparation with Er:YAG laser is recommended to enhance the durability of the bond of self-etch bonding systems to enamel. PMID:28144434

Comprehensive outsourcing biobanking facility to serve the international research community.

PubMed

Diaferia, Giuseppe R; Biunno, Ida; DeBlasio, Pasquale

2011-06-01

The validity of results from biomarker studies using archived specimens depends on the integrity of the specimens and the manner in which they are collected, processed, and stored. The management of a huge amount of biomaterial generated from research studies and clinical trials is becoming a very demanding task and many organizations are facing the choice between in-house storage and processing and outsourcing some activities. Storage and logistic functions are the prime targets for outsourcing, because to sustain these critical assets organizations must have the expertise, the dedicated qualified personnel, the proper quality control programs, and available resources to fulfill the mandatory requirements to maintain the integrity of the samples. External biobanks are dedicated and certified infrastructures (ISO, GMP, etc.) that apply efficient logistic and shipping activities, use validated standard operating procedures, install appropriate monitoring back-up systems, and, most of all, have room for expansion. Thus, the choice between in-house biobanking and outsourcing cannot be exclusively based on a financial decision; it must also consider (i) type of collection/project, (ii) logistic complexity (number and locations of collection sites), (iii) safety requirements, (iv) functional expertise, and (v) business priorities.

Moisture storage and transport properties of preservative treated and untreated southern pine wood

Treesearch

Samuel L. Zelinka; Samuel V. Glass; Charles R. Boardman; Dominique Derome

2016-01-01

Moisture storage and transport properties of southern pine (Pinus spp.) wood were measured for implementation into hygrothermal models. Specimens were untreated or pressure-treated with alkaline copper quaternary (ACQ) preservative. Moisture storage was characterized with sorption isotherms in the hygroscopic region (high capillary pressures) and...

Stability of selected hematology variables in canine blood kept at room temperature in EDTA for 24 and 48 hours.

PubMed

Médaille, C; Briend-Marchal, A; Braun, J P

2006-03-01

Most hematologic analyses are performed within a short time of blood sampling, but samples collected at the end of a week may have to be stored for up to 2 days. The stability of hematologic constituents is poorly documented. The objective of this study was to compare the results of RBC, WBC and platelet counts, hemoglobin (Hgb) concentration, and MCV before and after storage of canine blood at room temperature for 24 and 48 hours. One hundred fifty-two K3-EDTA canine blood specimens from 2 veterinary hospitals were analyzed within 4 hours of collection, then 24 and 48 hours later with a Coulter T540 hematology analyzer. Results were compared by Passing-Bablock agreement, difference plots, and according to their classification as normal or abnormal based on reference intervals. RBC count and Hgb concentration were stable for the duration of the study. Differences in WBC and platelet counts varied with the specimen, independently of the initial value. MCV increased consistently over the 2 days. However, only a few results were misclassified. Whole blood specimens stored for up to 2 days at room temperature are suitable for cell counts and Hgb measurement. However, potential variations have to be known to avoid misinterpretations, especially near the decision limits.

NASA Bioculture System: From Experiment Definition to Flight Payload

NASA Technical Reports Server (NTRS)

Sato, Kevin Y.; Almeida, Eduardo; Austin, Edward M.

2014-01-01

Starting in 2015, the NASA Bioculture System will be available to the science community to conduct cell biology and microbiology experiments on ISS. The Bioculture System carries ten environmentally independent Cassettes, which house the experiments. The closed loop fluids flow path subsystem in each Cassette provides a perfusion-based method for maintain specimen cultures in a shear-free environment by using a biochamber based on porous hollow fiber bioreactor technology. Each Cassette contains an incubator and separate insulated refrigerator compartment for storage of media, samples, nutrients and additives. The hardware is capable of fully automated or manual specimen culturing and processing, including in-flight experiment initiation, sampling and fixation, up to BSL-2 specimen culturing, and the ability to up to 10 independent cultures in parallel for statistical analysis. The incubation and culturing of specimens in the Bioculture System is a departure from standard laboratory culturing methods. Therefore, it is critical that the PI has an understanding the pre-flight test required for successfully using the Bioculture System to conduct an on-orbit experiment. Overall, the PI will conduct a series of ground tests to define flight experiment and on-orbit implementation requirements, verify biocompatibility, and determine base bioreactor conditions. The ground test processes for the utilization of the Bioculture System, from experiment selection to flight, will be reviewed. Also, pre-flight test schedules and use of COTS ground test equipment (CellMax and FiberCell systems) and the Bioculture System will be discussed.

Clinical evaluation of high-risk HPV detection on self-samples using the indicating FTA-elute solid-carrier cartridge.

PubMed

Geraets, D T; van Baars, R; Alonso, I; Ordi, J; Torné, A; Melchers, W J G; Meijer, C J L M; Quint, W G V

2013-06-01

High-risk human papillomavirus (hrHPV) testing in cervical screening is usually performed on physician-taken cervical smears in liquid-based medium. However, solid-state specimen carriers allow easy, non-hazardous storage and transportation and might be suitable for self-collection by non-responders in screening and in low-resource settings. We evaluated the adequacy of self-collected cervicovaginal (c/v) samples using a Viba-brush stored on an Indicating FTA-elute cartridge (FTA-based self-sampling) for hrHPV testing in women referred to a gynecology clinic due to an abnormal smear. 182 women accepted to self-collect a c/v sample. After self-sampling, a physician obtained a conventional liquid-based cervical smear. Finally, women were examined by colposcopy and a biopsy was taken when clinically indicated. Self-samples required only simple DNA elution, and DNA was extracted from physician-obtained samples. Both samples were tested for 14 hrHPVs by GP5+/6+-EIA-LQ Test and SPF(10)-DEIA-LiPA(25). Both assays detected significantly more hrHPV in physician-collected specimens than in self-collected samples (75.3% and 67.6% by SPF(10); 63.3% and 53.3% by GP5+/6+, respectively). The combination of physician-collected specimen and GP5+/6+ testing demonstrated the optimal balance in sensitivity (98.0%) and specificity (48.1%) for CIN2+ detection in this referral population. A test system of FTA-based self-collection and SPF(10) hrHPV detection approached this sensitivity (95.9%) and specificity (42.9%). These results show that the clinical performance of hrHPV detection is determined by both the sample collection system and the test method. FTA-based self-collection with SPF(10) testing might be valuable when a liquid-based medium cannot be used, but requires further investigation in screening populations. Copyright © 2013 Elsevier B.V. All rights reserved.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.

PubMed

Wu, Gary D; Lewis, James D; Hoffmann, Christian; Chen, Ying-Yu; Knight, Rob; Bittinger, Kyle; Hwang, Jennifer; Chen, Jun; Berkowsky, Ronald; Nessel, Lisa; Li, Hongzhe; Bushman, Frederic D

2010-07-30

Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80 degrees C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method.

Contribution of postpolymerization conditioning and storage environments to the mechanical properties of three interim restorative materials.

PubMed

Thompson, Geoffrey A; Luo, Qing

2014-09-01

Because polymer-based interim restorative materials are weak, even well-made restorations sometimes fail before the definitive restoration is ready for insertion. Therefore, knowing which fabrication procedures and service conditions affect mechanical properties is important, particularly over an extended period. The purpose of this study was to evaluate the effect of thermal treatment, surface sealing, thermocycling, storage media, storage temperature, and age on autopolymerizing poly(methylmethacrylate) and bis-acryl interim restorative materials. Outcome measures were flexural strength, Vickers surface microhardness, and impact strength. Flexural strength and microhardness of poly(methylmethacrylate) (Jet Acrylic) and 2 bis-acryl-composite resin (Protemp 3 Garant and Integrity) interim restorative materials were evaluated as affected by storage media, storage temperature, storage time, thermocycling, postpolymerization thermal treatment, or application of a surface sealer. In total, 2880 beam specimens (25×2×2 mm) were fabricated. Mechanical property analyses were made at 10 days, 30 days, 6 months, and 1 year after specimen preparation. Flexural strength was determined by using a 3-point bending test in a universal testing machine with a 1 kN load cell at a crosshead speed of 5.0 mm min(-1). Fracture specimens were recovered and used for determining Vickers microhardness. Measurements were made with a 0.1 N load and 15 second dwell time. Three microhardness measurements were made for each specimen, and the mean was used for reporting Vickers microhardness. Notched impact specimens (64×12.7×6.35 mm) were fabricated from Jet, Protemp 3 Garant, and Integrity interim restorative materials, yielding 288 impact specimens. Impact strengths were assessed at 10 days, 30 days, 6 months, and 1 year with a 2 J pendulum. The effects of the various experimental treatments were determined and rank ordered with analysis of variance, F ratios, and least square means differences Student t tests (α=.05). All experimental treatments investigated had significant effects on flexural strength, with material (P<.001) and thermocycling (P<.001) being dominant. Moreover, all experimental treatments investigated had a significant overall impact on Vickers microhardness with material (P<.001) and Palaseal glaze (P<.001) showing large effects. Material (P<.001) and age (P=.010) had a significant effect on impact strength. Mechanical properties of some interim polymeric materials can be improved by postpolymerization heat treatments or surface glazing. This procedure may extend the useful lifetime of some bis-acryl interim restorations. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Stability of Synthetic Cathinones in Urine.

PubMed

Glicksberg, Lindsay; Kerrigan, Sarah

2018-03-01

In this report, we evaluate the concentration, pH, temperature and analyte-dependent effects on cathinone stability in preserved human urine. A total of 22 synthetic cathinones were evaluated at 100 ng/mL and 1,000 ng/mL in pH 4 and pH 8 urine over 6 months. Specimens were stored at -20°C, 4°C, 20°C and 32°C. The stability of synthetic cathinones was highly dependent on urine pH and storage temperature. Cathinones were considerably more stable in acidic urine (pH 4) at low temperature. In alkaline urine (pH 8) at 32°C, significant losses (>20%) were observed within hours for the majority of drugs. In contrast, all drugs were stable in frozen and refrigerated urine at pH 4 for the duration of the study. These results highlight the importance of sample storage and the potential for pre-analytical changes in concentration during routine shipping and handling of specimens. Significant structural influence was also observed. Cathinones bearing a tertiary amine (pyrrolidine group) were significantly more stable than their secondary amine counterparts. The methylenedioxy group also exerted a significant stabilizing effect on both the tertiary and secondary amines. In the absence of the methylenedioxy group, no significant differences in stability were observed between the unsubstituted and ring substituted secondary amines. Half-lives at ambient temperature in pH 8 urine ranged from 9 h (3-fluoromethcathinone) to 4.3 months (methylenedioxypyrovalerone and 3,4-methylenedioxy-α-pyrrolidinobutiophenone), demonstrating the importance of analyte dependence, and the dual stabilizing effect of both the pyrollidine and methylenedioxy groups. Biological evidence may be subjected to a variety of environmental conditions prior to, and during transport to the forensic laboratory. These findings demonstrate the inherent instability of certain cathinone species in biological evidence under some conditions. Moreover, this study highlights the need for quantitative drug findings in toxicological investigations to be interpreted cautiously, and within the context of specimen storage and integrity.

Characterization of water sorption, solubility, and roughness of silorane- and methacrylate-based composite resins.

PubMed

Giannini, M; Di Francescantonio, M; Pacheco, R R; Cidreira Boaro, L C; Braga, R R

2014-01-01

The objective of this study was to evaluate the surface roughness (SR), water sorption (WS), and solubility (SO) of four composite resins after finishing/polishing and after one year of water storage. Two low-shrinkage composites (Filtek Silorane [3M ESPE] and Aelite LS [Bisco Inc]) and two composites of conventional formulations (Heliomolar and Tetric N-Ceram [Ivoclar Vivadent]) were tested. Their respective finishing and polishing systems (Sof-Lex Discs, 3M ESPE; Finishing Discs Kit, Bisco Inc; and Astropol F, P, HP, Ivoclar Vivadent) were used according to the manufacturers' instructions. Ten disc-shaped specimens of each composite resin were made for each evaluation. Polished surfaces were analyzed using a profilometer after 24 hours and one year. For the WS and SO, the discs were stored in desiccators until constant mass was achieved. Specimens were then stored in water for seven days or one year, at which time the mass of each specimen was measured. The specimens were dried again and dried specimen mass determined. The WS and SO were calculated from these measurements. Data were analyzed by two-way analysis of variance and Tukey post hoc test (α=0.05). Filtek Silorane showed the lowest SR, WS, and SO means. Water storage for one year increased the WS means for all composite resins tested. The silorane-based composite resin results were better than those obtained for methacrylate-based resins. One-year water storage did not change the SR and SO properties in any of the composite resins.

Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex.

PubMed

Liang, Xiao; Chigerwe, Munashe; Hietala, Sharon K; Crossley, Beate M

2014-06-01

In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI=0.89-0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (-27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P≥0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency. Copyright © 2014 Elsevier B.V. All rights reserved.

Influence of degradation conditions on dentin bonding durability of three universal adhesives.

PubMed

Sai, Keiichi; Shimamura, Yutaka; Takamizawa, Toshiki; Tsujimoto, Akimasa; Imai, Arisa; Endo, Hajime; Barkmeier, Wayne W; Latta, Mark A; Miyazaki, Masashi

2016-11-01

This study aims to determine dentin bonding durability of universal adhesives using shear bond strength (SBS) tests under various degradation conditions. G-Premio Bond (GP, GC), Scotchbond Universal (SU, 3M ESPE) and All Bond Universal (AB, Bisco) were compared with conventional two-step self-etch adhesive Clearfil SE Bond (SE, Kuraray Noritake Dental). Bonded specimens were divided into three groups of ten, and SBSs with bovine dentin were determined after the following treatments: 1) Storage in distilled water at 37°C for 24h followed by 3000, 10,000, 20,000 or 30,000 thermal cycles (TC group), 2) Storage in distilled water at 37°C for 3 months, 6 months or 1year (water storage, WS group) and 3) Storage in distilled water at 37°C for 24h (control). SE bonded specimens showed significantly higher SBSs than universal adhesives, regardless of TC or storage periods, although AB specimens showed significantly increased SBSs after 30,000 thermal cycles. In comparisons of universal adhesives under control and degradation conditions, SBS was only reduced in SU after 1year of WS. Following exposure of various adhesive systems to degradation conditions of thermal cycling and long term storage, SBS values of adhesive systems varied primarily with degradation period. Although universal adhesives have lower SBSs than the two-step self-etch adhesive SE, the present data indicate that the dentin bonding durability of universal adhesives in self-etch mode is sufficient for clinical use. Copyright © 2016 Elsevier Ltd. All rights reserved.

The influence of storage time and temperature on the measurement of serum, plasma and urine osmolality.

PubMed

Bezuidenhout, Karla; Rensburg, Megan A; Hudson, Careen L; Essack, Younus; Davids, M Razeen

2016-07-01

Many clinical laboratories require that specimens for serum and urine osmolality determination be processed within 3 h of sampling or need to arrive at the laboratory on ice. This protocol is based on the World Health Organization report on sample storage and stability, but the recommendation lacks good supporting data. We studied the effect of storage temperature and time on osmolality measurements. Blood and urine samples were obtained from 16 patients and 25 healthy volunteers. Baseline serum, plasma and urine osmolality measurements were performed within 30 min. Measurements were then made at 3, 6, 12, 24 and 36 h on samples stored at 4-8℃ and room temperature. We compared baseline values with subsequent measurements and used difference plots to illustrate changes in osmolality. At 4-8℃, serum and plasma osmolality were stable for up to 36 h. At room temperature, serum and plasma osmolality were very stable for up to 12 h. At 24 and 36 h, changes from baseline osmolality were statistically significant and exceeded the total allowable error of 1.5% but not the reference change value of 4.1%. Urine osmolality was extremely stable at room temperature with a mean change of less than 1 mosmol/kg at 36 h. Serum and plasma samples can be stored at room temperature for up to 36 h before measuring osmolality. Cooling samples to 4-8℃ may be useful when delays in measurement beyond 12 h are anticipated. Urine osmolality is extremely stable for up to 36 h at room temperature. © The Author(s) 2015.

Occlusal loading and cross-linking effects on dentin collagen degradation in physiological conditions.

PubMed

Turco, Gianluca; Frassetto, Andrea; Fontanive, Luca; Mazzoni, Annalisa; Cadenaro, Milena; Di Lenarda, Roberto; Tay, Franklin R; Pashley, David H; Breschi, Lorenzo

2016-02-01

This study evaluated the ability of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) to improve the stability of demineralized dentin collagen matrices when subjected to mechanical cycling by means of Chewing Simulation (CS). Demineralized dentin disks were randomly assigned to four groups (N=4): (1) immersion in artificial saliva at 37°C for 30 days; (2) pre-treatment with 0.5 M EDC for 60 s, then stored as in Group 1; (3) CS challenge (50 N occlusal load, 30 s occlusal time plus 30 s with no load, for 30 days); (4) pre-treatment with 0.5 M EDC as in Group 2 and CS challenge as in Group 3. Collagen degradation was evaluated by sampling storage media for ICTP and CTX telopeptides. EDC treated specimens showed no significant telopeptides release, irrespective of the aging method. Cyclic stressing of EDC-untreated specimens caused significantly higher ICTP release at day 1, compared to static storage, while by days 3 and 4, the ICTP release in the cyclic group fell significantly below the static group, and then remained undetectable from 5 to 30 days. CTX release in the cyclic groups, on EDC-untreated control specimens was always lower than in the static group in days 1-4, and then fell to undetectable for 30 days. This study showed that chewing stresses applied to control untreated demineralized dentin increased degradation of collagen in terms of CTX release, while collagen crosslinking agents may prevent dentin collagen degradation, irrespective of simulated occlusal function. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Effect of artificial aging on the surface roughness and microhardness of resin-based materials.

PubMed

Santos, M Jacinta M C; Rêgo, Heleine Maria Chagas; Mukhopadhyay, Anuradha; El Najjar, Mai; Santos, Gildo C

2016-01-01

This study sought to verify the effects of aging on the surface roughness (Ra) and microhardness (Knoop hardness number [KHN]) of resin-based restorative materials protected with a surface sealer. Disc specimens of 2 resin-modified glass ionomers (RMGIs) and 1 composite resin (CR) were fabricated in a metal mold. Specimens of each material were divided into 1 group that was covered with surface sealer and 1 group that was not. Both groups of each material were then subdivided according to whether they were stored (aged) in cola or distilled water. Surface roughness and KHN values were obtained from each specimen before and after storage. After aging of the specimens, significantly higher Ra values were observed in the 2 RMGIs when they were not covered with a surface sealer, while the CR was not affected. The KHN values varied by materials and storage conditions (with and without a surface sealer). All the groups with a surface sealer exhibited increased Ra values after aging.

A novel design for storage of inner stress by colloidal processing on rock-like materials

NASA Astrophysics Data System (ADS)

Chen, Weichang; Wang, Sijing; Lekan Olatayo, Afolagboye; Fu, Huanran

2018-06-01

Inner stress exists in rocks, affecting rock engineering, yet has received very little attention and quantitative investigation because of uncertainty about its characteristics. Previous studies have suggested that the inner stresses of rock materials are closely related to their physical state variation. In this work, a novel mold was designed to simulate the storage process of inner stress in specimens composed of quartz sands and epoxy. Then, thermal tests were carried out to change the physical state of the specimens, and expansion of the specimens was monitored. The results indicated that inner stress could be partly locked by the mold and it could also be released by heating. It can be inferred from the analysis that one necessary condition of storage and release of inner stress is physical state variation. Additionally, by using an XRD method, the variations in the interplanar spacing of the quartz sands were detected, and the results reflect that inner stress could be locked-in aggregates (quartz sands) by a cement constraint (solid epoxy). The inner stress stored in quartz sands was calculated using height and interplanar spacing variations.

Translational Research in Pediatrics IV: Solid Tissue Collection and Processing.

PubMed

Gillio-Meina, Carolina; Zielke, H Ronald; Fraser, Douglas D

2016-01-01

Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality. Copyright © 2016 by the American Academy of Pediatrics.

Effects of the density and homogeneity in NIRS crop moisture estimation

NASA Astrophysics Data System (ADS)

Lenzini, Nicola; Rovati, Luigi; Ferrari, Luca

2017-06-01

Near-infrared spectroscopy (NIRS) is widely used in fruits and vegetables quality evaluation. This technique is also used for the analysis of alfalfa, a crop that occupies a position of great importance in the agricultural field. In particular for the storage, moisture content is a key parameter for the crops and for this reason its monitoring is very important during the harvesting phase. Usually optical methods like NIRS are well suitable in laboratory frameworks where the specimen is properly prepared, while their application during the harvesting phase presents several diffculties. A lot of influencing factors, such as density and degree of homogeneity can affect the moisture evaluation. In this paper we present the NIRS analysis of alfalfa specimens with different values of moisture and density, as well as the obtained results. To study scattering and absorption phenomena, the forward and backward scattered light from the sample have been spectrally analyzed.

Rapid and effective processing of blood specimens for diagnostic PCR using filter paper and Chelex-100.

PubMed Central

Polski, J M; Kimzey, S; Percival, R W; Grosso, L E

1998-01-01

AIM: To provide a more efficient method for isolating DNA from peripheral blood for use in diagnostic DNA mutation analysis. METHODS: The use of blood impregnated filter paper and Chelex-100 in DNA isolation was evaluated and compared with standard DNA isolation techniques. RESULTS: In polymerase chain reaction (PCR) based assays of five point mutations, identical results were obtained with DNA isolated routinely from peripheral blood and isolated using the filter paper and Chelex-100 method. CONCLUSION: In the clinical setting, this method provides a useful alternative to conventional DNA isolation. It is easily implemented and inexpensive, and provides sufficient, stable DNA for multiple assays. The potential for specimen contamination is reduced because most of the steps are performed in a single microcentrifuge tube. In addition, this method provides for easy storage and transport of samples from the point of acquisition. PMID:9893748

Rapid and effective processing of blood specimens for diagnostic PCR using filter paper and Chelex-100.

PubMed

Polski, J M; Kimzey, S; Percival, R W; Grosso, L E

1998-08-01

To provide a more efficient method for isolating DNA from peripheral blood for use in diagnostic DNA mutation analysis. The use of blood impregnated filter paper and Chelex-100 in DNA isolation was evaluated and compared with standard DNA isolation techniques. In polymerase chain reaction (PCR) based assays of five point mutations, identical results were obtained with DNA isolated routinely from peripheral blood and isolated using the filter paper and Chelex-100 method. In the clinical setting, this method provides a useful alternative to conventional DNA isolation. It is easily implemented and inexpensive, and provides sufficient, stable DNA for multiple assays. The potential for specimen contamination is reduced because most of the steps are performed in a single microcentrifuge tube. In addition, this method provides for easy storage and transport of samples from the point of acquisition.

12-month color stability of enamel, dentine, and enamel-dentine samples after bleaching.

PubMed

Wiegand, Annette; Drebenstedt, Steffi; Roos, Malgorzata; Magalhães, Ana Carolina; Attin, Thomas

2008-12-01

The study aimed to quantify the color regression of enamel (E), dentine (D), and combined enamel-dentine (ED) of differently bleached ED specimens over a period of 12 months in vitro. Two ED samples were obtained from the labial surfaces of bovine teeth and prepared to a standardized thickness with the enamel and dentine layer each 1 mm. The ED samples were distributed on four groups (each n = 80), in which the different bleaching products were applied on enamel (1, Whitestrips; 2, Illuminé 15%; 3, Opalescence Xtra Boost) or dentine surfaces (4, mixture of sodium perborate/distilled water). Eighty ED samples were not bleached (control). Color (L*a*b*) of ED was assessed at baseline, subsequently after bleaching and at 3, 6, and 12 months of storage after bleaching (each 20 samples/group). E and D samples were prepared by removing the dentine or enamel layer of ED samples to allow for separate color analysis. Bleaching resulted in a significant color change (Delta E) of ED specimens. Within the observation period, Delta L but not Delta b declined to baseline. L* values of E and D samples also declined and were not significantly different from control samples after 12 months, while b* values did not decrease to baseline. Generally, no differences between the bleaching agents could be observed. Color change of enamel, dentine, and combined ED of in vitro bleached tooth samples is not stable over time with regard to lightness. However, yellowness did not return to baseline within 1 year.

Novel infrastructure for sepsis biomarker research in critically ill neonates and children.

PubMed

Juskewitch, Justin E; Enders, Felicity T; Abraham, Roshini S; Huskins, W Charles

2013-02-01

Sepsis biomarker research requires an infrastructure to identify septic patients efficiently and to collect and store specimens properly. We developed a novel infrastructure to study biomarkers of sepsis in children. Patients in pediatric and neonatal intensive care units were enrolled prospectively; enrollment information was stored in a secure, remotely accessible database. Researchers were notified of electronic medical record (EMR) orders for blood cultures (a surrogate for a diagnostic evaluation of suspected sepsis) by a page triggered by the order. Staff confirmed patient enrollment and remotely submitted an EMR order for collection of study specimens simultaneous with the blood culture. Specimens were processed and stored by a mobile clinical research unit. Over 2 years, 2029 patients were admitted; 138 were enrolled. Staff received pages for 95% of blood cultures collected from enrolled patients. The median time between the blood culture order and collection was 34 minutes (range 9-241). Study specimens were collected simultaneously with 41 blood cultures. The median times between specimen collection and storage for flow cytometry and cytokine analysis were 33 minutes (range 0-82) and 52 minutes (range 28-98), respectively. This novel infrastructure facilitated prompt, proper collection and storage of specimens for sepsis biomarker analysis. © 2013 Wiley Periodicals, Inc.

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider.

PubMed

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen's age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.

The essential work of fracture of thermoplastic orthodontic retainer materials.

PubMed

Pascual, Albert L; Beeman, Cynthia S; Hicks, E Preston; Bush, Heather M; Mitchell, Richard J

2010-05-01

To investigate whether oral cleansing agents affect the essential work of fracture (EWF) and plastic work of fracture (PWF) for two types of orthodontic thermoplastic retainer materials. Polyethylene-terephthalate-glycol (PETG; Tru-Tain Splint) and polypropylene/ethylene-propylene rubber (PP-EPR) blend (Essix-C+) sheets were compared. For each material, six sets of 25 sheets were thermoformed into double-edge-notched-tension specimens; subsets of five specimens were formed with internotch distances (L) equal to 6, 8, 10, 12, or 14 mm, respectively. Sets were stored (160 hours, 25 degrees C) in air (DRY), distilled water (DW), Original Listerine (LIS), mint Crest ProHealth (CPH), 3% hydrogen peroxide (HP), or Polident solution (POL). Specimens were fractured in tension at 2.54 mm/min. Areas under load-elongation curves were measured to determine total work of fracture (W(f)). Linear regressions (W(f) vs L [n = 25]) yielded intercepts (EWF) and slopes (PWF). Ninety-five percent confidence intervals were used to evaluate differences in EWF and PWF estimates. PP-EPR blends showed higher EWFs after storage in HP vs storage in DW. PP-EPR blend showed higher EWFs after storage in CPH vs PETG. After HP storage, PP-EPR exhibited lower PWFs than with any other storage conditions. PP-EPR exhibited higher PWFs than PETG after storage in DRY, DW, and LIS. Compared with DW, none of the cleansers decreased the energy to initiate fracture. With one exception, no cleanser decreased the energy to continue plastic fracture extension. In PP-EPR blend, increased resistance to fracture initiation was observed with CPH and HP, yet, surprisingly, HP decreased resistance to plastic fracture growth.

21 CFR 58.130 - Conduct of a nonclinical laboratory study.

Code of Federal Regulations, 2010 CFR

2010-04-01

... specimen in a manner that precludes error in the recording and storage of data. (d) Records of gross... that specimen histopathologically. (e) All data generated during the conduct of a nonclinical laboratory study, except those that are generated by automated data collection systems, shall be recorded...

21 CFR 58.130 - Conduct of a nonclinical laboratory study.

Code of Federal Regulations, 2013 CFR

2013-04-01

... specimen in a manner that precludes error in the recording and storage of data. (d) Records of gross... that specimen histopathologically. (e) All data generated during the conduct of a nonclinical laboratory study, except those that are generated by automated data collection systems, shall be recorded...

21 CFR 58.130 - Conduct of a nonclinical laboratory study.

Code of Federal Regulations, 2011 CFR

2011-04-01

... specimen in a manner that precludes error in the recording and storage of data. (d) Records of gross... that specimen histopathologically. (e) All data generated during the conduct of a nonclinical laboratory study, except those that are generated by automated data collection systems, shall be recorded...

Effect of thermocycling with or without 1 year of water storage on retentive strengths of luting cements for zirconia crowns.

PubMed

Ehlers, Vicky; Kampf, Gabriel; Stender, Elmar; Willershausen, Brita; Ernst, Claus-Peter

2015-06-01

Bond stability between zirconia crowns and luting cement and between cement and dentin is a main concern; however, only limited evidence is available as to its longevity. The purpose of this in vitro study was to measure the retentive strengths of 7 self-adhesive cements (RelyX Unicem Aplicap, RelyX Unicem Clicker, RelyX Unicem 2 Automix, iCEM, Maxcem Elite, Bifix SE, SpeedCem), 2 adhesive cements with self-etch primers (Panavia 21, SEcure), 1 glass ionomer cement (Ketac Cem), 1 resin-modified glass ionomer cement (Meron Plus), and 1 zinc phosphate cement for luting zirconia crowns (LAVA) to extracted teeth after thermocycling with or without 1 year of water storage. Two-hundred-forty extracted human molars (2 treatments; n=10 per cement) were prepared in a standardized manner. All cements were used according to the manufacturers' recommendations. The intaglios of the crowns were treated with airborne-particle abrasion. After thermocycling (×5000, 5°C/55°C) with or without 1 year of water storage, the cemented ceramic crowns were removed by using a Zwick universal testing device. Statistical analyses were done with the Wilcoxon rank sum and the 2-independent-samples Kolmogorov-Smirnov test. Median retentive strengths [MPa] for specimens thermocycled only/thermocycled with 1 year of water storage were as follows: Panavia 21: 1.7/2.5, SEcure: 3.0/3.0, RelyX Unicem Aplicap: 3.1/3.4, RelyX Unicem Clicker: 4.1/4.2, RelyX Unicem 2 Automix: 3.8/3.1, iCEM: 2.3/2.7, Maxcem Elite: 3.0/3.2, Bifix SE: 1.7/1.7, SpeedCem: 1.3/1.6, Meron Plus: 3.1/2.7, Ketac Cem: 1.4/1.4, and zinc phosphate cement: 1.1/1.6. Statistically significant differences were found only among specimens thermocycled only or thermocycled with 1-year water storage (P<.001). Significant differences in retentive strengths were observed among cements after thermocycling only or thermocycling with 1 year of water storage, but not for the effect of the additional 1 year of water storage. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

The Effect of Artificial Aging on The Bond Strength of Heat-activated Acrylic Resin to Surface-treated Nickel-chromium-beryllium Alloy.

PubMed

Al Jabbari, Youssef S; Zinelis, Spiros; Al Taweel, Sara M; Nagy, William W

2016-01-01

The debonding load of heat-activated polymethylmethacrylate (PMMA) denture base resin material to a nickel-chromium-beryllium (Ni-Cr-Be) alloy conditioned by three different surface treatments and utilizing two different commercial bonding systems was investigated. Denture resin (Lucitone-199) was bonded to Ni-Cr-Be alloy specimens treated with Metal Primer II, the Rocatec system with opaquer and the Rocatec system without opaquer. Denture base resin specimens bonded to non-treated sandblasted Ni-Cr-Be alloy were used as controls. Twenty samples for each treatment condition (80 specimens) were tested. The 80 specimens were divided into two categories, thermocycled and non-thermocycled, containing four groups of ten specimens each. The non-thermocycled specimens were tested after 48 hours' storage in room temperature water. The thermocycled specimens were tested after 2,000 cycles in 4°C and 55°C water baths. The debonding load was calculated in Newtons (N), and collected data were subjected by non parametric test Kruskal-Wallis One Way Analysis of Variance on Ranks and Dunn's post hoc test at the α = 0.05. The Metal Primer II and Rocatec system without opaquer groups produced significantly higher bond strengths (119.9 and 67.6 N), respectively, than did the sandblasted and Rocatec system with opaquer groups, where the bond strengths were 2.6 N and 0 N, respectively. The Metal Primer II was significantly different from all other groups (P<0.05). The bond strengths of all groups were significantly decreased (P<0.05) after thermocycling. Although thermocycling had a detrimental effect on the debonding load of all surface treatments tested, the Metal Primer II system provided higher values among all bonding systems tested, before and after thermocycling.

Comparison of FecalSwab and ESwab Devices for Storage and Transportation of Diarrheagenic Bacteria

PubMed Central

Kaukoranta, Suvi-Sirkku

2014-01-01

Using a collection (n = 12) of ATCC and known stock isolates, as well as 328 clinical stool specimens, we evaluated the ESwab and the new FecalSwab liquid-based microbiology (LBM) devices for storing and transporting diarrheagenic bacteria. The stock isolates were stored in these swab devices up to 48 h at refrigeration (4°C) or room (∼25°C) temperature and up to 3 months at −20°C or −70°C. With the clinical stool specimens, the performances of the ESwab and FecalSwab were compared to those of routinely used transport systems (Amies gel swabs and dry containers). At a refrigeration temperature, all isolates survived in FecalSwab up to 48 h, while in ESwab, only 10 isolates (83.3%) out of 12 survived. At −70°C, all isolates in FecalSwab were recovered after 3 months of storage, whereas in ESwab, none of the isolates were recovered. At −20°C, neither of the swab devices preserved the viability of stock isolates after 2 weeks of storage, and at room temperature, 7 (58.3%) of the stock isolates were recovered in both transport devices after 48 h. Of the 328 fecal specimens, 44 (13.4%) were positive for one of the common diarrheagenic bacterial species with all transport systems used. Thus, the suitability of the ESwab and FecalSwab devices for culturing fresh stools was at least equal to those of the Amies gel swabs and dry containers. Although the ESwab was shown to be an option for collecting and transporting fecal specimens, the FecalSwab device had clearly better preserving properties under different storage conditions. PMID:24740083

Detection of human papillomavirus DNA in urine. A review of the literature.

PubMed

Vorsters, A; Micalessi, I; Bilcke, J; Ieven, M; Bogers, J; Van Damme, P

2012-05-01

The detection of human papillomavirus (HPV) DNA in urine, a specimen easily obtained by a non-invasive self-sampling method, has been the subject of a considerable number of studies. This review provides an overview of 41 published studies; assesses how different methods and settings may contribute to the sometimes contradictory outcomes; and discusses the potential relevance of using urine samples in vaccine trials, disease surveillance, epidemiological studies, and specific settings of cervical cancer screening. Urine sampling, storage conditions, sample preparation, DNA extraction, and DNA amplification may all have an important impact on HPV DNA detection and the form of viral DNA that is detected. Possible trends in HPV DNA prevalence in urine could be inferred from the presence of risk factors or the diagnosis of cervical lesions. HPV DNA detection in urine is feasible and may become a useful tool but necessitates further improvement and standardization.

Influence of Different Post-Plasma Treatment Storage Conditions on the Shear Bond Strength of Veneering Porcelain to Zirconia

PubMed Central

Lee, Mun-Hwan; Min, Bong Ki; Son, Jun Sik; Kwon, Tae-Yub

2016-01-01

This in vitro study investigated whether different storage conditions of plasma-treated zirconia specimens affect the shear bond strength of veneering porcelain. Zirconia plates were treated with a non-thermal atmospheric argon plasma (200 W, 600 s). Porcelain veneering (2.38 mm in diameter) was performed immediately (P-I) or after 24 h storage in water (P-W) or air (P-A) on the treated surfaces (n = 10). Untreated plates were used as the control. Each group was further divided into two subgroups according to the application of a ceramic liner. All veneered specimens underwent a shear bond strength (SBS) test. In the X-ray photoelectron spectroscopy (XPS) analysis, the oxygen/carbon ratios of the plasma-treated groups increased in comparison with those of the control group. When a liner was not used, the three plasma-treated groups showed significantly higher SBS values than the control group (p < 0.001), although group P-A exhibited a significantly lower value than the other two groups (p < 0.05). The liner application negatively affected bonding in groups P-I and P-W (p < 0.05). When the veneering step was delayed after plasma treatment of zirconia, storage of the specimens in water was effective in maintaining the cleaned surfaces for optimal bonding with the veneering porcelain. PMID:28787841

AMS Radiocarbon Dating of Large Za Baobabs (Adansonia za) of Madagascar

PubMed Central

Patrut, Adrian; Patrut, Roxana T.; Danthu, Pascal; Leong Pock-Tsy, Jean-Michel; Rakosy, Laszlo; Lowy, Daniel A.; von Reden, Karl F.

2016-01-01

The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old. PMID:26760300

AMS Radiocarbon Dating of Large Za Baobabs (Adansonia za) of Madagascar.

PubMed

Patrut, Adrian; Patrut, Roxana T; Danthu, Pascal; Leong Pock-Tsy, Jean-Michel; Rakosy, Laszlo; Lowy, Daniel A; von Reden, Karl F

2016-01-01

The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.

Mechanical properties of haynes alloy 188 after 22,500 hours of exposure to LiF-22CaF2 and vacuum at 1093 K

NASA Astrophysics Data System (ADS)

Whittenberger, J. D.

1994-12-01

As a continuation of a study of a space-based thermal energy storage system centered on a LiF-CaF2 eutectic salt contained by Haynes alloy 188, this Co-base superalloy was subjected to molten salt, its vapor, and vacuum for 22,500 h at 1093 K. Samples from all three exposure conditions were tensile tested between 77 to 1200 K; in addition, vacuum and molten-salt exposed specimens were vacuum creep rupture tested at 1050 K. Comparison of these mechanical properties with those measured for the as-received alloy reveals no evidence for degradation beyond that ascribed to simple thermal aging of Haynes alloy 188. This behavior is identical to the 10,000 h results (Ref 3); hence, Haynes alloy 188 is a suitable containment material for an eutectic LiF-CaF2 thermal energy storage salt.

Prevalence of Pre-Analytical Errors in Clinical Chemistry Diagnostic Labs in Sulaimani City of Iraqi Kurdistan

PubMed Central

2017-01-01

Background Laboratory testing is roughly divided into three phases: a pre-analytical phase, an analytical phase and a post-analytical phase. Most analytical errors have been attributed to the analytical phase. However, recent studies have shown that up to 70% of analytical errors reflect the pre-analytical phase. The pre-analytical phase comprises all processes from the time a laboratory request is made by a physician until the specimen is analyzed at the lab. Generally, the pre-analytical phase includes patient preparation, specimen transportation, specimen collection and storage. In the present study, we report the first comprehensive assessment of the frequency and types of pre-analytical errors at the Sulaimani diagnostic labs in Iraqi Kurdistan. Materials and Methods Over 2 months, 5500 venous blood samples were observed in 10 public diagnostic labs of Sulaimani City. The percentages of rejected samples and types of sample inappropriateness were evaluated. The percentage of each of the following pre-analytical errors were recorded: delay in sample transportation, clotted samples, expired reagents, hemolyzed samples, samples not on ice, incorrect sample identification, insufficient sample, tube broken in centrifuge, request procedure errors, sample mix-ups, communication conflicts, misinterpreted orders, lipemic samples, contaminated samples and missed physician’s request orders. The difference between the relative frequencies of errors observed in the hospitals considered was tested using a proportional Z test. In particular, the survey aimed to discover whether analytical errors were recorded and examine the types of platforms used in the selected diagnostic labs. Results The analysis showed a high prevalence of improper sample handling during the pre-analytical phase. In appropriate samples, the percentage error was as high as 39%. The major reasons for rejection were hemolyzed samples (9%), incorrect sample identification (8%) and clotted samples (6%). Most quality control schemes at Sulaimani hospitals focus only on the analytical phase, and none of the pre-analytical errors were recorded. Interestingly, none of the labs were internationally accredited; therefore, corrective actions are needed at these hospitals to ensure better health outcomes. Internal and External Quality Assessment Schemes (EQAS) for the pre-analytical phase at Sulaimani clinical laboratories should be implemented at public hospitals. Furthermore, lab personnel, particularly phlebotomists, need continuous training on the importance of sample quality to obtain accurate test results. PMID:28107395

Prevalence of Pre-Analytical Errors in Clinical Chemistry Diagnostic Labs in Sulaimani City of Iraqi Kurdistan.

PubMed

Najat, Dereen

2017-01-01

Laboratory testing is roughly divided into three phases: a pre-analytical phase, an analytical phase and a post-analytical phase. Most analytical errors have been attributed to the analytical phase. However, recent studies have shown that up to 70% of analytical errors reflect the pre-analytical phase. The pre-analytical phase comprises all processes from the time a laboratory request is made by a physician until the specimen is analyzed at the lab. Generally, the pre-analytical phase includes patient preparation, specimen transportation, specimen collection and storage. In the present study, we report the first comprehensive assessment of the frequency and types of pre-analytical errors at the Sulaimani diagnostic labs in Iraqi Kurdistan. Over 2 months, 5500 venous blood samples were observed in 10 public diagnostic labs of Sulaimani City. The percentages of rejected samples and types of sample inappropriateness were evaluated. The percentage of each of the following pre-analytical errors were recorded: delay in sample transportation, clotted samples, expired reagents, hemolyzed samples, samples not on ice, incorrect sample identification, insufficient sample, tube broken in centrifuge, request procedure errors, sample mix-ups, communication conflicts, misinterpreted orders, lipemic samples, contaminated samples and missed physician's request orders. The difference between the relative frequencies of errors observed in the hospitals considered was tested using a proportional Z test. In particular, the survey aimed to discover whether analytical errors were recorded and examine the types of platforms used in the selected diagnostic labs. The analysis showed a high prevalence of improper sample handling during the pre-analytical phase. In appropriate samples, the percentage error was as high as 39%. The major reasons for rejection were hemolyzed samples (9%), incorrect sample identification (8%) and clotted samples (6%). Most quality control schemes at Sulaimani hospitals focus only on the analytical phase, and none of the pre-analytical errors were recorded. Interestingly, none of the labs were internationally accredited; therefore, corrective actions are needed at these hospitals to ensure better health outcomes. Internal and External Quality Assessment Schemes (EQAS) for the pre-analytical phase at Sulaimani clinical laboratories should be implemented at public hospitals. Furthermore, lab personnel, particularly phlebotomists, need continuous training on the importance of sample quality to obtain accurate test results.

Color stability comparison of silicone facial prostheses following disinfection.

PubMed

Goiato, Marcelo Coelho; Pesqueira, Aldiéris Alves; dos Santos, Daniela Micheline; Zavanelli, Adriana Cristina; Ribeiro, Paula do Prado

2009-04-01

The purpose of this study was to evaluate the color stability of two silicones for use in facial prostheses, under the influence of chemical disinfection and storage time. Twenty-eight specimens were obtained half made from Silastic MDX 4-4210 silicone and the other half from Silastic 732 RTV silicone. The specimens were divided into four groups: Silastic 732 RTV and MDX 4-4210 with disinfection three times a week with Efferdent and Sliastic 732 RTV and MDX 4-4210 disinfected with neutral soap. Color stability was analyzed by spectrophotometry, immediately and 2 months after making the specimens. After obtaining the results, ANOVA and Tukey test with 1% reliability were used for statistical analysis. Statistical differences between mean color values were observed. Disinfection with Efferdent did not statistically influence the mean color values. The factors of storage time and disinfection statistically influenced color stability; disinfection acts as a bleaching agent in silicone materials.

Self-sealing of thermal fatigue and mechanical damage in fiber-reinforced composite materials

NASA Astrophysics Data System (ADS)

Moll, Jericho L.

Fiber reinforced composite tanks provide a promising method of storage for liquid oxygen and hydrogen for aerospace applications. The inherent thermal fatigue of these vessels leads to the formation of microcracks, which allow gas phase leakage across the tank walls. In this dissertation, self-healing functionality is imparted to a structural composite to effectively seal microcracks induced by both mechanical and thermal loading cycles. Two different microencapsulated healing chemistries are investigated in woven glass fiber/epoxy and uni-weave carbon fiber/epoxy composites. Self-healing of mechanically induced damage was first studied in a room temperature cured plain weave E-glass/epoxy composite with encapsulated dicyclopentadiene (DCPD) monomer and wax protected Grubbs' catalyst healing components. A controlled amount of microcracking was introduced through cyclic indentation of opposing surfaces of the composite. The resulting damage zone was proportional to the indentation load. Healing was assessed through the use of a pressure cell apparatus to detect nitrogen flow through the thickness direction of the damaged composite. Successful healing resulted in a perfect seal, with no measurable gas flow. The effect of DCPD microcapsule size (51 microm and 18 microm) and concentration (0--12.2 wt%) on the self-sealing ability was investigated. Composite specimens with 6.5 wt% 51 microm capsules sealed 67% of the time, compared to 13% for the control panels without healing components. A thermally stable, dual microcapsule healing chemistry comprised of silanol terminated poly(dimethyl siloxane) plus a crosslinking agent and a tin catalyst was employed to allow higher composite processing temperatures. The microcapsules were incorporated into a satin weave E-glass fiber/epoxy composite processed at 120°C to yield a glass transition temperature of 127°C. Self-sealing ability after mechanical damage was assessed for different microcapsule sizees (25 microm and 42 microm) and concentrations (0--11 vol%). Incorporating 9 vol% 42 microm capsules or 11 vol% 25 microm capsules into the composite matrix leads to 100% of the samples sealing. The effect of microcapsule concentration on the short beam strength, storage modulus, and glass transition temperature of the composite specimens was also investigated. The thermally stable tin catalyzed poly(dimethyl siloxane) healing chemistry was then integrated into a [0/90]s uniweave carbon fiber/epoxy composite. Thermal cycling (-196°C to 35°C) of these specimens lead to the formation of microcracks, over time, formed a percolating crack network from one side of the composite to the other, resulting in a gas permeable specimen. Crack damage accumulation and sample permeability was monitored with number of cycles for both self-healing and traditional non-healing composites. Crack accumulation occurred at a similar rate for all sample types tested. A 63% increase in lifetime extension was achieved for the self-healing specimens over traditional non-healing composites.

Effects of long duration exposure to simulated space environment on nonmetallic materials properties

NASA Technical Reports Server (NTRS)

Peacock, C. L., Jr.; Whitaker, A. F.

1983-01-01

Nonmetallic materials specimens from the Viking program were tested in situ invacuo after continuous thermal vacuum exposure from 1971/1972 to the present. Eleven tests were done on appropriate specimens of 30 materials; however, no single material received all the tests. Some specimens also were exposed to 1 or 2.5 MeV electrons at differing fluences before testing. Baseline exposure data is reported for graphite/epoxy specimens that were exposed to vacuum since 1974. These materials were transferred to the thermal vacuum storage facility for future in situ testing and irradiation. Thin G/E specimens were tensile tested after thermal-vacuum cycling exposure. Photomicrographic examinations and SEM analyses were done on the failed specimens.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

PubMed Central

2010-01-01

Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80°C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method. PMID:20673359

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

PubMed Central

Amir, Amnon; Metcalf, Jessica L.; Amato, Katherine R.; Xu, Zhenjiang Zech; Humphrey, Greg

2016-01-01

ABSTRACT Immediate freezing at −20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods—95% ethanol, FTA cards, and the OMNIgene Gut kit—can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive. PMID:27822526

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.

PubMed

Song, Se Jin; Amir, Amnon; Metcalf, Jessica L; Amato, Katherine R; Xu, Zhenjiang Zech; Humphrey, Greg; Knight, Rob

2016-01-01

Immediate freezing at -20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods-95% ethanol, FTA cards, and the OMNIgene Gut kit-can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive.

40 CFR 160.190 - Storage and retrieval of records and data.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Storage and retrieval of records and data. 160.190 Section 160.190 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... soil, water, and plants, and wet specimens of blood, urine, feces, and biological fluids, do not need...

A review of international biobanks and networks: success factors and key benchmarks.

PubMed

Vaught, Jim; Kelly, Andrea; Hewitt, Robert

2009-09-01

Biobanks and biobanking networks are involved in varying degrees in the collection, processing, storage, and dissemination of biological specimens. This review outlines the approaches that 16 of the largest biobanks and biobanking networks in Europe, North America, Australia, and Asia have taken to collecting and distributing human research specimens and managing scientific initiatives while covering operating costs. Many are small operations that exist as either a single or a few freezers in a research laboratory, hospital clinical laboratory, or pathology suite. Larger academic and commercial biobanks operate to support large clinical and epidemiological studies. Operational and business models depend on the medical and research missions of their institutions and home countries. Some national biobanks operate with a centralized physical biobank that accepts samples from multiple locations. Others operate under a "federated" model where each institution maintains its own collections but agrees to list them on a central shared database. Some collections are "project-driven" meaning that specimens are collected and distributed to answer specific research questions. "General" collections are those that exist to establish a reference collection, that is, not to meet particular research goals but to be available to respond to multiple requests for an assortment of research uses. These individual and networked biobanking systems operate under a variety of business models, usually incorporating some form of partial cost recovery, while requiring at least partial public or government funding. Each has a well-defined biospecimen-access policy in place that specifies requirements that must be met-such as ethical clearance and the expertise to perform the proposed experiments-to obtain samples for research. The success of all of these biobanking models depends on a variety of factors including well-defined goals, a solid business plan, and specimen collections that are developed according to strict quality and operational controls.

Collection and storage of urine specimens for measurement of urolithiasis risk factors.

PubMed

Wu, Wenqi; Yang, Dong; Tiselius, Hans-Goran; Ou, Lili; Mai, Zanlin; Chen, Kang; Zhu, Hanliang; Xu, Shaohong; Zhao, Zhijian; Zeng, Guohua

2015-02-01

To evaluate how different methods for storage and preservation of urine samples affected the outcome of analysis of risk factors for stone formation. Spot urine samples were collected from 21 healthy volunteers. Each fresh urine sample was divided into ten 10-mL aliquots: 2 without preservative, 2 with thymol, 2 with toluene, 2 with hydrochloric acid (HCl), and 2 with sodium azide. One sample of each pair was stored at 4 °C and the other at room temperature. The concentrations of calcium, magnesium, sodium, phosphate, urate, oxalate, citrate, and pH in each urine sample were analyzed immediately after collection (0 hour) and after 24 and 48 hours. There were no significant differences in calcium, oxalate, magnesium, phosphate, sodium, urate or pH (without acidification) between samples with different preservation methods (P >.05). Urinary citrate, however, was significantly lower in the urine collected with HCl than when other preservatives were used, both at room temperature and at 4 °C. Urine pH was significantly higher after 48 hours than after 24 hours, whether the samples were stored at room temperature or at 4 °C. Antibacterial preservatives (eg, thymol or toluene) can be recommended as preservatives for 24-hour urine collections. Ideally, the samples should be stored at 4 °C. When HCl is used as a preservative, it seems essential to neutralize the samples before analysis. This is particularly obvious with the chromatographic method used for analysis of citrate that was used in this study. Copyright © 2015 Elsevier Inc. All rights reserved.

An evaluation of benthic macroinvertebrate biomass methodology : Part 1. Laboratory analytical methods.

PubMed

Mason, W T; Lewis, P A; Weber, C I

1983-03-01

Evaluation of analytical methods employed for wet weight (live or preserved samples) of benthic macroinvertebrates reveals that centrifugation at 140 x gravity for one minute yields constant biomass estimates. Less relative centrifugal force increases chance of incomplete removal of body moisture and results in weighing error, while greater force may rupture fragile macroinvertebrates, such as mayflies. Duration of specimen exposure in ethanol, formalin, and formol (formaling-ethanol combinations) causes significant body weight loss with within 48 hr formalin and formol cause less body weight loss than ethanol. However, as all preservatives tested cause body weight loss, preservation time of samples collected for comparative purposes should be treated uniformly. Dry weight estimates of macroinvertebrates are not significantly affected by kind of preservative or duration of exposure. Constant dry weights are attained by oven drying at 103 °C at a minimum of four hours or vacuum oven drying (15 inches of mercury pressure) at 103 °C for a minimum of one hour. Although requiring more time in preparation than oven drying and inalterably changing specimen body shape, freeze drying (10 microns pressure, -55 °C, 24 hr) provides constant dry weights and is advantageous for long term sample storage by minimizing curatorial attention. Constant ash-free dry weights of macroinvertebrate samples are attained by igniting samples at 500-550 °C for a minimum of one hour with slow cooling to room temperature in desiccators before weighing.

Novel application of digital microfluidics for the detection of biotinidase deficiency in newborns.

PubMed

Graham, Carrie; Sista, Ramakrishna S; Kleinert, Jairus; Wu, Ning; Eckhardt, Allen; Bali, Deeksha; Millington, David S; Pamula, Vamsee K

2013-12-01

Newborn screening for biotinidase deficiency can be performed using a fluorometric enzyme assay on dried blood spot specimens. As a pre-requisite to the consolidation of different enzymatic assays onto a single platform, we describe here a novel analytical method for detecting biotinidase deficiency using the same digital microfluidic cartridge that has already been demonstrated to screen for five lysosomal storage diseases (Pompe, Fabry, Gaucher, Hurler and Hunter) in a multiplex format. A novel assay to quantify biotinidase concentration in dried blood spots (DBS) was developed and optimized on the digital microfluidic platform using proficiency testing samples from the Centers for Disease Control and Prevention. The enzymatic assay uses 4-methylumbelliferyl biotin as the fluorogenic substrate. Biotinidase deficiency assays were performed on normal (n=200) and deficient (n=7) newborn DBS specimens. Enzymatic activity analysis of biotinidase deficiency revealed distinct separation between normal and affected DBS specimens using digital microfluidics and these results matched the expected activity. This study has demonstrated performance of biotinidase deficiency assays by measurement of 4-methylumbelliferyl product on a digital microfluidic platform. Due to the inherent ease in multiplexing on such a platform, consolidation of other fluorometric assays onto a single cartridge may be realized. © 2013.

Mayfield v. Dalton.

PubMed

1997-03-27

The U.S. Court of Appeals for the Ninth Circuit vacated a case in which the Department of Defense's compulsory taking of blood and tissue specimens from armed services members was claimed to be an unreasonable search and seizure under the Fourth Amendment. Mayfield and Vlacovsky were on active duty in the U.S. Marines when they challenged the military's order to give up blood and tissue samples for its DNA Registry, a repository for identification of remains of soldiers killed on duty. Mayfield and Vlacovsky also feared the possibility of discrimination from genetic information concerning propensity for disease. Between the decision of the federal district court and oral argument in this case, Mayfield and Vlacovsky had gone off active duty and joined the reserves. The court found the issue to be moot because Mayfield and Vlacovsky were not subject to the DNA collection program except in the remote possibility that they returned to active duty in an emergency situation. Also, between the two cases, the Department of Defense had shortened its specimen storage policy from 75 to 50 years and added the option of destroying the specimens at the donor's request upon separation from the service.

The effect of human blood on the setting and surface micro-hardness of calcium silicate cements.

PubMed

Song, Minju; Yue, Wonyoung; Kim, Soyeon; Kim, Wooksung; Kim, Yaelim; Kim, Jeong-Woong; Kim, Euiseong

2016-11-01

The purpose of the present study was to evaluate the effects of human blood on the setting and microhardness of calcium silicate cements. Three types of silicate-based cements were used: ProRoot MTA (PMTA), OrthoMTA (OMTA), and RetroMTA (RMTA). Mixed cement was placed into polyethylene molds with lengths of 2 and 4 mm. After storage for 4 days under three different storage conditions, i.e., saline, saline after 5 min of human blood, and human blood, the polyethylene molds were removed. With the specimens set, the surface microhardness was measured using a Vickers microhardness tester, crystalline structure was analyzed with X-ray diffraction (XRD), and the surface characteristics were examined with scanning electron microscopy (SEM). All specimens of 4 mm in length were set with all materials, and the blood groups exhibited lower microhardnesses than did the saline groups (p < 0.05). Among the 2-mm specimens that were stored in blood, the numbers of specimens that set were significantly different across the materials (p < 0.001). Regarding the microhardnesses of the RMTA and OMTA groups, there were no significant differences between storage conditions. For the PMTA group, only one specimen that was set in the blood group exhibited reduced microhardness. XRD showed changes of crystalline structure in the PMTA and OMTA blood group, whereas RMTA did not. SEM analysis revealed more rounded and homogeneous structures and demonstrated a clear lack of acicular or needle-like crystals in the PMTA and OMTA blood groups, while RMTA did not reveal substantial differences between the saline- and blood-stored groups. Blood contamination detrimentally affected the surface microhardnesses of all materials; furthermore, among the 2-mm specimens, blood contamination interfered with normal setting. Therefore, RMTA might be a more suitable choice when blood contamination is unavoidable due to limited depth. Clinical relevance RetroMTA might be a more suitable choice in situations in which blood contamination is unavoidable.

Effect of surface modifications on the bond strength of zirconia ceramic with resin cement resin.

PubMed

Hallmann, Lubica; Ulmer, Peter; Lehmann, Frank; Wille, Sebastian; Polonskyi, Oleksander; Johannes, Martina; Köbel, Stefan; Trottenberg, Thomas; Bornholdt, Sven; Haase, Fabian; Kersten, Holger; Kern, Matthias

2016-05-01

Purpose of this in vitro study was to evaluate the effect of surface modifications on the tensile bond strength between zirconia ceramic and resin. Zirconia ceramic surfaces were treated with 150-μm abrasive alumina particles, 150-μm abrasive zirconia particles, argon-ion bombardment, gas plasma, and piranha solution (H2SO4:H2O2=3:1). In addition, slip casting surfaces were examined. Untreated surfaces were used as the control group. Tensile bond strengths (TBS) were measured after water storage for 3 days or 150 days with additional 37,500 thermal cycling for artificial aging. Statistical analyses were performed with 1-way and 3-way ANOVA, followed by comparison of means with the Tukey HSD test. After storage in distilled water for three days at 37 °C, the highest mean tensile bond strengths (TBS) were observed for zirconia ceramic surfaces abraded with 150-μm abrasive alumina particles (TBS(AAP)=37.3 MPa, TBS(CAAP)=40.4 MPa), and 150-μm abrasive zirconia particles (TBS(AZP)=34.8 MPa, TBS(CAZP)=35.8 MPa). Also a high TBS was observed for specimens treated with argon-ion bombardment (TBS(BAI)=37.8 MPa). After 150 days of storage, specimens abraded with 150-μm abrasive alumina particles and 150-μm abrasive zirconia particles revealed high TBS (TBS(AAP)=37.6 MPa, TBS(CAAP)=33.0 MPa, TBS(AZP)=22.1 MPa and TBS(CAZP)=22.8 MPa). A high TBS was observed also for specimens prepared with slip casting (TBS(SC)=30.0 MPa). A decrease of TBS was observed for control specimens (TBS(UNT)=12.5 MPa, TBS(CUNT)=9.0 MPa), specimens treated with argon-ion bombardment (TBS(BAI)=10.3 MPa) and gas plasma (TBS(GP)=11.0 MPa). A decrease of TBS was observed also for specimens treated with piranha solution (TBS(PS)=3.9 MPa, TBS(CPS)=4.1 MPa). A significant difference in TBS after three days storage was observed for specimens treated with different methods (p<0.001). Thermal cycling significantly reduced TBS for all groups (p<0.001) excluding groups: AAP(p>0.05), CAAP(p>0.05) and SC(p>0.05). However, the failure patterns of debonded specimens prepared with 150-μm abrasive zirconia particles were 96.7% cohesive. Treatment of zirconia ceramic surfaces with abrasive zirconia particles is a promising method to increase the tensile bond strength without significant damage of the ceramic surface itself. An alternative promising method is slip casting. Copyright © 2016 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Use of fluorescence and scanning electron microscopy as tools in teaching biology

NASA Astrophysics Data System (ADS)

Ghosh, Nabarun; Silva, Jessica; Vazquez, Aracely; Das, A. B.; Smith, Don W.

2011-06-01

Recent nationwide surveys reveal significant decline in students' interest in Math and Sciences. The objective of this project was to inspire young minds in using various techniques involved in Sciences including Scanning Electron Microscopy. We used Scanning Electron Microscope in demonstrating various types of Biological samples. An SEM Tabletop model in the past decade has revolutionized the use of Scanning Electron Microscopes. Using SEM Tabletop model TM 1000 we studied biological specimens of fungal spores, pollen grains, diatoms, plant fibers, dust mites, insect parts and leaf surfaces. We also used fluorescence microscopy to view, to record and analyze various specimens with an Olympus BX40 microscope equipped with FITC and TRITC fluorescent filters, a mercury lamp source, DP-70 digital camera with Image Pro 6.0 software. Micrographs were captured using bright field microscopy, the fluoresceinisothiocyanate (FITC) filter, and the tetramethylrhodamine (TRITC) filter settings at 40X. A high pressure mercury lamp or UV source was used to excite the storage molecules or proteins which exhibited autofluorescence. We used fluorescent microscopy to confirm the localization of sugar beet viruses in plant organs by viewing the vascular bundles in the thin sections of the leaves and other tissues. We worked with the REU summer students on sample preparation and observation on various samples utilizing the SEM. Critical Point Drying (CPD) and metal coating with the sputter coater was followed before observing some cultured specimen and the samples that were soft in textures with high water content. SEM Top allowed investigating the detailed morphological features that can be used for classroom teaching. Undergraduate and graduate researchers studied biological samples of Arthropods, pollen grains and teeth collected from four species of snakes using SEM. This project inspired the research students to pursue their career in higher studies in science and 45% of the undergraduates participated in this project entered Graduate school.

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider

PubMed Central

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population. PMID:26309219

Effect of bacterial collagenase on resin-dentin bonds degradation.

PubMed

Toledano, Manuel; Osorio, Raquel; Osorio, Estrella; Aguilera, Fátima S; Yamauti, Monica; Pashley, David H; Tay, Franklin

2007-12-01

The objective of this study is to evaluate the effect of a bacterial collagenase on the degradation of resin-dentin bonds. Human dentin surfaces were bonded with: an etch-&-rinse self-priming adhesive (SB), a two-step self-etching primer/adhesive (SEB), and a 1-step self-etching adhesive (OUB). Composite build-ups were constructed. The bonded teeth were stored (24 h, 3 months, 1 year) in distilled water or in a buffered bacterial collagenase solution. Half of the specimens were stored as intact bonded teeth (Indirect Exposure/IE). The other half were sectioned into beams prior to storage (Direct Exposure/DE). After storage the intact teeth were sectioned into beams and all specimens were tested for microtensile bond strengths (MTBS). ANOVA and multiple comparisons tests were performed. Fractographic analysis was performed by scanning electron microscopy. The inclusion of bacterial collagenase in the storing solution did not lower the MTBS values over those seen in specimens stored in water. SB and SEB bonds strength were equal, and were superior to OUB. After 3 months of DE, SB and OUB bonded specimens showed decreases in MTBS; similar reductions required 1 year for SEB/DE. MTBS did not decrease in IE specimens except for OUB. Resin and collagen dissolution were evident in DE groups after storing.

The stability of iso-α-acids and reduced iso-α-acids in stored blood specimens.

PubMed

Rodda, Luke N; Gerostamoulos, Dimitri; Drummer, Olaf H

2014-06-01

The long-term stability of the iso-α-acids, and three structurally similar but chemically altered iso-α-acids (known as 'reduced iso-α-acids' and consisting of the rho-, tetrahydro- and hexahydro-iso-α-acid groups) were investigated in whole blood. Pools of blank blood spiked with the four beer-specific ingredient congener groups at two different concentration levels were stored at 20°C, 4°C and -20°C; and extracted in duplicate in weeks 1, 3, 5 and 8, using a previously published method. A loss of 15% of the initial concentration was considered to indicate possible instability and losses greater than 30% demonstrated significant losses. The individual analytes within the four iso-α-acid groups were also measured to determine which iso-α-acids were subject to greater degradation and were responsible for the overall group instability. All four iso-α-acid groups showed significant losses after 8 weeks of storage under room temperature conditions in particularly the natural iso-α-acid group where major losses were observed (96% and 85% losses for low and high concentrations, respectively). Some degradation in all iso-α-acid groups were seen at 4°C samples predominantly due to the 'n' analogs of the groups showing an increased instability in blood. The -20°C storage conditions resulted in minimal changes in concentrations of all analytes. Higher than frozen storage temperatures can result in substantial changes on the stability of the iso-α-acid type groups in blood. The aim of this study was to highlight the stabilities of the IAA analytes in order to assist in the interpretation of IAA in stored blood specimens. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

NDE to Manage Atmospheric SCC in Canisters for Dry Storage of Spent Fuel: An Assessment

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

Meyer, Ryan M.; Pardini, Allan F.; Cuta, Judith M.

2013-09-01

This report documents efforts to assess representative horizontal (Transuclear NUHOMS®) and vertical (Holtec HI-STORM) storage systems for the implementation of non-destructive examination (NDE) methods or techniques to manage atmospheric stress corrosion cracking (SCC) in canisters for dry storage of used nuclear fuel. The assessment is conducted by assessing accessibility and deployment, environmental compatibility, and applicability of NDE methods. A recommendation of this assessment is to focus on bulk ultrasonic and eddy current techniques for direct canister monitoring of atmospheric SCC. This assessment also highlights canister regions that may be most vulnerable to atmospheric SCC to guide the use of bulkmore » ultrasonic and eddy current examinations. An assessment of accessibility also identifies canister regions that are easiest and more difficult to access through the ventilation paths of the concrete shielding modules. A conceivable sampling strategy for canister inspections is to sample only the easiest to access portions of vulnerable regions. There are aspects to performing an NDE inspection of dry canister storage system (DCSS) canisters for atmospheric SCC that have not been addressed in previous performance studies. These aspects provide the basis for recommendations of future efforts to determine the capability and performance of eddy current and bulk ultrasonic examinations for atmospheric SCC in DCSS canisters. Finally, other important areas of investigation are identified including the development of instrumented surveillance specimens to identify when conditions are conducive for atmospheric SCC, characterization of atmospheric SCC morphology, and an assessment of air flow patterns over canister surfaces and their influence on chloride deposition.« less

Rapid test by liquid chromatography/tandem mass spectrometry to evaluate equine urine reactivity towards 17beta-OH steroids.

PubMed

Fidani, Marco; Casagni, Eleonora; Montana, Marco; Pasello, Emanuela; Pecoraro, Chiara; Gambaro, Veniero

2006-01-01

Bacteria frequently found in equine urine samples may cause degradation of 17beta-OH steroids. A simple liquid chromatography/tandem mass spectrometry (LC/MS/MS) method has been developed to evaluate the microbiological contamination of equine urine as a marker of poor storage conditions. Norethandrolone was used as the internal standard, and the linearity, sensitivity, precision and accuracy of the method were evaluated. 17beta-OH oxidation was demonstrated for testosterone, nandrolone, trenbolone and boldenone, but did not occur in alpha-epimers such as alpha-boldenone and epitestosterone, demonstrating the stereoselectivity of the reaction. A rapid test was performed by spiking one of the four 17beta-OH steroids in samples of diluted equine urine. The steroids were transformed into their respective ketones in the presence of bacterial activity. The test allows direct injection of diluted samples into the LC/MS system, without the need for prior extraction. Results show that the best method of storage is freezing at -18 degrees C. Urine specimens should be analyzed as soon as possible after thawing. This allows bacterial degradation of equine urine to be arrested temporarily, so that the urine can be used for qualitative or quantitative analysis of 17beta-OH steroids.

A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen

PubMed Central

Pilotte, Nils; Baumer, Ben; Grant, Jessica; Asbjornsdottir, Kristjana; Schaer, Fabian; Hu, Yan; Aroian, Raffi; Walson, Judd; Williams, Steven A.

2018-01-01

Background Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. Methodology Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against “no preservative” controls and the “gold standard” of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. Conclusions At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity, inhibitor resistance, preservative cost, shipping requirements, sample infectivity, and labor costs should be considered when deciding upon an appropriate method for the storage of fecal specimens for subsequent PCR analysis. Balancing logistical factors and the need to preserve the target DNA, we believe that under most circumstances 95% ethanol provides the most pragmatic choice for preserving stool samples in the field. PMID:29346412

Glass fibre-reinforced composite laced with chlorhexidine digluconate and yeast adhesion.

PubMed

Waltimo, T; Luo, G; Samaranayake, L P; Vallittu, P K

2004-02-01

The aim of this study was to lace dental glass fibre reinforced composite (FRC) prepreg with chlorhexidine digluconate and to examine the adherence of common oral fungal pathogen Candida albicans to FRC made of the prepreg. Four different test and control material groups each comprising 16 test specimens ((5.0 x 5.0 x 0.8) mm3) each were used as substrates for C. albicans adherence. A porous polymer pre-impregnated woven glass fibre prepreg was laced with solution of chlorhexidine gluconate and it was used with autopolymerized denture base polymer to fabricate FRC test specimens. Control group (Group 1) consisted of FRC test specimens stored in water. In Group 2, the test specimens were stored in 10% chlorhexidine digluconate solution for 24 h. Group 3 consisted of specimens fabricated using such fibre reinforcements which were pre-soaked in 20% chlorhexidine digluconate and dried before preparation with denture base resin, and followed by storage of the specimens in water. Group 4 was similar to Group 3 but instead of water storage the specimens were immersed in 10% chlorhexidine digluconate for 24 h. For the candidal adhesion assay the test and control specimens were incubated in standardized suspensions of four different strains of C. albicans, rinsed and prepared for light-microscopy. The mean number of adherent cells in each group was counted microscopically and analysed statistically. There were significantly (P < 0.05) more adherent C. albicans cells found in Group 1 than in the other three groups which did not differ significantly from each other. The lowest numbers of adherent cells were found in Group 3. Pretreating the porous polymer pre-impregnated glass fibre reinforcement with chlorhexidine digluconate result in reduction in the number of adherent yeast cells on the surface FRC material.

Viscoelastic properties of human and bovine articular cartilage: a comparison of frequency-dependent trends.

PubMed

Temple, Duncan K; Cederlund, Anna A; Lawless, Bernard M; Aspden, Richard M; Espino, Daniel M

2016-10-06

The purpose of this study was to compare the frequency-dependent viscoelastic properties of human and bovine cartilage. Full-depth cartilage specimens were extracted from bovine and human femoral heads. Using dynamic mechanical analysis, the viscoelastic properties of eight bovine and six human specimens were measured over the frequency range 1 Hz to 88 Hz. Significant differences between bovine and human cartilage viscoelastic properties were assessed using a Mann-Whitney test (p < 0.05). Throughout the range of frequencies tested and for both species, the storage modulus was greater than the loss modulus and both were frequency-dependent. The storage and loss moduli of all human and bovine cartilage specimens presented a logarithmic relationship with respect to frequency. The mean human storage modulus ranged from 31.9 MPa to 43.3 MPa, while the mean bovine storage modulus ranged from 54.0 MPa to 80.5 MPa; bovine storage moduli were 1.7 to 1.9 times greater than the human modulus. Similarly, the loss modulus of bovine cartilage was 2.0 to 2.1 times greater than human. The mean human loss modulus ranged from 5.3 MPa to 8.5 MPa while bovine moduli ranged from 10.6 MPa to 18.1 MPa. Frequency-dependent viscoelastic trends of bovine articular cartilage were consistent with those of human articular cartilage; this includes a similar frequency dependency and high-frequency plateau. Bovine cartilage was, however, 'stiffer' than human by a factor of approximately 2. With these provisos, bovine articular cartilage may be a suitable dynamic model for human articular cartilage.

Physicochemical hair conformation of patients with Sanfilippo disease type IIIA.

PubMed

Charan, R K; Nauer, G; Wagner, U; Klabuschnig, A; Lubec, G

1986-01-01

Sanfilippo disease type IIIA is an inborn error of metabolism with a deficiency in the heparan sulfamidase. Besides severe psychomotor retardation hair changes are obligatory. Hair is found to be coarse like a brush. We applied X-ray diffraction and infrared spectroscopy to characterize the conformation of hair samples of Sanfilippo patients. In healthy subjects as well as in the affected hair samples we found the wave numbers of structural relevance 1450, 1500, 1630, 1730, the pair 2337 and 2362, the quadruplet 2850, 2870, 2917, 2930 and 3080 cm-1. Also on X-ray diffraction analysis no differences could be detected. Though morphological-macroscopically and microscopically-changes were described for Sanfilippo hair samples, we could not find any change in supramolecular structure. The physical properties of coarseness of those hair specimen seems to be due to differences in the structural assembly of hair fibres and storage of heparan sulfate.

Monitoring CO2 penetration and storage in the brine-saturated low permeable sandstone by the geophysical exploration technologies

NASA Astrophysics Data System (ADS)

Honda, H.; Mitani, Y.; Kitamura, K.; Ikemi, H.; Imasato, M.

2017-12-01

Carbon dioxide (CO2) capture and storage (CCS) plays a vital role in reducing greenhouse gas emissions. In the northern part of Kyushu region of Japan, complex geological structure (Coalfield) is existed near the CO2 emission source and has 1.06 Gt of CO2 storage capacity. The geological survey shows that these layers are formed by low permeable sandstone. It is necessary to monitor the CO2 behavior and clear the mechanisms of CO2 penetration and storage in the low permeable sandstone. In this study, measurements of complex electrical impedance (Z) and elastic wave velocity (P-wave velocity: Vp) were conducted during the supercritical CO2 injection experiment into the brine-saturated low permeable sandstone. The experiment conditions were as follows; Confining pressure: 20 MPa, Initial pore pressure: 10 MPa, 40 °, CO2 injection rate: 0.01 to 0.5 mL/min. Z was measured in the center of the specimen and Vp were measured at three different heights of the specimen at constant intervals. In addition, we measured the longitudinal and lateral strain at the center of the specimen, the pore pressure and CO2 injection volume (CO2 saturation). During the CO2 injection, the change of Z and Vp were confirmed. In the drainage terms, Vp decreased drastically once CO2 reached the measurement cross section.Vp showed the little change even if the flow rate increased (CO2 saturation increased). On the other hand, before the CO2 front reached, Z decreased with CO2-dissolved brine. After that, Z showed continuously increased as the CO2 saturation increased. From the multi-parameter (Hydraulic and Rock-physics parameters), we revealed the detail CO2 behavior in the specimen. In the brine-saturated low permeable sandstone, the slow penetration of CO2 was observed. However, once CO2 has passed, the penetration of CO2 became easy in even for brine-remainded low permeable sandstone. We conclude low permeable sandstone has not only structural storage capacity but also residual tapping (Capillary trapping) capacity. There is a positive possibility to conduct CCS in the low-quality reservoir (low permeable sandstone).

Impact of Collection and Storage of Lung Tumor Tissue on Whole Genome Expression Profiling

PubMed Central

Freidin, Maxim B.; Bhudia, Neesa; Lim, Eric; Nicholson, Andrew G.; Cookson, William O.; Moffatt, Miriam F.

2012-01-01

Gene expression profiling could assist in revealing biomarkers of lung cancer prognosis and progression. The handling of biological samples may strongly influence global gene expression, a fact that has not been addressed in many studies. We sought to investigate the changes in gene expression that may occur as a result of sample processing time and conditions. Using Illumina Human WG-6 arrays, we quantified gene expression in lung carcinoma samples from six patients obtained at chest opening before and immediately after lung resection with storage in RNAlater [T1a(CO) and T1b(LR)], after receipt of the sample for histopathology, placed in RNAlater [T2a(HP)]; snap frozen [T2b(HP.SF)]; or snap frozen and stored for 1 week [T2c(HP.SFA)], as well as formalin-fixed, paraffin-embedded (FFPE) block samples. Sampling immediately after resection closely represented the tissue obtained in situ, with only 1% of genes differing more than twofold [T1a(CO) versus T1b(LR)]. Delaying tissue harvest for an average of 30 minutes from the operating theater had a significant impact on gene expression, with approximately 25% of genes differing between T1a(CO) and T2a(HP). Many genes previously identified as lung cancer biomarkers were altered during this period. Examination of FFPE specimens showed minimal correlation with fresh samples. This study shows that tissue collection immediately after lung resection with conservation in RNAlater is an optimal strategy for gene expression profiling. PMID:22240448

Arrhenius equation modeling for the shelf life prediction of tomato paste containing a natural preservative.

PubMed

Jafari, Seid Mahdi; Ganje, Mohammad; Dehnad, Danial; Ghanbari, Vahid; Hajitabar, Javad

2017-12-01

The shelf life of tomato paste with microencapsulated olive leaf extract was compared with that of samples containing a commercial preservative by accelerated shelf life testing. Based on previous studies showing that olive leaf extract as a rich source of phenolic compounds can have antimicrobial properties, application of its encapsulated form to improve the storage stability of tomato paste is proposed here. Regarding total soluble solids, the control and the sample containing 1000 µg g -1 sodium benzoate had the lowest (Q 10  = 1.63) and highest (Q 10  = 1.88) sensitivity to temperature changes respectively; also, the microencapsulated sample containing 1000 µg g -1 encapsulated olive leaf extract (Q 10  = 1.83) followed the sample containing 1000 µg g -1 sodium benzoate in terms of the highest kinetic rates. In the case of consistency, the lowest and highest activation energies (E a ) corresponded to samples containing 1000 µg g -1 non-encapsulated olive leaf extract and 1000 µg g -1 microencapsulated olive leaf extract respectively. Interestingly, samples containing microencapsulated olive leaf extract could maintain the original quality of the tomato paste very well, while those with non-encapsulated olive leaf extract rated the worst performance (among all specimens) in terms of maintaining their quality indices for a long time period. Overall, the shelf life equation was able to predict the consistency index of all tomato paste samples during long-time storage with high precision. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Blood gas testing and related measurements: National recommendations on behalf of the Croatian Society of Medical Biochemistry and Laboratory Medicine.

PubMed

Dukić, Lora; Kopčinović, Lara Milevoj; Dorotić, Adrijana; Baršić, Ivana

2016-10-15

Blood gas analysis (BGA) is exposed to risks of errors caused by improper sampling, transport and storage conditions. The Clinical and Laboratory Standards Institute (CLSI) generated documents with recommendations for avoidance of potential errors caused by sample mishandling. Two main documents related to BGA issued by the CLSI are GP43-A4 (former H11-A4) Procedures for the collection of arterial blood specimens; approved standard - fourth edition, and C46-A2 Blood gas and pH analysis and related measurements; approved guideline - second edition. Practices related to processing of blood gas samples are not standardized in the Republic of Croatia. Each institution has its own protocol for ordering, collection and analysis of blood gases. Although many laboratories use state of the art analyzers, still many preanalytical procedures remain unchanged. The objective of the Croatian Society of Medical Biochemistry and Laboratory Medicine (CSMBLM) is to standardize the procedures for BGA based on CLSI recommendations. The Working Group for Blood Gas Testing as part of the Committee for the Scientific Professional Development of the CSMBLM prepared a set of recommended protocols for sampling, transport, storage and processing of blood gas samples based on relevant CLSI documents, relevant literature search and on the results of Croatian survey study on practices and policies in acid-base testing. Recommendations are intended for laboratory professionals and all healthcare workers involved in blood gas processing.

Blood gas testing and related measurements: National recommendations on behalf of the Croatian Society of Medical Biochemistry and Laboratory Medicine

PubMed Central

Dukić, Lora; Kopčinović, Lara Milevoj; Dorotić, Adrijana; Baršić, Ivana

2016-01-01

Blood gas analysis (BGA) is exposed to risks of errors caused by improper sampling, transport and storage conditions. The Clinical and Laboratory Standards Institute (CLSI) generated documents with recommendations for avoidance of potential errors caused by sample mishandling. Two main documents related to BGA issued by the CLSI are GP43-A4 (former H11-A4) Procedures for the collection of arterial blood specimens; approved standard – fourth edition, and C46-A2 Blood gas and pH analysis and related measurements; approved guideline – second edition. Practices related to processing of blood gas samples are not standardized in the Republic of Croatia. Each institution has its own protocol for ordering, collection and analysis of blood gases. Although many laboratories use state of the art analyzers, still many preanalytical procedures remain unchanged. The objective of the Croatian Society of Medical Biochemistry and Laboratory Medicine (CSMBLM) is to standardize the procedures for BGA based on CLSI recommendations. The Working Group for Blood Gas Testing as part of the Committee for the Scientific Professional Development of the CSMBLM prepared a set of recommended protocols for sampling, transport, storage and processing of blood gas samples based on relevant CLSI documents, relevant literature search and on the results of Croatian survey study on practices and policies in acid-base testing. Recommendations are intended for laboratory professionals and all healthcare workers involved in blood gas processing. PMID:27812301

Degradation of Multimode Adhesive System Bond Strength to Artificial Caries-Affected Dentin Due to Water Storage.

PubMed

Follak, A C; Miotti, L L; Lenzi, T L; Rocha, R O; Soares, F Z

The purpose of this study was to evaluate the influence of water storage on bond strength of multimode adhesive systems to artificially induced caries-affected dentin. One hundred twelve sound bovine incisors were randomly assigned to 16 groups (n=7) according to the dentin condition (sound; SND, artificially induced caries-affected dentin; CAD, cariogenic challenge by pH cycling for 14 days); the adhesive system (SU, Scotchbond Universal Adhesive; AB, All-Bond Universal; PB, Prime & Bond Elect; SB, Adper Single Bond 2; and CS, Clearfil SE Bond), and the etching strategy (etch-and-rinse and self-etch). All adhesive systems were applied under manufacturer's instructions to flat dentin surfaces, and a composite block was built up on each dentin surface. After 24 hours of water storage, the specimens were sectioned into stick-shaped specimens (0.8 mm 2 ) and submitted to a microtensile test immediately (24 hours) or after six months of water storage. Bond strength data (MPa) were analyzed using three-way repeated-measures analysis of variance and post hoc Tukey test (α=5%), considering each substrate separately (SND and CAD). The etching strategy did not influence the bond strength of multimode adhesives, irrespective of the dentin condition. Water storage only reduced significantly the bond strength to CAD. The degradation of bond strength due to water storage was more pronounced in CAD, regardless of the etching strategy.

Method for on-line evaluation of materials using prompt gamma ray analysis

DOEpatents

Akers, Douglas W [Idaho Falls, ID

2009-12-08

A method for evaluating a material specimen comprises: Mounting a neutron source and a detector adjacent the material specimen; bombarding the material specimen with neutrons from the neutron source to create prompt gamma rays within the material specimen, some of the prompt gamma rays being emitted from the material specimen, some of the prompt gamma rays resulting in the formation of positrons within the material specimen by pair production; collecting positron annihilation data by detecting with the detector at least one emitted annihilation gamma ray resulting from the annihilation of a positron; storing the positron annihilation data on a data storage system for later retrieval and processing; and continuing to collect and store positron annihilation data, the continued collected and stored positron annihilation data being indicative of an accumulation of lattice damage over time.

Effect of water storage on ultimate tensile strength and mass changes of universal adhesives.

PubMed

Bahrololumi, Nazanin; Beglou, Amirreza; Najafi-Abrandabadi, Ahmad; Sadr, Alireza; Sheikh-Al-Eslamian, Seyedeh-Mahsa; Ghasemi, Amir

2017-01-01

The aim of the present study was to evaluate the influence of water storage on micro tensile strength (µTS) and mass changes (MC) of two universal adhesives. 10 disk-shaped specimens were prepared for each adhesive; Scotchbond Universal (SCU) All-Bond Universal (ABU) and Adper Single Bond 2 (SB2). At the baseline and after 1 day and 28 days of water storage, their mass were measured and compared to estimate water sorption and solubility. For µTS test, 20 dumbbell shaped specimens were also prepared for each adhesive in two subgroups of 1 day and 28 days water storage. MC was significantly lower for SCU and ABU than SB2 ( P < 0.05) at both time intervals. In all three adhesives, the MC was significantly lower at 28 days compared to that at 1 day ( P < 0.05). Similarly, µTS was significantly higher for SCU and ABU than SB2 at both storage intervals ( P < 0.05). After 28 days, µTS increased significantly for universal adhesives ( P < 0.05). MC and µTS of adhesives were both material and time dependent when stored in water; both universal adhesives showed less water sorption and higher values of µTS than the control group. Key words: Absorption, dental adhesives, dentin-bonding agents, solubility, tensile strength.

Vaginal Prostate Specific Antigen (PSA) Is a Useful Biomarker of Semen Exposure Among HIV-Infected Ugandan Women.

PubMed

Woolf-King, Sarah E; Muyindike, Winnie; Hobbs, Marcia M; Kusasira, Adrine; Fatch, Robin; Emenyonu, Nneka; Johnson, Mallory O; Hahn, Judith A

2017-07-01

The practical feasibility of using prostate specific antigen (PSA) as a biomarker of semen exposure was examined among HIV-infected Ugandan women. Vaginal fluids were obtained with self-collected swabs and a qualitative rapid test (ABAcard ® p30) was used to detect PSA. Trained laboratory technicians processed samples on-site and positive PSA tests were compared to self-reported unprotected vaginal sex (UVS) in the last 48 h. A total of 77 women submitted 126 samples for PSA testing at up to three study visits. Of these samples, 31 % (n = 39/126) were PSA positive, and 64 % (n = 25/39) of the positive PSA samples were accompanied by self-report of no UVS at the study visit the PSA was collected. There were no reported difficulties with specimen collection, storage, or processing. These findings provide preliminary data on high levels of misreported UVS among HIV-infected Ugandan women using practically feasible methods for PSA collection and processing.

KRAS detection in colonic tumors by DNA extraction from FTA paper: the molecular touch-prep.

PubMed

Petras, Melissa L; Lefferts, Joel A; Ward, Brian P; Suriawinata, Arief A; Tsongalis, Gregory J

2011-12-01

DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue is usually more degraded and contains more polymerase chain reaction (PCR) inhibitors than DNA isolated from nonfixed tissue. In addition, the tumor size and cellular heterogeneity found in tissue sections can often impact testing for molecular biomarkers. As a potential remedy to this situation, we evaluated the use of Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA for use in a real-time PCR-based KRAS mutation assay. Eleven colon tumor samples were collected by making a cut into the fresh tumor and applying the Whatman FTA paper to the cut surface. Matched FFPE tissue blocks from these tumors were also collected for comparison. KRAS mutation analysis was carried out using the Applied Biosystems 7500 Fast Real-time PCR System using 7 independent custom TaqMan PCR assays. Of the 11 colon tumors sampled, 6 were positive for KRAS mutations in both the Whatman FTA paper preparations and corresponding FFPE samples. Whatman FTA paper cards for collection of colorectal tumor samples before tissue fixation and for isolation of DNA have many advantages including ease of use, intrinsic antimicrobial properties, long storage potential (stability of DNA over time), and a faster turnaround time for results. Extracted DNA should be suitable for most molecular diagnostic assays that use PCR techniques. This novel means of DNA preservation from surgical specimens would benefit from additional study and validation as a dependable and practical technique to preserve specimens for molecular testing.

Long-term in vitro reactivity for HLA antibodies and comparison of detection using serum vs. plasma

PubMed Central

Norris, Philip J.; Lee, Jar-How; Carrick, Danielle M.; Gottschall, Jerome L.; Lebedeva, Mila; de Castro, B.R.; Kleinman, Steven H.; Busch, Michael P.

2010-01-01

BACKGROUND HLA antibodies are a possible cause of transfusion-related acute lung injury (TRALI), and fluorescent bead assays are often used for antibody detection. Serum is the manufacturer’s recommended sample, but plasma may be easier to obtain for studies of HLA antibody prevalence and TRALI case investigations. STUDY DESIGN AND METHODS Specimens were obtained from 44 multiparous females positive for HLA antibodies by lymphocytotoxicity testing at least 13 years prior, and from 1,000 contemporary blood donors. Screening tests were performed using a Luminex-based assay. In addition to comparing results obtained with paired plasma and serum samples, the effects of storage at 4 °C for one week and of multiple freeze-thaw cycles were evaluated. RESULTS Of 42 evaluable subjects with HLA antibodies documented >13 years earlier, only 1 showed loss of detectable antibodies, with 39 (93%) positive in the screening assay for class I and 24 (57%) positive in the screening assay for HLA class II antibodies. In 968 evaluable contemporary donors, 291 screened positive for HLA class I and 206 for HLA class II antibodies using a low assay cut-off. Screening test concordance using paired plasma and serum samples was high, particularly for subjects with higher level antibodies. Refrigeration of samples for one week did not significantly affect assay results, while repeated freeze-thaw cycles caused a decrement in signal level. CONCLUSION Serum and plasma samples gave concordant results in the majority of cases, particularly for specimens with higher-level antibodies. High-level HLA antibodies were present in most individuals for over 13 years. PMID:18980615

Viscoelastic characterization of thin-film polymers exposed to low Earth orbit

NASA Technical Reports Server (NTRS)

Letton, Alan; Farrow, Allan; Strganac, Thomas

1993-01-01

The materials made available through the Long Duration Exposure Facility (LDEF) satellite provide a set of specimens that can be well characterized and have a known exposure history with reference to atomic oxygen and ultraviolet radiation exposure. Mechanical characteristics measured from control samples and exposed samples provide a data base for predicting the behavior of polymers in low earth orbit. Samples of 1.0 mil thick low density polyethylene were exposed to the low earth orbit environment for a period of six years. These materials were not directly exposed to ram atomic oxygen and offer a unique opportunity for measuring the effect of atomic oxygen and UV radiation on mechanical properties with little concern to the effect of erosion. The viscoelastic characteristics of these materials were measured and compared to the viscoelastic characteristics of control samples. To aid in differentiating the effects of changes in crystallinity resulting from thermal cycling, from the effects of changes in chemical structure resulting from atomic oxygen/UV attack to the polymer, a second set of control specimens, annealed to increase crystallinity, were measured as well. The resulting characterization of these materials will offer insight into the impact of atomic oxygen/UV on the mechanical properties of polymeric materials. The viscoelastic properties measured for the control, annealed, and exposed specimens were the storage and loss modulus as a function of frequency and temperature. From these datum is calculated the viscoelastic master curve derived using the principle of time/temperature superposition. Using the master curve, the relaxation modulus is calculated using the method of Ninomiya and Ferry. The viscoelastic master curve and the stress relaxation modulus provide a direct measure of the changes in the chemical or morphological structure. In addition, the effect of these changes on long-term and short-term mechanical properties is known directly. It should be noted that the dependence on directionality for the polymer films was considered since these films were manufactured by a blown-film process.

Stability studies of amphetamine and ephedrine derivatives in urine.

PubMed

Jiménez, C; de la Torre, R; Ventura, M; Segura, J; Ventura, R

2006-10-20

Knowledge of the stability of drugs in biological specimens is a critical consideration for the interpretation of analytical results. Identification of proper storage conditions has been a matter of concern for most toxicology laboratories (both clinical and forensic), and the stability of drugs of abuse has been extensively studied. This concern should be extended to other areas of analytical chemistry like antidoping control. In this work, the stability of ephedrine derivatives (ephedrine, norephedrine, methylephedrine, pseudoephedrine, and norpseudoephedrine), and amphetamine derivatives (amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine (MDA), and 3,4-methylenedioxymethamphetamine (MDMA)) in urine has been studied. Spiked urine samples were prepared for stability testing. Urine samples were quantified by GC/NPD or GC/MS. The homogeneity of each batch of sample was verified before starting the stability study. The stability of analytes was evaluated in sterilized and non-sterilized urine samples at different storage conditions. For long-term stability testing, analyte concentration in urine stored at 4 degrees C and -20 degrees C was determined at different time intervals for 24 months for sterile urine samples, and for 6 months for non-sterile samples. For short-term stability testing, analyte concentration was evaluated in liquid urine stored at 37 degrees C for 7 days. The effect of repeated freezing (at -20 degrees C) and thawing (at room temperature) was also studied in sterile urine for up to three cycles. No significant loss of the analytes under study was observed at any of the investigated conditions. These results show the feasibility of preparing reference materials containing ephedrine and amphetamine derivatives to be used for quality control purposes.

[Study of the reineta protein modifications (Brama australis), put under freezing and storage to -18 degrees C and -30 degrees C].

PubMed

Abugoch, Lilian; Quitral, Vilma; Larraín, M Angélica; Vinagre, Julia; Kriukov, Andrei; Chávez, Gloria

2006-12-01

The objective of the present work was to study functional and thermal properties of reineta (Brama australis) frozen meat, analysed by water retention capacity (WRC), gel forming capacity (GFC), texture, emulsifying capacity and differential scanning calorimetry (DSC). For this study, reineta fillets were obtained and extracted by the same conditions, and cutted, packaged, frozen and stored at -18 degrees C and -30 degrees C for 7 months. The results obtained, showed that there were no signifficant differences in the responses to thermal treatment for all the specimens. For samples frozen at -18 degrees C and -30 degrees C, the protein contents were 23.5 + 0.0 and 25.4 + 1.0%, respectively. The WRC values were 0.45 + 0.1 and 1.59 +/- 0.0 g water/g protein, respectively. The gel forming capacity was only present in the fresh samples, whereas the frozen stored ones only form protein aggregates. The emulsifying capacity was between 960 and 1400 g oil / g protein, and the storage time increased this value. The miosin denaturation temperature (Td) and denaturation enthalpy (?H), obtained by DSC, fluctuated between 39.2 +/- 0.5 to 44.8 +/- 0.8 degrees C and 1.12 +/- 0.3 to 0.52 +/- 0.2 J/g, respectively. The actina values were between 71.0 +/- 0.6 to 75.3 +/- 0.5 degrees C and between 0.5 +/- 0.1 to 0.7 +/- 0.1 J/g. Cooperativity decreased as the storage time increased. This is showing a certain degree of protein displacement. The values found by thermal analyses showed a direct relationship with the functional properties, both decreasing with storage time.

Stress Corrosion Cracking Susceptibility of 304L Substrate and 308L Weld Metal Exposed to a Salt Spray

PubMed Central

Hsu, Chia-Hao; Chen, Tai-Cheng; Huang, Rong-Tan; Tsay, Leu-Wen

2017-01-01

304 stainless steels (SS) were considered as the materials for a dry storage canister. In this study, ER (Electrode Rod) 308L was utilized as the filler metal for the groove and overlay welds of a 304L stainless steel substrate, which was prepared via a gas tungsten arc-welding process in multiple passes. The electron backscatter diffraction (EBSD) map was used to identify the inherent microstructures in distinct specimens. U-bend and weight-loss tests were conducted by testing the 304L substrates and welds in a salt spray containing 5 wt % NaCl at 80 °C to evaluate their susceptibility to stress corrosion cracking (SCC). Generally, the weight loss of the ER 308L deposit was higher than that of the 304L substrate in a salt spray in the same sample-prepared condition. The dissolution of the skeletal structure in the fusion zone (FZ) was responsible for a greater weight loss of the 308L deposit, especially for the cold-rolled and sensitized specimen. Cold rolling was detrimental and sensitization after cold rolling was very harmful to the SCC resistance of the 304L substrate and 308L deposit. Overall, the SCC susceptibility of each specimen was correlated with its weight loss in each group. PMID:28772547

Outbreak of viral hemorrhagic fever caused by dengue virus type 3 in Al-Mukalla, Yemen.

PubMed

Madani, Tariq A; Abuelzein, El-Tayeb M E; Al-Bar, Hussein M S; Azhar, Esam I; Kao, Moujahed; Alshoeb, Haj O; Bamoosa, Alabd R

2013-03-14

Investigations were conducted by the authors to explore an outbreak of viral hemorrhagic fever (VHF) reported in 2010 from Al-Mukalla city, the capital of Hadramout in Yemen. From 15-17 June 2010, the outbreak investigation period, specimens were obtained within 7 days after onset of illness of 18 acutely ill patients hospitalized with VHF and 15 household asymptomatic contacts of 6 acute cases. Additionally, 189 stored sera taken from acutely ill patients with suspected VHF hospitalized in the preceding 12 months were obtained from the Ministry of Health of Yemen. Thus, a total of 222 human specimens were collected; 207 specimens from acute cases and 15 specimens from contacts. All samples were tested with RT-PCR for dengue (DENV), Alkhumra (ALKV), Rift Valley Fever (RVFV), Yellow Fever (YFV), and Chikungunya (CHIKV) viruses. Samples were also tested for DENV IgM, IgG, and NS1-antigen. Medical records of patients were reviewed and demographic, clinical, and laboratory data was collected. Of 207 patients tested, 181 (87.4%) patients were confirmed to have acute dengue with positive dengue NS1-antigen (97 patients, 46.9%) and/or IgM (163 patients, 78.7%). Of the 181 patients with confirmed dengue, 100 (55.2%) patients were IgG-positive. DENV RNA was detected in 2 (1%) patients with acute symptoms; both samples were molecularly typed as DENV type 3. No other VHF viruses were detected. For the 15 contacts tested, RT-PCR tests for the five viruses were negative, one contact was dengue IgM positive, and another one was dengue IgG positive. Of the 181 confirmed dengue patients, 120 (66.3%) patients were males and the median age was 24 years. The most common manifestations included fever (100%), headache (94.5%), backache (93.4%), malaise (88.4%), arthralgia (85.1%), myalgia (82.3%), bone pain (77.9%), and leukopenia (76.2%). Two (1.1%) patients died. DENV-3 was confirmed to be the cause of an outbreak of VHF in Al-Mukalla. It is important to use both IgM and NS1-antigen tests to confirm acute dengue particularly under the adverse field conditions, where proper storage and transportation of specimens are missing, which substantially reduce the sensitivity of the RT-PCR for detecting DENV RNA.

Outbreak of viral hemorrhagic fever caused by dengue virus type 3 in Al-Mukalla, Yemen

PubMed Central

2013-01-01

Background Investigations were conducted by the authors to explore an outbreak of viral hemorrhagic fever (VHF) reported in 2010 from Al-Mukalla city, the capital of Hadramout in Yemen. Methods From 15–17 June 2010, the outbreak investigation period, specimens were obtained within 7 days after onset of illness of 18 acutely ill patients hospitalized with VHF and 15 household asymptomatic contacts of 6 acute cases. Additionally, 189 stored sera taken from acutely ill patients with suspected VHF hospitalized in the preceding 12 months were obtained from the Ministry of Health of Yemen. Thus, a total of 222 human specimens were collected; 207 specimens from acute cases and 15 specimens from contacts. All samples were tested with RT-PCR for dengue (DENV), Alkhumra (ALKV), Rift Valley Fever (RVFV), Yellow Fever (YFV), and Chikungunya (CHIKV) viruses. Samples were also tested for DENV IgM, IgG, and NS1-antigen. Medical records of patients were reviewed and demographic, clinical, and laboratory data was collected. Results Of 207 patients tested, 181 (87.4%) patients were confirmed to have acute dengue with positive dengue NS1-antigen (97 patients, 46.9%) and/or IgM (163 patients, 78.7%). Of the 181 patients with confirmed dengue, 100 (55.2%) patients were IgG-positive. DENV RNA was detected in 2 (1%) patients with acute symptoms; both samples were molecularly typed as DENV type 3. No other VHF viruses were detected. For the 15 contacts tested, RT-PCR tests for the five viruses were negative, one contact was dengue IgM positive, and another one was dengue IgG positive. Of the 181 confirmed dengue patients, 120 (66.3%) patients were males and the median age was 24 years. The most common manifestations included fever (100%), headache (94.5%), backache (93.4%), malaise (88.4%), arthralgia (85.1%), myalgia (82.3%), bone pain (77.9%), and leukopenia (76.2%). Two (1.1%) patients died. Conclusions DENV-3 was confirmed to be the cause of an outbreak of VHF in Al-Mukalla. It is important to use both IgM and NS1-antigen tests to confirm acute dengue particularly under the adverse field conditions, where proper storage and transportation of specimens are missing, which substantially reduce the sensitivity of the RT-PCR for detecting DENV RNA. PMID:23497142

Burkholderia pseudomallei traced to water treatment plant in Australia.

PubMed

Inglis, T J; Garrow, S C; Henderson, M; Clair, A; Sampson, J; O'Reilly, L; Cameron, B

2000-01-01

Burkholderia pseudomallei was isolated from environmental specimens 1 year after an outbreak of acute melioidosis in a remote coastal community in northwestern Australia. B. pseudomallei was isolated from a water storage tank and from spray formed in a pH-raising aerator unit. Pulsed-field gel electrophoresis confirmed the aerator and storage tank isolates were identical to the outbreak strain, WKo97.

Mumps Cases and Outbreaks

MedlinePlus

... Providers Laboratory Testing for Mumps Infection Specimen Collection, Storage, and ... SC, TN, TX, UT, VA, VT, WA, WI, and WV **Preliminary data reported to CDC. Mumps outbreaks are not reportable. * ...

Effect of water storage on the silanization in porcelain repair strength.

PubMed

Berry, T; Barghi, N; Chung, K

1999-06-01

This study examined the long-term water storage affect of silanization on shear bond strength of composite resin to porcelain. One hundred and sixty square-shaped specimens were fabricated and sanded flat sequentially with silicone carbide papers. The specimens were then placed into four groups and 16 subgroups of 10 specimens each randomly. Four commercially available silane systems, two one-mix and two two-mix, were tested in this study. Teflon tubes with an internal diameter of 2.97 mm and 2 mm in height were filled with a dual cure composite resin (Mirage FLC), placed on the silanated surfaces and light-cured for 120 s. Specimens were stored in room temperature water and subjected to shear bond strength testing after 24 h, 1 week, 1 month and 3 month periods of immersion. An Instron Universal testing machine with a crosshead speed of 0.5 mm/min was used for the testing. The mean values of the shear bond strengths ranged from 4.38 MPa (24-h period) to 23.90 MPa (3-month period). ANOVA and Scheffe' tests were used to analyse data with confidence level at 95%. All groups recorded an increase in bond strength after one week as compared with the 24-h period (P<0.05). With the exception of a one-mix system, all systems showed significantly higher bond strength at 3 weeks as compared with the 24-h and 1-week water storage periods. In conclusion, bond strength of composite resin to porcelain resulting from silanization of porcelain increased during the experimental period. The bond strength also varied for different silanes used in this study.

Biospecimen repositories and cytopathology.

PubMed

Krishnamurthy, Savitri

2015-03-01

Biospecimen repositories are important for the advancement of biomedical research. Literature on the potential for biobanking of fine-needle aspiration, gynecologic, and nongynecologic cytology specimens is very limited. The potential for biobanking of these specimens as valuable additional resources to surgically excised tissues appears to be excellent. The cervicovaginal specimens that can be used for biobanking include Papanicolaou-stained monolayer preparations and residual material from liquid-based cytology preparations. Different types of specimen preparations of fine-needle aspiration and nongynecologic specimens, including Papanicolaou-stained and Diff-Quik-stained smears, cell blocks. and dedicated passes/residual material from fine-needle aspiration stored frozen in a variety of solutions, can be used for biobanking. Because of several gaps in knowledge regarding the standard of operative procedures for the procurement, storage, and quality assessment of cytology specimens, further studies as well as national conferences and workshops are needed not only to create awareness but also to facilitate the use of cytopathology specimens for biobanking. © 2014 American Cancer Society.

NERVA irradiation program. GTR 23, volume 1: Combined effects of reactor radiation and cryogenic temperature on NERVA structural materials

NASA Technical Reports Server (NTRS)

Mcdaniel, R. H.; Bradford, E. W.; Lewis, J. H.; Wattier, J. B.

1973-01-01

Specimens fabricated from structural materials that were candidates for certain NERVA applications were irradiated in liquid nitrogen (LN2), liquid hydrogen (LH2), water, and air. The specimens irradiated in LN2 were stored in LN2 and finally tested in LN2, or at some higher temperature in a few instances. The specimens irradiated in LH2 underwent an unplanned warmup while in storage so this portion of the test was lost; some specimens were tested in LN2 but none were tested in LH2. The Ground Test Reactor was the radiation source. The test specimens consisted mainly of tensile and fracture toughness specimens of several different materials, but other types of specimens such as tear, flexure, springs, and lubricant were also irradiated. Materials tested include Hastelloy X, Al, Ni steel, steel, Be, ZrC, Ti-6Al-4V, CuB, and Ti-5Al-2.5Sn.

Dimensional changes of acrylic resin denture bases: conventional versus injection-molding technique.

PubMed

Gharechahi, Jafar; Asadzadeh, Nafiseh; Shahabian, Foad; Gharechahi, Maryam

2014-07-01

Acrylic resin denture bases undergo dimensional changes during polymerization. Injection molding techniques are reported to reduce these changes and thereby improve physical properties of denture bases. The aim of this study was to compare dimensional changes of specimens processed by conventional and injection-molding techniques. SR-Ivocap Triplex Hot resin was used for conventional pressure-packed and SR-Ivocap High Impact was used for injection-molding techniques. After processing, all the specimens were stored in distilled water at room temperature until measured. For dimensional accuracy evaluation, measurements were recorded at 24-hour, 48-hour and 12-day intervals using a digital caliper with an accuracy of 0.01 mm. Statistical analysis was carried out by SPSS (SPSS Inc., Chicago, IL, USA) using t-test and repeated-measures ANOVA. Statistical significance was defined at P<0.05. After each water storage period, the acrylic specimens produced by injection exhibited less dimensional changes compared to those produced by the conventional technique. Curing shrinkage was compensated by water sorption with an increase in water storage time decreasing dimensional changes. Within the limitations of this study, dimensional changes of acrylic resin specimens were influenced by the molding technique used and SR-Ivocap injection procedure exhibited higher dimensional accuracy compared to conventional molding.

[Quality Management and Quality Specifications of Laboratory Tests in Clinical Studies--Challenges in Pre-Analytical Processes in Clinical Laboratories].

PubMed

Ishibashi, Midori

2015-01-01

The cost, speed, and quality are the three important factors recently indicated by the Ministry of Health, Labour and Welfare (MHLW) for the purpose of accelerating clinical studies. Based on this background, the importance of laboratory tests is increasing, especially in the evaluation of clinical study participants' entry and safety, and drug efficacy. To assure the quality of laboratory tests, providing high-quality laboratory tests is mandatory. For providing adequate quality assurance in laboratory tests, quality control in the three fields of pre-analytical, analytical, and post-analytical processes is extremely important. There are, however, no detailed written requirements concerning specimen collection, handling, preparation, storage, and shipping. Most laboratory tests for clinical studies are performed onsite in a local laboratory; however, a part of laboratory tests is done in offsite central laboratories after specimen shipping. As factors affecting laboratory tests, individual and inter-individual variations are well-known. Besides these factors, standardizing the factors of specimen collection, handling, preparation, storage, and shipping, may improve and maintain the high quality of clinical studies in general. Furthermore, the analytical method, units, and reference interval are also important factors. It is concluded that, to overcome the problems derived from pre-analytical processes, it is necessary to standardize specimen handling in a broad sense.

Dimensional Changes of Acrylic Resin Denture Bases: Conventional Versus Injection-Molding Technique

PubMed Central

Gharechahi, Jafar; Asadzadeh, Nafiseh; Shahabian, Foad; Gharechahi, Maryam

2014-01-01

Objective: Acrylic resin denture bases undergo dimensional changes during polymerization. Injection molding techniques are reported to reduce these changes and thereby improve physical properties of denture bases. The aim of this study was to compare dimensional changes of specimens processed by conventional and injection-molding techniques. Materials and Methods: SR-Ivocap Triplex Hot resin was used for conventional pressure-packed and SR-Ivocap High Impact was used for injection-molding techniques. After processing, all the specimens were stored in distilled water at room temperature until measured. For dimensional accuracy evaluation, measurements were recorded at 24-hour, 48-hour and 12-day intervals using a digital caliper with an accuracy of 0.01 mm. Statistical analysis was carried out by SPSS (SPSS Inc., Chicago, IL, USA) using t-test and repeated-measures ANOVA. Statistical significance was defined at P<0.05. Results: After each water storage period, the acrylic specimens produced by injection exhibited less dimensional changes compared to those produced by the conventional technique. Curing shrinkage was compensated by water sorption with an increase in water storage time decreasing dimensional changes. Conclusion: Within the limitations of this study, dimensional changes of acrylic resin specimens were influenced by the molding technique used and SR-Ivocap injection procedure exhibited higher dimensional accuracy compared to conventional molding. PMID:25584050

Proposal of a punch biopsy protocol as a pre-requisite for the establishment of a tissue bank from resected esophageal tumors.

PubMed

Bonavina, Luigi; Laface, Letizia; Picozzi, Stefano; Nencioni, Marco; Siboni, Stefano; Bona, Davide; Sironi, Andrea; Sorba, Francesca; Clemente, Claudio

2010-09-01

With the development of tissue banking, a need for homogeneous methods of collection, processing, and storage of tissue has emerged. We describe the implementation of a biological bank in a high-volume, tertiary care University referral center for esophageal cancer surgery. We also propose an original punch biopsy technique of the surgical specimen. The method proved to be simple, reproducible, and not expensive. Unified standards for specimen collection are necessary to improve results of specimen-based diagnostic testing and research in surgical oncology.

Effect of water storage on ultimate tensile strength and mass changes of universal adhesives

PubMed Central

Bahrololumi, Nazanin; Najafi-Abrandabadi, Ahmad; Sadr, Alireza; Sheikh-Al-Eslamian, Seyedeh-Mahsa; Ghasemi, Amir

2017-01-01

Background The aim of the present study was to evaluate the influence of water storage on micro tensile strength (µTS) and mass changes (MC) of two universal adhesives. Material and Methods 10 disk-shaped specimens were prepared for each adhesive; Scotchbond Universal (SCU) All-Bond Universal (ABU) and Adper Single Bond 2 (SB2). At the baseline and after 1 day and 28 days of water storage, their mass were measured and compared to estimate water sorption and solubility. For µTS test, 20 dumbbell shaped specimens were also prepared for each adhesive in two subgroups of 1 day and 28 days water storage. Results MC was significantly lower for SCU and ABU than SB2 (P < 0.05) at both time intervals. In all three adhesives, the MC was significantly lower at 28 days compared to that at 1 day (P < 0.05). Similarly, µTS was significantly higher for SCU and ABU than SB2 at both storage intervals (P < 0.05). After 28 days, µTS increased significantly for universal adhesives (P < 0.05). Conclusions MC and µTS of adhesives were both material and time dependent when stored in water; both universal adhesives showed less water sorption and higher values of µTS than the control group. Key words:Absorption, dental adhesives, dentin-bonding agents, solubility, tensile strength. PMID:28149468

Room temperature degradation of YBa2Cu3O(7-x) superconductors in varying relative humidity environments

NASA Technical Reports Server (NTRS)

Hooker, M. W.; Wise, S. A.; Carlberg, I. A.; Stephens, R. M.; Simchick, R. T.; Farjami, A.

1993-01-01

An aging study was performed to determine the stability of YBa2Cu3O(7-x) ceramics in humid environments at 20 C. In this study, fired ceramic specimens were exposed to humidity levels ranging from 30.5 to 100 percent for 2-, 4-, and 6-week time intervals. After storage under these conditions, the specimens were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and electrical resistance measurements. At every storage condition evaluated, the fired ceramics were found to interact with H2O present in the surrounding environment, resulting in the decomposition of the YBa2Cu3O(7-x) phase. XRD data showed that BaCO3, CuO, and Y2BaCuO5 were present after aging and that the peak intensities of these impurity phases increased both with increasing humidity level and with increasing time of exposure. Additionally, SEM analyses of the ceramic microstructures after aging revealed the development of needle-like crystallites along the surface of the test specimens after aging. Furthermore, the superconducting transition temperature T(sub c) was found to decrease both with increasing humidity level and with increasing time of exposure. All the specimens aged at 30.5, 66, and 81 percent relative humidity exhibited superconducting transitions above 80 K, although these values were reduced by the exposure to the test conditions. Conversely, the specimens stored in direct contact with water (100 percent relative humidity) exhibited no superconducting transitions.

Burkholderia pseudomallei traced to water treatment plant in Australia.

PubMed Central

Inglis, T. J.; Garrow, S. C.; Henderson, M.; Clair, A.; Sampson, J.; O'Reilly, L.; Cameron, B.

2000-01-01

Burkholderia pseudomallei was isolated from environmental specimens 1 year after an outbreak of acute melioidosis in a remote coastal community in northwestern Australia. B. pseudomallei was isolated from a water storage tank and from spray formed in a pH-raising aerator unit. Pulsed-field gel electrophoresis confirmed the aerator and storage tank isolates were identical to the outbreak strain, WKo97. PMID:10653571

Stability of Zika virus in urine: Specimen processing considerations and implications for the detection of RNA targets in urine.

PubMed

Tan, Susanna K; Sahoo, Malaya K; Milligan, Stephen B; Taylor, Nathaniel; Pinsky, Benjamin A

2017-10-01

Detection of Zika virus (ZIKV) RNA in urine is of increasing interest for the diagnosis of ZIKV infection. Pre-analytical variables can significantly impact the stability of RNA in urine. To determine optimal specimen processing protocols that would maximize detection of ZIKV RNA in urine by real-time, reverse transcriptase PCR, we investigated the effect of temperature, initial ZIKV concentration, use of nucleic acid stabilizers, and time on ZIKV RNA levels. Urine samples from healthy donors were spiked with ZIKV using the Exact Diagnostics ® ZIKV Verification Panel, a commercially available panel composed of heat-inactivated ZIKV, at concentrations of 5.0 log 10 copies/mL (ZIKV-high) and 4.0 log 10 copies/mL (ZIKV-low). Samples were stored at room temperature, 4°C, or -80°C and frozen aliquots were exposed to no stabilizer (urine), Buffer ATL (Qiagen, Germantown, MD), or DNA/RNA Shield (Zymo Research, Irvine, CA). ZIKV RNA levels in urine declined steadily at room temperature, though was not significant by 48h (ZIKV-high, p=0.09; ZIKV-low, p=0.20). ZIKV RNA titers were consistently higher when stored at 4°C, suggesting that storage at 4°C can slow the progression of RNA degradation. Freezing urine samples at -80°C resulted in a significant loss of detectable ZIKV RNA in the ZIKV-low group. ZIKV RNA was detected in 5/6 replicates at 3days, 1/6 replicates at 10days, and 1/3 replicates at 30days, with findings reproducible on repeat testing. Presence of either nucleic acid stabilizer in urine corrected this effect, and resulted in recovery of ZIKV RNA in all replicates. Use of a nucleic acid stabilizer in the ZIKV-high group did not add incremental benefit for the detection or quantitation of ZIKV RNA. ZIKV RNA is prone to degradation in urine with loss of detectable virus even when specimens are frozen at -80°C for 10days. Detection of ZIKV-positive urine samples, particularly those containing low ZIKV titers may be aided with the addition of a nucleic acid stabilizer during urine specimen processing. Copyright © 2017. Published by Elsevier B.V.

Bond durability of universal adhesive to bovine enamel using self-etch mode.

PubMed

Suzuki, Soshi; Takamizawa, Toshiki; Imai, Arisa; Tsujimoto, Akimasa; Sai, Keiichi; Takimoto, Masayuki; Barkmeier, Wayne W; Latta, Mark A; Miyazaki, Masashi

2018-04-01

The purpose of this study was to examine the enamel bond durability of universal adhesives in the self-etch mode under 2-year water storage and thermal cycling conditions. Three commercially available universal adhesives and a gold standard two-step self-etch adhesive were used. Ten specimens of bovine enamel were prepared per test group, and shear bond strength (SBS) was measured to determine the bonding durability after thermal cycling (TC) or long-term water storage (WS). The bonded specimens were divided into three groups: (1) specimens subjected to TC, where the bonded specimens were stored in 37 °C distilled water for 24 h before being subjected to 3000, 10,000, 20,000 or 30,000 TC; (2) specimens stored in 37 °C distilled water for 3 months, 6 months, 1 year or 2 year; and (3) specimens stored in 37 °C distilled water for 24 h, serving as a baseline. The two-step self-etch adhesive showed significantly higher SBS than the universal adhesives tested, regardless of the type of degradation method. All universal adhesives showed no significant enamel SBS reductions in TC and WS, when compared to baseline and the other degradation conditions. Compared to the bond strengths obtained with the two-step self-etch adhesive, significantly lower bond strengths were obtained with universal adhesives. However, the enamel bond durability of universal adhesives was relatively stable under both degradation conditions tested. The present data indicate that the enamel bond durability of universal adhesives in the self-etch mode might be sufficient for clinical use.

Atomic force microscopy and tridimensional topography analysis of human enamel after resinous infiltration and storage in water.

PubMed

Taher, Nadia M

2013-04-01

To evaluate the effect of water storage on surface roughness (Ra) of human enamel after treatment with resin infiltrant and fissure sealant, by utilizing atomic force microscopy (AFM) and microtomography. This study was conducted after registration and ethical approval clarification at the College of Dentistry Research Center, King Saud University, Riyadh, Kingdom of Saudi Arabia between January 2011 and August 2011. Thirty enamel surface specimens were prepared from caries-free human premolar teeth. Specimens were divided into 3 groups: Group I, was the control; Group II, a resin infiltrant (Icon) was applied on the enamel surfaces; and Group III, the teeth were treated with fissure sealant (SealRite). All specimens were stored in distilled water for 6 months and then, subjected to AFM Veeco CP11 1.2 analysis. A few specimens were scanned by skyscan-1072-x-ray microtomography. The Ra mean readings were recorded and statistical analysis was performed with the Statistical Package for Social Sciences Version 16 at the significance level of p<0.05. No significant differences in the mean Ra were recorded among the 3 groups, (Group I = 0.21+/-0.057), (Group II = 0.23+/-0.075), and (Group III = 0.20+/-0.039) at p=0.747. The AFM images of enamel surface show thin and inhomogeneous Icon resin in Group II, meanwhile, the SealRite in Group III showed a homogeneous layer in all specimens. The microtomography supported the findings of the AFM images. The persistence of the SealRite in all specimens revealed its low solubility in water and its protective effect on enamel surface.

Measuring influenza RNA quantity after prolonged storage or multiple freeze/thaw cycles.

PubMed

Granados, Andrea; Petrich, Astrid; McGeer, Allison; Gubbay, Jonathan B

2017-09-01

In this study, we aim to determine what effects prolonged storage and repeated freeze/thaw cycles have on the stability of influenza A(H1N1)pdm09 (influenza A/H1N1)RNA. Cloned influenza A/H1N1 RNA transcripts were serially diluted from 8.0-1.0 log 10 copies/μl. RT-qPCR was used to measure RNA loss in transcripts stored at -80°C, -20°C, 4°C and 25°C for up to 84days or transcripts undergoing a total of 10 freeze/thaw cycles. Viral load was measured in clinical specimens stored at-80°C for three years (n=89 influenza A RNA extracts; n=35 primary specimens) and in 10 clinical specimens from the 2015/2016 influenza season that underwent 7 freeze/thaw cycles. RNA stored at -80°C, -20°C, 4°C and 25°C is stable for up to 56, 56, 21, and 7days respectively or up to 9 freeze/thaw cycles when stored at -80°C. There is no difference in viral load in clinical specimens that have been stored for up to three years at -80°C if they are re-extracted. Similarly, clinical specimens undergoing up to 7 freeze/thaw cycles are stable if they are re-extracted between cycles. Influenza specimens can be stored for up to three years at -80°C or undergo up to 7 freeze/thaw cycles without loss of RNA quantity if re-extracted. Copyright © 2017 Elsevier B.V. All rights reserved.

Do Serum Creatinine Levels Show Clinically Significant Fluctuations on Serial Determinations on the Siemens Advia 1800 Analyzer?

PubMed

Levitan, Daniel; Harper, Aaron E; Sun, Yi; Scarpa Carniello, Jose V; Momeni, Amir; Kagan, Joshua; Alexis, Herol; Eid, Ikram; Harris, Loretta; Marshal, Barbara; Tafani, Edlira; Pincus, Matthew

2017-01-01

The goal of this work was to determine whether there are clinically significant fluctuations in the level of serum creatinine on serial determinations, especially in the borderline range (1.1-1.3 mg/dl), after specimen storage. Sixty-one serum samples were analyzed. They were divided into three categories based on the initial serum creatinine measurement: low (≤1.0 mg/dl), borderline (1.1-1.3 mg/dl), and high (≥1.4 mg/dl). The specimens were stored at 4°C and run on the Siemens Advia 1800 chemistry analyzer on days 1, 3, and 11. Statistical comparisons of the three groups were made using the unpaired t-test, yielding a two-tailed P-value for each group comparison. The P-values ranged from 0.0829 to 0.3892, indicating no statistically significant difference between the standard deviations of each group. Mild-to-moderate fluctuations in precision occur in successive serum creatinine determinations. The overwhelming majority of these fluctuations should not affect clinical decision making. © 2016 Wiley Periodicals, Inc.

Distribution law of temperature changes during methane adsorption and desorption in coal using infrared thermography technology

NASA Astrophysics Data System (ADS)

Zhao, Dong; Chen, Hao; An, Jiangfei; Zhou, Dong; Feng, Zengchao

2018-05-01

Gas adsorption and desorption is a thermodynamic process that takes place within coal as temperature changes and that is related to methane (CH4) storage. As infrared thermographic technology has been applied in this context to measure surface temperature changes, the aim of this research was to further elucidate the distribution law underlying this process as well as the thermal effects induced by heat adsorption and desorption in coal. Specimens of two different coal ranks were used in this study, and the surface temperature changes seen in the latter were detected. A contour line map was then drawn on the basis of initial results enabling a distribution law of temperature changes for samples. The results show that different regions of coal sample surfaces exhibit different heating rates during the adsorption process, but they all depends on gas storage capacity to a certain extent. It proposes a correlation coefficient that expresses the relationship between temperature change and gas adsorption capacity that could also be used to evaluate the feasibility of coalbed CH4 extraction in the field. And finally, this study is deduced a method to reveal the actual adsorption capacity of coal or CH4 reservoirs in in situ coal seams.

Vintage venoms: proteomic and pharmacological stability of snake venoms stored for up to eight decades.

PubMed

Jesupret, Clémence; Baumann, Kate; Jackson, Timothy N W; Ali, Syed Abid; Yang, Daryl C; Greisman, Laura; Kern, Larissa; Steuten, Jessica; Jouiaei, Mahdokht; Casewell, Nicholas R; Undheim, Eivind A B; Koludarov, Ivan; Debono, Jordan; Low, Dolyce H W; Rossi, Sarah; Panagides, Nadya; Winter, Kelly; Ignjatovic, Vera; Summerhayes, Robyn; Jones, Alun; Nouwens, Amanda; Dunstan, Nathan; Hodgson, Wayne C; Winkel, Kenneth D; Monagle, Paul; Fry, Bryan Grieg

2014-06-13

For over a century, venom samples from wild snakes have been collected and stored around the world. However, the quality of storage conditions for "vintage" venoms has rarely been assessed. The goal of this study was to determine whether such historical venom samples are still biochemically and pharmacologically viable for research purposes, or if new sample efforts are needed. In total, 52 samples spanning 5 genera and 13 species with regional variants of some species (e.g., 14 different populations of Notechis scutatus) were analysed by a combined proteomic and pharmacological approach to determine protein structural stability and bioactivity. When venoms were not exposed to air during storage, the proteomic results were virtually indistinguishable from that of fresh venom and bioactivity was equivalent or only slightly reduced. By contrast, a sample of Acanthophis antarcticus venom that was exposed to air (due to a loss of integrity of the rubber stopper) suffered significant degradation as evidenced by the proteomics profile. Interestingly, the neurotoxicity of this sample was nearly the same as fresh venom, indicating that degradation may have occurred in the free N- or C-terminus chains of the proteins, rather than at the tips of loops where the functional residues are located. These results suggest that these and other vintage venom collections may be of continuing value in toxin research. This is particularly important as many snake species worldwide are declining due to habitat destruction or modification. For some venoms (such as N. scutatus from Babel Island, Flinders Island, King Island and St. Francis Island) these were the first analyses ever conducted and these vintage samples may represent the only venom ever collected from these unique island forms of tiger snakes. Such vintage venoms may therefore represent the last remaining stocks of some local populations and thus are precious resources. These venoms also have significant historical value as the Oxyuranus venoms analysed include samples from the first coastal taipan (Oxyuranus scutellatus) collected for antivenom production (the snake that killed the collector Kevin Budden), as well as samples from the first Oxyuranus microlepidotus specimen collected after the species' rediscovery in 1976. These results demonstrate that with proper storage techniques, venom samples can retain structural and pharmacological stability. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of freeze-thawing on magnetic resonance imaging T2* of freshly harvested bovine patellar tendon

PubMed Central

Pownder, Sarah L.; Shah, Parina H.; Potter, Hollis G.

2015-01-01

Background Analysis of fresh specimens in research studies is ideal; however, it is often necessary to freeze samples for evaluation at a later time. Limited evaluation of the effect of freeze-thawing of tendon tissue samples on inherent magnetic resonance imaging (MRI) parameters, such as ultrashort echo time (UTE) T2* values, have been performed to date. Methods This study performed UTE MRI on 14 bovine patellar tendons at harvest and after four consecutive freeze-thaw cycles. Results Results demonstrated a small but significant reduction (12%) in tendon T2* values after the first freeze thaw cycle, but not after successive cycles. Tendons from juvenile animals with open physis had a significant reduction of T2* following a single freeze thaw cycle, P<0.0001. Conclusions The results of this study emphasize the importance of using uniform tendon storage protocols when using UTE MRI in preclinical models. PMID:26029639

Method Optimization for Extracting High-Quality RNA From the Human Pancreas Tissue.

PubMed

Jun, Eunsung; Oh, Juyun; Lee, Song; Jun, Hye-Ryeong; Seo, Eun Hye; Jang, Jin-Young; Kim, Song Cheol

2018-06-01

Nucleic acid sequencing is frequently used to determine the molecular basis of diseases. Therefore, proper storage of biological specimens is essential to inhibit nucleic acid degradation. RNA isolated from the human pancreas is generally of poor quality because of its high concentration of endogenous RNase. In this study, we optimized the method for extracting high quality RNA from paired tumor and normal pancreatic tissues obtained from eight pancreatic cancer patients post-surgery. RNA integrity number (RIN) was checked to evaluate the integrity of RNA, we tried to extract the RNA with an RIN value of 8 or higher that allows for the latest genetic analysis. The effect of several parameters, including the method used for tissue lysis, RNAlater treatment, tissue weight at storage, and the time to storage after surgical resection, on the quantity and quality of RNA extracted was examined. Data showed that the highest quantity of RNA was isolated using a combination of manual and mechanical methods of tissue lysis. Additionally, sectioning the tissues into small pieces (<100 mg) and treating them with RNAlater solution prior to storage increased RNA stability. Following these guidelines, high quality RNA was obtained from 100% (8/8) of tumor tissues and 75% (6/8) of normal tissues. High-quality RNA was still stable under repeated freezing and thawing. The application of these results during sample handling and storage in clinical settings will facilitate the genetic diagnosis of diseases and their subsequent treatment. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols

PubMed Central

Shiwa, Yuh; Hachiya, Tsuyoshi; Furukawa, Ryohei; Ohmomo, Hideki; Ono, Kanako; Kudo, Hisaaki; Hata, Jun; Hozawa, Atsushi; Iwasaki, Motoki; Matsuda, Koichi; Minegishi, Naoko; Satoh, Mamoru; Tanno, Kozo; Yamaji, Taiki; Wakai, Kenji; Hitomi, Jiro; Kiyohara, Yutaka; Kubo, Michiaki; Tanaka, Hideo; Tsugane, Shoichiro; Yamamoto, Masayuki; Sobue, Kenji; Shimizu, Atsushi

2016-01-01

Differences in DNA collection protocols may be a potential confounder in epigenome-wide association studies (EWAS) using a large number of blood specimens from multiple biobanks and/or cohorts. Here we show that pre-analytical procedures involved in DNA collection can induce systematic bias in the DNA methylation profiles of blood cells that can be adjusted by cell-type composition variables. In Experiment 1, whole blood from 16 volunteers was collected to examine the effect of a 24 h storage period at 4°C on DNA methylation profiles as measured using the Infinium HumanMethylation450 BeadChip array. Our statistical analysis showed that the P-value distribution of more than 450,000 CpG sites was similar to the theoretical distribution (in quantile-quantile plot, λ = 1.03) when comparing two control replicates, which was remarkably deviated from the theoretical distribution (λ = 1.50) when comparing control and storage conditions. We then considered cell-type composition as a possible cause of the observed bias in DNA methylation profiles and found that the bias associated with the cold storage condition was largely decreased (λadjusted = 1.14) by taking into account a cell-type composition variable. As such, we compared four respective sample collection protocols used in large-scale Japanese biobanks or cohorts as well as two control replicates. Systematic biases in DNA methylation profiles were observed between control and three of four protocols without adjustment of cell-type composition (λ = 1.12–1.45) and no remarkable biases were seen after adjusting for cell-type composition in all four protocols (λadjusted = 1.00–1.17). These results revealed important implications for comparing DNA methylation profiles between blood specimens from different sources and may lead to discovery of disease-associated DNA methylation markers and the development of DNA methylation profile-based predictive risk models. PMID:26799745

Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols.

PubMed

Shiwa, Yuh; Hachiya, Tsuyoshi; Furukawa, Ryohei; Ohmomo, Hideki; Ono, Kanako; Kudo, Hisaaki; Hata, Jun; Hozawa, Atsushi; Iwasaki, Motoki; Matsuda, Koichi; Minegishi, Naoko; Satoh, Mamoru; Tanno, Kozo; Yamaji, Taiki; Wakai, Kenji; Hitomi, Jiro; Kiyohara, Yutaka; Kubo, Michiaki; Tanaka, Hideo; Tsugane, Shoichiro; Yamamoto, Masayuki; Sobue, Kenji; Shimizu, Atsushi

2016-01-01

Differences in DNA collection protocols may be a potential confounder in epigenome-wide association studies (EWAS) using a large number of blood specimens from multiple biobanks and/or cohorts. Here we show that pre-analytical procedures involved in DNA collection can induce systematic bias in the DNA methylation profiles of blood cells that can be adjusted by cell-type composition variables. In Experiment 1, whole blood from 16 volunteers was collected to examine the effect of a 24 h storage period at 4°C on DNA methylation profiles as measured using the Infinium HumanMethylation450 BeadChip array. Our statistical analysis showed that the P-value distribution of more than 450,000 CpG sites was similar to the theoretical distribution (in quantile-quantile plot, λ = 1.03) when comparing two control replicates, which was remarkably deviated from the theoretical distribution (λ = 1.50) when comparing control and storage conditions. We then considered cell-type composition as a possible cause of the observed bias in DNA methylation profiles and found that the bias associated with the cold storage condition was largely decreased (λ adjusted = 1.14) by taking into account a cell-type composition variable. As such, we compared four respective sample collection protocols used in large-scale Japanese biobanks or cohorts as well as two control replicates. Systematic biases in DNA methylation profiles were observed between control and three of four protocols without adjustment of cell-type composition (λ = 1.12-1.45) and no remarkable biases were seen after adjusting for cell-type composition in all four protocols (λ adjusted = 1.00-1.17). These results revealed important implications for comparing DNA methylation profiles between blood specimens from different sources and may lead to discovery of disease-associated DNA methylation markers and the development of DNA methylation profile-based predictive risk models.

Establishment of a cervical cancer bio-bank for the Chinese population: from project-based sample collection to routine management.

PubMed

Yang, Ru; Li, Xiong; Zhou, Hang; Jia, Yao; Zhou, Jin; Huang, Kecheng; Tang, Fangxu; Hu, Ting; Shen, Jian; Chen, Zhilan; Wang, Shaoshuai; Sun, Haiying; Guo, Lili; Wang, Lin; Wang, Hui; Ma, Ding; Li, Shuang

2015-08-01

There is an increasing need for the establishment of a cervical cancer bio-bank that will facilitate both clinical and basic research. The cervical cancer bio-bank was first established in January 1999 and included two stages. First, a GWAS-based sample collection was conducted with special emphasis on the diagnosis and the retrieval of the corresponding bio-specimens, especially blood samples. Second, clinical data and their corresponding bio-specimens were routinely collected and handled. Notably, these bio-specimens also included samples from Wufeng Tujia Autonomous County, which has the highest incidence of cervical cancer in China. The specimens were collected from patients with cervical cancer and those with cervical intraepithelial neoplasia, while the control samples were collected from normal individuals. With special emphasis on clinical data and blood samples for the GWAS analysis, the collection of other bio-specimens was slow, and the pairing of specimens and clinical data was poor during the first stage. However, in the second stage, the pairing of the clinical data and its corresponding bio-specimens improved. At present, the samples procured and preserved in the bio-bank cover most regions of China and different ethnic groups for both the normal controls and cervical cancer patients of different pathological categories. This bio-bank of cervical cancer specimens from the Chinese population will greatly promote the studies of cervical cancer in China.

Long-term storage and safe retrieval of human papillomavirus DNA using FTA elute cards.

PubMed

Barth, Heidi; Morel, Adrien; Mougin, Christiane; Averous, Gerlinde; Legrain, Michèle; Fender, Muriel; Risch, Simone; Fafi-Kremer, Samira; Velten, Michel; Oudet, Pierre; Baldauf, Jean-Jacques; Stoll-Keller, Françoise

2016-03-01

Biobanking or collection and storage of specimens for future research purposes have become an essential tool in many fields of biomedical research and aims to provide a better understanding of disease mechanisms as well as the identification of disease-specific biomarkers that can navigate in complex diseases. In this study, we assessed the use of Flinders Technology Associates (FTA) cards as a long-term storage device for cervical specimens with suspected human papillomavirus (HPV) infections. HPV detection and genotyping results in liquid-based transport media were compared to HPV results from FTA cards. The overall agreement for the presence of any HPV infection between liquid-based medium and FTA cards stored for 1 year at ambient temperature was 100%. Reproducibility analysis of HPV detection and genotyping from FTA cards demonstrated that FTA cards are a reliable medium to store and preserve viral nucleic acids. Biobanking of cervical cells on FTA cards may provide a key resource for epidemiological and retrospective HPV studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Vaccine storage in the community: a study in central Italy.

PubMed Central

Grasso, M.; Ripabelli, G.; Sammarco, M. L.; Manfredi Selvaggi, T. M.; Quaranta, A.

1999-01-01

Maintaining the vaccine cold chain is an essential part of a successful immunization programme, but in developed countries faulty procedures may occur more commonly than is generally believed. A survey was conducted in a health district in central Italy to assess the methods of vaccine transportation and storage. Of 52 primary vaccination offices inspected, 39 (76.5%) had a refrigerator for vaccine storage but only 17 (33.3%) kept records of received and stored doses. None of the seven main offices selected for monitoring had a maximum and minimum thermometer and none monitored the internal temperature of the refrigerator. Moreover, other faulty procedures, such as the storage of food and laboratory specimens in vaccine refrigerators and the storage of vaccines on refrigerator door shelves, indicated that the knowledge and practice of vaccine storage and handling were often inadequate. PMID:10327715

An outbreak of viral gastroenteritis on a cruise ship.

PubMed

McEvoy, M; Blake, W; Brown, D; Green, J; Cartwright, R

1996-12-06

Three hundred and seventy-eight passengers reported gastroenteritis during four cruises in the western Mediterranean on consecutive weeks of 1995. The rate at which cases were reported each day increased on the fourth cruise. The ship's owner commissioned an epidemiological investigation from the PHLS Communicable Disease Surveillance Centre. Cases reported explosive vomiting and diarrhoea, which lasted from 24 hours to five days, and were suggestive of viral gastroenteritis. No food handlers reported illness, but enquiries suggested that some had been ill and treated themselves. No bacterial pathogens were isolated from faecal specimens provided by cases or from water, food, and environmental samples taken from the galley. Small round structured viruses (SRSV) were identified by reverse transcriptase polymerase chain reaction in two faecal specimens and one specimen of vomit from people who became ill during the fourth cruise. SRSV was also identified in one faecal specimen by electron microscopy. Environmental inspection revealed inappropriate food handling, hygiene, and storage. During one 24 hour period no chlorine was detectable in the water. A case control study conducted on the fourth cruise sought details of exposure to various foodstuffs, unbottled water, and various parts of the ship. No significant associations were found between illness and any exposures. The evidence strongly suggested a continuing outbreak of SRSV infection transmitted from person to person. Some passengers remained on board for a second week and could have transmitted their infection to new arrivals. The ship was cleared and disinfected at the end of the fourth cruise in order to interrupt transmission. Fewer than 10 cases presented in each of the fifth and sixth cruises.

Monitoring mercury in two South African herbaria.

PubMed

Kataeva, Maria; Panichev, Nikolay; van Wyk, Abraham E

2009-01-15

Mercury [Hg] emissions from old plant collections treated with mercuric chloride (HgCl(2)) may present a high health risk for staff working in certain herbaria. The present study evaluated Hg concentrations in ambient air, plant specimens and biological samples from staff working in the Pretoria National Herbarium (PRE) and the H.G.W.J. Schweickerdt Herbarium (PRU), University of Pretoria. Biological samples from a group of 15 people exposed to HgCl(2) in herbaria and a non-exposed control group of five people were studied. Additionally, plant samples from herbarium specimens treated and non-treated with HgCl(2) were analysed. Plant materials treated with HgCl(2) had persistent high concentrations of Hg in the range of 114-432 microg g(-1), whereas untreated materials were in the range of 0.20-0.45 microg g(-1). The HgCl(2)-treated plant specimens induced elevated concentrations of Hg into the herbarium rooms near storage cabinets, where up to 1 microg m(-3) of Hg was measured in the air of both herbaria. However, no significant difference in mean Hg concentrations in hair was found between herbarium workers and members of the control group, 0.46 and 0.64 microg g(-1) respectively (p0.05, Student's t-test). For both groups, Hg concentrations were lower than that indicated by the World Health Organization [WHO] for non-exposed adults, namely 2 microg g(-1). The mean concentration of total Hg in urine from the mercury-exposed herbarium group, 2.28 microg g(-1) creatinine, was significantly higher than in the control group, 1.05 microg g(-1) of creatinine. For both populations, the concentrations of Hg in their urine were below the threshold Hg values set by the WHO, i.e., 5 microg g(-1) creatinine. We concluded that there was no strong response by individual herbarium staff from long-term exposure to Hg concentrations in the range of 0.28-1.1 microg m(-3).

Evaluation of Discoloration Removal by Polishing Resin Composites Submitted to Staining in Different Drink Solutions

PubMed Central

Spina, Denis Roberto Falcão; Grossi, João Ricardo Almeida; Cunali, Rafael Schlögel; Baratto Filho, Flares; da Cunha, Leonardo Fernandes; Gonzaga, Carla Castiglia; Correr, Gisele Maria

2015-01-01

The aim of this study was to evaluate the discoloration effects of water, cola-based soft drink, coffee, and wine on resin composites used in restorative dentistry and the possibility of removing the stain with chair side manual polishing. The A2 shade of three materials was tested. Disc specimens were prepared. A spectrophotometer was used to measure the baseline CIE-Lab color parameters of each material (n=10) 24 hours after sample preparation. Samples were then immersed in a cola-based soft drink, coffee, or wine for 1 hour every day, for 30 days. For the remaining hours, the specimens were stored in distilled water. In the control group, the specimens were immersed in water for the whole period. The color differences (ΔE) were calculated after 7 and 30 days of storage, and after polishing with coarse Sof-Lex discs, and analyzed by two-way ANOVA with repeated measures and Tukey's HSD test (α=0.05). Luna presented higher ΔE values (3.41)a followed by Durafill (2.82)b and Herculite (2.24)c. For the drink solutions, ΔE values were higher for wine (4.40)a followed by coffee (2.59)b and for cola-based soft drink (2.23)c and water (2.13)c which were statistically similar. For time, ΔE values were higher for 30 days (3.97)a and then for 7 days (2.48)b and after polishing (2.04)c. The results indicate that color stability is material dependent. The types of drinks that patients consume also influence the color stability of restorative materials. PMID:27347551

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

PubMed

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

2018-05-05

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

Pooling Cervical Swabs and Testing by Ligase Chain Reaction Are Accurate and Cost-Saving Strategies for Diagnosis of Chlamydia trachomatis

PubMed Central

Kapala, J.; Copes, D.; Sproston, A.; Patel, J.; Jang, D.; Petrich, A.; Mahony, J.; Biers, K.; Chernesky, M.

2000-01-01

Specimen pooling to achieve efficiency when testing urine specimens for Chlamydia trachomatis nucleic acids has been suggested. We pooled endocervical swabs from 1,288 women and also tested individual swabs by ligase chain reaction (LCR). Out of 53 positive specimens, pools of 4 or 8 specimens missed two positives, providing 96.2% accuracy compared to individual test results. Dilution and positive-control spiking experiments showed that negative specimens with inhibitors of LCR in the pool reduced the signal. Conversely, two extra positives, detected only through pooling, were negative by individual testing but became positive after storage, suggesting that fresh positive specimens with labile inhibitors may be positive in a pool because of dilution of inhibitors. For this population of women with a 4% prevalence of C. trachomatis infection, substantial savings in cost of reagents (55 to 63%) and technologist time (50 to 63%) made pooling strategies a desirable alternative to individual testing. PMID:10878029

Preparation And Analysis Of Specimens Of Ablative Materials

NASA Technical Reports Server (NTRS)

Solomon, William C.

1994-01-01

Procedure for chemical analysis of specimens of silicone-based ablative thermal-insulation materials SLA-561 and MA25 involves acid digestion of specimens to prepare them for analysis by inductively-coupled-plasma/atomic-emission spectroscopy (ICP/AES). In comparison with atomic-absorption spectroscopy (AAS), ICP/AES is faster and more accurate than AAS. Results of analyses stored in data base, used to trace variations in concentrations of chemical elements in materials during long-term storage, and used in timely manner in investigations of failures. Acid-digestion portion of procedure applied to other thermal-insulation materials containing room-temperature-vulcanizing silicones and enables instrumental analysis of these materials.

Integrative specimen information service - a campus-wide resource for tissue banking, experimental data annotation, and analysis services.

PubMed

Schadow, Gunther; Dhaval, Rakesh; McDonald, Clement J; Ragg, Susanne

2006-01-01

We present the architecture and approach of an evolving campus-wide information service for tissues with clinical and data annotations to be used and contributed to by clinical researchers across the campus. The services provided include specimen tracking, long term data storage, and computational analysis services. The project is conceived and sustained by collaboration among researchers on the campus as well as participation in standards organizations and national collaboratives.

The Effect of SnCl2/AmF Pretreatment on Short- and Long-Term Bond Strength to Eroded Dentin

PubMed Central

Zumstein, Katrin; Peutzfeldt, Anne; Lussi, Adrian

2018-01-01

This study investigated the effect of SnCl2/AmF pretreatment on short- and long-term bond strength of resin composite to eroded dentin mediated by two self-etch, MDP-containing adhesive systems. 184 dentin specimens were produced from extracted human molars. Half the specimens (n = 92) were artificially eroded, and half were left untreated. For both substrates, half the specimens were pretreated with SnCl2/AmF, and half were left untreated. The specimens were treated with Clearfil SE Bond or Scotchbond Universal prior to application of resin composite. Microtensile bond strength (μTBS) was measured after 24 h or 1 year. Failure mode was detected and EDX was performed. μTBS results were statistically analyzed (α = 0.05). μTBS was significantly influenced by the dentin substrate (eroded < noneroded dentin) and storage time (24 h > 1 year; p < 0.0001) but not by pretreatment with SnCl2/AmF or adhesive system. The predominant failure mode was adhesive failure at the dentin-adhesive interface. The content of Sn was generally below detection limit. Pretreatment with SnCl2/AmF did not influence short- and long-term bond strength to eroded dentin. Bond strength was reduced after storage for one year, was lower to eroded dentin than to noneroded dentin, and was similar for the two adhesive systems.

The effectiveness of BD Vacutainer® Plus Urinalysis Preservative Tubes in preservation of urine for chemical strip analysis and particle counting.

PubMed

Ekşioğlu, Merve Kaymak; Madenci, Özlem Çakır; Yücel, Nihal; Elçi, Abdullah; Turhan, Bülent; Orhan, Gani; Orçun, Asuman

2016-01-01

The aim of this study was to evaluate the stability of urine collected in preservative tubes for chemistry strip analyses and particle counting to determine whether the transport of urine samples with all of their constituents is possible. 275 pathologic urine specimens were included. Each urine sample was evaluated after 4, 8, 12, 24, and 48 hours of storage in BD Vacutainer(®) Plus Urinalysis Preservative (BD UAP) tubes and compared with refrigeration at 4 °C. All analyses were peformed on H-800 and FUS-200 automatic modular urine analyzers (Dirui Industry, Changchun, China). The kappa coefficients (κ), false positive (FP) and false negative (FN) rates were evaluated. κ > 0.8 was accepted as good agreement. Haemoglobin (Hb), leucocyte esterase (LE), and protein (Pro) analyses should be performed within 4 hours, whereas glucose (Glc) was stable until the end of 48 hours in both storage conditions. Nitrite (Nit) was well preserved in BD UAP tubes for 24 hours but was stable only up to 8 hours at 4 °C. Bilirubin (Bil) had very high FN rates even at 4 hours in both conditions. The particle counting showed high FN rates for white blood cells (WBC) and red blood cells (RBC), whereas squamous epithelial cells (EC) were stable up to 8 hours in both conditions. Preanalytical requirements for both urine chemical strip analyses and particle counting in a unique sample were not met in either condition. Thus, the transfer of urine samples for centralization of urinalysis is not yet feasible.

Experimentally Induced Repeated Anhydrobiosis in the Eutardigrade Richtersius coronifer.

PubMed

Czernekova, Michaela; Jönsson, K Ingemar

2016-01-01

Tardigrades represent one of the main animal groups with anhydrobiotic capacity at any stage of their life cycle. The ability of tardigrades to survive repeated cycles of anhydrobiosis has rarely been studied but is of interest to understand the factors constraining anhydrobiotic survival. The main objective of this study was to investigate the patterns of survival of the eutardigrade Richtersius coronifer under repeated cycles of desiccation, and the potential effect of repeated desiccation on size, shape and number of storage cells. We also analyzed potential change in body size, gut content and frequency of mitotic storage cells. Specimens were kept under non-cultured conditions and desiccated under controlled relative humidity. After each desiccation cycle 10 specimens were selected for analysis of morphometric characteristics and mitosis. The study demonstrates that tardigrades may survive up to 6 repeated desiccations, with declining survival rates with increased number of desiccations. We found a significantly higher proportion of animals that were unable to contract properly into a tun stage during the desiccation process at the 5th and 6th desiccations. Also total number of storage cells declined at the 5th and 6th desiccations, while no effect on storage cell size was observed. The frequency of mitotic storage cells tended to decline with higher number of desiccation cycles. Our study shows that the number of consecutive cycles of anhydrobiosis that R. coronifer may undergo is limited, with increased inability for tun formation and energetic constraints as possible causal factors.

Influence of artificial saliva on abrasive wear and microhardness of dental composites filled with nanoparticles.

PubMed

Mayworm, Camila D; Camargo, Sérgio S; Bastian, Fernando L

2008-09-01

The aim of this study is to compare the wear resistance and hardness of two dental nanohybrid composites and to evaluate the influence of artificial saliva storage on those properties. Specimens were made from two commercial nanohybrid dental composites (Esthet-X-Dentsply and Filtek Supreme-3M). Abrasion tests were carried out in a ball-cratering machine (three body abrasion) and microscopic analysis of the wear surfaces was made using optical and scanning electron microscopy; hardness was quantified by Vickers hardness test. Those tests were repeated on specimens stored in artificial saliva. Results show that the wear rate of the studied materials is within 10(-7)mm(3)/Nmm range, one of the composites presenting wear rate twice as large as the other. After storage in artificial saliva, the wear resistance increases for both materials. Microhardness of the composites is around 52 and 64HV, Esthet-X presents higher hardness values than Filtek Supreme. After storage in artificial saliva, the microhardness of both materials decreases. Data were analyzed using ANOVA test, p < or = 0.05. Artificial saliva storage increases the materials' wear resistance, suggesting that in both materials bulk post-cure takes place and saliva absorption occurs only on the surface of the composites. This effect was confirmed by comparing the Vickers hardness before and after artificial saliva treatment and FTIR analyses. Surface microhardness of the composites decreases after storage in artificial saliva whereas bulk microhardness of the materials increases.

Experimentally Induced Repeated Anhydrobiosis in the Eutardigrade Richtersius coronifer

PubMed Central

2016-01-01

Tardigrades represent one of the main animal groups with anhydrobiotic capacity at any stage of their life cycle. The ability of tardigrades to survive repeated cycles of anhydrobiosis has rarely been studied but is of interest to understand the factors constraining anhydrobiotic survival. The main objective of this study was to investigate the patterns of survival of the eutardigrade Richtersius coronifer under repeated cycles of desiccation, and the potential effect of repeated desiccation on size, shape and number of storage cells. We also analyzed potential change in body size, gut content and frequency of mitotic storage cells. Specimens were kept under non-cultured conditions and desiccated under controlled relative humidity. After each desiccation cycle 10 specimens were selected for analysis of morphometric characteristics and mitosis. The study demonstrates that tardigrades may survive up to 6 repeated desiccations, with declining survival rates with increased number of desiccations. We found a significantly higher proportion of animals that were unable to contract properly into a tun stage during the desiccation process at the 5th and 6th desiccations. Also total number of storage cells declined at the 5th and 6th desiccations, while no effect on storage cell size was observed. The frequency of mitotic storage cells tended to decline with higher number of desiccation cycles. Our study shows that the number of consecutive cycles of anhydrobiosis that R. coronifer may undergo is limited, with increased inability for tun formation and energetic constraints as possible causal factors. PMID:27828978

Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture.

PubMed

Iroh Tam, Pui-Ying; Hernandez-Alvarado, Nelmary; Schleiss, Mark R; Hassan-Hanga, Fatimah; Onuchukwu, Chuma; Umoru, Dominic; Obaro, Stephen K

2016-01-01

Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS) is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR) assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture. Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples. A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%). One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4-90.1%) and 62.5% (95% CI 24.5-91.5%), respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%). Among these, six were positive for a non-S. pneumoniae pathogen on culture. Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite growth of a non-S. pneumoniae pathogen on culture. A precise definition of what constitutes a positive result is required to avoid falsely over-identifying specimens.

Bond strength to dentin with artificial carious lesions: influence of caries detecting dye.

PubMed

Palma, R G; Turbino, M L; Matson, E; Powers, J M

1998-06-01

To evaluate the influence of dyes for caries detection on tensile bond strength of adhesive materials to artificial carious dentin. Buccal and lingual enamel of human molars were removed leaving intact dentin surfaces. The entire surface of each specimen was covered with nail varnish, keeping a window area of 4 x 4 mm. Artificial carious lesions were induced with acidified gel. Three dyes (0.5% basic fuchsin; Caries Finder and Cari-D-Tect) were used according to manufacturers' recommendations. Specimens were etched with 35% phosphoric acid for 20 s, washed and dried, leaving a wet dentin surface. The adhesive system (Prime & Bond 2.0) was applied in two layers and light-cured. Restorative materials (TPH Spectrum, Dyract, Advance) were bonded using a 3-mm diameter inverted-cone mold. Control groups were made without dye. Eight samples were tested for each group. After 24 hrs of storage in distilled water, the samples were debonded using a testing machine at 0.5 mm/min crosshead speed. ANOVA and Tukey-Kramer test showed that TPH Spectrum (0.73 MPa) and Dyract (0.74 MPa) had similar bond strengths, and both were higher than Advance (0.0 MPa), which was statistically different (P < 0.01). The use of the dyes did not cause any changes in tensile bond strength for any tested materials.

Texture of Frozen Food

NASA Astrophysics Data System (ADS)

Wani, Kohmei

Quantitative determination of textural quality of frozen food due to freezing and storage conditions is complicated,since the texture is consisted of multi-dimensiona1 factors. The author reviewed the importance of texture in food quality and the factors which is proposed by a priori estimation. New classification of expression words of textural properties by subjective evaluation and an application of four elements mechanical model for analysis of physical characteristics was studied on frozen meat patties. Combination of freezing-thawing condition on the subjective properties and physiochemical characteristics of beef lean meat and hamachi fish (Yellow-tail) meat was studied. Change of the plasticity and the deformability of these samples differed by freezing-thawing rate and cooking procedure. Also optimum freezing-thawing condition was differed from specimens.

Fog interception by Ball moss (Tillandsia recurvata)

NASA Astrophysics Data System (ADS)

Guevara-Escobar, A.; Cervantes-Jiménez, M.; Suzán-Azpiri, H.; González-Sosa, E.; Hernández-Sandoval, L.; Malda-Barrera, G.; Martínez-Díaz, M.

2011-08-01

Interception losses are a major influence in the water yield of vegetated areas. For most storms, rain interception results in less water reaching the ground. However, fog interception can increase the overall water storage capacity of the vegetation and once the storage is exceeded, fog drip is a common hydrological input. Fog interception is disregarded in water budgets of semiarid regions, but for some plant communities, it could be a mechanism offsetting evaporation losses. Tillandsia recurvata is a cosmopolitan epiphyte adapted to arid habitats where fog may be an important water source. Therefore, the interception storage capacity by T. recurvata was measured in controlled conditions and applying simulated rain or fog. Juvenile, vegetative specimens were used to determine the potential upperbound storage capacities. The storage capacity was proportional to dry weight mass. Interception storage capacity (Cmin) was 0.19 and 0.56 mm for rainfall and fog respectively. The coefficients obtained in the laboratory were used together with biomass measurements for T. recurvata in a xeric scrub to calculate the depth of water intercepted by rain. T. recurvata contributed 20 % to the rain interception capacity of their shrub hosts: Acacia farnesiana and Prosopis laevigata and; also potentially intercepted 4.8 % of the annual rainfall. Nocturnal stomatic opening in T. recurvata is not only relevant for CO2 but for water vapor, as suggested by the higher weight change of specimens wetted with fog for 1 h at dark in comparison to those wetted during daylight (543 ± 77 vs. 325 ± 56 mg, p = 0.048). The storage capacity of T. recurvata leaf surfaces could increase the amount of water available for evaporation, but as this species colonise montane forests, the effect could be negative on water recharge, because potential storage capacity is very high, in the laboratory experiments it took up to 12 h at a rate of 0.26 l h-1 to reach saturation conditions when fog was applied.

Method and apparatus for supercooling and solidifying substances

NASA Technical Reports Server (NTRS)

Lacy, L. L.; Robinson, M. B.; Rathz, T. J.; Katz, L.; Nisen, D. B. (Inventor)

1983-01-01

An enclosure provides a containerless environment in which a sample specimen is positioned. The specimen is heated in the containerless environment, and the specimen melt is dropped through the tube in which it cools by radiation. The tube is alternatively backfilled with an inert gas whereby the specimen melt cools by both radiation and convection during its free fall. During the free fall, the sample is in a containerless, low-gravity environment which enhances supercooling in the sample and prevents sedimentation and thermal convection influences. The sample continues to supercool until nucleation occurs which is detected by silicon photovoltaic detectors. The sample solidifies after nucleation and becomes completely solid before entering the detachable catcher. The amount of supercooling of the specimen can be measured by knowing the cooling ratio and determining the time for nucleation to occur.

Urine analysis concerning xenon for doping control purposes.

PubMed

Thevis, Mario; Piper, Thomas; Geyer, Hans; Schaefer, Maximilian S; Schneemann, Julia; Kienbaum, Peter; Schänzer, Wilhelm

2015-01-15

On September 1(st) 2014, a modified Prohibited List as established by the World Anti-Doping Agency (WADA) became effective featuring xenon as a banned substance categorized as hypoxia-inducible factor (HIF) activator. Consequently, the analysis of xenon from commonly provided doping control specimens such as blood and urine is desirable, and first data on the determination of xenon from urine in the context of human sports drug testing, are presented. In accordance to earlier studies utilizing plasma as doping control matrix, urine was enriched to saturation with xenon, sequentially diluted, and the target analyte was detected as supported by the internal standard d6 -cyclohexanone by means of gas chromatography/triple quadrupole mass spectrometry (GC/MS/MS) using headspace injection. Three major xenon isotopes at m/z 128.9, 130.9 and 131.9 were targeted in (pseudo) selected reaction monitoring mode enabling the unambiguous identification of the prohibited substance. Assay characteristics including limit of detection (LOD), intraday/interday precision, and specificity as well as analyte recovery under different storage conditions were determined. Proof-of-concept data were generated by applying the established method to urine samples collected from five patients before, during and after (up to 48 h) xenon-based general anesthesia. Xenon was traceable in enriched human urine samples down to the detection limit of approximately 0.5 nmol/mL. The intraday and interday imprecision values of the method were found below 25%, and specificity was demonstrated by analyzing 20 different blank urine samples that corroborated the fitness-for-purpose of the analytical approach to unequivocally detect xenon at non-physiological concentrations in human urine. The patients' urine specimens returned 'xenon-positive' test results up to 40 h post-anesthesia, indicating the limits of the expected doping control detection window. Since xenon has been considered a prohibited substance according to WADA regulations in September 2014, its analysis from common specimens of routine sports drug testing is desirable. In previous studies, its traceability in whole blood and plasma was shown, and herein a complementary approach utilizing doping control urine samples for the GC/MS/MS analysis of xenon was reported. Copyright © 2014 John Wiley & Sons, Ltd.

Even with rehydration, preservation in ethanol influences the mechanical properties of bone and how bone responds to experimental manipulation.

PubMed

Vesper, Evan O; Hammond, Max A; Allen, Matthew R; Wallace, Joseph M

2017-04-01

Typically, bones are harvested at the time of animal euthanasia and stored until mechanical testing. However, storage methods are not standardized, and differential effects on mechanical properties are possible between methods. The goal of this study was to investigate the effects that two common preservation methods (freezing wrapped in saline-soaked gauze and refrigerating ethanol fixed samples) have on bone mechanical properties in the context of an in vitro ribosylation treatment designed to modify mechanical integrity. It was hypothesized that there would be an interactive effect between ribose treatment and preservation method. Tibiae from twenty five 11week old female C57BL/6 mice were separated into 2 preservation groups. Micro-CT scans of contralateral pairs assessed differences in geometry prior to storage. After 7weeks of storage, bones in each pair of tibiae were soaked in a solution containing either 0M or 0.6M ribose for 1week prior to 4 point bending tests. There were no differences in any cortical geometric parameters between contralateral tibiae. There was a significant main effect of ethanol fixation on displacement to yield (-16.3%), stiffness (+24.5%), strain to yield (-13.9%), and elastic modulus (+18.5%) relative to frozen specimens. There was a significant main effect of ribose treatment for yield force (+13.9%), ultimate force (+9.2%), work to yield (+22.2%), yield stress (+14.1%), and resilience (+21.9%) relative to control-soaked bones. Postyield displacement, total displacement, postyield work, total work, total strain, and toughness were analyzed separately within each preservation method due to significant interactions. For samples stored frozen, all six properties were lower in the ribose-soaked group (49%-68%) while no significant effects of ribose were observed in ethanol fixed bones. Storage in ethanol likely caused changes to the collagen matrix which prevented or masked the embrittling effects of ribosylation that were seen in samples stored frozen wrapped in saline-soaked gauze. These data illustrate the clear importance of maintaining hydration if the eventual goal is to use bones for mechanical assessments and further show that storage in ethanol can alter potential to detect effects of experimental manipulation (in this case ribosylation). Copyright © 2017 Elsevier Inc. All rights reserved.

Methodological considerations for implementation of lymphocyte subset analysis in a clinical reference laboratory.

PubMed

Muirhead, K A; Wallace, P K; Schmitt, T C; Frescatore, R L; Franco, J A; Horan, P K

1986-01-01

As the diagnostic utility of lymphocyte subset analysis has been recognized in the clinical research laboratory, a wide variety of reagents and cell preparation, staining and analysis methods have also been described. Methods that are perfectly suitable for analysis of smaller sample numbers in the biological or clinical research setting are not always appropriate and/or applicable in the setting of a high volume clinical reference laboratory. We describe here some of the specific considerations involved in choosing a method for flow cytometric analysis which minimizes sample preparation and data analysis time while maximizing sample stability, viability, and reproducibility. Monoclonal T- and B-cell reagents from three manufacturers were found to give equivalent results for a reference population of healthy individuals. This was true whether direct or indirect immunofluorescence staining was used and whether cells were prepared by Ficoll-Hypaque fractionation (FH) or by lysis of whole blood. When B cells were enumerated using a polyclonal anti-immunoglobulin reagent, less cytophilic immunoglobulin staining was present after lysis than after FH preparation. However, both preparation methods required additional incubation at 37 degrees C to obtain results concordant with monoclonal B-cell reagents. Standard reagents were chosen on the basis of maximum positive/negative separation and the availability of appropriate negative controls. The effects of collection medium and storage conditions on sample stability and reproducibility of subset analysis were also assessed. Specimens collected in heparin and stored at room temperature in buffered medium gave reproducible results for 3 days after specimen collection, using either FH or lysis as the preparation method. General strategies for instrument optimization, quality control, and biohazard containment are also discussed.

46 CFR 164.009-15 - Test procedure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... material, is less than 47 mm, the specimens prepared consist of layers of the sample. (3) If the sample is a composite material and has a height that is not 50 ±3mm, the layers of the specimen prepared are proportional in thickness to the layers of the sample. (4) The top and bottom faces of each specimen prepared...

Molecular epidemiology biomarkers-Sample collection and processing considerations

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

Holland, Nina T.; Pfleger, Laura; Berger, Eileen

2005-08-07

Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are inmore » place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century.« less

Evaluation of the FTA carrier device for human papillomavirus testing in developing countries.

PubMed

Gonzalez, Paula; Cortes, Bernal; Quint, Wim; Kreimer, Aimée R; Porras, Carolina; Rodríguez, Ana Cecilia; Jimenez, Silvia; Herrero, Rolando; Struijk, Linda; Hildesheim, Allan; Melchers, Willem

2012-12-01

Liquid-based methods for the collection, transportation, and storage of cervical cells are cumbersome and expensive and involve laborious DNA extraction. An FTA cartridge is a solid carrier device, easier to handle and allowing simple DNA elution for human papillomavirus (HPV) testing. HPV-DNA results from cervical specimens collected in PreservCyt medium (Hologic, Inc.) and the indicating FTA elute cartridge were compared in an area where transportation and storage may affect the performance of the test. Cervical cells from 319 young adult women enrolled in the Costa Rica Vaccine Trial were collected by a nurse using a Cervex brush (Roberts), which was placed on the FTA cartridge and subsequently rinsed in 20 ml of PreservCyt medium. Two 0.5-ml PreservCyt aliquots were frozen for HPV-PCR testing; the FTA cartridges were kept at room temperature. HPV-DNA detection and typing was performed using SPF(10) PCR/DEIA (DNA enzyme immunoassay detection of amplimers)/LiPA(25) system. The percent agreement, agreement among positives, and kappas were estimated. Positivity was higher for FTA compared to PreservCyt specimens (54.5% versus 45.8%, P < 0.001). For oncogenic types, the overall agreement was 0.92, the agreement between positives was 0.74, and the kappa was 0.79. For individual HPV types, the overall agreement ranged from 0.97 to 1.00. We did not observe reduced cytology adequacy when specimen collection for cytology was preceded by FTA collection for HPV testing. HPV-DNA detection from FTA cartridges is broadly comparable to detection from PC medium. The higher HPV detection observed for FTA-collected specimens should be explored further. FTA cartridges could provide a simpler and more cost-effective method for cervical cell collection, storage, and transportation for HPV-DNA detection in research settings in developing countries.

Evaluation of the FTA Carrier Device for Human Papillomavirus Testing in Developing Countries

PubMed Central

Cortes, Bernal; Quint, Wim; Kreimer, Aimée R.; Porras, Carolina; Rodríguez, Ana Cecilia; Jimenez, Silvia; Herrero, Rolando; Struijk, Linda; Hildesheim, Allan; Melchers, Willem

2012-01-01

Liquid-based methods for the collection, transportation, and storage of cervical cells are cumbersome and expensive and involve laborious DNA extraction. An FTA cartridge is a solid carrier device, easier to handle and allowing simple DNA elution for human papillomavirus (HPV) testing. HPV-DNA results from cervical specimens collected in PreservCyt medium (Hologic, Inc.) and the indicating FTA elute cartridge were compared in an area where transportation and storage may affect the performance of the test. Cervical cells from 319 young adult women enrolled in the Costa Rica Vaccine Trial were collected by a nurse using a Cervex brush (Roberts), which was placed on the FTA cartridge and subsequently rinsed in 20 ml of PreservCyt medium. Two 0.5-ml PreservCyt aliquots were frozen for HPV-PCR testing; the FTA cartridges were kept at room temperature. HPV-DNA detection and typing was performed using SPF10 PCR/DEIA (DNA enzyme immunoassay detection of amplimers)/LiPA25 system. The percent agreement, agreement among positives, and kappas were estimated. Positivity was higher for FTA compared to PreservCyt specimens (54.5% versus 45.8%, P < 0.001). For oncogenic types, the overall agreement was 0.92, the agreement between positives was 0.74, and the kappa was 0.79. For individual HPV types, the overall agreement ranged from 0.97 to 1.00. We did not observe reduced cytology adequacy when specimen collection for cytology was preceded by FTA collection for HPV testing. HPV-DNA detection from FTA cartridges is broadly comparable to detection from PC medium. The higher HPV detection observed for FTA-collected specimens should be explored further. FTA cartridges could provide a simpler and more cost-effective method for cervical cell collection, storage, and transportation for HPV-DNA detection in research settings in developing countries. PMID:22993174

Intrinsic material property differences in bone tissue from patients suffering low-trauma osteoporotic fractures, compared to matched non-fracturing women.

PubMed

Vennin, S; Desyatova, A; Turner, J A; Watson, P A; Lappe, J M; Recker, R R; Akhter, M P

2017-04-01

Osteoporotic (low-trauma) fractures are a significant public health problem. Over 50% of women over 50yrs. of age will suffer an osteoporotic fracture in their remaining lifetimes. While current therapies reduce skeletal fracture risk by maintaining or increasing bone density, additional information is needed that includes the intrinsic material strength properties of bone tissue to help develop better treatments, since measurements of bone density account for no more than ~50% of fracture risk. The hypothesis tested here is that postmenopausal women who have sustained osteoporotic fractures have reduced bone quality, as indicated with measures of intrinsic material properties compared to those who have not fractured. Transiliac biopsies (N=120) were collected from fracturing (N=60, Cases) and non-fracturing postmenopausal women (N=60, age- and BMD-matched Controls) to measure intrinsic material properties using the nano-indentation technique. Each biopsy specimen was embedded in epoxy resin and then ground, polished and used for the nano-indentation testing. After calibration, multiple indentations were made using quasi-static (hardness, modulus) and dynamic (storage and loss moduli) testing protocols. Multiple indentations allowed the median and variance to be computed for each type of measurement for each specimen. Cases were found to have significantly lower median values for cortical hardness and indentation modulus. In addition, cases showed significantly less within-specimen variability in cortical modulus, cortical hardness, cortical storage modulus and trabecular hardness, and more within-specimen variability in trabecular loss modulus. Multivariate modeling indicated the presence of significant independent mechanical effects of cortical loss modulus, along with variability of cortical storage modulus, cortical loss modulus, and trabecular hardness. These results suggest mechanical heterogeneity of bone tissue may contribute to fracture resistance. Although the magnitudes of differences in the intrinsic properties were not overwhelming, this is the first comprehensive study to investigate, and compare the intrinsic properties of bone tissue in fracturing and non-fracturing postmenopausal women. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of a whitening agent application on enamel bond strength of self-etching primer systems.

PubMed

Miyazaki, Masashi; Sato, Hikaru; Sato, Tomomi; Moore, B Keith; Platt, Jeffrey A

2004-06-01

Though reduction in bond strength after tooth whitening has been reported, little is known about it's effect on enamel bond strength of two-step bonding systems that exclude phosphoric acid etching prior to bonding agent application. The purpose of this study was to determine the effect of whitening procedure using an in-office whitening agent on enamel bond strength of self-etching primer systems. Three self-etching primer systems, Imperva Fluoro Bond, Mac Bond II, Clearfil SE Bond, and a one-bottle adhesive system Single Bond as a control material, were used. Bovine mandibular incisors were mounted in self-curing resin and the facial enamel or dentin surfaces were ground wet on 600-grit SiC paper. An in-office whitening agent, Hi-Lite was applied on the tooth surface according to the manufacturer's instruction. Bonding procedures were done soon after rinsing off the whitening agent or after 24 hours storage in distilled water. Specimens without whitening procedure were prepared as controls. Fifteen specimens per test group were stored in 37 degrees C distilled water for 24 hours, then shear tested at a crosshead speed of 1.0 mm/minute. One-way ANOVA followed by Duncan multiple range test were used for statistical analysis of the results. For the specimens made soon after rinsing off the whitening agent, a significant decrease in enamel bond strength was observed for all the bonding systems used. For the specimens made after 24 hours storage in water, a small decrease in enamel bond strength was observed and no significant differences were found compared to those of controls (without whitening). From the results of this study, enamel bond strengths of the self-etching primer systems might be affected to a lesser degree after rinsing with water followed by 24 hours storage in water.

Spiking of serum specimens with exogenous reporter peptides for mass spectrometry based protease profiling as diagnostic tool.

PubMed

Findeisen, Peter; Peccerella, Teresa; Post, Stefan; Wenz, Frederik; Neumaier, Michael

2008-04-01

Serum is a difficult matrix for the identification of biomarkers by mass spectrometry (MS). This is due to high-abundance proteins and their complex processing by a multitude of endogenous proteases making rigorous standardisation difficult. Here, we have investigated the use of defined exogenous reporter peptides as substrates for disease-specific proteases with respect to improved standardisation and disease classification accuracy. A recombinant N-terminal fragment of the Adenomatous Polyposis Coli (APC) protein was digested with trypsin to yield a peptide mixture for subsequent Reporter Peptide Spiking (RPS) of serum. Different preanalytical handling of serum samples was simulated by storage of serum samples for up to 6 h at ambient temperature, followed by RPS, further incubation under standardised conditions and testing for stability of protease-generated MS profiles. To demonstrate the superior classification accuracy achieved by RPS, a pilot profiling experiment was performed using serum specimens from pancreatic cancer patients (n = 50) and healthy controls (n = 50). After RPS six different peak categories could be defined, two of which (categories C and D) are modulated by endogenous proteases. These latter are relevant for improved classification accuracy as shown by enhanced disease-specific classification from 78% to 87% in unspiked and spiked samples, respectively. Peaks of these categories presented with unchanged signal intensities regardless of preanalytical conditions. The use of RPS generally improved the signal intensities of protease-generated peptide peaks. RPS circumvents preanalytical variabilities and improves classification accuracies. Our approach will be helpful to introduce MS-based proteomic profiling into routine laboratory testing.

Non-destructive trace element microanalysis of as-received cometary nucleus samples using synchrotron x ray fluorescence

NASA Technical Reports Server (NTRS)

Sutton, S. R.

1989-01-01

The Synchrotron X ray Fluorescence (SXRF) microprobe at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, will be an excellent instrument for non-destructive trace element analyses of cometary nucleus samples. Trace element analyses of as-received cometary nucleus material will also be possible with this technique. Bulk analysis of relatively volatile elements will be important in establishing comet formation conditions. However, as demonstrated for meteorites, microanalyses of individual phases in their petrographic context are crucial in defining the histories of particular components in unequilibrated specimens. Perhaps most informative in comparing cometary material with meteorites will be the halogens and trace metals. In-situ, high spatial resolution microanalyses will be essential in establishing host phases for these elements and identifying terrestrial (collection/processing) overprints. The present SXRF microprobe is a simple, yet powerful, instrument in which specimens are excited with filtered, continuum synchrotron radiation from a bending magnet on a 2.5 GeV electron storage ring. A refrigerated cell will be constructed to permit analyses at low temperatures. The cell will consist essentially of an air tight housing with a cold stage. Kapton windows will be used to allow the incident synchrotron beam to enter the cell and fluorescent x rays to exit it. The cell will be either under vacuum or continuous purge by ultrapure helium during analyses. Several other improvements of the NSLS microprobe will be made prior to the cometary nucleus sample return mission that will greatly enhance the sensitivity of the technique.

Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery.

PubMed

Saigusa, Daisuke; Okamura, Yasunobu; Motoike, Ikuko N; Katoh, Yasutake; Kurosawa, Yasuhiro; Saijyo, Reina; Koshiba, Seizo; Yasuda, Jun; Motohashi, Hozumi; Sugawara, Junichi; Tanabe, Osamu; Kinoshita, Kengo; Yamamoto, Masayuki

2016-01-01

Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens' pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases.

Oxytocin Levels in Community-Collected Saliva Samples Transported by Dry Versus Wet Ice.

PubMed

Howland, Lois C; Pickler, Rita H; Sullenbarger, Brent A; Connelly, Cynthia D

2018-01-01

Oxytocin (OT), a neuropeptide produced primarily in the hypothalamus, is associated with both critical physiological and psychological processes, particularly stress and feelings of affiliation. Increasingly, researchers are seeking ways to reliably incorporate OT as an outcome biomarker in clinical research. Previously, OT levels were measured in plasma or urine. Recently, researchers have measured this biomarker in saliva, particularly when conducting research in clinical and community settings. In spite of increased interest in the use of salivary OT in clinical research, procedures for handling, transport, and analysis of specimens vary. It is not known if significant OT protein degradation occurs if samples are initially transported on wet ice before being frozen. The aim of this study is to evaluate the effect of transport media (wet vs. dry ice) on OT levels derived from saliva collected from 12 postpartum women residing in the community. Saliva collected from each participant was divided between two microcentrifuge tubes (MIDSCI, Valley Park, MO), one placed on wet ice and one on dry ice for transport from the participant's home to the laboratory freezer. Time from collection to storage freezer was recorded. Laboratory personnel, blinded to method of transport, batch processed the samples. No significant differences in OT levels were found by transport method. Despite large interperson variations in OT levels, there were negligible intraperson variations. Although further research is required to identify factors (including transport time) related to interperson variation, this study supports the use of wet ice as a means of transporting salivary OT specimens in community-based research.

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

PubMed

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

2017-05-01

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

Cross-sectional examination of the damage zone in impacted specimens of carbon/epoxy and carbon/PEEK composites

NASA Technical Reports Server (NTRS)

Nettles, A. T.; Magold, N. J.

1990-01-01

Drop weight impact testing was utilized to inflict damage on eight-ply bidirectional and unidirectional samples of carbon/epoxy and carbon/PEEK (polyetheretherketone) test specimens with impact energies ranging from 0.80 J to 1.76 J. The impacting tip was of a smaller diameter (4.2-mm) than those used in most previous studies, and the specimens were placed with a diamond wheel wafering saw through the impacted area perpendicular to the outer fibers. Photographs at 12 x magnification were taken of these cross-sections and examined. The results on the bidirectional samples show little damage until 1.13 J, at which point delaminations were seen in the epoxy specimens. The PEEK specimens showed less delamination than the epoxy specimens for a given impact energy level. The unidirectional specimens displayed more damage than the bidirectional samples for a given impact energy, with the PEEK specimens showing much less damage than the epoxy material.

Fatigue Behavior of Porous Ti-6Al-4V Made by Laser-Engineered Net Shaping.

PubMed

Razavi, Seyed Mohammad Javad; Bordonaro, Giancarlo G; Ferro, Paolo; Torgersen, Jan; Berto, Filippo

2018-02-12

The fatigue behavior and fracture mechanisms of additively manufactured Ti-6Al-4V specimens are investigated in this study. Three sets of testing samples were fabricated for the assessment of fatigue life. The first batch of samples was built by using Laser-Engineered Net Shaping (LENS) technology, a Direct Energy Deposition (DED) method. Internal voids and defects were induced in a second batch of samples by changing LENS machine processing parameters. Fatigue performance of these samples is compared to the wrought Ti-6Al-4V samples. The effects of machine-induced porosity are assessed on mechanical properties and results are presented in the form of SN curves for the three sets of samples. Fracture mechanisms are examined by using Scanning Electron Microscopy (SEM) to characterize the morphological characteristics of the failure surface. Different fracture surface morphologies are observed for porous and non-porous specimens due to the combination of head write speed and laser power. Formation of defects such as pores, unmelted regions, and gas entrapments affect the failure mechanisms in porous specimens. Non-porous specimens exhibit fatigue properties comparable with that of the wrought specimens, but porous specimens are found to show a tremendous reduced fatigue strength.

XRD Analysis of Cement Paste Samples Exposed to the Simulated Environment of a Deep Repository - 12239

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

Ferreira, Eduardo G.A.; Marumo, Julio T.; Vicente, Roberto

2012-07-01

Portland cement materials are widely used as engineered barriers in repositories for radioactive waste. The capacity of such barriers to avoid the disposed of radionuclides to entering the biosphere in the long-term depends on the service life of those materials. Thus, the performance assessment of structural materials under a series of environmental conditions prevailing at the environs of repositories is a matter of interest. The durability of cement paste foreseen as backfill in a deep borehole for disposal of disused sealed radioactive sources is investigated in the development of the repository concept. Results are intended to be part of themore » body of evidence in the safety case of the proposed disposal technology. This paper presents the results of X-Ray Diffraction (XRD) Analysis of cement paste exposed to varying temperatures and simulated groundwater after samples received the radiation dose that the cement paste will accumulate until complete decay of the radioactive sources. The XRD analysis of cement paste samples realized in this work allowed observing some differences in the results of cement paste specimens that were submitted to different treatments. The cluster analysis of results was able to group tested samples according to the applied treatments. Mineralogical differences, however, are tenuous and, apart from ettringite, are hardly observed. The absence of ettringite in all the seven specimens that were kept in dry storage at high temperature had hardly occurred by natural variations in the composition of hydrated cement paste because ettringite is observed in all tested except the seven specimens. Therefore this absence is certainly the result of the treatments and could be explained by the decomposition of ettringite. Although the temperature of decomposition is about 110-120 deg. C, it may be initially decomposed to meta-ettringite, an amorphous compound, above 50 deg. C in the absence of water. Influence of irradiation on the mineralogical composition was not observed when the treatment was analyzed individually or when analyzed under the possible synergic effect with other treatments. However, the radiation dose to which specimens were exposed is only a fraction of the accumulated dose in cement paste until complete decay of some sources. Therefore, in the short term, the conditions deemed to prevail in the repository environment may not influence the properties of cement paste at detectable levels. Under the conditions presented in this work, it is not possible to predict the long term evolution of these properties. (authors)« less

Results of a pilot study using self-collected mid-turbinate nasal swabs for detection of influenza virus infection among pregnant women.

PubMed

Thompson, Mark G; Ferber, Jeannette R; Odouli, Roxana; David, Donna; Shifflett, Pat; Meece, Jennifer K; Naleway, Allison L; Bozeman, Sam; Spencer, Sarah M; Fry, Alicia M; Li, De-Kun

2015-05-01

We evaluated the feasibility of asking pregnant women to self-collect and ship respiratory specimens. In a preliminary laboratory study, we compared the RT-PCR cycle threshold (CT) values of influenza A and B viruses incubated at 4 storage temperatures (from 4 to 35°C) for 6 time periods (8, 24, 48, 72, and 168 hours and 30 days), resulting in 24 conditions that were compared to an aliquot tested after standard freezing (-20°C) (baseline condition). In a subsequent pilot study, during January-February, 2014, we delivered respiratory specimen collection kits to 53 pregnant women with a medically attended acute respiratory illness using three delivery methods. CT values were stable after storage at temperatures <27°C for up to 72 hours for influenza A viruses and 48 hours for influenza B viruses. Of 53 women who received kits during the pilot, 89% collected and shipped nasal swabs as requested. However, 30% (14/47) of the women took over 2 days to collect and ship their specimen. The human control gene, ribonuclease P (RNase P), was detected in 100% of nasal swab specimens. However, the mean CT values for RNase P (26.5, 95% confidence interval [CI] = 26.0-27.1) and for the 8 influenza A virus positives in our pilot (32.2, 95% CI = 28.9-35.5) were significantly higher than the CTs observed in our 2010-2012 study using staff-collected nasal pharyngeal swabs (P-values < 0.01). Self-collection of respiratory specimens is a promising research method, but further research is needed to quantify the sensitivity and specificity of the approach. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Field study of dried blood spot specimens for HIV-1 drug resistance genotyping.

PubMed

Parry, C M; Parkin, N; Diallo, K; Mwebaza, S; Batamwita, R; DeVos, J; Bbosa, N; Lyagoba, F; Magambo, B; Jordan, M R; Downing, R; Zhang, G; Kaleebu, P; Yang, C; Bertagnolio, S

2014-08-01

Dried blood spots (DBS) are an alternative specimen type for HIV drug resistance genotyping in resource-limited settings. Data relating to the impact of DBS storage and shipment conditions on genotyping efficiency under field conditions are limited. We compared the genotyping efficiencies and resistance profiles of DBS stored and shipped at different temperatures to those of plasma specimens collected in parallel from patients receiving antiretroviral therapy in Uganda. Plasma and four DBS cards from anti-coagulated venous blood and a fifth card from finger-prick blood were prepared from 103 HIV patients with a median viral load (VL) of 57,062 copies/ml (range, 1,081 to 2,964,191). DBS were stored at ambient temperature for 2 or 4 weeks or frozen at -80 °C and shipped from Uganda to the United States at ambient temperature or frozen on dry ice for genotyping using a broadly sensitive in-house method. Plasma (97.1%) and DBS (98.1%) stored and shipped frozen had similar genotyping efficiencies. DBS stored frozen (97.1%) or at ambient temperature for 2 weeks (93.2%) and shipped at ambient temperature also had similar genotyping efficiencies. Genotyping efficiency was reduced for DBS stored at ambient temperature for 4 weeks (89.3%, P = 0.03) or prepared from finger-prick blood and stored at ambient temperature for 2 weeks (77.7%, P < 0.001) compared to DBS prepared from venous blood and handled similarly. Resistance profiles were similar between plasma and DBS specimens. This report delineates the optimal DBS collection, storage, and shipping conditions and opens a new avenue for cost-saving ambient-temperature DBS specimen shipments for HIV drug resistance (HIVDR) surveillances in resource-limited settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Effects of 6 months of aging in water on hardness and surface roughness of two microhybrid dental composites.

PubMed

de Moraes, Rafael Ratto; Marimon, José Laurindo Machado; Schneider, Luis Felipe; Sinhoreti, Mário Alexandre Coelho; Correr-Sobrinho, Lourenço; Bueno, Márcia

2008-06-01

This study assessed the effect of 6 months of aging in water on surface roughness and surface/subsurface hardness of two microhybrid resin composites. Filtek Z250 and Charisma were tested. Cylindrical specimens were obtained and stored in distilled water for 24 hours or 6 months, at 37 degrees C. For Knoop hardness evaluation, the specimens were transversely wet-flattened, and indentations were made on surface and subsurface layers. Data were submitted to three-way ANOVA and Tukey's test (alpha < or = 0.05). Surface roughness baseline measurements were made at 24 hours and repeated after 6 months of storage. Data were submitted to repeated measures ANOVA and Tukey's test (alpha < or = 0.05). Surface hardness (KHN, kg/mm(2)) means (+/- standard deviation) ranged from 55 +/- 1 to 49 +/- 4 for Z250 and from 50 +/- 2 to 41 +/- 3 for Charisma, at 24 hours and 6 months, respectively. Subsurface means ranged from 58 +/- 2 to 61 +/- 3 for Z250 and from 50 +/- 1 to 54 +/- 2 for Charisma, at 24 hours and 6 months. For both composites, the aged specimens presented significantly softer surfaces (p < 0.01). For the subsurface hardness, alteration after storage was detected only for Charisma, which presented a significant rise in hardness (p < 0.01). Z250 presented significantly harder surface and subsurface layers in comparison with Charisma. Surface roughness (Ra, mum) means ranged from 0.07 +/- 0.00 to 0.07 +/- 0.01 for Z250 and from 0.06 +/- 0.01 to 0.07 +/- 0.01 for Charisma, at 24 hours and 6 months, respectively. For both composites, no significant roughness alteration was detected during the study (p= 0.386). The 6-month period of storage in water presented a significant softening effect on the surfaces of the composites, although no significant deleterious alteration was detected for the subsurface hardness. In addition, the storage period had no significant effect on the surface roughness of the materials.

Lifecycle Verification of Tank Liner Polymers

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

Anovitz, Lawrence; Smith, Barton

2014-03-01

This report describes a method that was developed for the purpose of assessing the durability of thermoplastic liners used in a Type IV hydrogen storage tank during the tank s expected service life. In the method, a thermoplastic liner specimen is cycled between the maximum and minimum expected working temperatures while it is differentially pressurized with high-pressure hydrogen gas. The number of thermal cycling intervals corresponds to those expected within the tank s design lifetime. At prescribed intervals, hydrogen permeation measurements are done in situ to assess the ability of the liner specimen to maintain its hydrogen barrier properties andmore » to model its permeability over the tank lifetime. Finally, the model is used to assess whether the steady-state leakage rate in the tank could potentially exceed the leakage specification for hydrogen fuel cell passenger vehicles. A durability assessment was performed on a specimen of high-density polyethylene (HDPE) that is in current use as a tank liner. Hydrogen permeation measurements were performed on several additional tank liner polymers as well as novel polymers proposed for use as storage tank liners and hydrogen barrier materials. The following technical barriers from the Fuel Cell Technologies Program MYRDD were addressed by the project: D. Durability of on-board storage systems lifetime of at least 1500 cycles G. Materials of construction vessel containment that is resistant to hydrogen permeation M. Lack of Tank Performance Data and Understanding of Failure Mechanisms And the following technical targets1 for on-board hydrogen storage systems R&D were likewise addressed: Operational cycle life (1/4 tank to full) FY 2017: 1500 cycles; Ultimate: 1500 cycles Environmental health & safety Permeation and leakage: Meets or exceeds applicable standards Loss of useable H2: FY 2017: 0.05 g/h/kg H2; Ultimate: 0.05 g/h/kg H2« less

Gas chromatographic column for the storage of sample profiles

NASA Technical Reports Server (NTRS)

Dimandja, J. M.; Valentin, J. R.; Phillips, J. B.

1994-01-01

The concept of a sample retention column that preserves the true time profile of an analyte of interest is studied. This storage system allows for the detection to be done at convenient times, as opposed to the nearly continuous monitoring that is required by other systems to preserve a sample time profile. The sample storage column is essentially a gas chromatography column, although its use is not the separation of sample components. The functions of the storage column are the selective isolation of the component of interest from the rest of the components present in the sample and the storage of this component as a function of time. Using octane as a test substance, the sample storage system was optimized with respect to such parameters as storage and readout temperature, flow rate through the storage column, column efficiency and storage time. A 3-h sample profile was collected and stored at 30 degrees C for 20 h. The profile was then retrieved, essentially intact, in 5 min at 130 degrees C.

Changes in surface characteristics of two different resin composites after 1 year water storage: An SEM and AFM study.

PubMed

Tekçe, Neslihan; Pala, Kansad; Demirci, Mustafa; Tuncer, Safa

2016-11-01

To evaluate changes in surface characteristics of two different resin composites after 1 year of water storage using a profilometer, Vickers hardness, scanning electron microscopy (SEM), and atomic force microscopy (AFM). A total of 46 composite disk specimens (10 mm in diameter and 2 mm thick) were fabricated using Clearfil Majesty Esthetic and Clearfil Majesty Posterior (Kuraray Medical Co, Tokyo, Japan). Ten specimens from each composite were used for surface roughness and microhardness tests (n = 10). For each composite, scanning electron microscope (SEM, n = 2) and atomic force microscope (AFM, n = 1) images were obtained after 24 h and 1 year of water storage. The data were analyzed using two-way analysis of variance and a post-hoc Bonferroni test. Microhardness values of Clearfil Majesty Esthetic decreased significantly (78.15-63.74, p = 0.015) and surface roughness values did not change after 1 year of water storage (0.36-0.39, p = 0.464). Clearfil Majesty Posterior microhardness values were quite stable (138.74-137.25, p = 0.784), and surface roughness values increased significantly (0.39-0.48, p = 0.028) over 1 year. One year of water storage caused microhardness values for Clearfil Majesty Esthetic to decrease and the surface roughness of Clearfil Majesty Posterior increased. AFM and SEM images demonstrated surface detoration of the materials after 1 year and ensured similar results with the quantitative test methods. SCANNING 38:694-700, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR

PubMed Central

Kim, Young-gon; Kim, Min Young; Park, Kwisung; Cho, Chi Hyun; Yoon, Soo Young; Nam, Myung Hyun; Lee, Chang Kyu; Cho, Yun-Jung; Lim, Chae Seung

2016-01-01

ABSTRACT Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens (P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies. PMID:27807150

Color Stability of the Bulk-Fill Composite Resins with Different Thickness in Response to Coffee/Water Immersion

PubMed Central

Sheikh-Al-Eslamian, Seyedeh Mahsa; Hasani, Elham; Abrandabadi, Ahmad Najafi

2016-01-01

We aimed to evaluate the color stability of bulk-fill and conventional composite resin with respect to thickness and storage media. Twenty specimens of a conventional composite resin (6 mm diameter and 2 mm thick) and 40 specimens of the bulk-fill Tetric EvoCeram composite resin at two different thicknesses (6 mm diameter and 2 mm thick or 4 mm thick, n = 20) were prepared. The specimens were stored in distilled water during the study period (28 d). Half of the specimens were remained in distilled water and the other half were immersed in coffee solution 20 min/d and kept in distilled water between the cycles. Color changes (ΔE) were measured using the CIE L ⁎ a ⁎ b ⁎ color space and a digital imaging system at 1, 7, 14, and 28 days of storage. Data were analyzed using Two-way ANOVA and Tukey's HSD post hoc test (P < 0.05). Composite resins showed significant increase in color changes by time (bulk-fill > conventional; P < 0.001). Coffee exhibited significantly more staining susceptibility than that of distilled water (P < 0.001). There was greater color changes with increasing the increment thickness, which was significant at 14 (P < 0.001) and 28 d (P < 0.01). Color change of bulk-fill composite resin was greater than that of the conventional one after coffee staining and is also a function of increment thicknesses. PMID:27403163

Study of damage to red blood cells exposed to different doses of γ-ray irradiation.

PubMed

Xu, Deyi; Peng, Mingxi; Zhang, Zhe; Dong, Guofei; Zhang, Yiqin; Yu, Hongwei

2012-07-01

The aims of this research were to study alterations in the ultrastructure of red blood cells, the changes in concentrations of plasma electrolytes and the killing effect of lymphocytes in samples of blood exposed to different doses of γ-ray irradiation. Blood samples were treated with different doses of γ-ray irradiation and then preserved for different periods. Specimens were prepared for standard electron microscopy and transmission electron microscopy. At the same time, changes in the concentrations of Na(+), K(+) and Cl(-) and pH values in the plasma as well as Fas and FasL expression of lymphocytes before and after irradiation were determined. The proportions of reversibly and irreversibly transformed cells, for example, echinocytes, sphero-echinocytes, and degenerated forms, increased with increasing doses of irradiation and storage period, while the number of discocyte shaped red blood cells decreased. The change in K(+) concentration was greater than that of Na+ or Cl(-) after irradiation and was dosage-dependent. Plasma pH was influenced by different doses of radiation and storage time. After exposure to (137)Cs γ-irradiation, the expression of both Fas and FasL in lymphocytes differed significantly from that in the control group: the expression was positively correlated with irradiation dose (r=0.95, 0.96), but no significant difference in the Fas/FasL ratio was observed (P>0.05). We conclude that the ultrastructure of red blood cells is not changed obviously by irradiation with some doses of γ-rays and various periods of storage. However, irradiation does have some dose-dependent and time-dependent adverse effects on the erythrocytes.

Two-year interfacial bond durability and nanoleakage of repaired silorane-based resin composite.

PubMed

Mobarak, E; El-Deeb, H

2013-01-01

To investigate the effect of silane primer application, intermediate adhesive agent/repair composite, and storage period on the interfacial microtensile bond strength (μTBS) of repaired silorane-based resin composite compared with unrepaired composites and on the nanoleakage. Forty-eight 1-month-old substrate specimens from Filtek P90 were roughened, etched, and distributed over two groups (n=24) based on receiving silane (Clearfil Ceramic Primer) or not. Then, half of the specimens (n=12) were repaired with P90 System Adhesive/Filtek P90 and the other half with Adper Scotchbond Multipurpose adhesive/Filtek Z250 resin composite. Within each repair category, repaired specimens were stored in artificial saliva at 37°C for either 24 hours (n=6) or two years before being serially sectioned into sticks (0.6 ± 0.01 mm(2)). From each specimen, two sticks were prepared for nanoleakage determination and four sticks were used for μTBS testing. Additional unrepaired specimens from each composite (n=12) were made to determine the cohesive strength at 24 hours and two years. Mean μTBS were calculated and statistically analyzed. Modes of failure were also determined. General linear model analysis revealed no significant effect for the silane priming, intermediate adhesive agent/repair composite, and storage period or for their interactions on the μTBS values of the repaired specimens. There was no significant difference between the cohesive strength of Filtek P90 and Filtek Z250; both were significantly higher than all repaired categories. At 24 hours, nanoleakage was not detected when silorane-based composite was repaired with the same material. However, after two years, all repair categories showed nanoleakage. Silane application has no effect on μTBS and nanoleakage. Durability of the interfacial bond of repaired silorane-based resin composite appeared successful regardless of the chemistry of the intermediate adhesive agent/composite used for repair. However, nanoleakage was detected early when a different repair intermediate adhesive agent/composite was used.

Apparatus for transporting hazardous materials

DOEpatents

Osterman, Robert A.; Cox, Robert

1992-01-01

An apparatus and method are provided for selectively receiving, transporting, and releasing one or more radioactive or other hazardous samples for analysis on a differential thermal analysis (DTA) apparatus. The apparatus includes a portable sample transporting apparatus for storing and transporting the samples and includes a support assembly for supporting the transporting apparatus when a sample is transferred to the DTA apparatus. The transporting apparatus includes a storage member which includes a plurality of storage chambers arrayed circumferentially with respect to a central axis. An adjustable top door is located on the top side of the storage member, and the top door includes a channel capable of being selectively placed in registration with the respective storage chambers thereby permitting the samples to selectively enter the respective storage chambers. The top door, when closed, isolates the respective samples within the storage chambers. A plurality of spring-biased bottom doors are located on the bottom sides of the respective storage chambers. The bottom doors isolate the samples in the respective storage chambers when the bottom doors are in the closed position. The bottom doors permit the samples to leave the respective storage chambers from the bottom side when the respective bottom doors are in respective open positions. The bottom doors permit the samples to be loaded into the respective storage chambers after the analysis for storage and transport to a permanent storage location.

Comparative Evaluation of Marginal Discrepancy in Tooth Colored Self Cure Acrylic Provisional Restorations With and Without Reinforcement of Glass Beads: An In-Vitro Study.

PubMed

Yasangi, Manoj Kumar; Mannem, Dhanalakshmi; Bommireddy, Vikram Simha; Neturi, Sirisha; Ravoori, Srinivas; Jyothi

2015-05-01

This invitro study was conducted to compare and evaluate marginal discrepancy in two types of tooth colored self cure provisional restorative materials {DPI&UNIFAST TRAD} before and after reinforcement of glass beads. The aim of the present study was to evaluate and compare marginal discrepancy in two types of provisional restorative materials (DPI and UNI FAST TRAD) before and after reinforcement with Glass beads. Tooth shaped resin copings were fabricated on custom made brass metal die. A total of 60 resin copings were fabricated in which 30 samples were prepared with DPI and 30 samples with UNIFAST material. Each group of 30 samples were divided in to two sub groups in which 15 samples were prepared with glass bead reinforcement and 15 samples without reinforcement. The marginal discrepancy was evaluated with photomicroscope {Reichet Polyvar 2 met} by placing the resin copings on custom made brass resin coping holder. Measurements obtained were statistically analysed by unpaired t-test to know any significance between two variables. Unreinforced DPI specimens had shown lower marginal discrepancy (442.82) than reinforced specimens (585.77). Unreinforced UNIFAST specimens have shown high values of marginal discrepancy (592.83) than reinforced specimens (436.35). p-value between reinforced and unreinforced specimens of DPI (p=0.0013) and UNIFAST (p= 0.0038) has shown statistical significance. This in-vitro study revealed that unreinforced DPI specimens have shown lower marginal discrepancy than reinforced specimens and unreinforced UNIFAST specimens have shown higher values of marginal discrepancy than reinforced specimens.

Influence of the artificial saliva storage on 3-D surface texture characteristics of contemporary dental nanocomposites.

PubMed

Ţălu, Ştefan; Bramowicz, Miroslaw; Kulesza, Slawomir; Lainović, Tijana; Vilotić, Marko; Blažić, Larisa

2016-11-01

The aim of this study was to analyse the influence of the artificial saliva on a three-dimensional (3-D) surface texture of contemporary dental composites. The representatives of four composites types were tested: nanofilled (Filtek Ultimate Body, FUB), nanohybrid (Filtek Z550, FZ550), microfilled (Gradia Direct, GD) and microhybrid (Filtek Z250, FZ250). The specimens were polymerised and polished by the multistep protocol (SuperSnap, Shofu). Their surface was examined, before and after 3 weeks' exposure to artificial saliva storage. The surface texture was analysed using the atomic force microscope (AFM). The obtained images were processed to calculate the areal autocorrelation function (AACF), anisotropy ratio S tr (texture aspect ratio), and structure function (SF). The log-log plots of SF were used to calculate fractal properties, such as fractal dimension D, and pseudo-topothesy K. The analysis showed changes in surface anisotropy ratio S tr values, which became higher, whereas the S q roughness (root-mean-square) reduced after the artificial saliva storage. All the samples exhibited bifractal structure before the saliva treatment, but only half of them remained bifractal afterwards (GD, FZ250), whereas the other half turned into a monofractal (FUB, FZ550). The cube-count fractal dimension D cc was found to be material- and treatment-insensitive. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Non-01 Vibrio cholerae infections in Cancun, Mexico.

PubMed

Finch, M J; Valdespino, J L; Wells, J G; Perez-Perez, G; Arjona, F; Sepulveda, A; Bessudo, D; Blake, P A

1987-03-01

To determine the role of Vibrio cholerae as a cause of diarrheal illness in Cancun, Mexico, an investigation was conducted in July and August 1983. Although toxigenic V. cholerae 01 were not found, non-01 V. cholerae were isolated from 22 (16%) of 134 stools from persons with diarrheal illness and none of 22 stools from well persons; 58 (92%) of 63 sewage samples; 12 (86%) of 14 untreated well water samples; a home storage tank for treated water; and 5 (21%) of 24 samples of raw seafood. None of the V. cholerae isolates from patients were toxigenic. The illness occurred mainly in small children, and were characterized principally by diarrhea and abdominal pain. No patient was seriously ill, and all recovered without sequelae. Seven different serotypes of non-01 V. cholerae were isolated from the stool specimens, and Smith serotype 12 accounted for 10 (46%) of the 22 isolates. A matched-pair case-control study found that cases were more likely than controls to have eaten home prepared gelatin (P = 0.03, OR = 5/0) and seafood (P = 0.06, OR = 4/0).

Coccidian oöcysts as type-specimens: long-term storage in aqueous potassium dichromate solution preserves DNA.

PubMed

Williams, R B; Thebo, P; Marshall, R N; Marshall, J A

2010-05-01

Preservation of the exogenous oöcyst stage of coccidian parasites (phylum Apicomplexa N.D. Levine, 1970) as type-specimens of newly described species has long been problematical. Conventional fixatives have proved unsatisfactory, and compromises such as embedding oöcysts in resin or photographing them are not entirely appropriate for various reasons. As an alternative, chilled potassium dichromate solution (normally used in the laboratory to prevent putrefaction of temporary preparations of live oöcysts) has been tested as a long-term preservative of sporulated oöcysts of Eimeria brunetti P.P. Levine, 1942, E. maxima Tyzzer, 1929, E. mitis Tyzzer, 1929, E. necatrix Johnson, 1930, E. praecox Johnson, 1930 and E. tenella (Railliet & Lucet, 1891) (suborder Eimeriorina Léger, 1911; family Eimeriidae Minchin, 1903). Oöcysts from faeces of chickens Gallus gallus (Linnaeus) were placed in 2.5% w/v aqueous potassium dichromate solution (PDS) and stored in the dark at 4 +/- 2 degrees C. After 23 years in storage, oöcysts of each species were administered orally to chickens and failed to initiate infections, indicating that the oöcysts were dead. Nevertheless, after about 24 years, DNA was still recoverable from the oöcysts, and the original species identifications made by classic parasitological methods were confirmed by polymerase chain reaction assays. Furthermore, after almost 25 years, microscopical examination revealed that the walls and internal structures remained well preserved in 83-98% of the oöcysts of the six species investigated. Hence, PDS is potentially suitable for the long-term preservation of sporulated coccidian oöcysts as type-specimens for taxonomic purposes. The samples used in this study are now in the care of the Natural History Museum, London, UK. It is recommended that they be monitored in like manner, by suitably qualified scientists, at intervals of about 5 years to assess their state of preservation and the recoverability of DNA. Enough material is available to monitor it until it is at least 100 years old.

The effectiveness of BD Vacutainer® Plus Urinalysis Preservative Tubes in preservation of urine for chemical strip analysis and particle counting

PubMed Central

Ekşioğlu, Merve Kaymak; Madenci, Özlem Çakır; Yücel, Nihal; Elçi, Abdullah; Turhan, Bülent; Orhan, Gani; Orçun, Asuman

2016-01-01

Introduction The aim of this study was to evaluate the stability of urine collected in preservative tubes for chemistry strip analyses and particle counting to determine whether the transport of urine samples with all of their constituents is possible. Materials and methods 275 pathologic urine specimens were included. Each urine sample was evaluated after 4, 8, 12, 24, and 48 hours of storage in BD Vacutainer® Plus Urinalysis Preservative (BD UAP) tubes and compared with refrigeration at 4 °C. All analyses were peformed on H-800 and FUS-200 automatic modular urine analyzers (Dirui Industry, Changchun, China). The kappa coefficients (κ), false positive (FP) and false negative (FN) rates were evaluated. κ > 0.8 was accepted as good agreement. Results Haemoglobin (Hb), leucocyte esterase (LE), and protein (Pro) analyses should be performed within 4 hours, whereas glucose (Glc) was stable until the end of 48 hours in both storage conditions. Nitrite (Nit) was well preserved in BD UAP tubes for 24 hours but was stable only up to 8 hours at 4 °C. Bilirubin (Bil) had very high FN rates even at 4 hours in both conditions. The particle counting showed high FN rates for white blood cells (WBC) and red blood cells (RBC), whereas squamous epithelial cells (EC) were stable up to 8 hours in both conditions. Conclusions Preanalytical requirements for both urine chemical strip analyses and particle counting in a unique sample were not met in either condition. Thus, the transfer of urine samples for centralization of urinalysis is not yet feasible. PMID:27346967

Unreliable alcohol testing in a shipping safety programme.

PubMed

Helander, Anders; Hagelberg, Charlotte Asker; Beck, Olof; Petrini, Björn

2009-08-10

Within a maritime alcohol and drug testing programme, a case showing an unphysiological urine ethanol concentration (235 mmol/L, 10.8 g/L) was found. The sample contained low levels of the ethanol metabolites ethyl glucuronide (EtG) and ethyl sulphate (EtS) which confirmed prior drinking, but also tested positive for the fermenting yeast Candida albicans which suggested post-sampling ethanol formation. This and other questionable cases prompted investigation of the suitability of urine alcohol testing for the intended application. Besides the routine measurements of ethanol, illicit drugs and creatinine, randomly selected ethanol-positive and ethanol-negative urines collected within the maritime programme were checked for the presence of EtG and EtS and for fungal and bacterial growth. Data on sample handling and storage was also gathered. Ten of 15 (67%) ethanol-positive and 4 of 9 (44%) ethanol-negative urines contained yeast and/or bacteria. Among the ethanol-positive cases, 4 (27%) were obviously false positives because EtG and EtS were not detected. Microbial action as the reason for false-high ethanol concentrations was indicated in other cases. When 17 bacteria-infected but fungi-negative urines were supplemented with glucose and stored for 1 week at 21 degrees C, ethanol was formed in 2 specimens containing Escherichia coli and E. coli plus P. aeruginosa. In these samples, EtG was also formed on storage while EtS was not. The routines employed for urine collection and handling within this substance abuse programme caused many false-positive identifications of alcohol use with unintended medico-legal consequences. Unpreserved urines stored without cooling should not be used for alcohol testing, given the high risk for microbial interference.

Characterization of some biological specimens using TEM and SEM

NASA Astrophysics Data System (ADS)

Ghosh, Nabarun; Smith, Don W.

2009-05-01

The advent of novel techniques using the Transmission and Scanning Electron Microscopes improved observation on various biological specimens to characterize them. We studied some biological specimens using Transmission and Scanning Electron Microscopes. We followed negative staining technique with Phosphotungstic acid using bacterial culture of Bacillus subtilis. Negative staining is very convenient technique to view the structural morphology of different samples including bacteria, phage viruses and filaments in a cell. We could observe the bacterial cell wall and flagellum very well when trapped the negative stained biofilm from bacterial culture on a TEM grid. We cut ultra thin sections from the fixed root tips of Pisum sativum (Garden pea). Root tips were pre fixed with osmium tetroxide and post fixed with uranium acetate and placed in the BEEM capsule for block making. The ultrathin sections on the grid under TEM showed the granular chromatin in the nucleus. The protein bodies and large vacuoles with the storage materials were conspicuous. We followed fixation, critical point drying and sputter coating with gold to view the tissues with SEM after placing on stubs. SEM view of the leaf surface of a dangerous weed Tragia hispida showed the surface trichomes. These trichomes when break on touching releases poisonous content causing skin irritation. The cultured tissue from in vitro culture of Albizia lebbeck, a tree revealed the regenerative structures including leaf buds and stomata on the tissue surface. SEM and TEM allow investigating the minute details characteristic morphological features that can be used for classroom teaching.

Novel Formulations of Phase Change Materials—Epoxy Composites for Thermal Energy Storage

PubMed Central

Alvarez Feijoo, Miguel Angel

2018-01-01

This research aimed to evaluate the thermal properties of new formulations of phase change materials (PCMs)-epoxy composites, containing a thickening agent and a thermally conductive phase. The composite specimens produced consisted of composites fabricated using (a) inorganic PCMs (hydrated salts), epoxy resins and aluminum particulates or (b) organic PCM (paraffin), epoxy resins, and copper particles. Differential Scanning Calorimetry (DSC) was used to analyze the thermal behavior of the samples, while hardness measurements were used to determine changes in mechanical properties at diverse PCM and conductive phase loading values. The results indicate that the epoxy matrix can act as a container for the PCM phase without hindering the heat-absorbing behavior of the PCMs employed. Organic PCMs presented reversible phase transformations over multiple cycles, an advantage that was lacking in their inorganic counterparts. The enthalpy of the organic PCM-epoxy specimens increased linearly with the PCM content in the matrix. The use of thickening agents prevented phase segregation issues and allowed the fabrication of specimens containing up to 40% PCM, a loading significantly higher than others reported. The conductive phase seemed to improve the heat transfer and the mechanical properties of the composites when present in low percentages (<10 wt %); however, given its mass, the enthalpy detected in the composites was reduced as their loading further increased. The conductive phase combination (PCM + epoxy resin + hardener + thickening agent) presents great potential as a heat-absorbing material at the temperatures employed. PMID:29373538

Novel Formulations of Phase Change Materials-Epoxy Composites for Thermal Energy Storage.

PubMed

Arce, Maria Elena; Alvarez Feijoo, Miguel Angel; Suarez Garcia, Andres; Luhrs, Claudia C

2018-01-26

This research aimed to evaluate the thermal properties of new formulations of phase change materials (PCMs)-epoxy composites, containing a thickening agent and a thermally conductive phase. The composite specimens produced consisted of composites fabricated using (a) inorganic PCMs (hydrated salts), epoxy resins and aluminum particulates or (b) organic PCM (paraffin), epoxy resins, and copper particles. Differential Scanning Calorimetry (DSC) was used to analyze the thermal behavior of the samples, while hardness measurements were used to determine changes in mechanical properties at diverse PCM and conductive phase loading values. The results indicate that the epoxy matrix can act as a container for the PCM phase without hindering the heat-absorbing behavior of the PCMs employed. Organic PCMs presented reversible phase transformations over multiple cycles, an advantage that was lacking in their inorganic counterparts. The enthalpy of the organic PCM-epoxy specimens increased linearly with the PCM content in the matrix. The use of thickening agents prevented phase segregation issues and allowed the fabrication of specimens containing up to 40% PCM, a loading significantly higher than others reported. The conductive phase seemed to improve the heat transfer and the mechanical properties of the composites when present in low percentages (<10 wt %); however, given its mass, the enthalpy detected in the composites was reduced as their loading further increased. The conductive phase combination (PCM + epoxy resin + hardener + thickening agent) presents great potential as a heat-absorbing material at the temperatures employed.

Molecular detection and serotyping of infectious bronchitis virus from FTA filter paper.

PubMed

Moscoso, Hugo; Raybon, Erine O; Thayer, Stephan G; Hofacre, Charles L

2005-03-01

We investigated the feasibility of using Flinders Technology Associates (FTA) filter cards for the storage of allantoic fluid containing an infectious bronchitis virus (IBV), such as Arkansas-DPI, Connecticut, and Massachusetts, and for their identification by reverse transcriptase (RT)-polymerase chain reaction (PCR) and characterization by restriction fragment length polymorphism (RFLP) or nucleotide sequencing. FTA paper is a cotton-based cellulose membrane containing lyophilized chemicals that lyses many types of bacteria and viruses. IBV was inactivated upon contact with the FTA, as shown by the inability of the virus to be propagated in embryonating chicken eggs. RT-PCR of the S1 gene showed that viral RNA in allantoic fluid remained stable after storage on FTA filter cards and that the stability was time and temperature sensitive for the large (1700 base pair [bp]) but not the small (383 bp) PCR products. Analysis of the amplified products showed that molecular characterization is feasible in allantoic fluid stored on FTA under nonfavorable environmental conditions (41 C) for at least 15 days. The use of FTA cards for the collection, transport, and storage of IBV-containing samples is safe, inexpensive, and adequate for molecular diagnosis. We propose that specimens coming from overseas on FTA cards would be first analyzed by RT-PCR with primers yielding a 1700-bp product followed by RFLP of the positive cases. Negative cases would be analyzed with primers yielding a 383-bp product (to exdude detrimental effect of the storage conditions) followed by nucleotide sequencing of the positive cases.

Preparing rock powder specimens of controlled size distribution

NASA Technical Reports Server (NTRS)

Blum, P.

1968-01-01

Apparatus produces rock powder specimens of the size distribution needed in geological sampling. By cutting grooves in the surface of the rock sample and then by milling these shallow, parallel ridges, the powder specimen is produced. Particle size distribution is controlled by changing the height and width of ridges.

Establishment and operation of a biorepository for molecular epidemiologic studies in Costa Rica.

PubMed

Cortés, Bernal; Schiffman, Mark; Herrero, Rolando; Hildesheim, Allan; Jiménez, Silvia; Shea, Katheryn; González, Paula; Porras, Carolina; Fallas, Greivin; Rodríguez, Ana Cecilia

2010-04-01

The Proyecto Epidemiológico Guanacaste (PEG) has conducted several large studies related to human papillomavirus (HPV) and cervical cancer in Guanacaste, Costa Rica in a long-standing collaboration with the U.S. National Cancer Institute. To improve molecular epidemiology efforts and save costs, we have gradually transferred technology to Costa Rica, culminating in state-of-the-art laboratories and a biorepository to support a phase III clinical trial investigating the efficacy of HPV 16/18 vaccine. Here, we describe the rationale and lessons learned in transferring molecular epidemiologic and biorepository technology to a developing country. At the outset of the PEG in the early 1990s, we shipped all specimens to repositories and laboratories in the United States, which created multiple problems. Since then, by intensive personal interactions between experts from the United States and Costa Rica, we have successfully transferred liquid-based cytology, HPV DNA testing and serology, chlamydia and gonorrhea testing, PCR-safe tissue processing, and viable cryopreservation. To accommodate the vaccine trial, a state-of-the-art repository opened in mid-2004. Approximately 15,000 to 50,000 samples are housed in the repository on any given day, and >500,000 specimens have been shipped, many using a custom-made dry shipper that permits exporting >20,000 specimens at a time. Quality control of shipments received by the NCI biorepository has revealed an error rate of <0.2%. Recently, the PEG repository has incorporated other activities; for example, large-scale aliquotting and long-term, cost-efficient storage of frozen specimens returned from the United States. Using Internet-based specimen tracking software has proven to be efficient even across borders. For long-standing collaborations, it makes sense to transfer the molecular epidemiology expertise toward the source of specimens. The successes of the PEG molecular epidemiology laboratories and biorepository prove that the physical and informatics infrastructures of a modern biorepository can be transferred to a resource-limited and weather-challenged region. Technology transfer is an important and feasible goal of international collaborations.

Fatigue Behavior of Porous Ti-6Al-4V Made by Laser-Engineered Net Shaping

PubMed Central

Bordonaro, Giancarlo G.; Berto, Filippo

2018-01-01

The fatigue behavior and fracture mechanisms of additively manufactured Ti-6Al-4V specimens are investigated in this study. Three sets of testing samples were fabricated for the assessment of fatigue life. The first batch of samples was built by using Laser-Engineered Net Shaping (LENS) technology, a Direct Energy Deposition (DED) method. Internal voids and defects were induced in a second batch of samples by changing LENS machine processing parameters. Fatigue performance of these samples is compared to the wrought Ti-6Al-4V samples. The effects of machine-induced porosity are assessed on mechanical properties and results are presented in the form of SN curves for the three sets of samples. Fracture mechanisms are examined by using Scanning Electron Microscopy (SEM) to characterize the morphological characteristics of the failure surface. Different fracture surface morphologies are observed for porous and non-porous specimens due to the combination of head write speed and laser power. Formation of defects such as pores, unmelted regions, and gas entrapments affect the failure mechanisms in porous specimens. Non-porous specimens exhibit fatigue properties comparable with that of the wrought specimens, but porous specimens are found to show a tremendous reduced fatigue strength. PMID:29439510

Planned Variation in Preanalytical Conditions to Evaluate Biospecimen Stability in the National Children’s Study (NCS)

PubMed Central

Mechanic, Leah; Mendez, Armando; Merrill, Lori; Rogers, John; Layton, Marnie; Todd, Deborah; Varanasi, Arti; O’Brien, Barbara; Meyer, William A.; Zhang, Ming; Schleicher, Rosemary L.; Moye, Jack

2014-01-01

BACKGROUND Preanalytical conditions encountered during collection, processing, and storage of biospecimens may influence laboratory results. The National Children’s Study (NCS) is a planned prospective cohort study of 100,000 families to examine the influence of a wide variety of exposures on child health. In developing biospecimen collection, processing, and storage procedures for the NCS, we identified several analytes of different biochemical categories for which it was unclear to what extent deviations from NCS procedures could influence measurement results. METHODS A pilot study was performed to examine effects of preanalytic sample handling conditions (delays in centrifugation, freezing delays, delays in separation from cells, additive delay, and tube type) on concentrations of eight different analytes. 2,825 measurements were made to assess 15 unique combinations of analyte and handling conditions in blood collected from 151 women of childbearing age (≥20 individuals per handling condition). RESULTS The majority of analytes were stable under the conditions evaluated. However, levels of plasma interleukin-6 and serum insulin were decreased in response to sample centrifugation delays of up to 5.5 hours post collection (P<0.0001). In addition, delays in freezing centrifuged plasma samples (comparing 24, 48 and 72 hours to immediate freezing) resulted in increased levels of adrenocorticotropic hormone (P=0.0014). CONCLUSIONS Determining stability of proposed analytes in response to preanalytical conditions and handling helps to ensure high-quality specimens for study now and in the future. The results inform development of procedures, plans for measurement of analytes, and interpretation of laboratory results. PMID:23924524

System and method for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J; Kertesz, Vilmos

2014-01-28

A system and method for laser desorption of an analyte from a specimen and capturing of the analyte in a suspended solvent to form a testing solution are described. The method can include providing a specimen supported by a desorption region of a specimen stage and desorbing an analyte from a target site of the specimen with a laser beam centered at a radiation wavelength (.lamda.). The desorption region is transparent to the radiation wavelength (.lamda.) and the sampling probe and a laser source emitting the laser beam are on opposite sides of a primary surface of the specimen stage. The system can also be arranged where the laser source and the sampling probe are on the same side of a primary surface of the specimen stage. The testing solution can then be analyzed using an analytical instrument or undergo further processing.

Rock and Core Repository Coming Digital

NASA Astrophysics Data System (ADS)

Maicher, Doris; Fleischer, Dirk; Czerniak, Andreas

2016-04-01

In times of whole city centres being available by a mouse click in 3D to virtually walk through, reality sometimes becomes neglected. The reality of scientific sample collections not being digitised to the essence of molecules, isotopes and electrons becomes unbelievable to the upgrowing generation of scientists. Just like any other geological institute the Helmholtz Centre for Ocean Research GEOMAR accumulated thousands of specimen. The samples, collected mainly during marine expeditions, date back as far as 1964. Today GEOMAR houses a central geological sample collection of at least 17 000 m of sediment core and more than 4 500 boxes with hard rock samples and refined sample specimen. This repository, having been dormant, missed the onset of the interconnected digital age. Physical samples without barcodes, QR codes or RFID tags need to be migrated and reconnected, urgently. In our use case, GEOMAR opted for the International Geo Sample Number IGSN as the persistent identifier. Consequentially, the software CurationDIS by smartcube GmbH as the central component of this project was selected. The software is designed to handle acquisition and administration of sample material and sample archiving in storage places. In addition, the software allows direct embedding of IGSN. We plan to adopt IGSN as a future asset, while for the initial inventory taking of our sample material, simple but unique QR codes act as "bridging identifiers" during the process. Currently we compile an overview of the broad variety of sample types and their associated data. QR-coding of the boxes of rock samples and sediment cores is near completion, delineating their location in the repository and linking a particular sample to any information available about the object. Planning is in progress to streamline the flow from receiving new samples to their curation to sharing samples and information publically. Additionally, interface planning for linkage to GEOMAR databases OceanRep (publications) and OSIS (expeditions) as well as for external data retrieval are in the pipeline. Looking ahead to implement IGSN, taking on board lessons learned from earlier generations, it will enable to comply with our institute's open science policy. Also it will allow to register newly collected samples already during ship expeditions. They thus receive their "birth certificate" contemporarily in this ever faster revolving scientific world.

Comparison of specimen adequacy and smear quality in oral smears prepared by manual liquid-based cytology and conventional methods

PubMed Central

Shukla, Surabhi; Einstein, A; Shukla, Abhilasha; Mishra, Deepika

2015-01-01

Background: Liquid-based cytology (LBC), recommended in the mass screening of potentially malignant cervical and oral lesions, suffers from high cost owing to the use of expensive automated devices and materials. Considering the need for cost-effective LBC techniques, we evaluated the efficacy of an inexpensive manual LBC (MLBC) technique against conventional cytological technique in terms of specimen adequacy and smear quality of oral smears. Materials and Methods: Cytological samples were collected from 21 patients using a cytobrush device. After preparation of a conventional smear, the brush containing the remaining sample was immersed in the preservative vial. The preserved material was processed by an MLBC technique and subsequently, direct smears were made from the prepared cell button. Both conventional and MLBC smears were stained by routine Papanicolaou technique and evaluated by an independent observer for the thickness of the smear, cellular distribution, resolution/clarity of cells, cellular staining characteristics and the presence of unsatisfactory background/artifacts. Each parameter was graded as satisfactory; or satisfactory, but limited; or unsatisfactory. Chi-square test was used to compare the values obtained (significance set at P ≤ 0.05). Results: MLBC technique produced a significant number of satisfactory smears with regard to cell distribution, clarity/resolution, staining characteristics and background/artifacts compared to conventional methods. Conclusions: MLBC is a cost-effective cytological technique that may produce oral smears with excellent cytomorphology and longer storage life. PMID:26980958

Osteoinduction on Acid and Heat Treated Porous Ti Metal Samples in Canine Muscle

PubMed Central

Kawai, Toshiyuki; Takemoto, Mitsuru; Fujibayashi, Shunsuke; Akiyama, Haruhiko; Tanaka, Masashi; Yamaguchi, Seiji; Pattanayak, Deepak K.; Doi, Kenji; Matsushita, Tomiharu; Nakamura, Takashi; Kokubo, Tadashi; Matsuda, Shuichi

2014-01-01

Samples of porous Ti metal were subjected to different acid and heat treatments. Ectopic bone formation on specimens embedded in dog muscle was compared with the surface characteristics of the specimen. Treatment of the specimens by H2SO4/HCl and heating at 600°C produced micrometer-scale roughness with surface layers composed of rutile phase of titanium dioxide. The acid- and heat-treated specimens induced ectopic bone formation within 6 months of implantation. A specimen treated using NaOH followed by HCl acid and then heat treatment produced nanometer-scale surface roughness with a surface layer composed of both rutile and anatase phases of titanium dioxide. These specimens also induced bone formation after 6 months of implantation. Both these specimens featured positive surface charge and good apatite-forming abilities in a simulated body fluid. The amount of the bone induced in the porous structure increased with apatite-forming ability and higher positive surface charge. Untreated porous Ti metal samples showed no bone formation even after 12 months. Specimens that were only heat treated featured a smooth surface composed of rutile. A mixed acid treatment produced specimens with micrometer-scale rough surfaces composed of titanium hydride. Both of them also showed no bone formation after 12 months. The specimens that showed no bone formation also featured almost zero surface charge and no apatite-forming ability. These results indicate that osteoinduction of these porous Ti metal samples is directly related to positive surface charge that facilitates formation of apatite on the metal surfaces in vitro. PMID:24520375

Device for high spatial resolution chemical analysis of a sample and method of high spatial resolution chemical analysis

DOEpatents

Van Berkel, Gary J.

2015-10-06

A system and method for analyzing a chemical composition of a specimen are described. The system can include at least one pin; a sampling device configured to contact a liquid with a specimen on the at least one pin to form a testing solution; and a stepper mechanism configured to move the at least one pin and the sampling device relative to one another. The system can also include an analytical instrument for determining a chemical composition of the specimen from the testing solution. In particular, the systems and methods described herein enable chemical analysis of specimens, such as tissue, to be evaluated in a manner that the spatial-resolution is limited by the size of the pins used to obtain tissue samples, not the size of the sampling device used to solubilize the samples coupled to the pins.

Identification of phlebotomine sand flies using one MALDI-TOF MS reference database and two mass spectrometer systems.

PubMed

Mathis, Alexander; Depaquit, Jérôme; Dvořák, Vit; Tuten, Holly; Bañuls, Anne-Laure; Halada, Petr; Zapata, Sonia; Lehrter, Véronique; Hlavačková, Kristýna; Prudhomme, Jorian; Volf, Petr; Sereno, Denis; Kaufmann, Christian; Pflüger, Valentin; Schaffner, Francis

2015-05-10

Rapid, accurate and high-throughput identification of vector arthropods is of paramount importance in surveillance programmes that are becoming more common due to the changing geographic occurrence and extent of many arthropod-borne diseases. Protein profiling by MALDI-TOF mass spectrometry fulfils these requirements for identification, and reference databases have recently been established for several vector taxa, mostly with specimens from laboratory colonies. We established and validated a reference database containing 20 phlebotomine sand fly (Diptera: Psychodidae, Phlebotominae) species by using specimens from colonies or field-collections that had been stored for various periods of time. Identical biomarker mass patterns ('superspectra') were obtained with colony- or field-derived specimens of the same species. In the validation study, high quality spectra (i.e. more than 30 evaluable masses) were obtained with all fresh insects from colonies, and with 55/59 insects deep-frozen (liquid nitrogen/-80 °C) for up to 25 years. In contrast, only 36/52 specimens stored in ethanol could be identified. This resulted in an overall sensitivity of 87 % (140/161); specificity was 100 %. Duration of storage impaired data counts in the high mass range, and thus cluster analyses of closely related specimens might reflect their storage conditions rather than phenotypic distinctness. A major drawback of MALDI-TOF MS is the restricted availability of in-house databases and the fact that mass spectrometers from 2 companies (Bruker, Shimadzu) are widely being used. We have analysed fingerprints of phlebotomine sand flies obtained by automatic routine procedure on a Bruker instrument by using our database and the software established on a Shimadzu system. The sensitivity with 312 specimens from 8 sand fly species from laboratory colonies when evaluating only high quality spectra was 98.3 %; the specificity was 100 %. The corresponding diagnostic values with 55 field-collected specimens from 4 species were 94.7 % and 97.4 %, respectively. A centralized high-quality database (created by expert taxonomists and experienced users of mass spectrometers) that is easily amenable to customer-oriented identification services is a highly desirable resource. As shown in the present work, spectra obtained from different specimens with different instruments can be analysed using a centralized database, which should be available in the near future via an online platform in a cost-efficient manner.

Comparative Evaluation of Marginal Discrepancy in Tooth Colored Self Cure Acrylic Provisional Restorations With and Without Reinforcement of Glass Beads: An In-Vitro Study

PubMed Central

Yasangi, Manoj Kumar; Mannem, Dhanalakshmi; Neturi, Sirisha; Ravoori, Srinivas; Jyothi

2015-01-01

Context This invitro study was conducted to compare and evaluate marginal discrepancy in two types of tooth colored self cure provisional restorative materials {DPI&UNIFAST TRAD} before and after reinforcement of glass beads. Aim The aim of the present study was to evaluate and compare marginal discrepancy in two types of provisional restorative materials (DPI and UNI FAST TRAD) before and after reinforcement with Glass beads. Materials and Methods Tooth shaped resin copings were fabricated on custom made brass metal die. A total of 60 resin copings were fabricated in which 30 samples were prepared with DPI and 30 samples with UNIFAST material. Each group of 30 samples were divided in to two sub groups in which 15 samples were prepared with glass bead reinforcement and 15 samples without reinforcement. The marginal discrepancy was evaluated with photomicroscope {Reichet Polyvar 2 met} by placing the resin copings on custom made brass resin coping holder. Results Measurements obtained were statistically analysed by unpaired t-test to know any significance between two variables. Unreinforced DPI specimens had shown lower marginal discrepancy (442.82) than reinforced specimens (585.77). Unreinforced UNIFAST specimens have shown high values of marginal discrepancy (592.83) than reinforced specimens (436.35). p-value between reinforced and unreinforced specimens of DPI (p=0.0013) and UNIFAST (p= 0.0038) has shown statistical significance. Conclusion This in-vitro study revealed that unreinforced DPI specimens have shown lower marginal discrepancy than reinforced specimens and unreinforced UNIFAST specimens have shown higher values of marginal discrepancy than reinforced specimens. PMID:26155574

Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota.

PubMed

Goddard, Amanda F; Staudinger, Benjamin J; Dowd, Scot E; Joshi-Datar, Amruta; Wolcott, Randall D; Aitken, Moira L; Fligner, Corinne L; Singh, Pradeep K

2012-08-21

Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx. Thus, contamination could confound results. Here, we compared culture-independent analyses of throat and sputum specimens to samples directly obtained from the lungs at the time of transplantation. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens. In contrast, upper-airway specimens from the same subjects contained higher levels of microbial diversity and organisms not typically considered CF pathogens. Furthermore, sputum exhibited day-to-day variation in the abundance of nontypical organisms, even in the absence of clinical changes. These findings suggest that oropharyngeal contamination could limit the accuracy of DNA-based measurements on upper-airway specimens. This work highlights the importance of sampling procedures for microbiome studies and suggests that methods that account for contamination are needed when DNA-based methods are used on clinical specimens.

Pre-analytical issues in the haemostasis laboratory: guidance for the clinical laboratories.

PubMed

Magnette, A; Chatelain, M; Chatelain, B; Ten Cate, H; Mullier, F

2016-01-01

Ensuring quality has become a daily requirement in laboratories. In haemostasis, even more than in other disciplines of biology, quality is determined by a pre-analytical step that encompasses all procedures, starting with the formulation of the medical question, and includes patient preparation, sample collection, handling, transportation, processing, and storage until time of analysis. This step, based on a variety of manual activities, is the most vulnerable part of the total testing process and is a major component of the reliability and validity of results in haemostasis and constitutes the most important source of erroneous or un-interpretable results. Pre-analytical errors may occur throughout the testing process and arise from unsuitable, inappropriate or wrongly handled procedures. Problems may arise during the collection of blood specimens such as misidentification of the sample, use of inadequate devices or needles, incorrect order of draw, prolonged tourniquet placing, unsuccessful attempts to locate the vein, incorrect use of additive tubes, collection of unsuitable samples for quality or quantity, inappropriate mixing of a sample, etc. Some factors can alter the result of a sample constituent after collection during transportation, preparation and storage. Laboratory errors can often have serious adverse consequences. Lack of standardized procedures for sample collection accounts for most of the errors encountered within the total testing process. They can also have clinical consequences as well as a significant impact on patient care, especially those related to specialized tests as these are often considered as "diagnostic". Controlling pre-analytical variables is critical since this has a direct influence on the quality of results and on their clinical reliability. The accurate standardization of the pre-analytical phase is of pivotal importance for achieving reliable results of coagulation tests and should reduce the side effects of the influence factors. This review is a summary of the most important recommendations regarding the importance of pre-analytical factors for coagulation testing and should be a tool to increase awareness about the importance of pre-analytical factors for coagulation testing.

Influence of storage conditions on aluminum concentrations in serum, dialysis fluid, urine, and tap water.

PubMed

Wilhelm, M; Ohnesorge, F K

1990-01-01

The influence of storage temperature, vessel type, and treatment on alterations of aluminum (Al) concentrations in serum, urine, and dialysis fluid samples was studied at three different concentrations for each sample over an 18-month period. Furthermore, the influence of acidification on Al levels in tap water, urine, and dialysis fluid samples was studied over a four-month period. Al was measured by atomic absorption spectrometry. Sample storage in glass vessels was unsuitable, whereas only minor alterations of Al levels were observed with storage in polypropylene tubes, polystyrene tubes, and Monovettes. By using appropriate plastic containers, acid washing of the vessels showed no improvement. Frozen storage was superior compared with 4 degrees C, whereas storage at -80 degrees C offered no advantage compared with storage at -20 degrees C. Acidification of tap water samples was necessary to stabilize Al levels during storage. No striking effect of acidification on Al levels in urine and dialysis fluid samples was found. It is concluded that longterm storage of serum, urine, tap water, and dialysis fluid samples is possible if appropriate conditions are used.

Cross-sectional TEM specimen preparation for W/B{sub 4}C multilayer sample using FIB

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

Mondal, Puspen, E-mail: puspen@rrcat.gov.in; Pradhan, P. C.; Tiwari, Pragya

2016-05-23

A recent emergence of a cross-beam scanning electron microscopy (SEM)/focused-ion-beam (FIB) system have given choice to fabricate cross-sectional transmission electron microscopy (TEM) specimen of thin film multilayer sample. A 300 layer pair thin film multilayer sample of W/B{sub 4}C was used to demonstrate the specimen lift-out technique in very short time as compared to conventional cross-sectional sample preparation technique. To get large area electron transparent sample, sample prepared by FIB is followed by Ar{sup +} ion polishing at 2 kV with grazing incident. The prepared cross-sectional sample was characterized by transmission electron microscope.

The Comparison of Sorption and Solubility Behavior of Four Different Resin Luting Cements in Different Storage Media.

PubMed

Giti, Rashin; Vojdani, Mahroo; Abduo, Jaafar; Bagheri, Rafat

2016-06-01

Structural integrity and dimensional stability are the key factors that determine the clinical success and durability of luting cements in the oral cavity. Sorption and solubility of self-adhesive resin luting cements in food-simulating solutions has not been studied sufficiently. This study aimed to compare the sorption and solubility of 2 conventional and 2 self-adhesive resin-based luting cements immersed in four different storage media. A total of 32 disc-shaped specimens were prepared from each of four resin luting cements; seT (SDI), Panavia F (Kuraray), Clearfil SA Cement (Kuraray), and Choice 2 (Bisco). Eight specimens of each material were immersed in all tested solutions including n-heptane 97%, distilled water, apple juice, or Listerine mouth wash. Sorption and solubility were measured by weighing the specimens before and after immersion and desiccation. Data were analyzed by SPSS version 18, using two-way ANOVA and Tukey's HSD test with p≤ 0.05 set as the level of significance. There was a statistically significant interaction between the materials and solutions. The effect of media on the sorption and solubility was material-dependent. While seT showed the highest values of the sorption in almost all solutions, Choice 2 showed the least values of sorption and solubility. Immersion in apple juice caused more sorption than other solutions (p≤ 0.05). The sorption and solubility behavior of the studied cements were significantly affected by their composition and the storage media. The more hydrophobic materials with higher filler content like Choice 2 resin cement showed the least sorption and solubility. Due to their lower sorption and solubility, these types of resin-based luting cements are recommended to be used clinically.

Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture

PubMed Central

Iroh Tam, Pui-Ying; Hernandez-Alvarado, Nelmary; Schleiss, Mark R.; Hassan-Hanga, Fatimah; Onuchukwu, Chuma; Umoru, Dominic; Obaro, Stephen K.

2016-01-01

Background Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS) is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR) assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture. Methods Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples. Results A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%). One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4–90.1%) and 62.5% (95% CI 24.5–91.5%), respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%). Among these, six were positive for a non-S. pneumoniae pathogen on culture. Conclusions Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite growth of a non-S. pneumoniae pathogen on culture. A precise definition of what constitutes a positive result is required to avoid falsely over-identifying specimens. PMID:27007889

Effect of double-layer application on dentin bond durability of one-step self-etch adhesives.

PubMed

Taschner, M; Kümmerling, M; Lohbauer, U; Breschi, L; Petschelt, A; Frankenberger, R

2014-01-01

The aim of this in vitro study was 1) to analyze the influence of a double-layer application technique of four one-step self-etch adhesive systems on dentin and 2) to determine its effect on the stability of the adhesive interfaces stored under different conditions. Four different one-step self-etch adhesives were selected for the study (iBondSE, Clearfil S(3) Bond, XenoV(+), and Scotchbond Universal). Adhesives were applied according to manufacturers' instructions or with a double-layer application technique (without light curing of the first layer). After bonding, resin-dentin specimens were sectioned for microtensile bond strength testing in accordance with the nontrimming technique and divided into 3 subgroups of storage: a) 24 hours (immediate bond strength, T0), b) six months (T6) in artificial saliva at 37°C, or c) five hours in 10 % NaOCl at room temperature. After storage, specimens were stressed to failure. Fracture mode was assessed under a light microscope. At T0, iBond SE showed a significant increase in microtensile bond strength when the double-application technique was applied. All adhesive systems showed reduced bond strengths after six months of storage in artificial saliva and after storage in 10% NaOCl for five hours; however at T6, iBond SE, Clearfil S(3) Bond, and XenoV(+) showed significantly higher microtensile bond strength results for the double-application technique compared with the single-application technique. Scotchbond Universal showed no difference between single- or double-application, irrespective of the storage conditions. The results of this study show that improvements in bond strength of one-step self-etch adhesives by using the double-application technique are adhesive dependent.

Influence of Different Dentin Substrate (Caries-Affected, Caries-Infected, Sound) on Long-Term μTBS.

PubMed

Costa, Ana Rosa; Garcia-Godoy, Franklin; Correr-Sobrinho, Lourenço; Naves, Lucas Zago; Raposo, Luís Henrique Araújo; Carvalho, Fabíola Galbiatti de; Sinhoreti, Mário Alexandre Coelho; Puppin-Rontani, Regina Maria

2017-01-01

The aim of this study was to evaluate the μTBS in different dentin substrates and water-storage periods. Twenty-four dentin blocks obtained from sound third molars were randomly divided into 3 groups: Sound dentin (Sd), Caries-affected dentin (Ca) and Caries-infected dentin (Ci). Dentin blocks from Ca and Ci groups were subjected to artificial caries development (S. mutans biofilm). The softest carious tissue was removed using spherical drills under visual inspection with Caries Detector solution (Ca group). It was considered as Ci (softer and deeply red stained dentin) and Ca (harder and slightly red stained dentin). The Adper Single Bond 2 adhesive system was applied and Z350 composite blocks were built in all groups. Teeth were stored in deionized water for 24 h at 37 ºC and sectioned into beams (1.0 mm2 section area). The beams from each tooth were randomly divided into three storages periods: 24 h, 6 months or 1 year. Specimens were submitted to µTBS using EZ test machine at a crosshead speed of 1.0 mm/min. Failure mode was examined by SEM. Data from µTBS were submitted to split plot two-way ANOVA and Tukey's HSD tests (a=0.05). The µTBS (MPa) of Sd (41.2) was significantly higher than Ca (32.4) and Ci (27.2), regardless of storage. Ca and Ci after 6 months and 1 year, presented similar µTBS. Mixed and adhesive failures predominated in all groups. The highest µTBS values (48.1±9.1) were found for Sd at 24 h storage. Storage of specimens decreased the µTBS values for all conditions.

Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.

PubMed

Pisarska, Margareta D; Akhlaghpour, Marzieh; Lee, Bora; Barlow, Gillian M; Xu, Ning; Wang, Erica T; Mackey, Aaron J; Farber, Charles R; Rich, Stephen S; Rotter, Jerome I; Chen, Yii-der I; Goodarzi, Mark O; Guller, Seth; Williams, John

2016-11-01

Multiple testing to understand global changes in gene expression based on genetic and epigenetic modifications is evolving. Chorionic villi, obtained for prenatal testing, is limited, but can be used to understand ongoing human pregnancies. However, optimal storage, processing and utilization of CVS for multiple platform testing have not been established. Leftover CVS samples were flash-frozen or preserved in RNAlater. Modifications to standard isolation kits were performed to isolate quality DNA and RNA from samples as small as 2-5 mg. RNAlater samples had significantly higher RNA yields and quality and were successfully used in microarray and RNA-sequencing (RNA-seq). RNA-seq libraries generated using 200 versus 800-ng RNA showed similar biological coefficients of variation. RNAlater samples had lower DNA yields and quality, which improved by heating the elution buffer to 70 °C. Purification of DNA was not necessary for bisulfite-conversion and genome-wide methylation profiling. CVS cells were propagated and continue to express genes found in freshly isolated chorionic villi. CVS samples preserved in RNAlater are superior. Our optimized techniques provide specimens for genetic, epigenetic and gene expression studies from a single small sample which can be used to develop diagnostics and treatments using a systems biology approach in the prenatal period. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

Detection of EGFR and KRAS mutations in fine-needle aspirates stored on Whatman FTA cards: is this the tool for biobanking cytological samples in the molecular era?

PubMed

da Cunha Santos, Gilda; Liu, Ni; Tsao, Ming-Sound; Kamel-Reid, Suzanne; Chin, Kayu; Geddie, William R

2010-12-25

The aims of this study were to compare the quality of DNA recovered from fine-needle aspirates (FNAs) stored on Whatman FTA cards with that retrieved from corresponding cell blocks and to determine whether the DNA extracted from the cards is suitable for multiple mutation analyses. FNAs collected from 18 resected lung tumors and cell suspensions from 4 lung cancer cell lines were placed on FTA Indicating Micro Cards and further processed to produce paired formalin-fixed paraffin-embedded (FFPE) cell blocks. Fragment analysis was used for the detection of EGFR exon 19 deletion, and direct sequencing for detection of EGFR exon 21 L858R mutation and exon 2 deletion of KRAS. Corresponding FFPE tissue sections from 2 resection specimens were also tested. Analyses were successful with all FNAs and lung cancer-derived cell lines collected on cards. Polymerase chain reaction failed in 2 cell blocks. For FNAs collected on cards, 5 cases showed EGFR and 3 showed KRAS mutations. Eleven cases were wild type. With cell blocks, 4 cases were found to harbor KRAS and 4 harbored EGFR mutations. All lung cancer-derived cell lines tested positive for their respective mutations, and there was complete agreement between card and cell block FNA samples for EGFR exon 21. For EGFR exon 19, 1 of 18 cases showed discordant results between the card and cell block, and for KRAS 1 of 17. The two resection specimens tested gave concordant results with the FTA card. Storage of cytologic material on FTA cards can maximize and simplify sample procurement for multiple mutational analyses with results similar to those from cell blocks.

A Multivariate Evaluation of Factors Affecting the Quality of Freshly Frozen Tissue Specimens.

PubMed

Wang, Tong-Hong; Chen, Chin-Chuan; Liang, Kung-Hao; Chen, Chi-Yuan; Chuang, Wen-Yu; Ueng, Shir-Hwa; Chu, Pao-Hsien; Huang, Chung-Guei; Chen, Tse-Ching; Hsueh, Chuen

2017-08-01

Well-prepared and preserved freshly frozen specimens are indispensable materials for clinical studies. To manage specimen quality and to understand the factors potentially affecting specimen quality during preservation processes, we analyzed the quality of RNA and genomic DNA of various tissues collected between 2002 and 2011 in Linkou Chang Gung Memorial Hospital, Taiwan. During this period, a total of 1059 freshly frozen specimens from eight major cancer categories were examined. It was found that preservation duration, organ origin, and tissue type could all influence the quality of RNA samples. The increased preservation period correlated with decreased RNA quality; the brain, breast, and stomach RNA specimens displayed faster degradation rates than those of other organs, and RNA specimens isolated from tumor tissues were apparently more stable than those of other tissues. These factors could all be used as quality predictors of RNA quality. In contrast, almost all analyses revealed that the genomic DNA samples had good quality, which was not influenced by the aforementioned factors. The results assisted us in determining preservation factors that affect specimen quality, which could provide evidence for improving processes of sample collection and preservation. Furthermore, the results are also useful for researchers to adopt as the evaluation criteria for choosing specimen collection and preservation strategies.

Evaluation of specimen preservatives for DNA analyses of bees

USGS Publications Warehouse

Frampton, M.; Droege, S.; Conrad, T.; Prager, S.; Richards, M.H.

2008-01-01

Large-scale insect collecting efforts that are facilitated by the use of pan traps result in large numbers of specimens being collected. Storage of these specimens can be problematic if space and equipment are limited. In this study, we investigated the effects of various preservatives (alcohol solutions and DMSO) on the amount and quality of DNA extracted from bees (specifically Halictidae, Apidae, and Andrenidae). In addition, we examined the amount and quality of DNA obtained from bee specimens killed and stored at -80 degrees C and from specimens stored for up to 24 years in ethanol. DNA quality was measured in terms of how well it could be PCR-amplified using a set of mitochondrial primers that are commonly used in insect molecular systematics. Overall the best methods of preservation were ultra-cold freezing and dimethyl sulfoxide, but these are both expensive and in the case of ultra-cold freezing, somewhat impractical for field entomologists. Additionally, dimethyl sulfoxide was shown to have adverse effects on morphological characters that are typically used for identification to the level of species. We therefore recommend that the best alternative is 95% ethanol, as it preserves bee specimens well for both morphological and molecular studies.

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging.

PubMed

Nakasako, Masayoshi; Takayama, Yuki; Oroguchi, Tomotaka; Sekiguchi, Yuki; Kobayashi, Amane; Shirahama, Keiya; Yamamoto, Masaki; Hikima, Takaaki; Yonekura, Koji; Maki-Yonekura, Saori; Kohmura, Yoshiki; Inubushi, Yuichi; Takahashi, Yukio; Suzuki, Akihiro; Matsunaga, Sachihiro; Inui, Yayoi; Tono, Kensuke; Kameshima, Takashi; Joti, Yasumasa; Hoshi, Takahiko

2013-09-01

We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.

Evaluation of Sampling Recommendations From the Influenza Virologic Surveillance Right Size Roadmap for Idaho.

PubMed

Rosenthal, Mariana; Anderson, Katey; Tengelsen, Leslie; Carter, Kris; Hahn, Christine; Ball, Christopher

2017-08-24

The Right Size Roadmap was developed by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention to improve influenza virologic surveillance efficiency. Guidelines were provided to state health departments regarding representativeness and statistical estimates of specimen numbers needed for seasonal influenza situational awareness, rare or novel influenza virus detection, and rare or novel influenza virus investigation. The aim of this study was to compare Roadmap sampling recommendations with Idaho's influenza virologic surveillance to determine implementation feasibility. We calculated the proportion of medically attended influenza-like illness (MA-ILI) from Idaho's influenza-like illness surveillance among outpatients during October 2008 to May 2014, applied data to Roadmap-provided sample size calculators, and compared calculations with actual numbers of specimens tested for influenza by the Idaho Bureau of Laboratories (IBL). We assessed representativeness among patients' tested specimens to census estimates by age, sex, and health district residence. Among outpatients surveilled, Idaho's mean annual proportion of MA-ILI was 2.30% (20,834/905,818) during a 5-year period. Thus, according to Roadmap recommendations, Idaho needs to collect 128 specimens from MA-ILI patients/week for situational awareness, 1496 influenza-positive specimens/week for detection of a rare or novel influenza virus at 0.2% prevalence, and after detection, 478 specimens/week to confirm true prevalence is ≤2% of influenza-positive samples. The mean number of respiratory specimens Idaho tested for influenza/week, excluding the 2009-2010 influenza season, ranged from 6 to 24. Various influenza virus types and subtypes were collected and specimen submission sources were representative in terms of geographic distribution, patient age range and sex, and disease severity. Insufficient numbers of respiratory specimens are submitted to IBL for influenza laboratory testing. Increased specimen submission would facilitate meeting Roadmap sample size recommendations. ©Mariana Rosenthal, Katey Anderson, Leslie Tengelsen, Kris Carter, Christine Hahn, Christopher Ball. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 24.08.2017.

Evaluation of Sampling Recommendations From the Influenza Virologic Surveillance Right Size Roadmap for Idaho

PubMed Central

2017-01-01

Background The Right Size Roadmap was developed by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention to improve influenza virologic surveillance efficiency. Guidelines were provided to state health departments regarding representativeness and statistical estimates of specimen numbers needed for seasonal influenza situational awareness, rare or novel influenza virus detection, and rare or novel influenza virus investigation. Objective The aim of this study was to compare Roadmap sampling recommendations with Idaho’s influenza virologic surveillance to determine implementation feasibility. Methods We calculated the proportion of medically attended influenza-like illness (MA-ILI) from Idaho’s influenza-like illness surveillance among outpatients during October 2008 to May 2014, applied data to Roadmap-provided sample size calculators, and compared calculations with actual numbers of specimens tested for influenza by the Idaho Bureau of Laboratories (IBL). We assessed representativeness among patients’ tested specimens to census estimates by age, sex, and health district residence. Results Among outpatients surveilled, Idaho’s mean annual proportion of MA-ILI was 2.30% (20,834/905,818) during a 5-year period. Thus, according to Roadmap recommendations, Idaho needs to collect 128 specimens from MA-ILI patients/week for situational awareness, 1496 influenza-positive specimens/week for detection of a rare or novel influenza virus at 0.2% prevalence, and after detection, 478 specimens/week to confirm true prevalence is ≤2% of influenza-positive samples. The mean number of respiratory specimens Idaho tested for influenza/week, excluding the 2009-2010 influenza season, ranged from 6 to 24. Various influenza virus types and subtypes were collected and specimen submission sources were representative in terms of geographic distribution, patient age range and sex, and disease severity. Conclusions Insufficient numbers of respiratory specimens are submitted to IBL for influenza laboratory testing. Increased specimen submission would facilitate meeting Roadmap sample size recommendations. PMID:28838883

A Study on the Influence of Process Parameters on the Viscoelastic Properties of ABS Components Manufactured by FDM Process

NASA Astrophysics Data System (ADS)

Dakshinamurthy, Devika; Gupta, Srinivasa

2018-04-01

Fused Deposition Modelling (FDM) is a fast growing Rapid Prototyping (RP) technology due to its ability to build parts having complex geometrical shape in reasonable time period. The quality of built parts depends on many process variables. In this study, the influence of three FDM process parameters namely, slice height, raster angle and raster width on viscoelastic properties of Acrylonitrile Butadiene Styrene (ABS) RP-specimen is studied. Statistically designed experiments have been conducted for finding the optimum process parameter setting for enhancing the storage modulus. Dynamic Mechanical Analysis has been used to understand the viscoelastic properties at various parameter settings. At the optimal parameter setting the storage modulus and loss modulus of the ABS-RP specimen was 1008 and 259.9 MPa respectively. The relative percentage contribution of slice height and raster width on the viscoelastic properties of the FDM-RP components was found to be 55 and 31 % respectively.

Use of pure nickel and LiOH for thermal energy storage

NASA Technical Reports Server (NTRS)

Whittenberger, J. D.

1988-01-01

The solid to liquid phase transformation of LiOH has been proposed as an ideal candidate thermal energy storage media for a Rankine Cycle powered electrical generation unit envisioned in Space Station based solar dynamic systems. Due to the corrosive nature of molten hydroxides, long term containment of LiOH is of concern. Pure nickel is thought to be a suitably resistant material, and a program has been instituted to measure the effects of prolonged exposure of liquid and gaseous LiOH on the mechanical properties of pure nickel alloys. Results to date indicate that negligible weight and thickness changes occurred in Ni alloys exposed to LiOH for as long as 2500 hr at 775 K, and essentially no difference in 77-900 K tensile properties could be detected between LiOH exposed and vacuum annealed Ni specimens. Although there was little sign of outward damage, microstructural examination revealed that all hydroxide contaminated tensile test specimens had surface connected intergranular cracks along the gage lengths. Two other potential problems, which have strong implications with respect to a LiOH/Ni energy storage system, were also noted during the corrosion experiments. In particular stress corrosion cracking of weld joints in pressurized vessel and permeation of hydrogen through nickel were observed.

Quality specification in haematology: the automated blood cell count.

PubMed

Buttarello, Mauro

2004-08-02

Quality specifications for automated blood cell counts include topics that go beyond the traditional analytic stage (imprecision, inaccuracy, quality control) and extend to pre- and post-analytic phases. In this review pre-analytic aspects concerning the choice of anticoagulants, maximum conservation times and differences between storage at room temperature or at 4 degrees C are considered. For the analytic phase, goals for imprecision and bias obtained with various approaches (ratio to biologic variation, state of the art, specific clinical situations) are evaluated. For the post-analytic phase, medical review criteria (algorithm, decision limit and delta check) and the structure of the report (general part and comments), which constitutes the formal act through which a laboratory communicates with clinicians, are considered. K2EDTA is considered the anticoagulant of choice for automated cell counts. Regarding storage, specimens should be analyzed as soon as possible. Storage at 4 degrees C may stabilize specimens from 24 to 72 h when complete blood count (CBC) and differential leucocyte count (DLC) is performed. For precision, analytical goals based on the state of the art are acceptable while for bias this is satisfactory only for some parameters. In haematology quality specifications for pre- and analytical phases are important, but the review criteria and the quality of the report play a central role in assuring a definite clinical value.

Genus Level Identification of Mycobacteria from Clinical Specimens by Using an Easy-To-Handle Mycobacterium-Specific PCR Assay

PubMed Central

Stauffer, Fritz; Haber, Heinrich; Rieger, Armin; Mutschlechner, Robert; Hasenberger, Petra; Tevere, Vincent J.; Young, Karen K. Y.

1998-01-01

An easy-to-handle Mycobacterium-specific PCR assay for detection of the presence of a wide range of mycobacterial species in clinical samples was evaluated. The performance of the genus probe was compared with the performance of probes specific for Mycobacterium tuberculosis and Mycobacterium avium and with that of standard culture. In addition, the utility of an internal control in monitoring amplification inhibitors was studied. Of 545 respiratory and 325 nonrespiratory specimens (a total of 870 specimens), 58 (6.7%) showed the presence of amplification inhibitors, as determined by a negative result for the internal control. Of these 58 specimens, 31 (53%) were stool specimens; other material, even citrate blood after lysis of erythrocytes, did not pose a problem with regard to inhibition of PCR amplification. Eighty-one of the remaining 812 specimens had a positive Mycobacterium culture result. Of these culture-positive specimens, 58 (71.6%) showed a positive result with the Mycobacterium genus-specific probe. Seventy-two samples had a positive result with the Mycobacterium-specific probe but a negative culture result. Of these 72 samples, 26 samples were regarded as true positive, either because the M. tuberculosis- or M. avium-specific probe was also positive at the same time or because other specimens from the same patient taken at the same time were culture positive. The sensitivity of the Mycobacterium-specific probe was 78.5% and the specificity was 93.5%. This study showed that pretesting of clinical specimens for mycobacteria to the genus level with a Mycobacterium-specific probe offers the routine clinical laboratory the possibility of detecting tuberculous and nontuberculous mycobacteria with one test. Furthermore, specimens testing positive with the genus-specific probe can be immediately identified with species-specific probes. PMID:9508282

Clinical biochemistry laboratory rejection rates due to various types of preanalytical errors.

PubMed

Atay, Aysenur; Demir, Leyla; Cuhadar, Serap; Saglam, Gulcan; Unal, Hulya; Aksun, Saliha; Arslan, Banu; Ozkan, Asuman; Sutcu, Recep

2014-01-01

Preanalytical errors, along the process from the beginning of test requests to the admissions of the specimens to the laboratory, cause the rejection of samples. The aim of this study was to better explain the reasons of rejected samples, regarding to their rates in certain test groups in our laboratory. This preliminary study was designed on the rejected samples in one-year period, based on the rates and types of inappropriateness. Test requests and blood samples of clinical chemistry, immunoassay, hematology, glycated hemoglobin, coagulation and erythrocyte sedimentation rate test units were evaluated. Types of inappropriateness were evaluated as follows: improperly labelled samples, hemolysed, clotted specimen, insufficient volume of specimen and total request errors. A total of 5,183,582 test requests from 1,035,743 blood collection tubes were considered. The total rejection rate was 0.65 %. The rejection rate of coagulation group was significantly higher (2.28%) than the other test groups (P < 0.001) including insufficient volume of specimen error rate as 1.38%. Rejection rates of hemolysis, clotted specimen and insufficient volume of sample error were found to be 8%, 24% and 34%, respectively. Total request errors, particularly, for unintelligible requests were 32% of the total for inpatients. The errors were especially attributable to unintelligible requests of inappropriate test requests, improperly labelled samples for inpatients and blood drawing errors especially due to insufficient volume of specimens in a coagulation test group. Further studies should be performed after corrective and preventive actions to detect a possible decrease in rejecting samples.

Inhibition of atmospheric corrosion of mild steel by sodium benzoate treatment

NASA Astrophysics Data System (ADS)

Kahraman, Ramazan

2002-02-01

The objective of this study was to evaluate the effectiveness of sodium benzoate as an inhibitor to slow down or prevent atmospheric corrosion/discoloration of the local mild steel during storage in the Arabian Gulf region. Test specimens were prepared from locally produced reinforcing steel products. The inhibitor solution was applied on steel specimens at a concentration of 100 mM for 1 day at room temperature. Wooden exposure racks were used to hold as-received and inhibitor-treated specimens during atmospheric exposure for different periods. Corrosion was evaluated through weight loss determination and electrochemical technique. As expected, the Arabian Gulf atmosphere was corrosive on the as-received local mild steel. On the other hand, treatment of steel with sodium benzoate lowered its corrosion rate during initial days of its exposure to atmosphere. However, atmospheric corrosion inhibition performance of sodium benzoate deteriorated with exposure time after 30 or more days of atmospheric exposure, and the corrosion rates of sodium benzoate-treated specimens reached that of the unprotected specimens at the end of 90 days of atmospheric exposure.

Storage of cell samples for ToF-SIMS experiments-How to maintain sample integrity.

PubMed

Schaepe, Kaija; Kokesch-Himmelreich, Julia; Rohnke, Marcus; Wagner, Alena-Svenja; Schaaf, Thimo; Henss, Anja; Wenisch, Sabine; Janek, Jürgen

2016-06-25

In order to obtain comparable and reproducible results from time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of biological cells, the influence of sample preparation and storage has to be carefully considered. It has been previously shown that the impact of the chosen preparation routine is crucial. In continuation of this work, the impact of storage needs to be addressed, as besides the fact that degradation will unavoidably take place, the effects of different storage procedures in combination with specific sample preparations remain largely unknown. Therefore, this work examines different wet (buffer, water, and alcohol) and dry (air-dried, freeze-dried, and critical-point-dried) storage procedures on human mesenchymal stem cell cultures. All cell samples were analyzed by ToF-SIMS immediately after preparation and after a storage period of 4 weeks. The obtained spectra were compared by principal component analysis with lipid- and amino acid-related signals known from the literature. In all dry storage procedures, notable degradation effects were observed, especially for lipid-, but also for amino acid-signal intensities. This leads to the conclusion that dried samples are to some extent easier to handle, yet the procedure is not the optimal storage solution. Degradation proceeds faster, which is possibly caused by oxidation reactions and cleaving enzymes that might still be active. Just as well, wet stored samples in alcohol struggle with decreased signal intensities from lipids and amino acids after storage. Compared to that, the wet stored samples in a buffered or pure aqueous environment revealed no degradation effects after 4 weeks. However, this storage bears a higher risk of fungi/bacterial contamination, as sterile conditions are typically not maintained. Thus, regular solution change is recommended for optimized storage conditions. Not directly exposing the samples to air, wet storage seems to minimize oxidation effects, and hence, buffer or water storage with regular renewal of the solution is recommended for short storage periods.

Storage of cell samples for ToF-SIMS experiments—How to maintain sample integrity

PubMed Central

Schaepe, Kaija; Kokesch-Himmelreich, Julia; Rohnke, Marcus; Wagner, Alena-Svenja; Schaaf, Thimo; Henss, Anja; Wenisch, Sabine; Janek, Jürgen

2016-01-01

In order to obtain comparable and reproducible results from time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of biological cells, the influence of sample preparation and storage has to be carefully considered. It has been previously shown that the impact of the chosen preparation routine is crucial. In continuation of this work, the impact of storage needs to be addressed, as besides the fact that degradation will unavoidably take place, the effects of different storage procedures in combination with specific sample preparations remain largely unknown. Therefore, this work examines different wet (buffer, water, and alcohol) and dry (air-dried, freeze-dried, and critical-point-dried) storage procedures on human mesenchymal stem cell cultures. All cell samples were analyzed by ToF-SIMS immediately after preparation and after a storage period of 4 weeks. The obtained spectra were compared by principal component analysis with lipid- and amino acid-related signals known from the literature. In all dry storage procedures, notable degradation effects were observed, especially for lipid-, but also for amino acid-signal intensities. This leads to the conclusion that dried samples are to some extent easier to handle, yet the procedure is not the optimal storage solution. Degradation proceeds faster, which is possibly caused by oxidation reactions and cleaving enzymes that might still be active. Just as well, wet stored samples in alcohol struggle with decreased signal intensities from lipids and amino acids after storage. Compared to that, the wet stored samples in a buffered or pure aqueous environment revealed no degradation effects after 4 weeks. However, this storage bears a higher risk of fungi/bacterial contamination, as sterile conditions are typically not maintained. Thus, regular solution change is recommended for optimized storage conditions. Not directly exposing the samples to air, wet storage seems to minimize oxidation effects, and hence, buffer or water storage with regular renewal of the solution is recommended for short storage periods. PMID:26810048

Internet of Things technology-based management methods for environmental specimen banks.

PubMed

Peng, Lihong; Wang, Qian; Yu, Ang

2015-02-01

The establishment and management of environmental specimen banks (ESBs) has long been a problem worldwide. The complexity of specimen environment has made the management of ESB likewise complex. Through an analysis of the development and management of ESBs worldwide and in light of the sophisticated Internet of Things (IOT) technology, this paper presents IOT technology-based ESB management methods. An IOT technology-based ESB management system can significantly facilitate ESB ingress and egress management as well as long-term storage management under quality control. This paper elaborates on the design of IOT technology-based modules, which can be used in ESB management to achieve standardized, smart, information-based ESB management. ESB management has far-reaching implications for environmental management and for research in environmental science.

The influence of storage time and pH variation on water sorption by different composite resins.

PubMed

Gusmão, George Mário de Araújo Silva; De Queiroz, Thiago Vinicius Veras; Pompeu, Guilherme Ferrer; Menezes Filho, Paulo Fonseca; da Silva, Cláudio Heliomar Vicente

2013-01-01

The objective of this work was to assess the influence of storage time and pH cycling on water sorption by different composite resins. Nine resin brands were selected and divided into groups: G1-ROK (SDI), G2-ICE (SDI), G3-GLACIER (SDI), G4-Z350 (3M/ESPE), G5-Z250 (3M/ESPE), G6-TPH 3 (DENTSPLY), G7-ESTHET X (DENTSPLY), G8-SUPRAFILL (SSWHITE), and G9-MASTERFILL (BIODINΒMICS). Ninety specimens, ten per group, were obtained using an aluminum matrix. Specimens measured 10 mm diameter × 2 mm width. The groups were divided into subgroups according to the immersion solution: A - control (n = 05) stored in artificial saliva pH = 7.0 and B-test (n = 05) submitted to seven consecutive days of pH cycling (cariogenic challenger) that consisted of immersion in a pH° = 4.3 solution for 6 h followed by immersion in a pH¹ =7.0 solution for 18 h and stored in artificial saliva pH = 7.0 until the end of the experiment. The specimens were weighed on six occasions: T 0 (after fabrication), T 1 (24 h), T 2 (7 days), T 3 (15 days), T 4 (30 days), T 5 (60 days), and then analyzed. The water sorption was determined by the weight difference between the specimens at the time intervals. The mean weight gain was exactly the same for both the subgroups within group G4. The highest means for the control subgroup were found in groups: G1, G5, G7, G8, and G9. For the pH cycling subgroup, the highest means were found in G2, G3, and G6; however, significant differences between the subgroups compared to the mean-weight gain were found for G1, G5, and G7. The water sorption of composite resins is dependent upon their storage time. The pH cycling created a significant impact on resins G1, G5, and G7. The sorption and solubility of composite resins vary according to their chemical composition.

Was it poisoning?

PubMed

Flanagan, R J

The aim of post-mortem toxicology is to help establish the role that drugs or other poisons played in a death, or in events immediately before death. If self-poisoning is suspected then the diagnosis may be straightforward and all that may be required is confirmation of the agents involved. If the cause of death is not immediately obvious, however, then suspicion of possible poisoning is of course crucial. Blood sampling (needle aspiration, peripheral vein, e.g. femoral, ideally after proximal ligation) before opening the body, minimises the risk of sample contamination with, for example, gut contents or urine. The site of blood sampling should always be recorded. Other specimens (stomach contents, urine, liver, vitreous humor) may also be valuable and may be needed to corroborate unexpected or unusual findings in the absence of other evidence. The availability of ante-mortem specimens should not preclude post-mortem sampling. Appropriate sample preservation, transport, and storage are mandatory. Interpretation of post-mortem toxicology must take into account what is known of the clinical pharmacology, including pharmacokinetics, and toxicology of the agent(s) in question, the circumstances under which death occurred including the possible mechanism(s) of exposure, and other factors such as the sample(s) analysed and the analytical methods used. It was thought that concentrations of poisons measured in blood obtained at autopsy reflected the situation peri-mortem. However, we now know that changes may occur in the composition of body fluids, even peripheral blood, after death. Such changes are likely to be greater with centrally-acting drugs such as clozapine with large volumes of distribution, and may perhaps be minimised by prompt refrigeration of the body and performing the autopsy quickly. Better training in analytical toxicology is needed for pathologists and others who may be called upon to interpret toxicological data for the Courts. Undue reliance on quantitative results is likely to confuse sooner rather than later, especially in the case of centrally-acting drugs such as opioids and clozapine. Remember that the question is normally "was it poisoning?" or "was it an overdose?"--and not--"is it a fatal level"?

40 CFR 160.130 - Conduct of a study.

Code of Federal Regulations, 2014 CFR

2014-07-01

... manner that precludes error in the recording and storage of data. (d) In animal studies where... available to a pathologist when examining that specimen histopathologically. (e) All data generated during the conduct of a study, except those that are generated by automated data collection systems, shall be...

40 CFR 160.130 - Conduct of a study.

Code of Federal Regulations, 2012 CFR

2012-07-01

... manner that precludes error in the recording and storage of data. (d) In animal studies where... available to a pathologist when examining that specimen histopathologically. (e) All data generated during the conduct of a study, except those that are generated by automated data collection systems, shall be...

An improved FIB sample preparation technique for site-specific plan-view specimens: A new cutting geometry.

PubMed

Li, Chen; Habler, Gerlinde; Baldwin, Lisa C; Abart, Rainer

2018-01-01

Focused ion beam (FIB) sample preparation technique in plan-view geometry allows direct correlations of the atomic structure study via transmission electron microscopy with micrometer-scale property measurements. However, one main technical difficulty is that a large amount of material must be removed underneath the specimen. Furthermore, directly monitoring the milling process is difficult unless very large material volumes surrounding the TEM specimen site are removed. In this paper, a new cutting geometry is introduced for FIB lift-out sample preparation with plan-view geometry. Firstly, an "isolated" cuboid shaped specimen is cut out, leaving a "bridge" connecting it with the bulk material. Subsequently the two long sides of the "isolated" cuboid are wedged, forming a triangular prism shape. A micromanipulator needle is used for in-situ transfer of the specimen to a FIB TEM grid, which has been mounted parallel with the specimen surface using a simple custom-made sample slit. Finally, the grid is transferred to the standard FIB grid holder for final thinning with standard procedures. This new cutting geometry provides clear viewing angles for monitoring the milling process, which solves the difficulty of judging whether the specimen has been entirely detached from the bulk material, with the least possible damage to the surrounding materials. With an improved success rate and efficiency, this plan-view FIB lift-out specimen preparation technique should have a wide application for material science. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evaluation of a commercial ligase chain reaction assay for the diagnosis of pulmonary and extra-pulmonary tuberculosis.

PubMed

Viveiros, M; Pinheiro, S; Moreira, P; Pacheco, T; Brum, L

1999-06-01

Egas Moniz Hospital, Lisbon, Portugal. To evaluate the Ligase Chain Reaction (LCx) Mycobacterium tuberculosis Assay for the direct detection of M. tuberculosis complex in respiratory specimens after smear observation, and its suitability for non-respiratory clinical specimens. Analysis of 156 specimens collected from 123 patients with pulmonary tuberculosis and/or extrapulmonary involvement. Among 93 pulmonary secretions and 63 extra-pulmonary samples and after resolution of discrepancies based on clinical and laboratory findings, two pulmonary samples from a patient with a diagnosis of sarcoidosis, four samples of cerebrospinal and one of seminal fluid were considered as false positives. Two tissue biopsy samples, one pericardial effusion and one pulmonary secretion from patients strongly suspected of having tuberculosis were considered as false negatives for the assay, without inhibition of amplification. All specimens yielding M. avium on culture were LCx negative. The LCx Mycobacterium tuberculosis Assay was found to be useful for the rapid identification of M. tuberculosis complex in all types of specimens. It revealed a high specificity both in pulmonary and extrapulmonary products, and a sensitivity of 97% for the pulmonary secretions and of 75% for the extra-pulmonary specimens, independently of the bacilloscopy results.

Influence of gross specimen sampling on the incidence of incidental prostatic carcinoma in cystoprostatectomy specimens of patients with bladder carcinoma.

PubMed

Mlakar, J; Volavšek, M

2016-03-01

Reported prostate cancer incidence rates vary greatly among cystoprostatectomy samples. We investigated how the thoroughness of prostate sampling influences prostatic carcinoma incidence in bladder cancer patients. In a retrospective study, 313 cystoprostatectomy cases of urinary bladder carcinoma were analysed for the presence of concurrent prostatic carcinoma. Patients were divided into two groups: patients who had undergone the operation before and after 2007, when a policy of preferably complete prostate sampling in cystoprostatectomy specimens was introduced at our institution. Cases processed after the 2007 recommended sampling changes had a significantly higher rate of incidental prostatic carcinoma and clinically significant prostatic carcinoma than the pre-2007 group (p < 0.0001 and p = 0.003, respectively). Complete prostate processing in cystoprostatectomy specimens results in a higher incidence of incidental prostatic carcinoma than with partial processing. More patients with clinically significant prostate cancer are consequently discovered. In conclusion, we believe that complete prostate sampling should be mandatory.

Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4{degrees}C

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

Haldeman, D.L.; Amy, P.S.; White, D.C.

1994-08-01

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4{degrees}C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at bothmore » sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage. 30 refs., 1 fig., 5 tabs.« less

The impact of long term freezing on the mechanical properties of porcine aortic tissue.

PubMed

O'Leary, Siobhan A; Doyle, Barry J; McGloughlin, Tim M

2014-09-01

Preservation of the native artery׳s functionality can be important in both clinical and experimental applications. Although, simple cryopreservation techniques offer an attractive solution to this problem, the extent to which freezing affects the tissue׳s properties is widely debated. Earlier assessments of the mechanical properties post-freezing have been limited by one or more of the following: small sample numbers, uncontrolled inter-specimen/animal variability, failure to account for the impact of potential errors in thickness measurements, short storage times and uniaxial test methods. Biaxial mechanical tests were performed on porcine aortic samples (n=89) extracted from superior, middle and inferior regions of five aortas, stored in isotonic saline at -20°C for 1 day, 1 week, 1, 6 and 12 months, thawed and retested. The sample׳s weight and thickness were also measured pre and post-freezing. A total of 178 tests were performed and elastic modulus was assessed by calculating the slope of the Cauchy stress-stretch curve at the low and high stretch regions in both the circumferential (θ) and longitudinal (L) directions. The weight of the samples increased post-freezing. However, in general, no significant difference was found between the elastic modulus of porcine aortic tissue before and after freezing at -20°C and was unaffected by storage time. Although more accurate measuring instruments are warranted to confirm this finding, minor changes to the elastic modulus as a result of freezing were negatively correlated with regional variances i.e. changes in the elastic modulus decreased from the superior to the inferior region. These results indicate that for applications which require preservation of the gross mechanical properties, storing the tissue at -20°C in isotonic saline, for an extended period of time, is acceptable. Copyright © 2014 Elsevier Ltd. All rights reserved.

A qualitative signature for early diagnosis of hepatocellular carcinoma based on relative expression orderings.

PubMed

Ao, Lu; Zhang, Zimei; Guan, Qingzhou; Guo, Yating; Guo, You; Zhang, Jiahui; Lv, Xingwei; Huang, Haiyan; Zhang, Huarong; Wang, Xianlong; Guo, Zheng

2018-04-23

Currently, using biopsy specimens to confirm suspicious liver lesions of early hepatocellular carcinoma are not entirely reliable because of insufficient sampling amount and inaccurate sampling location. It is necessary to develop a signature to aid early hepatocellular carcinoma diagnosis using biopsy specimens even when the sampling location is inaccurate. Based on the within-sample relative expression orderings of gene pairs, we identified a simple qualitative signature to distinguish both hepatocellular carcinoma and adjacent non-tumour tissues from cirrhosis tissues of non-hepatocellular carcinoma patients. A signature consisting of 19 gene pairs was identified in the training data sets and validated in 2 large collections of samples from biopsy and surgical resection specimens. For biopsy specimens, 95.7% of 141 hepatocellular carcinoma tissues and all (100%) of 108 cirrhosis tissues of non-hepatocellular carcinoma patients were correctly classified. Especially, all (100%) of 60 hepatocellular carcinoma adjacent normal tissues and 77.5% of 80 hepatocellular carcinoma adjacent cirrhosis tissues were classified to hepatocellular carcinoma. For surgical resection specimens, 99.7% of 733 hepatocellular carcinoma specimens were correctly classified to hepatocellular carcinoma, while 96.1% of 254 hepatocellular carcinoma adjacent cirrhosis tissues and 95.9% of 538 hepatocellular carcinoma adjacent normal tissues were classified to hepatocellular carcinoma. In contrast, 17.0% of 47 cirrhosis from non-hepatocellular carcinoma patients waiting for liver transplantation were classified to hepatocellular carcinoma, indicating that some patients with long-lasting cirrhosis could have already gained hepatocellular carcinoma characteristics. The signature can distinguish both hepatocellular carcinoma tissues and tumour-adjacent tissues from cirrhosis tissues of non-hepatocellular carcinoma patients even using inaccurately sampled biopsy specimens, which can aid early diagnosis of hepatocellular carcinoma. © 2018 The Authors. Liver International Published by John Wiley & Sons Ltd.

Effect of time on tensile bond strength of resin cement bonded to dentine and low-viscosity composite.

PubMed

Duarte, Rosângela Marques; de Goes, Mario Fernando; Montes, Marcos Antonio Japiassú Resende

2006-01-01

The purpose of this study was to evaluate the tensile bond strength (TBS) of Panavia F resin cement (PF) applied on dentine pre-treated with ED Primer (ED) and Clearfil Liner Bond 2V (CLB) coated with a layer of low-viscosity composite Protect Liner F (PLF) at 10 min, 24 h and 12 months after curing. The labial surfaces of 60 bovine lower incisors were ground to obtain a flat dentine surface, allowing a demarcation of a 4.0 mm-diameter area with adhesive tape. The teeth were randomly divided in six groups; ED was applied in groups A I, A II and A III and CLB was applied, followed by PLF, in groups B I, B II and B III. A resin composite rod with a wire loop was luted directly to the prepared surface of each group with PF. The specimens of groups A I and B I were submitted to TBS test after 10 min. Groups A II and B II were submitted to TBS test after 24 h storage and groups A III and B III were submitted to TBS test after 12 months storage. Each specimen was inspected by SEM and classified according to the failure mode. Additionally, two representative specimens of each failure mode were sectioned for a composite/dentine interface SEM evaluation. No significant statistical differences were observed among the groups at 10 min and 24 h. Groups A III and B III presented the lowest TBS values (p<0.05) after 12 months storage. PF on resin-coated dentin (PLF) showed the highest TBS values and was statistically different to PF on dentine for all the groups. The fracture pattern was generally cohesive on the adhesive/hybrid layer for groups A I, A II and A III and cohesive on composite resin for B I, B II and B III. The use of a less hydrophilic self-etching system to pre-treat dentine, coating with a low-viscosity composite layer prior luting with resin cement, may provide a protection of the hybridised complex, allowing a dentine seal during the 12 months storage period.

Effect of Energy Drinks on Discoloration of Silorane and Dimethacrylate-Based Composite Resins.

PubMed

Ahmadizenouz, Ghazaleh; Esmaeili, Behnaz; Ahangari, Zohreh; Khafri, Soraya; Rahmani, Aghil

2016-08-01

This study aimed to assess the effects of two energy drinks on color change (ΔE) of two methacrylate-based and a silorane-based composite resin after one week and one month. Thirty cubic samples were fabricated from Filtek P90, Filtek Z250 and Filtek Z350XT composite resins. All the specimens were stored in distilled water at 37°C for 24 hours. Baseline color values (L*a*b*) of each specimen were measured using a spectrophotometer according to the CIEL*a*b* color system. Ten randomly selected specimens from each composite were then immersed in the two energy drinks (Hype, Red Bull) and artificial saliva (control) for one week and one month. Color was re-assessed after each storage period and ΔE values were calculated. The data were analyzed using the Kruskal Wallis and Mann-Whitney U tests. Filtek Z250 composite showed the highest ΔE irrespective of the solutions at both time points. After seven days and one month, the lowest ΔE values were observed in Filtek Z350XT and Filtek P90 composites immersed in artificial saliva, respectively. The ΔE values of Filtek Z250 and Z350XT composites induced by Red Bull and Hype energy drinks were not significantly different. Discoloration of Filtek P90 was higher in Red Bull energy drink at both time points. Prolonged immersion time in all three solutions increased ΔE values of all composites. However, the ΔE values were within the clinically acceptable range (<3.3) at both time points.

[Aging of silorane- and methacrylate-based composite resins: effects on color and translucency].

PubMed

Liu, Chang; Pan, Jie; Lin, Hong; Shen, Song

2015-10-01

To evaluate the color stability and translucency of silorane-based low shrinkage composite after in vitro aging procedures of thermal cycling and water storage respectively, and to compare with those of conventional methacrylate-based posterior composite. Three light-cured composite resins, dimethacrylate-based composite A (Filtek™ Z350), B (Filtek™ P60) and silorane-based composite C (Filtek™ P90), were tested in this study. Ten specimens (10 mm in diameter, 1 mm in height) of each composite were prepared. The ten specimens in each group were then divided into two subgroups (n = 5). One subgroup underwent thermal cycling [(5.0 ± 0.5)~(55.0 ± 1.0) °C, 10 000 cycles] and the other was stored in 37 C° distilled water for 180 days. With a spectrophotometer, the CIE L * a * b * parameters of the specimens were tested before and after artificial aging against white, medium grey and black backgrounds, respectively. △E, TP and △TP were calculated and data were analyzed using independent-samples t test and partial analysis (P < 0.05). With regard to color stability, silorane-based composite showed color alteration above the clinically acceptable levels (△E > 3.3), and also showed higher △E with a statistically significant difference in comparison with the other composites (B and C) (P < 0.05) after artificial aging. With regard to translucency, composite C showed more alteration compared with composite B (P < 0.05) after thermal cycling. It may be concluded that the silorane-based composite underwent greater alteration with regard to color stability and translucency.

Diversity of sandflies (Psychodidae: Phlebotominae) captured in sandstone caves from Central Amazonia, Brazil.

PubMed

Alves, Veracilda Ribeiro; Freitas, Rui Alves de; Santos, Francisco Lima; Barrett, Toby Vincent

2011-05-01

In the present paper we describe the diversity of phlebotomine sandflies collected in three sandstone caves in the municipality of Presidente Figueiredo, state of Amazonas, Brazil. The phlebotomines were captured during 2006 with CDC light traps. Guano samples from inside the Gruta Refúgio do Maruaga were collected to investigate the presence of immature specimens. A total of 2,160 adult phlebotomines representing 15 species were captured. Pintomyia pacae was the dominant species in Gruta dos Animais (1,723 specimens) and Gruta dos Lages (50 specimens) and Deanemyia maruaga new comb (280 specimens) was the dominant species in Gruta Refúgio do Maruaga. A total of 18 guano samples were collected and seven of these samples included immature specimens. A total of 507 immature specimens were captured; 495 of these specimens were larvae and 12 were pupae. The presence of paca (Agouti paca) footprints near Gruta dos Animais and Gruta dos Lages suggests the association of Pi. pacae with this rodent. This finding may explain the abundance of Pi. pacae in these locations, while the species is relatively rare in the forest. Deanemyia maruaga is a cave species that uses guano to breed during its immature stages. Adult specimens of this species are apparently parthenogenetic and autogenous and represent the second record of parthenogenesis for the subfamily Phlebotominae.

Performance of universal adhesives on bonding to leucite-reinforced ceramic.

PubMed

Kim, Ryan Jin-Young; Woo, Jung-Soo; Lee, In-Bog; Yi, Young-Ah; Hwang, Ji-Yun; Seo, Deog-Gyu

2015-01-01

This study aimed to investigate the microshear bond strength of universal bonding adhesives to leucite-reinforced glass-ceramic. Leucite-reinforced glass-ceramic blocks were polished and etched with 9.5% hydrofluoric acid for 1 min. The specimens were assigned to one of four groups based on their surface conditioning (n = 16): 1) NC: negative control with no further treatment; 2) SBU: Single Bond Universal (3M ESPE); 3) ABU: ALL-BOND Universal (Bisco); and 4) PC: RelyX Ceramic Primer and Adper Scotchbond Multi-Purpose Adhesive (3M ESPE) as a positive control. RelyX Ultimate resin cement (3M ESPE) was placed on the pretreated ceramic and was light cured. Eight specimens from each group were stored in water for 24 h, and the remaining eight specimens were thermocycled 10,000 times prior to microshear bond strength evaluation. The fractured surfaces were examined by stereomicroscopy and scanning electron microscopy (SEM). After water storage and thermocycling, the microshear bond strength values decreased in the order of PC > SBU and ABU > NC (P < 0.05). Thermocycling significantly reduced the microshear bond strength, regardless of the surface conditioning used (P < 0.05). Cohesive failure in the ceramic and mixed failure in the ceramic and resin cement were observed in the fractured specimens. The percentage of specimens with cohesive failure after 24 h of water storage was: NC (50%), SBU (75%), ABU (75%), and PC (87%). After thermocycling, the percentage of cohesive failure in NC decreased to 25%; however, yet the percentages of the other groups remained the same. Although the bond strength between resin and hydrofluoric acid-etched glass ceramic was improved when universal adhesives were used, conventional surface conditioning using a separate silane and adhesive is preferable to a simplified procedure that uses only a universal adhesive for cementation of leucite-reinforced glass-ceramic.

Vibration damping characteristics of graphite/epoxy composites for large space structures

NASA Technical Reports Server (NTRS)

Gibson, R. F.

1982-01-01

Limited data on extensional and flexural damping of small specimens of graphite/epoxy and unreinforced epoxy resin were obtained. Flexural damping was measured using a forced vibration technique based on resonant flexural vibration of shaker excited double cantilever specimens. Extensional damping was measured by subjecting similar specimens to low frequency sinusoidal oscillation in a servohydraulic tensile testing machine while plotting load versus extensional strain. Damping was found to vary slowly and continuously over the frequency range 0.01 - 1000 Hz, and no drastic transitions were observed. Composite damping was found to be less than neat resin damping. Comparison of small specimen damping values with assembled column damping values seems to indicate that, for those materials, material damping is more important than joint damping. The data reported was limited not by the test apparatus, but by signal conditioning and data acquisition. It is believed that filtering of the strain gage signals and the use of digital storage with slow playback will make it possible to extend the frequency and amplitude ranges significantly.

Final Report for X-ray Diffraction Sample Preparation Method Development

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

Ely, T. M.; Meznarich, H. K.; Valero, T.

WRPS-1500790, “X-ray Diffraction Saltcake Sample Preparation Method Development Plan/Procedure,” was originally prepared with the intent of improving the specimen preparation methodology used to generate saltcake specimens suitable for XRD-based solid phase characterization. At the time that this test plan document was originally developed, packed powder in cavity supports with collodion binder was the established XRD specimen preparation method. An alternate specimen preparation method less vulnerable, if not completely invulnerable to preferred orientation effects, was desired as a replacement for the method.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2014-06-03

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2015-09-29

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J; Kertesz, Vilmos; Ovchinnikova, Olga S

2013-08-27

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

DEVELOPMENT OF THE U.S. EPA HEALTH EFFECTS RESEARCH LABORATORY FROZEN BLOOD CELL REPOSITORY PROGRAM

EPA Science Inventory

In previous efforts, we suggested that proper blood cell freezing and storage is necessary in longitudinal studies with reduced between tests error, for specimen sharing between laboratories and for convenient scheduling of assays. e continue to develop and upgrade programs for o...

40 CFR 792.130 - Conduct of a study.

Code of Federal Regulations, 2014 CFR

2014-07-01

... shall accompany the specimen in a manner that precludes error in the recording and storage of data. (d.... (e) All data generated during the conduct of a study, except those that are generated by automated data collection systems, shall be recorded directly, promptly, and legibly in ink. All data entries...

Degree of conversion and hardness of two different systems of the Vitrebond™ glass ionomer cement light cured with blue LED.

PubMed

Calixto, Luiz Rafael; Tonetto, Mateus Rodrigues; Pinto, Shelon Cristina Souza; Barros, Erico Damasceno; Borges, Alvaro Henrique; Lima, Fabricio Viana Pereira; de Andrade, Marcelo Ferrarezi; Bandéca, Matheus Coelho

2013-03-01

This study investigated the physicochemical properties of the new formulation of the glass ionomer cements through hardness test and degree of conversion by infrared spectroscopy (FTIR). Forty specimens (n = 40) were made in a metallic mold (4 mm diameter x 2 mm thickness) with two resin-modified glass ionomer cements, Vitrebond™ and Vitrebond™ Plus (3M/ ESPE). Each specimen was light cured with blue LED with power density of 500 mW/cm(2) during 30 s. Immediately after light curing, 24h, 48h and 7 days the hardness and degree of conversion was determined. The Vickers hardness was performed by the MMT-3 microhardness tester using load of 50 gm force for 30 seconds. For degree of conversion, the specimens were pulverized, pressed with KBr and analyzed with FT-IR (Nexus 470). The statistical analysis of the data by ANOVA showed that the Vitrebond™ and Vitrebond™ Plus were no difference significant between the same storage times (p > 0.05). For degree of conversion, the Vitrebond™ and Vitrebond™ Plus were statistically different in all storage times after light curing. The Vitrebond™ showed higher values than Vitrebond™ Plus (p < 0.05). The performance of Vitrebond™ had greater results for degree of conversion than Vitrebond™ Plus. The correlation between hardness and degree of conversion was no evidence in this study.

[Effect of three aging challenges on the bonding stability of resin-dentin interface using an etch-and-rinse adhesive].

PubMed

Xu, Shuai; Zhang, Ling; Li, Fang; Zhou, Wei; Chen, Yujiang; Chen, Jihua

2014-06-01

To systematically investigate the aging effect of thermocycling, water storage and bacteria aggression on the stability of resin-dentin bonds. Forty molars were sectioned perpendicularly to the axis of the teeth to expose the middle-coronal dentin surfaces. The dentin surfaces were then treated with Single Bond 2 and made a core build-up. According to random digits table, the bonding specimens were divided into four groups (n = 10) as follows: immediate control group, aging group with thermocycling for 5 000 times, aging group with artificial saliva storage for 6 months and aging group with bacteria aggression for 14 days. The specimens in each group were then subjected to microtensile bond strengths (µTBS) testing and nanoleakage evaluation respectively. After aging treatments, the three aging groups showed significantly lower µTBS than the immediate control group [(44.24 ± 12.75) MPa, P < 0.05]. The immediate control group also showed the lowest value of nanoleakage. The µTBS of aging group with bacteria aggression [(25.53 ± 7.39) MPa] was significantly lower than those of the other aging groups with artificial saliva storage[(29.72 ± 6.51) MPa] and thermocycling [(31.92 ± 11.87) MPa, P < 0.05]. There were no differences in the nanoleakage values among the three aging groups (P > 0.05). All the aging treatments with artificial saliva storage, thermocycling and bacteria aggression could accelerate the degradation of bonding interfaces between an etch-and-rinse adhesive and dentin. Bacteria aggression showed the most impairing effect on the stability of resin-dentin bonds.

A novel PNPLA2 mutation causes neutral lipid storage disease with myopathy (NLSDM) presenting muscular dystrophic features with lipid storage and rimmed vacuoles.

PubMed

Chen, J; Hong, D; Wang, Z; Yuan, Y

2010-01-01

Neutral lipid storage disease with myopathy (NLSDM) is a type of lipid storage myopathy arising due to a mutation in the PNPLA2 gene encoding an adipose triglyceride lipase responsible for the degradation of intracellular triglycerides. Herein, we report the cases of two siblings manifesting slowly progressive proximal and distal limb weakness in adulthood. One of the patients had dilated cardiomyopathy, hearing loss and short stature. Muscle specimens of the 2 patients revealed muscular dystrophic features with massive lipid droplets and numerous rimmed vacuoles in the fibers. A novel homozygous mutation IVS2+1G > A in the PNPLA2 gene was identified in the 2 cases, but not in the healthy familial individuals. The presence of massive lipid droplets with muscular dystrophic changes and rimmed vacuoles in muscle fibers might be one of the characteristic pathological changes of NLSDM.

Specimen dimensions influence the measurement of material properties in tendon fascicles.

PubMed

Legerlotz, Kirsten; Riley, Graham P; Screen, Hazel R C

2010-08-26

Stress, strain and modulus are regularly used to characterize material properties of tissue samples. However, when comparing results from different studies it is evident the reported material properties, particularly failure strains, vary hugely. The aim of our study was to characterize how and why specimen length and cross-sectional area (CSA) appear to influence failure stress, strain and modulus in fascicles from two functionally different tendons. Fascicles were dissected from five rat tails and five bovine foot extensors, their diameters determined by a laser micrometer, and loaded to failure at a range of grip-to-grip lengths. Strain to failure significantly decreased with increasing in specimen length in both rat and bovine fascicles, while modulus increased. Specimen length did not influence failure stress in rat tail fascicles, although in bovine fascicles it was significantly lower in the longer 40 mm specimens compared to 5 and 10mm specimens. The variations in failure strain and modulus with sample length could be predominantly explained by end-effects. However, it was also evident that strain fields along the sample length were highly variable and notably larger towards the ends of the sample than the mid-section even at distances in excess of 5mm from the gripping points. Failure strain, stress and modulus correlated significantly with CSA at certain specimen lengths. Our findings have implications for the mechanical testing of tendon tissue: while it is not always possible to control for fascicle length and/or CSA, these parameters have to be taken into account when comparing samples of different dimensions. 2010 Elsevier Ltd. All rights reserved.

A review of blood sample handling and pre-processing for metabolomics studies.

PubMed

Hernandes, Vinicius Veri; Barbas, Coral; Dudzik, Danuta

2017-09-01

Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biobanking of different body fluids within the frame of IVF-a standard operating procedure to improve reproductive biology research.

PubMed

Schenk, Michael; Huppertz, Berthold; Obermayer-Pietsch, Barbara; Kastelic, Darja; Hörmann-Kröpfl, Martina; Weiss, Gregor

2017-02-01

The aim of the present study was to develop a standard operating procedure (SOP) for the collection, transport, and storage of human cumulus cells, follicular fluid, blood serum, seminal plasma, embryo culture supernatant, and embryo culture supernatant control obtained within the IVF process under approved protocols and written informed consent from participating patients. The SOP was developed at the Kinderwunsch Institut Schenk, Dobl, Austria, together with Biobank Graz of the Medical University of Graz, Austria. The SOP provides comprehensive details of laboratory procedures and sampling of the different fluids within the IVF process. Furthermore, information on sample coding, references of involved laboratory techniques (e.g., oocyte retrieval with a Steiner-TAN needle), ethical approvals, and biobanking procedures are presented. The result of the present study is a standard operating procedure. The SOP ensures a professional way for collection and scientific use of IVF samples by the Kinderwunsch Institut Schenk, Dobl, Austria, and Biobank Graz of the Medical University of Graz, Austria. It can be used as a template for other institutions to unify specimen collection procedures in the field of reproductive health research.

Fiber-reinforced composite substructure: load-bearing capacity of an onlay restoration and flexural properties of the material.

PubMed

Garoushi, Sufyan K; Lassila, Lippo V J; Tezvergil, Arzu; Vallittu, Pekka K

2006-09-01

The aim of this study was to determine the static load-bearing capacity of composite resin onlay restorations made of particulate filler composite (PFC) with two different types of fiber-reinforced composite (FRC) substructures. In addition, flexural properties of the material combination and the effect of polymerization devices were tested. Specimens were prepared to simulate an onlay restoration, which consisted of 2 to 3 mm of FRC layer as a substructure (short random and continuous bidirectional fiber orientation) and a 1 mm surface layer of PFC. Control specimens were prepared from plain PFC. In Group A the specimens were incrementally polymerized only with a hand-light curing unit for 40 s, while in Group B the specimens were post-cured in a light-curing oven for 15 min before they were statically loaded with a steel ball. Bar-shaped test specimens were prepared to measure the flexural properties of material combination using a three-point bending test (ISO 10477). Analysis of variance (ANOVA) revealed all specimens with a FRC substructure have higher values of static load-bearing capacity and flexural properties than those obtained with plain PFC (p<0.001). The load-bearing capacity of all the specimens decreased after post-curing and water storage. Restorations made from a material combination of FRC and PFC showed better mechanical properties than those obtained with plain PFC.

Contamination with HIV antibody may be responsible for false positive results in specimens tested on automated platforms running HIV 4th generation assays in a region of high HIV prevalence.

PubMed

Hardie, Diana Ruth; Korsman, Stephen N; Hsiao, Nei-Yuan; Morobadi, Molefi Daniel; Vawda, Sabeehah; Goedhals, Dominique

2017-01-01

In South Africa where the prevalence of HIV infection is very high, 4th generation HIV antibody/p24 antigen combo immunoassays are the tests of choice for laboratory based screening. Testing is usually performed in clinical pathology laboratories on automated analysers. To investigate the cause of false positive results on 4th generation HIV testing platforms in public sector laboratories, the performance of two automated platforms was compared in a clinical pathology setting, firstly on routine diagnostic specimens and secondly on known sero-negative samples. Firstly, 1181 routine diagnostic specimens were sequentially tested on Siemens and Roche automated 4th generation platforms. HIV viral load, western blot and follow up testing were used to determine the true status of inconclusive specimens. Subsequently, known HIV seronegative samples from a single donor were repeatedly tested on both platforms and an analyser was tested for surface contamination with HIV positive serum to identify how suspected specimen contamination could be occurring. Serial testing of diagnostic specimens yielded 163 weakly positive or discordant results. Only 3 of 163 were conclusively shown to indicate true HIV infection. Specimen contamination with HIV antibody was suspected, based on the following evidence: the proportion of positive specimens increased on repeated passage through the analysers; viral loads were low or undetectable and western blots negative or indeterminate on problem specimens; screen negative, 2nd test positive specimens tested positive when reanalysed on the screening assay; follow up specimens (where available) were negative. Similarly, an increasing number of known negative specimens became (repeatedly) sero-positive on serial passage through one of the analysers. Internal and external analyser surfaces were contaminated with HIV serum, evidence that sample splashes occur during testing. Due to the extreme sensitivity of these assays, contamination with minute amounts of HIV antibody can cause a negative sample to test positive. Better contamination control measures are needed on analysers used in clinical pathology environments, especially in regions where HIV sero-prevalence is high.

Preservation of Fine-Needle Aspiration Specimens for Future Use in RNA-Based Molecular Testing

PubMed Central

Ladd, Amy C.; O'Sullivan-Mejia, Emerald; Lea, Tasha; Perry, Jessica; Dumur, Catherine I.; Dragoescu, Ema; Garrett, Carleton T.; Powers, Celeste N.

2015-01-01

Background The application of ancillary molecular testing is becoming more important for the diagnosis and classification of disease. The use of fine-needle aspiration (FNA) biopsy as the means of sampling tumors in conjunction with molecular testing could be a powerful combination. FNA is minimally invasive, cost effective, and usually demonstrates accuracy comparable to diagnoses based on excisional biopsies. Quality control (QC) and test validation requirements for development of molecular tests impose a need for access to pre-existing clinical samples. Tissue banking of excisional biopsy specimens is frequently performed at large research institutions, but few have developed protocols for preservation of cytologic specimens. This study aimed to evaluate cryopreservation of FNA specimens as a method of maintaining cellular morphology and ribonucleic acid (RNA) integrity in banked tissues. Methods FNA specimens were obtained from fresh tumor resections, processed by using a cryopreservation protocol, and stored for up to 27 weeks. Upon retrieval, samples were made into slides for morphological evaluation, and RNA was extracted and assessed for integrity by using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, Calif). Results Cryopreserved specimens showed good cell morphology and, in many cases, yielded intact RNA. Cases showing moderate or severe RNA degradation could generally be associated with prolonged specimen handling or sampling of necrotic areas. Conclusions FNA specimens can be stored in a manner that maintains cellular morphology and RNA integrity necessary for studies of gene expression. In addition to addressing quality control (QC) and test validation needs, cytology banks will be an invaluable resource for future molecular morphologic and diagnostic research studies. PMID:21287691

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.

PubMed

Blekhman, Ran; Tang, Karen; Archie, Elizabeth A; Barreiro, Luis B; Johnson, Zachary P; Wilson, Mark E; Kohn, Jordan; Yuan, Michael L; Gesquiere, Laurence; Grieneisen, Laura E; Tung, Jenny

2016-08-16

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples-unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.

Enamel remineralization effect of a dentifrice containing calcium sodium phosphosilicate: an optical coherence tomography observation.

PubMed

Matsuyoshi, Saki; Murayama, Ryosuke; Akiba, Shunsuke; Yabuki, Chiaki; Takamizawa, Toshiki; Kurokawa, Hiroyasu; Miyazaki, Masashi

2017-04-01

The purpose of this study was to examine the effects of a dentifrice containing 5% calcium sodium phosphosilicate (CSP) on the remineralization of the enamel using optical coherence tomography (OCT). Bovine incisors were sliced and shaped in a rectangular form. One group of five specimens was treated with undersaturated 0.1 M lactic acid buffer solution (pH 4.75) for 10 min and then placed in artificial saliva (pH 7.0) (De group). Other specimens were stored in solutions of toothpaste containing CSP for 10 min, followed by 10-min immersion in the lactic acid buffer solution twice a day before storage in artificial saliva (CSP group). An additional group was stored in only artificial saliva (control group). OCT imaging on the selected location of the enamel surface was performed. The peak intensity and width at 1/e 2 were recorded in each of the six areas on the sample and averaged, and the sample size of each group was six. The integrated value in units (dB × μm) was calculated in the area of peak intensity. The data for each group was subjected to one-way repeated-measures ANOVA and Tukey HSD tests (α = 0.05). The changes in integrated values of each group were different. A slight but significant increase in the integrated value was observed in the control group, whereas a slight but significant decrease in the value was observed the De group. Integrated values increased in the CSP group. Remineralization occurred upon immersion in the toothpaste containing CSP.

The TDR Tuberculosis Specimen Bank: a resource for diagnostic test developers.

PubMed

Nathanson, C-M; Cuevas, L E; Cunningham, J; Perkins, M D; Peeling, R W; Guillerm, M; Moussy, F; Ramsay, A

2010-11-01

The Special Programme for Research and Training in Tropical Diseases established a specimen bank in 1999 to support the development and evaluation of new tuberculosis (TB) diagnostic tools. To provide a narrative of the bank's development and discuss lessons learned, the bank's limitations and potential future applications. Collection sites were selected in high- and low-prevalence settings. Patients with TB symptoms, consenting to participate and to undergo human immunodeficiency virus testing were enrolled and diagnosed. Serum, sputum, saliva and urine samples were collected and sent to the bank's repositories. The bank has stocked 41,437 samples from 2524 patients at 11 sites worldwide. Ninety-five requests for specimens have been reviewed and 67 sets have been approved. Approved applicants have received sets of 20 or 200 samples. The bank allowed an evaluation of 19 commercial lateral flow tests and showed that none of them had broad global utility for TB diagnosis. The establishment and development of the specimen bank have provided a wealth of experience. It is fulfilling a need to provide quality specimens, but the type and number of samples may not fulfil the demands of future end-users. Plans are underway to review the mechanisms of specimen collection and distribution to maximise their impact on product development.

High-Throughput Testing of Urogenital and Extragenital Specimens for Detection of Chlamydia Trachomatis and Neisseria Gonorrhoeae with Cobas® CT/NG.

PubMed

Marlowe, Elizabeth M; Hardy, David; Krevolin, Mark; Gohl, Peter; Bertram, Alexander; Arcenas, Rodney; Seiverth, Britta; Schneider, Tanja; Liesenfeld, Oliver

2017-09-01

We compared the analytical and clinical performance of cobas ® CT/NG for use on the Cobas ® 6800/8800 Systems with the Cobas ® 4800 CT/NG Test from urogenital and extragenital specimens in over 12,000 specimens from both male and female subjects in Germany and the United States. The analytical sensitivity was ≤40 EB/ml for Chlamydia trachomatis (CT) and ≤1 CFU/ml for Neisseria gonorrhoeae (NG). Using clinical specimens, the overall percent agreement with the Cobas ® 4800 CT/NG Test was >98.5%. Across urogenital specimens, there were 93 discrepant specimens; 76 (93.8%) of 81 CT discrepant specimens were 6800+/4800- and 10 (83.3%) of 12 NG discrepant specimens were 6800+/4800-. Sequencing verified CT results for 45 (61.6%) of 73 samples positive by 6800 and 1 (20%) of 5 positive by 4800. Similarly, 7 (70.0%) of 10 NG samples positive by 6800 and 1 of 2 positive by 4800 were confirmed by sequencing. Among discrepant extragenital specimens (all 6800+/4800-), 7 (50%) of 14 oropharyngeal and 23 (76.7%) of 30 anorectal CT discordant samples were confirmed as CT positive by sequencing; all 8 anorectal and 20 (90.9%) of 22 oropharyngeal NG discordant results were also confirmed as NG positive. In conclusion, Cobas ® CT/NG for use on the Cobas ® 6800/8800 Systems provides high-throughput automated solutions for sexually transmitted infection (STI) screening programs.

Quality control of human tissues--experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank.

PubMed

Sandusky, George E; Teheny, Katie Heinz; Esterman, Mike; Hanson, Jeff; Williams, Stephen D

2007-01-01

The success of molecular research and its applications in both the clinical and basic research arenas is strongly dependent on the collection, handling, storage, and quality control of fresh human tissue samples. This tissue bank was set up to bank fresh surgically obtained human tissue using a Clinical Annotated Tissue Database (CATD) in order to capture the associated patient clinical data and demographics using a one way patient encryption scheme to protect patient identification. In this study, we determined that high quality of tissue samples is imperative for both genomic and proteomic molecular research. This paper also contains a brief compilation of the literature involved in the patient ethics, patient informed consent, patient de-identification, tissue collection, processing, and storage as well as basic molecular research generated from the tissue bank using good clinical practices. The current applicable rules, regulations, and guidelines for handling human tissues are briefly discussed. More than 6,610 cancer patients have been consented (97% of those that were contacted by the consenter) and 16,800 tissue specimens have been banked from these patients in 9 years. All samples collected in the bank were QC'd by a pathologist. Approximately 1,550 tissue samples have been requested for use in basic, clinical, and/or biomarker cancer research studies. Each tissue aliquot removed from the bank for a research study were evaluated by a second H&E, if the samples passed the QC, they were submitted for genomic and proteomic molecular analysis/study. Approximately 75% of samples evaluated were of high histologic quality and used for research studies. Since 2003, we changed the patient informed consent to allow the tissue bank to gather more patient clinical follow-up information. Ninety two percent of the patients (1,865 patients) signed the new informed consent form and agreed to be re-contacted for follow-up information on their disease state. In addition, eighty five percent of patients (1,584) agreed to be re-contacted to provide a biological fluid sample to be used for biomarker research.

Progressive Consent and Specimen Accrual Models to Address Sustainability: A Decade's Experience at an Oregon Biorepository.

PubMed

Ost, John A; Newton, Paul W; Neilson, Duncan R; Cioffi, Joseph A; Wackym, P Ashley; Perkins, R Serene

2017-02-01

The Legacy Biorepository is a College of American Pathologists-accredited biorepository operating within a seven-hospital healthcare system, with a decade's experience in specimen accrual, storage, and distribution. While standardization of our practices through accreditation remains a priority, we along with others face challenges with regard to sustainability. Purposeful changes in our consent process, which we term "progressive consent," are expected to improve sustainability and operational flexibility while increasing our scientific impact. Until 2015, informed consent was performed primarily by biorepository staff at an estimated time of 1 hour per case. After a process improvement exercise, we successfully changed our informed consent process to a modified front-door model, with use of material and data for research as an opt-in or opt-out selection on the institutional patient informed consent form provided to surgery patients in the healthcare system. Successful implementation of this change required the engagement and participation of multiple stakeholders in healthcare system leadership, hospital administration, research, legal, regulatory, and patient care levels. A modified front-door consent enabled us to collect an additional 38 specimens in the first two quarters of 2016, with a time commitment of 15.75 hours, a time savings per specimen increasing in Q2 over Q1. We estimate a potential savings of 43 hours in 2016. This progressive model allowed us to maintain our frozen sample collection while increasing the availability of paraffin-embedded tissue and bodily fluids. Augmenting our tissue collection added little expense per case (approximately half that of each frozen tissue aliquot) and increased the range of biospecimens collected. Biorepository financial sustainability is a critical issue. Thorough evaluation and modification of existing procedures and collection models, as well as cost recovery initiatives, can translate into savings. Sustainability, process improvement, and scientific impact broadly overlap and continue to require operational critique and implementation of strategic changes.

Saccharose solid matrix embedded proteins: a new method for sample preparation for X-ray absorption spectroscopy.

PubMed

Ascone, I; Sabatucci, A; Bubacco, L; Di Muro, P; Salvato, B

2000-01-01

In this study, solid samples of hemoglobin and hemocyanin have been prepared by embedding the proteins into a saccharose-based matrix. These materials have been developed specifically for specimens for X-ray absorption spectroscopy (XAS). The preservation of protein conformation and active site organization was tested, making comparisons between the solid and the corresponding liquid samples, using resonance Raman, infra red, fluorescence and XAS. The XAS spectra of irradiated solid and liquid samples were then compared, and the preservation of biological activity of the proteins during both preparation procedure and X-ray irradiation was assessed. In all cases, the measurements clearly demonstrate that protein solid samples are both structurally and functionally quite well preserved, much better than those in the liquid state. The saccharose matrix provides an excellent protection against X-ray damages, allowing for longer exposure to the X-ray beam. Moreover, the demonstrated long-term stability of samples permits their preparation and storage in optimal conditions, allowing for the repetition of data collection with the same sample in several experimental sessions. The very high protein concentration that can be reached results in a significantly better signal-to-noise ratio, particularly useful for high molecular weight proteins with a low metal-to-protein ratio. On the bases of the above-mentioned results, we propose the new method as a standard procedure for the preparation of biological samples to be used for XAS spectroscopy.

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

PubMed

Sproul, John S; Maddison, David R

2017-11-01

Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens. © 2017 John Wiley & Sons Ltd.

Evaluation of GeneXpert MTB/RIF for detection of Mycobacterium tuberculosis complex and rpo B gene in respiratory and non-respiratory clinical specimens at a tertiary care teaching hospital in Saudi Arabia.

PubMed

Somily, Ali M; Barry, Mazin A; Habib, Hanan A; Alotaibi, Fawzia E; Al-Zamil, Fahad A; Khan, Mohammed A; Sarwar, Mohammed S; Bakhash, Nawab D; Alrabiaah, Abdulkarim A; Shakoor, Zahid A; Senok, Abiola C

2016-12-01

To assess the performance of Xpert MTB/RIF, an automated molecular test for Mycobacterium tuberculosis (MTB) and resistance to rifampin (RIF), against smear microscopy and culture method for diagnosis of MTB infection. Methods: This is a retrospective analysis of 103 respiratory and 137 non-respiratory patient specimens suspected of tuberculosis at King Khalid University Hospital, Riyadh, Kingdom of Saudi Arabia performed between April 2014 and March 2015. Each sample underwent smear microscopy, mycobacterial culture, and GeneXpert MTB/RIF test. Results: Fifteen out of 103 respiratory samples were smear and culture positive, whereas 9 out of 137 non-respiratory samples were smear positive. Out of 9 smear positive specimens, 8 were also culture positive. All 15 culture positive respiratory samples were detected by Xpert MTB/RIF (sensitivity  and positive predictive value [PPV]=100%). Similarly, all 8 culture positive non-respiratory specimens were identified by Xpert MTB/RIF (sensitivity 100%; PPV 88.8%). The Xpert MTB/RIF detected only one false positive result in 88 smear negative respiratory specimens (specificity 98.9%; negative predictive value [NPV]= 100%). All 125 smear negative non-respiratory specimens tested negative by culture and Xpert MTB/RIF (sensitivity, specificity, PPV, NPV= 100%). Conclusion: The performance of Xpert MTB/RIF was comparable to the gold standard culture method for identification of MTB in both respiratory and non-respiratory clinical specimens.

Evaluation of GeneXpert MTB/RIF for detection of Mycobacterium tuberculosis complex and rpo B gene in respiratory and non-respiratory clinical specimens at a tertiary care teaching hospital in Saudi Arabia

PubMed Central

Somily, Ali M.; Barry, Mazin A.; Habib, Hanan A.; Alotaibi, Fawzia E.; Al-Zamil, Fahad A.; Khan, Mohammed A.; Sarwar, Mohammed S.; Bakhash, Nawab D.; Alrabiaah, Abdulkarim A.; Shakoor, Zahid A.; Senok, Abiola C.

2016-01-01

Objectives To assess the performance of Xpert MTB/RIF, an automated molecular test for Mycobacterium tuberculosis (MTB) and resistance to rifampin (RIF), against smear microscopy and culture method for diagnosis of MTB infection. Methods This is a retrospective analysis of 103 respiratory and 137 non-respiratory patient specimens suspected of tuberculosis at King Khalid University Hospital, Riyadh, Kingdom of Saudi Arabia performed between April 2014 and March 2015. Each sample underwent smear microscopy, mycobacterial culture, and GeneXpert MTB/RIF test. Results Fifteen out of 103 respiratory samples were smear and culture positive, whereas 9 out of 137 non-respiratory samples were smear positive. Out of 9 smear positive specimens, 8 were also culture positive. All 15 culture positive respiratory samples were detected by Xpert MTB/RIF (sensitivity and positive predictive value [PPV]=100%). Similarly, all 8 culture positive non-respiratory specimens were identified by Xpert MTB/RIF (sensitivity 100%; PPV 88.8%). The Xpert MTB/RIF detected only one false positive result in 88 smear negative respiratory specimens (specificity 98.9%; negative predictive value [NPV]= 100%). All 125 smear negative non-respiratory specimens tested negative by culture and Xpert MTB/RIF (sensitivity, specificity, PPV, NPV= 100%). Conclusion The performance of Xpert MTB/RIF was comparable to the gold standard culture method for identification of MTB in both respiratory and non-respiratory clinical specimens. PMID:27874159

[Effects of resting days on live poultry markets in controlling the avian influenza pollution].

PubMed

Liu, Hui; Chen, Zongqiu; Xiao, Xincai; Lu, Jianyun; Di, Biao; Li, Kuibiao; Wang, Hui; Luo, Lei; Yang, Zhicong

2014-07-01

To analyze the results of nine-round environmental specimen surveillance programs in five live poultry markets pre-, during and post the 'closing days' and to evaluate the effects of 'closing days' on live poultry markets regarding the control against avian influenza pollution. In January 2014, control measures including culling poultry, completely cleaning and disinfecting and a 'three-day-closing' measure were conducted in five live poultry markets which were found positive for H7N9 nucleic acid in the 1(st) round environmental specimen surveillance program. Second surveillance program was conducted after a thorough disinfection campaign was launched. Several times surveillance were conducted in one week, after the markets were reopened. RT-PCR was used to test the nucleic acid of HA, H5, H7 and H9 viruses. 654 specimens from the environment were collected and tested. During the first round surveillance program, positive rates for influenza A and H5/H7/H9 nucleic acid of poultry stalls appeared to be 94.44% and 61.11% respectively. The positive rates of poultry stalls reduced to 0 after the disinfection campaign but increased again after the markets reopened. The positive rate for influenza A of poultry stalls slightly increased from 50.00% in the third surveillance to 72.22% in the ninth surveillance (P > 0.05). The positive rate for H5/H7/H9 of poultry stalls showed a significantly increasing trend, from 0 in the third surveillance to 44.44% in the ninth surveillance (P < 0.01). The positive rates for influenza A and H5/H7/H9 nucleic acid of specimens were 28.89% and 17.78% respectively. The positive rate of specimens reduced to 0 after disinfection while increased again after reopening of the markets. The positive rate for influenza A of specimens slightly increased from 19.67% in the third surveillance to 27.54% in the ninth surveillance programs (P > 0.05). The positive rate for H5/H7/H9 of specimen showed a significant increasing trend, from 0 in the third surveillance to 8.70% in the ninth-round surveillance programs (P < 0.01). The positive rate for influenza A was the highest for slaughter- related specimens of 22.4% (35/156). The positive rates for influenza A from sewage and drinking water being collected on the later stage after the markets reopened (25.9%, 12.4%)were higher than those on the early stage (8.3%, 8.6%) (P > 0.05). The positive rate for influenza A of poultry stalls with overnight poultry storage (91.7%) was significant higher than that of poultry stalls without the overnight storage (33.3%). The positive rate for influenza A of poultry stalls in which simultaneously selling different kinds of poultry (85.7%) was significant higher than that of poultry stalls in which selling only one kind of poultry at one time (25.0%) (P < 0.05). Slaughter in live poultry markets posed a large risk of pollution diffusion. Sewage and drinking water showed an accumulation effect for avian influenza virus. Overnight poultry storage and selling different kinds of poultry at one time at the poultry stalls seemed the risk factors for avian influenza virus transmission. Complete cleaning, disinfecting and several 'closing days' for live poultry markets seemed effective in eliminating avian influenza virus. Once the markets were reopened, they seemed to be soon polluted again.

Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group.

PubMed

Tuck, Melissa K; Chan, Daniel W; Chia, David; Godwin, Andrew K; Grizzle, William E; Krueger, Karl E; Rom, William; Sanda, Martin; Sorbara, Lynn; Stass, Sanford; Wang, Wendy; Brenner, Dean E

2009-01-01

Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.

Changes in chroma of two indirect composite materials polymerized with different polymerization systems.

PubMed

Ayano, Michiya

2012-01-01

This study evaluated chroma change in two composite materials (Sinfony and Pearleste) polymerized with two different systems. Disk specimens were prepared using a metal halide unit (Hyper LII) and an exposure time of 60 to 180 s. The proprietary polymerization systems (Visio and Pearlcure systems) were used as the reference polymerization modes. After storage at 37°C for 24 h, CIE 1976 L*a*b* values were measured by using a dental chroma meter (ShadeEye NCC) with a gray background. The specimens were then immersed in water or tea. Color change from baseline to 4 weeks was evaluated by measuring ΔL*, Δa*, and Δb*, after which ΔE*(ab) values were calculated. The brightness of Sinfony specimens was reduced by tea immersion. The color of both materials shifted to yellow after tea immersion, although color change in Sinfony specimens was greater than that in Pearleste specimens. For both materials, color change was less after polymerization with the metal halide unit. In conclusion, Sinfony polymerized with the Hyper LII unit, and Pearleste polymerized with either system, were stable against discoloration due to tea immersion.

Evaluation of a new amplified enzyme immunoassay (EIA) for the detection of Chlamydia trachomatis in male urine, female endocervical swab, and patient obtained vaginal swab specimens

PubMed Central

Tanaka, M.; Nakayama, H.; Sagiyama, K.; Haraoka, M.; Yoshida, H.; Hagiwara, T.; Akazawa, K.; Naito, S.

2000-01-01

Aims—To compare the performance of a new generation dual amplified enzyme immunoassay (EIA) with a molecular method for the diagnosis of Chlamydia trachomatis, using a range of urogenital samples, and to assess the reliability of testing self collected vaginal specimens compared with clinician collected vaginal specimens. Methods—Two population groups were tested. For the first population group, first void urine samples were collected from 193 male patients with urethritis, and endocervical swabs were collected from 187 high risk commercial sex workers. All urine and endocervical specimens were tested by a conventional assay (IDEIA chlamydia), a new generation amplified immunoassay (IDEIA PCE chlamydia), and the Amplicor polymerase chain reaction (PCR). Discrepant results obtained among the three sample types were confirmed using a nested PCR test with a different plasmid target region. For the second population group, four swab specimens, including one patient obtained vaginal swab, two clinician obtained endocervical swabs, and one clinician obtained vaginal swab, were collected from 91 high risk sex workers. Self collected and clinician collected vaginal swabs were tested by IDEIA PCE chlamydia. Clinician obtained endocervical swabs were assayed by IDEIA PCE chlamydia and Amplicor PCR. Results—The performance of the IDEIA PCE chlamydia test was comparable to that of the Amplicor PCR test when male urine and female endocervical swab specimens were analysed. The relative sensitivities of IDEIA, IDEIA PCE, and Amplicor PCR on male first void urine specimens were 79.3%, 91.4%, and 100%, respectively. The relative sensitivities of the three tests on female endocervical specimens were 85.0%, 95.0%, and 100%, respectively. The positivity rates for patient collected vaginal specimens and clinician collected vaginal specimens by IDEIA PCE were 25.2% and 23.1%, respectively, whereas those for clinician collected endocervical swabs by PCR and IDEIA PCE were both 27.5%. Conclusions—IDEIA PCE chlamydia is a lower cost but sensitive alternative test to PCR for testing male urine samples and female endocervical swabs. In addition, self collected or clinician collected vaginal specimens tested by IDEIA PCE chlamydia are a reliable alternative to analysing endocervical specimens. Key Words: Chlamydia trachomatis • enzyme immunoassay • clinical specimens PMID:10889816

Recommendations for clinical biomarker specimen preservation and stability assessments.

PubMed

Dakappagari, Naveen; Zhang, Hui; Stephen, Laurie; Amaravadi, Lakshmi; Khan, Masood U

2017-04-01

With the wide use of biomarkers to enable critical drug-development decisions, there is a growing concern from scientific community on the need for a 'standardized process' for ensuring biomarker specimen stability and hence, a strong desire to share best practices on preserving the integrity of biomarker specimens in clinical trials and the design of studies to evaluate analyte stability. By leveraging representative industry experience, we have attempted to provide an overview of critical aspects of biomarker specimen stability commonly encountered during clinical development, including: planning of clinical sample collection procedures, clinical site training, selection of sample preservation buffers, shipping logistics, fit-for-purpose stability assessments in the analytical laboratory and presentation of case studies covering widely utilized biomarker specimen types.

Long-term stability and temporal trends of organic contaminants in four collections of mussel tissue frozen standard reference materials.

PubMed

Schantz, Michele M; Pugh, Rebecca S; Pol, Stacy S Vander; Wise, Stephen A

2015-04-01

The stability of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and chlorinated pesticides in frozen mussel tissue Standard Reference Materials (SRMs) stored at -80 °C was assessed by analyzing samples of SRM 1974, SRM 1974a, and SRM 1974b Organics in Mussel Tissue (Mytilus edulis) periodically over 25 y, 20 y, and 12 y, respectively. The most recent analyses were performed during the certification of the fourth release of this material, SRM 1974c. Results indicate the concentrations of these persistent organic pollutants have not changed during storage at -80 °C. In addition, brominated diphenyl ethers (BDEs) were quantified in each of the materials during this study. The stability information is important for on-going monitoring studies collecting large quantities of samples for future analyses (i.e., formally established specimen banking programs). Since all four mussel tissue SRMs were prepared from mussels collected at the same site in Dorchester Bay, MA, USA, the results provide a temporal trend study for these contaminants over a 17 year period (1987 to 2004).

Fully integrated multiplexed lab-on-a-card assay for enteric pathogens

NASA Astrophysics Data System (ADS)

Weigl, B. H.; Gerdes, J.; Tarr, P.; Yager, P.; Dillman, L.; Peck, R.; Ramachandran, S.; Lemba, M.; Kokoris, M.; Nabavi, M.; Battrell, F.; Hoekstra, D.; Klein, E. J.; Denno, D. M.

2006-01-01

Under this NIH-funded project, we are developing a lab-on-a-card platform to identify enteric bacterial pathogens in patients presenting with acute diarrhea, with special reference to infections that might be encountered in developing countries. Component functions that are integrated on this platform include on-chip immunocapture of live or whole pathogens, multiplexed nucleic acid amplification and on-chip detection, sample processing to support direct use of clinical specimens, and dry reagent storage and handling. All microfluidic functions are contained on the lab card. This new diagnostic test will be able to rapidly identify and differentiate Shigella dysenteriae serotype 1, Shigella toxin-producing Escherichia coli, E. coli 0157, Campylobacter jejuni, and Salmonella and Shigella species. This presentation will report on progress to date on sample and bacteria processing methodologies, identification and validation of capture antibodies and strategy for organism immunocapture, identification and validation of specific polymerase chain reaction (PCR) primer sequences for over 200 clinical isolates of enteric pathogens, and implementation of on-chip nucleic acid extraction for a subset of those pathogens.

Efficacy of different whitening modalities on bovine enamel and dentin.

PubMed

Wiegand, Annette; Vollmer, Doreen; Foitzik, Magdalena; Attin, Rengin; Attin, Thomas

2005-06-01

Previous studies have shown that bleaching treatment may be efficient in both enamel and dentin, but it is still unknown how much the subsurface dentin contributes to the color change of teeth. This in vitro study evaluated the whitening effect of different external bleaching agents on enamel-dentin slabs and subsurface dentin. Ninety bovine teeth were distributed among six groups (A, Opalescence 10%; B, Opalescence PF 15%; C, Opalescence Quick; D, Opalescence Extra Boost; E, Rapid White; F, Whitestrips). Two enamel-dentin specimens were prepared from the labial surface of each teeth. In one of the specimens enamel was removed, resulting in a dentin (CD) disc of 1 mm high. The labial and the pulpal sides of the second specimen were ground until the remaining enamel and dentin layers of the enamel-dentin sample (ED) were 1 mm each. Whitening treatment of the ED specimens was performed according to manufacturers' instructions. Pre- and posttreatment Lab values of ED samples were analyzed using CIE-Lab. Baseline Lab values of dentin were analyzed by evaluation of the CD specimen. Finally, enamel of the ED specimens was removed and color change of the exposed dentin (D) was recorded. For all treatment agents significant color changes (DeltaE) were observed for enamel-dentin samples and subsurface dentin specimens compared to controls. In groups A-D DeltaE was significantly higher in dentin than enamel-dentin. Furthermore, L and b values of bleached enamel-dentin and subsurface dentin samples differed significantly from baseline. Treatment with the tested external whitening bleaching agents resulted in color change of both enamel-dentin and subsurface dentin samples. The results indicate that color change of treated teeth might be highly influenced by color change of the subsurface dentin.

36 CFR 34.5 - Applicable regulations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Applicable regulations. 34.5 Section 34.5 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR EL... specimens. (6) 2.10Camping and food storage. (7) 2.11Picnicking. (8) 2.12Audio disturbances. (9) 2.13Fires...

Development of A 5,000 BBL, Rubberized Fabric Fuel Storage Tank, Collapsible,

DTIC Science & Technology

1981-04-01

Note l/ after soil burial. 6/ Reference fuel D is ASTM D-471, 60% iso-octane and 40% toluene. 7/ Retained after 56 days -25- i IGOODYEAR AEROSPACE 0 0...331.7) Pure. 9.I - 9.6 920 0() 09/O 0A) 2.7 ". paum Mese IEststa"t r.e ASIN 11-70 W1 I (ma) 7.3A -n-i I GAC 19-1337 Rev 2 USLE is (continmed) () The...the greater requirement. 5/ Method 5762 except that the specimens were prepared by Note 1/ after soil burial and the number of specimens was reduced

Sample storage-induced changes in the quantity and quality of soil labile organic carbon

PubMed Central

Sun, Shou-Qin; Cai, Hui-Ying; Chang, Scott X.; Bhatti, Jagtar S.

2015-01-01

Effects of sample storage methods on the quantity and quality of labile soil organic carbon are not fully understood even though their effects on basic soil properties have been extensively studied. We studied the effects of air-drying and frozen storage on cold and hot water soluble organic carbon (WSOC). Cold- and hot-WSOC in air-dried and frozen-stored soils were linearly correlated with those in fresh soils, indicating that storage proportionally altered the extractability of soil organic carbon. Air-drying but not frozen storage increased the concentrations of cold-WSOC and carbohydrate in cold-WSOC, while both increased polyphenol concentrations. In contrast, only polyphenol concentration in hot-WSOC was increased by air-drying and frozen storage, suggesting that hot-WSOC was less affected by sample storage. The biodegradability of cold- but not hot-WSOC was increased by air-drying, while both air-drying and frozen storage increased humification index and changed specific UV absorbance of both cold- and hot-WSOC, indicating shifts in the quality of soil WSOC. Our results suggest that storage methods affect the quantity and quality of WSOC but not comparisons between samples, frozen storage is better than air-drying if samples have to be stored, and storage should be avoided whenever possible when studying the quantity and quality of both cold- and hot-WSOC. PMID:26617054

Specimen rejection in laboratory medicine: Necessary for patient safety?

PubMed

Dikmen, Zeliha Gunnur; Pinar, Asli; Akbiyik, Filiz

2015-01-01

The emergency laboratory in Hacettepe University Hospitals receives specimens from emergency departments (EDs), inpatient services and intensive care units (ICUs). The samples are accepted according to the rejection criteria of the laboratory. In this study, we aimed to evaluate the sample rejection ratios according to the types of pre-preanalytical errors and collection areas. The samples sent to the emergency laboratory were recorded during 12 months between January to December, 2013 in which 453,171 samples were received and 27,067 specimens were rejected. Rejection ratios was 2.5% for biochemistry tests, 3.2% for complete blood count (CBC), 9.8% for blood gases, 9.2% for urine analysis, 13.3% for coagulation tests, 12.8% for therapeutic drug monitoring, 3.5% for cardiac markers and 12% for hormone tests. The most frequent rejection reasons were fibrin clots (28%) and inadequate volume (9%) for biochemical tests. Clotted samples (35%) and inadequate volume (13%) were the major causes for coagulation tests, blood gas analyses and CBC. The ratio of rejected specimens was higher in the EDs (40%) compared to ICUs (30%) and inpatient services (28%). The highest rejection ratio was observed in neurology ICU (14%) among the ICUs and internal medicine inpatient service (10%) within inpatient clinics. We detected an overall specimen rejection rate of 6% in emergency laboratory. By documentation of rejected samples and periodic training of healthcare personnel, we expect to decrease sample rejection ratios below 2%, improve total quality management of the emergency laboratory and promote patient safety.

Effectiveness of saliva and fingerprints as alternative specimens to urine and blood in forensic drug testing.

PubMed

Kuwayama, Kenji; Miyaguchi, Hajime; Yamamuro, Tadashi; Tsujikawa, Kenji; Kanamori, Tatsuyuki; Iwata, Yuko T; Inoue, Hiroyuki

2016-07-01

In forensic drug testing, it is important to immediately take biological specimens from suspects and victims to prove their drug intake. We evaluated the effectiveness of saliva and fingerprints as alternative specimens to urine and blood in terms of ease of sampling, drug detection sensitivity, and drug detection periods for each specimen type. After four commercially available pharmaceutical products were administered to healthy subjects, each in a single dose, their urine, blood, saliva, and fingerprints were taken at predetermined sampling times over approximately four weeks. Fourteen analytes (the administered drugs and their main metabolites) were extracted from each specimen using simple pretreatments, such as dilution and deproteinization, and were analyzed using liquid chromatography/mass spectrometry (LC/MS). Most of the analytes were detected in saliva and fingerprints, as well as in urine and blood. The time-courses of drug concentrations were similar between urine and fingerprints, and between blood and saliva. Compared to the other compounds, the acidic compounds, for example ibuprofen, acetylsalicylic acid, were more difficult to detect in all specimens. Acetaminophen, dihydrocodeine, and methylephedrine were detected in fingerprints at later sampling times than in urine. However, a relationship between the drug structures and their detection periods in each specimen was not found. Saliva and fingerprints could be easily sampled on site without using special techniques or facilities. In addition, fingerprints could be immediately analyzed after simple and rapid treatment. In cases where it would be difficult to immediately obtain urine and blood, saliva and fingerprints could be effective alternative specimens for drug testing. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

PubMed Central

Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

2017-01-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites, and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. PMID:28239968

Inhibition of Titanium In Fuming Nitric Acid

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

RITTENHOUSE, J. B.; PAPP, C. A.

1958-06-01

Storage tests were conducted to determine the effectiveness of oxygen in inhibiting the corrosion reaction of titanium in fuming nitric acid (FNA). In these tests, which were of 28 days duration at a temperature of 30 C, the samples investigated were ½-inch squares (0.020 inch thick) of commercially pure titanium (75A) and a binary 8 percent-manganese alloy (C110M). The specimens were stored in Teflon-lined aluminum pressure vessels at 50 percent ullage. The pressure vessels were of the following types: vented to the atmosphere, sealed with air in the vapor space, sealed with oxygen atmosphere in the vapor space, and equippedmore » for a 1-ml/minute oxygen flow through the vapor space. Finally, results of the investigation indicated no inhibition of titanium corrosion by oxygen, but confirmed the inhibiting effect of a water content of 1 to 2 percent by weight in the FNA.« less

Comparative Assessment of a Self-sampling Device and Gynecologist Sampling for Cytology and HPV DNA Detection in a Rural and Low Resource Setting: Malaysian Experience.

PubMed

Latiff, Latiffah A; Ibrahim, Zaidah; Pei, Chong Pei; Rahman, Sabariah Abdul; Akhtari-Zavare, Mehrnoosh

2015-01-01

This study was conducted to assess the agreement and differences between cervical self-sampling with a Kato device (KSSD) and gynecologist sampling for Pap cytology and human papillomavirus DNA (HPV DNA) detection. Women underwent self-sampling followed by gynecologist sampling during screening at two primary health clinics. Pap cytology of cervical specimens was evaluated for specimen adequacy, presence of endocervical cells or transformation zone cells and cytological interpretation for cells abnormalities. Cervical specimens were also extracted and tested for HPV DNA detection. Positive HPV smears underwent gene sequencing and HPV genotyping by referring to the online NCBI gene bank. Results were compared between samplings by Kappa agreement and McNemar test. For Pap specimen adequacy, KSSD showed 100% agreement with gynecologist sampling but had only 32.3% agreement for presence of endocervical cells. Both sampling showed 100% agreement with only 1 case detected HSIL favouring CIN2 for cytology result. HPV DNA detection showed 86.2%agreement (K=0.64, 95% CI 0.524-0.756, p=0.001) between samplings. KSSD and gynaecologist sampling identified high risk HPV in 17.3% and 23.9% respectively (p= 0.014). The self-sampling using Kato device can serve as a tool in Pap cytology and HPV DNA detection in low resource settings in Malaysia. Self-sampling devices such as KSSD can be used as an alternative technique to gynaecologist sampling for cervical cancer screening among rural populations in Malaysia.

Metallographic Characterization of Wrought Depleted Uranium

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

Forsyth, Robert Thomas; Hill, Mary Ann

Metallographic characterization was performed on wrought depleted uranium (DU) samples taken from the longitudinal and transverse orientations from specific locations on two specimens. Characterization of the samples included general microstructure, inclusion analysis, grain size analysis, and microhardness testing. Comparisons of the characterization results were made to determine any differences based on specimen, sample orientation, or sample location. In addition, the characterization results for the wrought DU samples were also compared with data obtained from the metallographic characterization of cast DU samples previously characterized. No differences were observed in microstructure, inclusion size, morphology, and distribution, or grain size in regard tomore » specimen, location, or orientation for the wrought depleted uranium samples. However, a small difference was observed in average hardness with regard to orientation at the same locations within the same specimen. The longitudinal samples were slightly harder than the transverse samples from the same location of the same specimen. This was true for both wrought DU specimens. Comparing the wrought DU sample data with the previously characterized cast DU sample data, distinct differences in microstructure, inclusion size, morphology and distribution, grain size, and microhardness were observed. As expected, the microstructure of the wrought DU samples consisted of small recrystallized grains which were uniform, randomly oriented, and equiaxed with minimal twinning observed in only a few grains. In contrast, the cast DU microstructure consisted of large irregularly shaped grains with extensive twinning observed in most grains. Inclusions in the wrought DU samples were elongated, broken and cracked and light and dark phases were observed in some inclusions. The mean inclusion area percentage for the wrought DU samples ranged from 0.08% to 0.34% and the average density from all wrought DU samples was 1.62E+04/cm 2. Inclusions in the cast DU samples were equiaxed and intact with light and dark phases observed in some inclusions. The mean inclusion area percentage for the cast DU samples ranged from 0.93% to 1.00% and the average density from all wrought DU samples was 2.83E+04/cm 2. The average mean grain area from all wrought DU samples was 141 μm 2 while the average mean grain area from all cast DU samples was 1.7 mm2. The average Knoop microhardness from all wrought DU samples was 215 HK and the average Knoop microhardness from all cast DU samples was 264 HK.« less

Surface sampling concentration and reaction probe with controller to adjust sampling position

DOEpatents

Van Berkel, Gary J.; ElNaggar, Mariam S.

2016-07-19

A method of analyzing a chemical composition of a specimen is described. The method can include providing a probe comprising an outer capillary tube and an inner capillary tube disposed co-axially within the outer capillary tube, where the inner and outer capillary tubes define a solvent capillary and a sampling capillary in fluid communication with one another at a distal end of the probe; contacting a target site on a surface of a specimen with a solvent in fluid communication with the probe; maintaining a plug volume proximate a solvent-specimen interface, wherein the plug volume is in fluid communication with the probe; draining plug sampling fluid from the plug volume through the sampling capillary; and analyzing a chemical composition of the plug sampling fluid with an analytical instrument. A system for performing the method is also described.

Storage Time and Urine Biomarker Levels in the ASSESS-AKI Study

PubMed Central

Liu, Kathleen D.; Siew, Edward D.; Reeves, W. Brian; Himmelfarb, Jonathan; Go, Alan S.; Hsu, Chi-yuan; Bennett, Michael R.; Devarajan, Prasad; Ikizler, T. Alp; Kaufman, James S.; Kimmel, Paul L.; Chinchilli, Vernon M.; Parikh, Chirag R.

2016-01-01

Background Although stored urine samples are often used in biomarker studies focused on acute and chronic kidney disease, how storage time impacts biomarker levels is not well understood. Methods 866 subjects enrolled in the NIDDK-sponsored ASsessment, Serial Evaluation, and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) Study were included. Samples were processed under standard conditions and stored at -70°C until analyzed. Kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), interleukin-18 (IL-18), and liver fatty acid binding protein (L-FABP) were measured in urine samples collected during the index hospitalization or an outpatient visit 3 months later. Mixed effects models were used to determine the effect of storage time on biomarker levels and stratified by visit. Results Median storage was 17.8 months (25–75% IQR 10.6–23.7) for samples from the index hospitalization and 14.6 months (IQR 7.3–20.4) for outpatient samples. In the mixed effects models, the only significant association between storage time and biomarker concentration was for KIM-1 in outpatient samples, where each month of storage was associated with a 1.7% decrease (95% CI -3% to -0.3%). There was no relationship between storage time and KIM-1 levels in samples from the index hospitalization. Conclusion There was no significant impact of storage time over a median of 18 months on urine KIM-1, NGAL, IL-18 or L-FABP in hospitalized samples; a statistically significant effect towards a decrease over time was noted for KIM-1 in outpatient samples. Additional studies are needed to determine whether longer periods of storage at -70°C systematically impact levels of these analytes. PMID:27788160

Storage Time and Urine Biomarker Levels in the ASSESS-AKI Study.

PubMed

Liu, Kathleen D; Siew, Edward D; Reeves, W Brian; Himmelfarb, Jonathan; Go, Alan S; Hsu, Chi-Yuan; Bennett, Michael R; Devarajan, Prasad; Ikizler, T Alp; Kaufman, James S; Kimmel, Paul L; Chinchilli, Vernon M; Parikh, Chirag R

2016-01-01

Although stored urine samples are often used in biomarker studies focused on acute and chronic kidney disease, how storage time impacts biomarker levels is not well understood. 866 subjects enrolled in the NIDDK-sponsored ASsessment, Serial Evaluation, and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) Study were included. Samples were processed under standard conditions and stored at -70°C until analyzed. Kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), interleukin-18 (IL-18), and liver fatty acid binding protein (L-FABP) were measured in urine samples collected during the index hospitalization or an outpatient visit 3 months later. Mixed effects models were used to determine the effect of storage time on biomarker levels and stratified by visit. Median storage was 17.8 months (25-75% IQR 10.6-23.7) for samples from the index hospitalization and 14.6 months (IQR 7.3-20.4) for outpatient samples. In the mixed effects models, the only significant association between storage time and biomarker concentration was for KIM-1 in outpatient samples, where each month of storage was associated with a 1.7% decrease (95% CI -3% to -0.3%). There was no relationship between storage time and KIM-1 levels in samples from the index hospitalization. There was no significant impact of storage time over a median of 18 months on urine KIM-1, NGAL, IL-18 or L-FABP in hospitalized samples; a statistically significant effect towards a decrease over time was noted for KIM-1 in outpatient samples. Additional studies are needed to determine whether longer periods of storage at -70°C systematically impact levels of these analytes.

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.

PubMed

Gupta, Vijayalaxmi; Holets-Bondar, Lesya; Roby, Katherine F; Enders, George; Tash, Joseph S

2015-01-01

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.

Distribution and Diversity of Soil Microfauna from East Antarctica: Assessing the Link between Biotic and Abiotic Factors

PubMed Central

Velasco-Castrillón, Alejandro; Schultz, Mark B.; Colombo, Federica; Gibson, John A. E.; Davies, Kerrie A.; Austin, Andrew D.; Stevens, Mark I.

2014-01-01

Terrestrial life in Antarctica has been described as some of the simplest on the planet, and mainly confined to soil microfaunal communities. Studies have suggested that the lack of diversity is due to extreme environmental conditions and thought to be driven by abiotic factors. In this study we investigated soil microfauna composition, abundance, and distribution in East Antarctica, and assessed correlations with soil geochemistry and environmental variables. We examined 109 soil samples from a wide range of ice-free habitats, spanning 2000 km from Framnes Mountains to Bailey Peninsula. Microfauna across all samples were patchily distributed, from complete absence of invertebrates to over 1600 specimens/gram of dry weight of soil (gdw), with highest microfauna abundance observed in samples with visible vegetation. Bdelloid rotifers were on average the most widespread found in 87% of sampled sites and the most abundant (44 specimens/gdw). Tardigrades occurred in 57% of the sampled sites with an abundance of 12 specimens/gdw. Nematodes occurred in 71% of samples with a total abundance of 3 specimens/gdw. Ciliates and mites were rarely found in soil samples, with an average abundance of 1.3 and 0.04 specimens/gdw, respectively. We found that microfaunal composition and abundance were mostly correlated with the soil geochemical parameters; phosphorus, NO3 − and salinity, and likely to be the result of soil properties and historic landscape formation and alteration, rather than the geographic region they were sampled from. Studies focusing on Antarctic biodiversity must take into account soil geochemical and environmental factors that influence population and species heterogeneity. PMID:24498126

Importance of sample preparation for molecular diagnosis of lyme borreliosis from urine.

PubMed

Bergmann, A R; Schmidt, B L; Derler, A-M; Aberer, E

2002-12-01

Urine PCR has been used for the diagnosis of Borrelia burgdorferi infection in recent years but has been abandoned because of its low sensitivity and the irreproducibility of the results. Our study aimed to analyze technical details related to sample preparation and detection methods. Crucial for a successful urine PCR were (i) avoidance of the first morning urine sample; (ii) centrifugation at 36,000 x g; and (iii) the extraction method, with only DNAzol of the seven different extraction methods used yielding positive results with patient urine specimens. Furthermore, storage of frozen urine samples at -80 degrees C reduced the sensitivity of a positive urine PCR result obtained with samples from 72 untreated erythema migrans (EM) patients from 85% in the first 3 months to <30% after more than 3 months. Bands were detected at 276 bp on ethidium bromide-stained agarose gels after amplification by a nested PCR. The specificity of bands for 32 of 33 samples was proven by hybridization with a GEN-ETI-K-DEIA kit and for a 10 further positive amplicons by sequencing. By using all of these steps to optimize the urine PCR technique, B. burgdorferi infection could be diagnosed by using urine samples from EM patients with a sensitivity (85%) substantially better than that of serological methods (50%). This improved method could be of future importance as an additional laboratory technique for the diagnosis of unclear, unrecognized borrelia infections and diseases possibly related to Lyme borreliosis.

The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: Standard operating procedures based on empirical analyses.

PubMed

Kanai, Yae; Nishihara, Hiroshi; Miyagi, Yohei; Tsuruyama, Tatsuhiro; Taguchi, Kenichi; Katoh, Hiroto; Takeuchi, Tomoyo; Gotoh, Masahiro; Kuramoto, Junko; Arai, Eri; Ojima, Hidenori; Shibuya, Ayako; Yoshida, Teruhiko; Akahane, Toshiaki; Kasajima, Rika; Morita, Kei-Ichi; Inazawa, Johji; Sasaki, Takeshi; Fukayama, Masashi; Oda, Yoshinao

2018-02-01

Genome research using appropriately collected pathological tissue samples is expected to yield breakthroughs in the development of biomarkers and identification of therapeutic targets for diseases such as cancers. In this connection, the Japanese Society of Pathology (JSP) has developed "The JSP Guidelines on the Handling of Pathological Tissue Samples for Genomic Research" based on an abundance of data from empirical analyses of tissue samples collected and stored under various conditions. Tissue samples should be collected from appropriate sites within surgically resected specimens, without disturbing the features on which pathological diagnosis is based, while avoiding bleeding or necrotic foci. They should be collected as soon as possible after resection: at the latest within about 3 h of storage at 4°C. Preferably, snap-frozen samples should be stored in liquid nitrogen (about -180°C) until use. When intending to use genomic DNA extracted from formalin-fixed paraffin-embedded tissue, 10% neutral buffered formalin should be used. Insufficient fixation and overfixation must both be avoided. We hope that pathologists, clinicians, clinical laboratory technicians and biobank operators will come to master the handling of pathological tissue samples based on the standard operating procedures in these Guidelines to yield results that will assist in the realization of genomic medicine. © 2018 The Authors. Pathology International published by Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

Specimen Collection and Submission Manual

DTIC Science & Technology

2016-06-01

immunoassays Specimen: tissue or bone marrow (100 mg); Whole EDTA blood or serum (0.5 ml) Nasopharyngeal or throat swab, dry or in transport medium; Sputum... Syndrome Coronavirus (MERS-CoV) – detection in clinical samples Methodology: molecular Specimen: If possible collect 3 specimen types (lower...guidelines-clinical-specimens.html) Shipping: ship cold on wet ice or ice packs. For delays exceeding 72 hours, ship frozen on dry ice. Turnaround: 1-2

46 CFR 153.935a - Storage of cargo samples.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 5 2014-10-01 2014-10-01 false Storage of cargo samples. 153.935a Section 153.935a Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SHIPS... § 153.935a Storage of cargo samples. (a) The master shall make sure that any cargo samples are stored in...

High-Throughput Testing of Urogenital and Extragenital Specimens for Detection of Chlamydia Trachomatis and Neisseria Gonorrhoeae with Cobas® CT/NG

PubMed Central

Marlowe, Elizabeth M.; Hardy, David; Krevolin, Mark; Gohl, Peter; Bertram, Alexander; Arcenas, Rodney; Seiverth, Britta; Schneider, Tanja; Liesenfeld, Oliver

2017-01-01

We compared the analytical and clinical performance of cobas® CT/NG for use on the Cobas® 6800/8800 Systems with the Cobas® 4800 CT/NG Test from urogenital and extragenital specimens in over 12,000 specimens from both male and female subjects in Germany and the United States. The analytical sensitivity was ≤40 EB/ml for Chlamydia trachomatis (CT) and ≤1 CFU/ml for Neisseria gonorrhoeae (NG). Using clinical specimens, the overall percent agreement with the Cobas® 4800 CT/NG Test was >98.5%. Across urogenital specimens, there were 93 discrepant specimens; 76 (93.8%) of 81 CT discrepant specimens were 6800+/4800– and 10 (83.3%) of 12 NG discrepant specimens were 6800+/4800–. Sequencing verified CT results for 45 (61.6%) of 73 samples positive by 6800 and 1 (20%) of 5 positive by 4800. Similarly, 7 (70.0%) of 10 NG samples positive by 6800 and 1 of 2 positive by 4800 were confirmed by sequencing. Among discrepant extragenital specimens (all 6800+/4800–), 7 (50%) of 14 oropharyngeal and 23 (76.7%) of 30 anorectal CT discordant samples were confirmed as CT positive by sequencing; all 8 anorectal and 20 (90.9%) of 22 oropharyngeal NG discordant results were also confirmed as NG positive. In conclusion, Cobas® CT/NG for use on the Cobas® 6800/8800 Systems provides high-throughput automated solutions for sexually transmitted infection (STI) screening programs. PMID:29034107

Japanese Wolves are Genetically Divided into Two Groups Based on an 8-Nucleotide Insertion/Deletion within the mtDNA Control Region.

PubMed

Ishiguro, Naotaka; Inoshima, Yasuo; Yanai, Tokuma; Sasaki, Motoki; Matsui, Akira; Kikuchi, Hiroki; Maruyama, Masashi; Hongo, Hitomi; Vostretsov, Yuri E; Gasilin, Viatcheslav; Kosintsev, Pavel A; Quanjia, Chen; Chunxue, Wang

2016-02-01

The mitochondrial DNA (mtDNA) control region (198- to 598-bp) of four ancient Canis specimens (two Canis mandibles, a cranium, and a first phalanx) was examined, and each specimen was genetically identified as Japanese wolf. Two unique nucleotide substitutions, the 78-C insertion and the 482-G deletion, both of which are specific for Japanese wolf, were observed in each sample. Based on the mtDNA sequences analyzed, these four specimens and 10 additional Japanese wolf samples could be classified into two groups- Group A (10 samples) and Group B (4 samples)-which contain or lack an 8-bp insertion/deletion (indel), respectively. Interestingly, three dogs (Akita-b, Kishu 25, and S-husky 102) that each contained Japanese wolf-specific features were also classified into Group A or B based on the 8-bp indel. To determine the origin or ancestor of the Japanese wolf, mtDNA control regions of ancient continental Canis specimens were examined; 84 specimens were from Russia, and 29 were from China. However, none of these 113 specimens contained Japanese wolf-specific sequences. Moreover, none of 426 Japanese modern hunting dogs examined contained these Japanese wolf-specific mtDNA sequences. The mtDNA control region sequences of Groups A and B appeared to be unique to grey wolf and dog populations.

Large-Scale Evaluation of the Immuno-Mycologics Lateral Flow and Enzyme-Linked Immunoassays for Detection of Cryptococcal Antigen in Serum and Cerebrospinal Fluid

PubMed Central

Hansen, Jessica; Slechta, E. Susan; Gates-Hollingsworth, Marcellene A.; Neary, Brandon; Barker, Adam P.; Bauman, Sean; Kozel, Thomas R.

2013-01-01

Cryptococcosis is a systemic infection caused by the pathogenic yeasts Cryptococcus neoformans and C. gattii. Detection of cryptococcal capsular antigen (CrAg) in serum and cerebrospinal fluid (CSF) plays an important diagnostic role. We prospectively compared the new Immuno-Mycologics Inc. (IMMY) lateral flow assay (LFA) and enzyme immunoassay (EIA) to our current CrAg test (Premier EIA; Meridian Bioscience Inc.). Discordant samples were retested with the latex-Cryptococcus antigen test (IMMY) and using serotype-specific monoclonal antibodies (MAbs). A total of 589 serum and 411 CSF specimens were tested in parallel. Qualitative agreement across assays was 97.7%. In all, 56 (41 serum and 15 CSF) samples were positive and 921 (527 serum and 394 CSF) samples were negative by all three assays. The 23 discrepant specimens were all Meridian EIA negative. Of 23 discordant specimens, 20 (87.0%) were positive by both the IMMY LFA and EIA, 2 were LFA positive only, and 1 was EIA positive only. Eleven discrepant specimens had adequate volume for latex agglutination (LA) testing; 8 were LA positive, and 3 were LA negative. LA-negative samples (2 CSF samples and 1 serum) had low IMMY LFA/EIA titers (≤1:10). Serotype-specific MAb analysis of the LA-positive samples suggested that these specimens contained CrAg epitopes similar to those of serotype C strains. In conclusion, the IMMY assays showed excellent overall concordance with the Meridian EIA. Assay performance differences were related to issues of analytic sensitivity and possible serotype bias. Incomplete access to patient-level data combined with low specimen volumes limited our ability to fully resolve discrepant results. PMID:23114703

Large-scale evaluation of the immuno-mycologics lateral flow and enzyme-linked immunoassays for detection of cryptococcal antigen in serum and cerebrospinal fluid.

PubMed

Hansen, Jessica; Slechta, E Susan; Gates-Hollingsworth, Marcellene A; Neary, Brandon; Barker, Adam P; Bauman, Sean; Kozel, Thomas R; Hanson, Kimberly E

2013-01-01

Cryptococcosis is a systemic infection caused by the pathogenic yeasts Cryptococcus neoformans and C. gattii. Detection of cryptococcal capsular antigen (CrAg) in serum and cerebrospinal fluid (CSF) plays an important diagnostic role. We prospectively compared the new Immuno-Mycologics Inc. (IMMY) lateral flow assay (LFA) and enzyme immunoassay (EIA) to our current CrAg test (Premier EIA; Meridian Bioscience Inc.). Discordant samples were retested with the latex-Cryptococcus antigen test (IMMY) and using serotype-specific monoclonal antibodies (MAbs). A total of 589 serum and 411 CSF specimens were tested in parallel. Qualitative agreement across assays was 97.7%. In all, 56 (41 serum and 15 CSF) samples were positive and 921 (527 serum and 394 CSF) samples were negative by all three assays. The 23 discrepant specimens were all Meridian EIA negative. Of 23 discordant specimens, 20 (87.0%) were positive by both the IMMY LFA and EIA, 2 were LFA positive only, and 1 was EIA positive only. Eleven discrepant specimens had adequate volume for latex agglutination (LA) testing; 8 were LA positive, and 3 were LA negative. LA-negative samples (2 CSF samples and 1 serum) had low IMMY LFA/EIA titers (≤1:10). Serotype-specific MAb analysis of the LA-positive samples suggested that these specimens contained CrAg epitopes similar to those of serotype C strains. In conclusion, the IMMY assays showed excellent overall concordance with the Meridian EIA. Assay performance differences were related to issues of analytic sensitivity and possible serotype bias. Incomplete access to patient-level data combined with low specimen volumes limited our ability to fully resolve discrepant results.

A Randomized Controlled Trial of a Novel Sheath Cryoprobe for Bronchoscopic Lung Biopsy in a Porcine Model.

PubMed

Yarmus, Lonny B; Semaan, Roy W; Arias, Sixto A; Feller-Kopman, David; Ortiz, Ricardo; Bösmüller, Hans; Illei, Peter B; Frimpong, Bernice O; Oakjones-Burgess, Karen; Lee, Hans J

2016-08-01

Transbronchial forceps biopsy (FBx) has been the preferred method for obtaining bronchoscopic lung biopsy specimens. Cryoprobe biopsy (CBx) has been shown to obtain larger and higher quality samples, but is limited by its inability to retrieve the sample through the working channel of the bronchoscope, requiring the bronchoscope to leave the airway for sample retrieval. We evaluated a novel device using a sheath cryobiopsy (SCBx). This method allows for specimen retrieval through the working channel of the bronchoscope, with the scope remaining inside the airway. This prospective, randomized controlled, single-blinded porcine study compared a 1.1-mm SCBx probe, a 1.9-mm CBx probe, and 2.0-mm FBx forceps. Assessment of histologic accessibility, sample quantity and quality, number of attempts to acquire and retrieve samples, cryoprobe activation time, fluoroscopy activation time, technical feasibility, and complications were compared. Samples adequate for standard pathologic processing were retrieved with 82.1% of the SCBx specimens, 82.9%% of the CBx specimens, and 30% of the FBx specimens. The histologic accessibility of both SCBx (P = .0002) and CBx (P = .0003) was superior to FBx. Procedure time for FBx was faster than for both SCBx and CBx, but SCBx was significantly faster than CBx (P < .0001). Fluoroscopy time was lower for both SCBx and CBx compared with FBx. There were no significant bleeding events. SCBx is a feasible technique providing a higher quality lung biopsy specimen compared with FBx and can successfully be retrieved through the working channel. Human studies are needed to further assess this technique with additional safety data. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Impact of specimen adequacy on the assessment of renal allograft biopsy specimens.

PubMed

Cimen, S; Geldenhuys, L; Guler, S; Imamoglu, A; Molinari, M

2016-01-01

The Banff classification was introduced to achieve uniformity in the assessment of renal allograft biopsies. The primary aim of this study was to evaluate the impact of specimen adequacy on the Banff classification. All renal allograft biopsies obtained between July 2010 and June 2012 for suspicion of acute rejection were included. Pre-biopsy clinical data on suspected diagnosis and time from renal transplantation were provided to a nephropathologist who was blinded to the original pathological report. Second pathological readings were compared with the original to assess agreement stratified by specimen adequacy. Cohen's kappa test and Fisher's exact test were used for statistical analyses. Forty-nine specimens were reviewed. Among these specimens, 81.6% were classified as adequate, 6.12% as minimal, and 12.24% as unsatisfactory. The agreement analysis among the first and second readings revealed a kappa value of 0.97. Full agreement between readings was found in 75% of the adequate specimens, 66.7 and 50% for minimal and unsatisfactory specimens, respectively. There was no agreement between readings in 5% of the adequate specimens and 16.7% of the unsatisfactory specimens. For the entire sample full agreement was found in 71.4%, partial agreement in 20.4% and no agreement in 8.2% of the specimens. Statistical analysis using Fisher's exact test yielded a P value above 0.25 showing that - probably due to small sample size - the results were not statistically significant. Specimen adequacy may be a determinant of a diagnostic agreement in renal allograft specimen assessment. While additional studies including larger case numbers are required to further delineate the impact of specimen adequacy on the reliability of histopathological assessments, specimen quality must be considered during clinical decision making while dealing with biopsy reports based on minimal or unsatisfactory specimens.

Development of fracture mechanics data for two hydrazine APU turbine wheel materials

NASA Technical Reports Server (NTRS)

Curbishley, G.

1975-01-01

The effects of high temperature, high pressure ammonia were measured on the fracture mechanics and fatigue properties of Astroloy and Rene' 41 turbine wheel materials. Also, the influence of protective coatings on these properties was investigated. Specimens of forged bar stock were subjected to LCF and HCF tests at 950 K (1250 F) and 3.4 MN/sq m (500 psig) pressure, in ammonia containing about 1.5 percent H2O. Aluminized samples (Chromizing Company's Al-870) and gold plated test bars were compared with uncoated specimens. Comparison tests were also run in air at 950 K (1250 F), but at ambient pressures. K sub IE and K sub TH were determined on surface flawed specimens in both the air and ammonia in both uncoated and gold plated conditions. Gold plated specimens exhibited better properties than uncoated samples, and aluminized test bars generally had lower properties. The fatigue properties of specimens tested in ammonia were higher than those tested in air, yet the K sub TH values of ammonia tested samples were lower than those tested in air. However, insufficient specimens were tested to develop significant design data.

Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification.

PubMed

Unger, Jakob; Merhof, Dorit; Renner, Susanne

2016-11-16

Global Plants, a collaborative between JSTOR and some 300 herbaria, now contains about 2.48 million high-resolution images of plant specimens, a number that continues to grow, and collections that are digitizing their specimens at high resolution are allocating considerable recourses to the maintenance of computer hardware (e.g., servers) and to acquiring digital storage space. We here apply machine learning, specifically the training of a Support-Vector-Machine, to classify specimen images into categories, ideally at the species level, using the 26 most common tree species in Germany as a test case. We designed an analysis pipeline and classification system consisting of segmentation, normalization, feature extraction, and classification steps and evaluated the system in two test sets, one with 26 species, the other with 17, in each case using 10 images per species of plants collected between 1820 and 1995, which simulates the empirical situation that most named species are represented in herbaria and databases, such as JSTOR, by few specimens. We achieved 73.21% accuracy of species assignments in the larger test set, and 84.88% in the smaller test set. The results of this first application of a computer vision algorithm trained on images of herbarium specimens shows that despite the problem of overlapping leaves, leaf-architectural features can be used to categorize specimens to species with good accuracy. Computer vision is poised to play a significant role in future rapid identification at least for frequently collected genera or species in the European flora.

An Open-Source Storage Solution for Cryo-Electron Microscopy Samples.

PubMed

Ultee, Eveline; Schenkel, Fred; Yang, Wen; Brenzinger, Susanne; Depelteau, Jamie S; Briegel, Ariane

2018-02-01

Cryo-electron microscopy (cryo-EM) enables the study of biological structures in situ in great detail and to solve protein structures at Ångstrom level resolution. Due to recent advances in instrumentation and data processing, the field of cryo-EM is a rapidly growing. Access to facilities and national centers that house the state-of-the-art microscopes is limited due to the ever-rising demand, resulting in long wait times between sample preparation and data acquisition. To improve sample storage, we have developed a cryo-storage system with an efficient, high storage capacity that enables sample storage in a highly organized manner. This system is simple to use, cost-effective and easily adaptable for any type of grid storage box and dewar and any size cryo-EM laboratory.

Sample holder for axial rotation of specimens in 3D microscopy.

PubMed

Bruns, T; Schickinger, S; Schneckenburger, H

2015-10-01

In common light microscopy, observation of samples is only possible from one perspective. However, especially for larger three-dimensional specimens observation from different views is desirable. Therefore, we are presenting a sample holder permitting rotation of the specimen around an axis perpendicular to the light path of the microscope. Thus, images can be put into a defined multidimensional context, enabling reliable three-dimensional reconstructions. The device can be easily adapted to a great variety of common light microscopes and is suitable for various applications in science, education and industry, where the observation of three-dimensional specimens is essential. Fluorescence z-projection images of copepods and ixodidae ticks at different rotation angles obtained by confocal laser scanning microscopy and light sheet fluorescence microscopy are reported as representative results. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Dimensional change in complete dentures fabricated by injection molding and microwave processing.

PubMed

Keenan, Phillip L J; Radford, David R; Clark, Robert K F

2003-01-01

Acrylic resin complete dentures undergo dimensional changes during polymerization. Techniques with injection molding and polymerization and microwave polymerization are reported to reduce these changes and thereby improve clinical fit. These dimensional changes need to be quantified. The purpose of this study was to compare differences in dimensional changes of simulated maxillary complete dentures during polymerization and storage in water after injection molding and conventional polymerization, or microwave polymerization against a control of conventionally packed and polymerized simulated maxillary complete dentures. Forty identical maxillary denture bases were prepared in dental wax with anatomic teeth. They were invested and the wax eliminated from the molds. Ten specimens each were randomly assigned to 1 of 4 groups. Group 1 was compression molded and conventionally polymerized; group 2 was injection molded and conventionally polymerized (Success); group 3 was injection molded and microwave polymerized (Acron MC); and group 4 was injection molded and microwave polymerized (Microbase). Intermolar width and changes in vertical dimension of occlusion, were determined after polymerization and after storage in water for 28 days. Measurements in triplicate were made between points scribed on the second molar teeth with a traveling microscope (accurate to 0.005 mm). Vertical dimension of occlusion was measured between points scribed on the upper and lower members of an articulator by use of an internal micrometer (accurate to 0.05 mm). Data were analyzed by use of a 1-way analysis of variance with Tukey post-hoc contrasts (P <.05). Polymerization contractions (intermolar widths) for each group were: group 1, -0.24%; group 2, -0.27%; group 3, -0.35%; and group 4, -0.37%. The Microbase specimens had greater shrinkage than conventionally polymerized specimens, but there were no significant differences between the groups. All injection methods had less postpolymerization increase in vertical dimension of occlusion (0.63 to 0.41 mm) than the conventional Trevalon control (0.74 mm), but only group 4 was significantly different (P<.004). After storage in water for 28 days, all specimens increased in vertical dimension of occlusion (0.10% to 0.16%) from polymerization techniques, but there were no significant differences between groups. Within the limitations of this study, injection molding resulted in a slightly less increase of vertical dimension of occlusion than conventional polymerization techniques, the difference being significant for Microbase compared with the conventional Trevalon control.

A Raman Microspectroscopy Study of Water and Trehalose in Spin-Dried Cells

PubMed Central

Abazari, Alireza; Chakraborty, Nilay; Hand, Steven; Aksan, Alptekin; Toner, Mehmet

2014-01-01

Long-term storage of desiccated nucleated mammalian cells at ambient temperature may be accomplished in a stable glassy state, which can be achieved by removal of water from the biological sample in the presence of glass-forming agents including trehalose. The stability of the glass may be compromised due to a nonuniform distribution of residual water and trehalose within and around the desiccated cells. Thus, quantification of water and trehalose contents at the single-cell level is critical for predicting the glass formation and stability for dry storage. Using Raman microspectroscopy, we estimated the trehalose and residual water contents in the microenvironment of spin-dried cells. Individual cells with or without intracellular trehalose were embedded in a solid thin layer of extracellular trehalose after spin-drying. We found strong evidence suggesting that the residual water was bound at a 2:1 water/trehalose molar ratio in both the extracellular and intracellular milieus. Other than the water associated with trehalose, we did not find any more residual water in the spin-dried sample, intra- or extracellularly. The extracellular trehalose film exhibited characteristics of an amorphous state with a glass transition temperature of ∼22°C. The intracellular milieu also dried to levels suitable for glass formation at room temperature. These findings demonstrate a method for quantification of water and trehalose in desiccated specimens using confocal Raman microspectroscopy. This approach has broad use in desiccation studies to carefully investigate the relationship of water and trehalose content and distribution with the tolerance to drying in mammalian cells. PMID:25418294

[Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

PubMed

Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

2006-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory.

Solid tissue culture for cytogenetic analysis: a collaborative survey for the Association of Clinical Cytogeneticists.

PubMed Central

Rodgers, C S; Creasy, M R; Fitchett, M; Maliszewska, C T; Pratt, N R; Waters, J J

1996-01-01

AIMS: To survey the diagnostic service provided by UK laboratories for the culture of solid tissue samples (excluding tumours) and in particular to examine the variation in culture success rates and the problems of maternal cell overgrowth. METHODS: Twenty seven laboratories took part in a collaborative survey during 1992. Each laboratory submitted data on up to a maximum of 60 consecutive specimens (n = 1361) over a six month period. RESULTS: Skin specimens, the largest category received (n = 520), were the most problematic (51% success rate). Culture success rates were significantly lower (43%) when skin specimens (n = 140) were transported dry to the laboratory. Success rates for skin specimens also varied, depending on the origin of the specimen, from 18% for intra-uterine deaths (IUD) (n = 94) to 85% for neonatal deaths (n = 33) and 83% for live patients (n = 54). Culture of selected extra-fetal tissues from IUD, stillbirths and following elective termination of pregnancy (TOP) gave comparable success rates to those achieved for skin samples from neonatal deaths and live births. Skewed sex ratios, female > male, were identified for products of conception (POC) (n = 298) and placental biopsy specimens (n = 97). CONCLUSIONS: By appropriate selection, transport and processing of tissues, and in particular by avoiding relying solely on skin samples from IUD, stillbirths and TOP, an increase in culture success rates for solid tissue samples submitted for cytogenetic analysis could be achieved. The high risk of maternal cell contamination from POC and placental biopsy specimens was also identified in this survey. PMID:8881913

Effect of monomer composition of polymer matrix on flexural properties of glass fibre-reinforced orthodontic archwire.

PubMed

Ohtonen, J; Vallittu, P K; Lassila, L V J

2013-02-01

To compare force levels obtained from glass fibre-reinforced composite (FRC) archwires. Specifically, FRC wires were compared with polymer matrices having different dimethacrylate monomer compositions. FRC material (E-glass provided by Stick Tech Ltd, Turku, Finland) with continuous unidirectional glass fibres and four different types of dimethacrylate monomer compositions for the resin matrix were tested. Cross-sectionally round FRC archwires fitting into the 0.3 mm slot of a bracket were divided into 16 groups with six specimens in each group. Glass fibres were impregnated by the manufacturer, and they were initially light-cured by hand light-curing unit or additionally post-cured in light-curing oven. The FRC archwire specimens were tested at 37°C according to a three-point bending test in dry and wet conditions using a span length of 10 mm and a crosshead speed of 1.0 mm/minute. The wires were loaded until final failure. The data were statistically analysed using analysis of variance (ANOVA). The dry FRC archwire specimens revealed higher load values than water stored ones, regardless of the polymer matrix. A majority of the FRC archwires showed higher load values after being post-cured. ANOVA revealed that the polymer matrix, curing method, and water storage had a significant effect (P < 0.05) on the flexural behaviour of the FRC archwire. Polymer matrix composition, curing method, and water storage affected the flexural properties and thus, force level and working range which could be obtained from the FRC archwire.

Influence of Hemostatic Solution on Bond Strength and Physicochemical Properties of Resin Cement.

PubMed

Araújo, Isabela Sousa de; Prado, Célio Jesus do; Raposo, Luís Henrique Araújo; Soares, Carlos José; Zanatta, Rayssa Ferreira; Torres, Carlos Rocha Gomes; Ruggiero, Reinaldo; Silva, Gisele Rodrigues da

2017-01-01

The aim of this study was to evaluate the degree of conversion, color stability, chemical composition, and bond strength of a light-cured resin cement contaminated with three different hemostatic solutions. Specimens were prepared for the control (uncontaminated resin cement) and experimental groups (resin cement contaminated with one of the hemostatic solutions) according to the tests. For degree of conversion, DC (n = 5) and color analyses (n = 10), specimens (3 mm in diameter and 2 mm thick) were evaluated by Fourier transform infrared spectroscopy (FTIR) and CIELAB spectrophotometry (L*, a*, b*), respectively. For elemental chemical analysis (n = 1), specimens (2 mm thick and 6 mm in diameter) were evaluated by x-ray energy-dispersive spectroscopy (EDS). The bond strengths of the groups were assessed by the microshear test (n = 20) in a leucite-reinforced glass ceramic substrate, followed by failure mode analysis by scanning electron microscopy (SEM). The mean values, except for the elemental chemical evaluation and failure mode, were evaluated by ANOVA and Tukey's HSD test. The color stability was influenced by storage time (p<0.001) and interaction between contamination and storage time (p<0.001). Hemostop and Viscostat Clear contamination did not affect the DC, however Viscostat increased the DC. Bond strength of the resin cement to ceramic was negatively affected by the contaminants (p<0.001). Contamination by hemostatic agents affected the bond strength, degree of conversion, and color stability of the light-cured resin cement tested.

[Expression of ATAD2 in different liver lesions and its clinical significance].

PubMed

Liu, F; Zhou, X; Ji, H H; Li, H; Xiang, F G

2017-05-20

Objective: To examine the expression of ATAD2 in different liver lesions and its clinical significance. Methods: ATAD2 expression in 60 hepatocellular carcinoma (HCC) surgical specimens (49 of which have concurrent liver cirrhosis), 43 HCC biopsy specimens, 2 high-grade liver dysplastic nodule specimens, 3 low-grade liver dysplastic nodule specimens, 50 liver cirrhosis tissue samples, and 20 normal liver tissue samples were measured using immunohistochemistry. The F-test, q-test, t-test, and chi-square test were used for statistical analysis of data. Results: ATAD2 was expressed in 56 HCC surgical specimens (93.33%), 35 HCC biopsy specimens (81.40%), and 2 high-grade liver dysplastic nodule specimens (2/2), but not in the low-grade liver dysplastic nodule, liver cirrhosis tissue, and normal liver tissue samples. The mean expression of ATAD2 was significantly higher in HCC tissues than in high-grade and low-grade liver dysplastic nodule tissues, liver cirrhosis tissue, and normal liver tissue ( F = 22.96, q = 3.138, 3.972, 12.272, and 9.101, respectively, all P < 0.01). There were no significant differences in the mean expression and positive expression rate of ATAD2 between HCC surgical and biopsy specimens ( t = 1.40, P > 0.05; χ ² = 3.47, P >0.05). Of the 35 HCC biopsy specimens that expressed ATAD2, the mean ATAD2 expression was ≥1% in 35 specimens (100%), ≥3% in 27 specimens (77.14%), and ≥5 % in 23 specimens (65.71%). In addition, among the pathological grade I-II HCC biopsy specimens, the mean ATAD2 expression was ≥1% in 28 specimens (100%), ≥3% in 22 specimens (62.86%), and ≥5% in 19 specimens (54.29%). Moreover, ATAD2 expression in HCC was associated with serum alpha-fetoprotein level, presence of hepatitis B virus surface antigen (HBsAg), and presence of concurrent liver cirrhosis ( t = 2.09, 2.30, and 2.18, respectively, all P < 0.05). Conclusion: ATAD2 may play an important role in HCC tumorigenesis, and may be involved in malignant transformation of cells. ATAD2 expression can be a valuable marker for differentiating the nature of lesions in liver biopsy tissues during clinical practice.

Degree and frequency of inhibition in a routine real-time PCR detecting Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia in Turkey.

PubMed

Döskaya, Mert; Caner, Ayse; Degirmenci, Aysu; Wengenack, Nancy L; Yolasigmaz, Aysegül; Turgay, Nevin; Ozensoy Töz, Seray; Gürüz, Yüksel

2011-07-01

Routine laboratory diagnosis of Pneumocystis jirovecii is currently achieved by PCR in almost all laboratories with sufficient equipment due to its high sensitivity and specificity compared to staining methods. A current issue that limits the reliability and sensitivity of PCR is the degree of inhibition caused by inhibitory substances in respiratory samples. The present study aimed to analyse the degree and frequency of inhibition in real-time PCR detecting P. jirovecii in respiratory specimens submitted to a Pneumocystis pneumonia (PcP) diagnosis laboratory in Ege University Medical School, Turkey. Between July 2009 and December 2010, 76 respiratory specimens [63 bronchoalveolar lavage (BAL) fluid, 10 sputum samples, two tracheal aspiration fluid and one thoracentesis fluid] obtained from 69 PcP-suspected patients were investigated for the presence of P. jirovecii using real-time PCR targeting the cdc2 gene. Of these samples, 42 of the specimens were stained and examined by microscopy according to the request of the clinicians. PCR was positive in 15 specimens in the initial run. Of the remaining 61 samples, 41 of them were negative with positive internal inhibition controls (i.e. true-negative group). The frequency of inhibition in the initial run was 26.31 % (20/76) as determined by spiked negative controls. All of the inhibited samples were resolved after 1 : 2, 1 : 5, 1 : 10 and 1 : 20 dilutions. P. jirovecii was detected by PCR in two inhibited specimens after retesting with diluted samples which were also positive by microscopy. The incidence of P. jirovecii in respiratory specimens was 22.36 % (17/76) as determined by real-time PCR and 7.14 % (3/42) by microscopy. Overall, the incidence of P. jirovecii in respiratory samples was 23.68 % (18/76) as detected by both methods. In conclusion, inclusion of spiked positive controls in each sample and retesting with diluted samples to resolve inhibition increased the reliability of the real-time PCR assay in terms of determining false-negative results and influencing the treatment of the patient. Furthermore, results of the present study determined for the first time the frequency and degree of inhibition in a real-time PCR detecting P. jirovecii in respiratory specimens during routine diagnosis of PcP.

Immunological screening of drugs of abuse and gas chromatographic-mass spectrometric confirmation of opiates and cocaine in hair.

PubMed

Segura, J; Stramesi, C; Redón, A; Ventura, M; Sanchez, C J; González, G; San, L; Montagna, M

1999-03-05

The work presents an analytical strategy to detect drugs of abuse in hair. It involves two sequential steps: a screening by a simple enzyme-linked immunosorbent assay (ELISA) methodology to detect opiates, cocaine and its metabolites, and benzodiacepines, followed by confirmation of opiates and cocaine metabolites in positive samples by gas chromatography coupled to mass spectrometry (GC-MS). In the same GC-MS run other drugs for substitution therapy (e.g. methadone and its main metabolite) can also be detected. After a double washing of hair samples with dichloromethane, hair specimens were cut into small pieces and 10 mg samples were incubated in 2 ml of methanol-trifluoroacetic acid (9:1) mixture, overnight at 37 degrees C. Aliquots of the extract were then evaporated, reconstituted in buffer and analysed according to the ELISA procedure. Confirmation involved solid-phase extraction of another fraction of the extract kept at -20 degrees C, derivatization with heptafluorobutyric anhydride and hexafluoroisopropanol and detection of cocaine, benzoylecgonine, ecgonine methylester, cocaethylene, morphine, codeine, 6-monoacetylmorphine, methadone and 2-ethylidene-1.5-dimethyl-3,3-diphenylpirrolidine (methadone metabolite) by selective ion monitoring after gas chromatographic separation. During the development of the method it was verified that no more than 10% of cocaine, opiates and benzodiacepines were lost when dichloromethane was used to wash real samples. The results also confirmed the increase of extractability power of TFA when it was added to methanol: the recovery for the analytes (cocaine and its metabolites and opiates) added to methanol-TFA alone was of the order of 90% except for benzoylecgonine (75%), and the recovery for the analytes added to methanol-TFA extract of drug-free hair was about 90% for all analytes except for benzoylecgonine and 6-MAM (around 70%). Regarding the stability of labile compounds, only small amounts of ecgonine methylester (2.3%) and morphine (7.2%) were produced, from cocaine and 6-MAM respectively, after the whole extraction procedure and two weeks of storage of methanol-TFA extracts at -20 degrees C. Satisfactory results were obtained when the procedures were applied to the analysis of external proficiency testing hair samples and actual specimens from drug addicts.

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

PubMed

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

2018-01-01

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

Analysis of polyfluoroalkyl substances and bisphenol A in dried blood spots by liquid chromatography tandem mass spectrometry.

PubMed

Ma, Wanli; Kannan, Kurunthachalam; Wu, Qian; Bell, Erin M; Druschel, Charlotte M; Caggana, Michele; Aldous, Kenneth M

2013-05-01

Dried blood spots (DBS), collected as part of the newborn screening program (NSP) in the USA, is a valuable resource for studies on environmental chemical exposures and associated health outcomes in newborns. Nevertheless, determination of concentrations of environmental chemicals in DBS requires assays with great sensitivity, as the typical volume of blood available on a DBS with 16-mm diameter disc is approximately 50 μL. In this study, we developed a liquid-liquid extraction and high-performance liquid chromatography/tandem mass spectrometry method for the detection of perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA), and bisphenol A (BPA) in DBS. The method was validated for accuracy, precision, and sensitivity, by spiking of target chemicals at different levels on Whatman 903 filter cards, which is used in the collection of DBS by the NSP. Contamination arising from collection, storage, and handling of DBS is an important issue to be considered in the analysis of trace levels of environmental chemicals in DBS. For the evaluation of the magnitude of background contamination, field blanks were prepared from unspotted portions of DBS filter cards collected by the NSP. The method was applied for the measurement of PFOS, PFOA, and BPA in 192 DBS specimens provided by NSP of New York State. PFOS and PFOA were detected in 100 % of the specimens analyzed. The concentrations of PFOS and PFOA measured in DBS were similar to those reported earlier in the whole blood samples of newborns. BPA was also found in 86 % of the specimens at concentrations ranging from 0.2 to 36 ng/mL (excluding two outliers). Further studies are needed to evaluate the sources of BPA exposures and health outcomes in newborns.

Effect of Energy Drinks on Discoloration of Silorane and Dimethacrylate-Based Composite Resins

PubMed Central

Ahmadizenouz, Ghazaleh; Esmaeili, Behnaz; Ahangari, Zohreh; Khafri, Soraya; Rahmani, Aghil

2016-01-01

Objectives: This study aimed to assess the effects of two energy drinks on color change (ΔE) of two methacrylate-based and a silorane-based composite resin after one week and one month. Materials and Methods: Thirty cubic samples were fabricated from Filtek P90, Filtek Z250 and Filtek Z350XT composite resins. All the specimens were stored in distilled water at 37°C for 24 hours. Baseline color values (L*a*b*) of each specimen were measured using a spectrophotometer according to the CIEL*a*b* color system. Ten randomly selected specimens from each composite were then immersed in the two energy drinks (Hype, Red Bull) and artificial saliva (control) for one week and one month. Color was re-assessed after each storage period and ΔE values were calculated. The data were analyzed using the Kruskal Wallis and Mann–Whitney U tests. Results: Filtek Z250 composite showed the highest ΔE irrespective of the solutions at both time points. After seven days and one month, the lowest ΔE values were observed in Filtek Z350XT and Filtek P90 composites immersed in artificial saliva, respectively. The ΔE values of Filtek Z250 and Z350XT composites induced by Red Bull and Hype energy drinks were not significantly different. Discoloration of Filtek P90 was higher in Red Bull energy drink at both time points. Conclusions: Prolonged immersion time in all three solutions increased ΔE values of all composites. However, the ΔE values were within the clinically acceptable range (<3.3) at both time points. PMID:28127318

The influence of total suction on the brittle failure characteristics of clay shales

NASA Astrophysics Data System (ADS)

Amann, F.; Linda, W.; Zimmer, S.; Thoeny, R.

2013-12-01

Clay shale testing is challenging and the results obtained from standard laboratory tests may not always reflect the strength of the clay shale in-situ. This is to a certain extend associated with the sensitivity of these rock types to desaturation processes during drilling, sample storage, and sample preparation. In this study the relationship between total suction, uniaxial compressive strength and Brazilian tensile (BTS) strength of cylindrical samples of Opalinus Clay was established in a systematic manner. Unconfined uniaxial compression and BTS tests were performed utilizing a servo-controlled testing procedure. Total suctions in the specimens was generated in air tight desiccators using supersaturated saline solutions which establish a relative humidity ranging from 20% to 99%. For unconfined compressive strength tests loading of the specimens occurred parallel to bedding. For BTS tests loading was either oriented normal or perpendicular to bedding. Both, the crack initiation and volumetric strain reversal threshold values were determined using volumetric and radial stress-strain methods. The results of BTS tests show that the tensile strength normal and perpendicular to bedding increases by a factor of approximately 3 when total suction is increased from 0 to 90 MPa (i.e. saturation decreases from 1.0 to 0.7) . Beyond 90 MPa total suction no further increase in tensile strength was observed, most probably due to shrinkage cracks which alter the tensile strength of the clay shale. Results obtained from UCS tests suggest that higher total suctions result in higher UCS values. Between total suctions of 0 to 90 MPa, the strength increase is almost linear (i.e. the UCS increases by a factor of 1.5 MPa). Beyond 90 MPa total suction no further strength increase was observed. A similar trend can be observed for crack initiation and crack damage values. In the same range of total suction the crack initiation stress increases by a factor of 5 (from 2 MPa to 10 MPa), and the crack damage stress increases by a factor of 2 (from 6 to 12 MPa). In addition to UCS tests, the water retention curve of intact and disturbed specimens was established. Here, results indicate that the drying path remains nearly unaffected by mechanical damage. However, the wetting path is considerably affected by mechanical damage.

Encapsulation of grape seed extract in polylactide microcapsules for sustained bioactivity and time-dependent release in dental material applications.

PubMed

Yourdkhani, Mostafa; Leme-Kraus, Ariene Arcas; Aydin, Berdan; Bedran-Russo, Ana Karina; White, Scott R

2017-06-01

To sustain the bioactivity of proanthocyanidins-rich plant-derived extracts via encapsulation within biodegradable polymer microcapsules. Polylactide microcapsules containing grape seed extract (GSE) were manufactured using a combination of double emulsion and solvent evaporation techniques. Microcapsule morphology, size distribution, and cross-section were examined via scanning electron microscopy. UV-vis measurements were carried out to evaluate the core loading and encapsulation efficiency of microcapsules. The bioactivity of extracts was evaluated after extraction from capsules via solvent partitioning one week or one year post-encapsulation process. Fifteen human molars were cut into 7mm×1.7mm×0.5mm thick mid-coronal dentin beams, demineralized, and treated with either encapsulated GSE, pristine GSE, or left untreated. The elastic modulus of dentin specimens was measured based on three-point bending experiments as an indirect assessment of the bioactivity of grape seed extracts. The effects of the encapsulation process and storage time on the bioactivity of extracts were analyzed. Polynuclear microcapsules with average diameter of 1.38μm and core loading of up to 38wt% were successfully manufactured. There were no statistically significant differences in the mean fold increase of elastic modulus values among the samples treated with encapsulated or pristine GSE (p=0.333), or the storage time (one week versus one year storage at room temperature, p=0.967). Polynuclear microcapsules containing proanthocyanidins-rich plant-derived extracts were prepared. The bioactivity of extracts was preserved after microencapsulation. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

An outbreak of febrile gastroenteritis associated with corn contaminated by Listeria monocytogenes.

PubMed

Aureli, P; Fiorucci, G C; Caroli, D; Marchiaro, G; Novara, O; Leone, L; Salmaso, S

2000-04-27

On May 21, 1997, numerous cases of febrile gastrointestinal illness were reported among the students and staff of two primary schools in northern Italy, all of whom had eaten at cafeterias served by the same caterer. We interviewed people who ate at the cafeterias about symptoms and foods consumed on May 20. There were no samples of foods left at the cafeterias, but we tested routine samples taken on May 20 by the caterer and environmental specimens at the catering plant. The hospitalized patients were tested for common enteropathogens and toxins. Of the 2189 persons interviewed (82 percent of those exposed), 1566 (72 percent) reported symptoms; of these, 292 (19 percent) were hospitalized. Among samples obtained from hospitalized patients, all but two of the stool specimens and all blood specimens were negative for common enteropathogens. Listeria monocytogenes was isolated from one blood specimen and from 123 of the 141 stool specimens. Consumption of a cold salad of corn and tuna was associated with the development of symptoms (relative risk, 6.19; 95 percent confidence interval, 4.81 to 7.98; P<0.001). L. monocytogenes was isolated from the caterer's sample of the salad and from environmental specimens collected from the catering plant. All listeria isolates were serotype 4b and were found to be identical on DNA analysis. Experimental contamination of sterile samples of the implicated foods showed that L. monocytogenes grew on corn when kept for at least 10 hours at 25 degrees C. Food-borne infection with L. monocytogenes can cause febrile illness with gastroenteritis in immunocompetent persons.

A novel cross-disciplinary multi-institute approach to translational cancer research: lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC).

PubMed

Patel, Ashokkumar A; Gilbertson, John R; Showe, Louise C; London, Jack W; Ross, Eric; Ochs, Michael F; Carver, Joseph; Lazarus, Andrea; Parwani, Anil V; Dhir, Rajiv; Beck, J Robert; Liebman, Michael; Garcia, Fernando U; Prichard, Jeff; Wilkerson, Myra; Herberman, Ronald B; Becich, Michael J

2007-06-08

The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium's intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers. The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions' IRB/HIPAA standards. Currently, this "virtual biorepository" has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium's web site. The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy.

A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

PubMed Central

Patel, Ashokkumar A.; Gilbertson, John R.; Showe, Louise C.; London, Jack W.; Ross, Eric; Ochs, Michael F.; Carver, Joseph; Lazarus, Andrea; Parwani, Anil V.; Dhir, Rajiv; Beck, J. Robert; Liebman, Michael; Garcia, Fernando U.; Prichard, Jeff; Wilkerson, Myra; Herberman, Ronald B.; Becich, Michael J.

2007-01-01

Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium’s intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers. Methods: The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions’ IRB/HIPAA standards. Results: Currently, this “virtual biorepository” has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium’s web site. Conclusions: The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy. PMID:19455246

Effect of photoactivated riboflavin on the biodegradation-resistance of root-dentin collagen.

PubMed

Priyadarshini, Balasankar Meera; Lu, Thong Beng; Fawzy, Amr S

2017-12-01

This study was conducted to evaluate the effect of UVA-activated 1% riboflavin solution on structural integrity; mechanical properties and stability; and collagenase-mediated collagen solubilisation resistance of demineralized root dentin collagen matrix. Root dentin specimens demineralized with 17% EDTA for 7days were treated with 1% RF for 1min followed by UVA photo-activation at intensity 7mW/cm 2 for 1min. Control specimens were completely devoid of riboflavin and/or UVA treatments. Specimens were challenged with bacterial collagenase type-I solution for different time-periods at 37°C. Collagen solubilisation resistance was evaluated in terms of hydroxyproline (HYP) liberation. Mechanical characterization of dentin specimens before and after 24h of exposure to collagenase solution was done in terms of apparent-elastic modulus (E appr ) and ultimate tensile strength (UTS). Variations in dentin collagen-network structure with exposure time in collagenase were visualized by TEM. Crosslinking dentin with UVA-activated riboflavin significantly decreased HYP release and increased E appr and UTS compared to control specimens with storage time in collagenase. Moreover, crosslinked specimens showed higher structural resistance to collagenase effect reflected from dense, well-formed collagen fibrils-network with characteristic collagen cross-banding. UVA-activated riboflavin treatment increased collagenase-mediated collagen degradation resistance and enhanced mechanical stability against collagenase challenges of root dentin after EDTA demineralization. Copyright © 2017 Elsevier B.V. All rights reserved.

40 CFR 80.1653 - Recordkeeping.

Code of Federal Regulations, 2014 CFR

2014-07-01

... this subpart O: (i) The location, date, time, and storage tank or truck identification for each sample... analytical testing: (i) The location, date, time, and storage tank or truck identification for each sample..., time, and storage tank or truck identification for each sample collected. (B) The name and title of the...

Comparison of four-hour and twenty-four-hour refrigerated storage of nonpotable water for fecal coliform analysis.

PubMed Central

Standridge, J H; Lesar, D J

1977-01-01

The problem of extending the storage time of water samples for fecal coliform analysis was addressed. Included in this report is a literature review of the storage problem. Twenty-eight samples were analyzed in replicate to determine the effect of 24-h storage of water samples at 4 degrees C. A new statistical approach to data analysis, coupled with the concept of practical acceptability, is presented. According to our results, many samples can successfully be stored at 4 degrees C for 24 h. PMID:335972

Changes in Postfermentation Quality during the Distribution Process of Anchovy ( Engraulis japonicus) Fish Sauce.

PubMed

Joung, Byung Chun; Min, Jin Gi

2018-06-01

In the present study, we evaluated the changes in quality that can occur during the distribution of nonheated anchovy ( Engraulis japonicus) fish sauce after packaging. The pH values of all samples ranged from 5.5 to 5.8, and there were no significant differences ( P > 0.05) in pH among the samples during storage regardless of storage temperature or salt concentration. The initial total volatile base nitrogen concentration in all samples after bottling was 115 to 121 mg/100 mL, but this concentration increased gradually with storage time. After 1 year of storage, total volatile base nitrogen concentration had increased to approximately 170% of the initial concentration (166 to 194 mg/100 mL). Amino nitrogen increased slightly during storage but was significantly lower than the increase in amino nitrogen during general anchovy fish sauce fermentation with anchovy flesh. Most of the free amino acids increased slightly during the storage period regardless of storage temperature or salt concentration, but tyrosine and histidine increased and then decreased during the storage period. The histamine concentration of the anchovy fish sauce at a salt concentration of 20% was 43.3 mg/100 mL initially, but after 1 year the histamine concentration was 89.7 mg/100 mL in samples stored at 10°C, 102.6 mg/100 mL in samples stored at 25°C, and 116.8 mg/100 mL in samples stored at 35°C . Changes in putrescine and cadaverine concentrations were similar to those in histamine; concentrations increased about twofold from the initial concentrations after 1 year of storage. However, the rate of increase in putrescine from 4 months after storage was very high, and cadaverine slightly decreased by 12 months of storage. High scores for umami and aroma sensory characteristics were given to samples stored at 10°C, but samples stored 35°C were given high scores for rancid. Despite the overall low scores for aroma and umami for samples stored at 35°C, the quality of the anchovy fish sauce as a fermented food was considered acceptable.

Comparison of Epidermal Growth Factor Receptor Mutations between Metastatic Lymph Node Diagnosed by EBUS-TBNA and Primary Tumor in Non-Small Cell Lung Cancer

PubMed Central

Kang, Hyo Jae; Hwangbo, Bin; Lee, Jin Soo; Kim, Moon Soo; Lee, Jong Mog; Lee, Geon-Kook

2016-01-01

Introduction Although the use of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is increasing for epidermal growth factor receptor (EGFR) testing in lung cancer, the discordance rate in EGFR mutations between lymph node (LN) samples obtained by EBUS-TBNA and primary tumor (PT) is not well known. Thus, we compared the EGFR mutation status of LN samples obtained by EBUS-TBNA and PTs to estimate the efficacy of using EBUS-TBNA specimens for EGFR testing in advanced, non-squamous, non-small cell lung cancer (NSCLC). Materials and Methods Using data of patients from the EBUS-TBNA database (N = 1914) obtained between January 2009 and January 2013, we identified 100 treatment-naïve, advanced, non-squamous NSCLC patients (stage 3 and 4) with matched LN specimens obtained by EBUS-TBNA and PT specimens. Of these, 74 patients with paired specimens were feasible for EGFR mutation analysis, which we performed using a direct sequencing method. Results Of the 74 cases, at least one major [exon 19 deleted (19del) and L858R] or minor (T790M, exon 20 insertion, and other point mutations) EGFR mutation was detected in 31 cases (41.9%), which included PT (n = 31, 41.9%) and LN (n = 28, 37.8%) specimens. Major mutations were detected in 25 PT (33.8%, 19del = 13, L858R = 12) and 22 LN (29.8%, 19del = 11, L858R = 11) specimens. The discordance rate in major mutations between matched PT and LN specimens was 4.1% (3/74). Among minor mutations, T790M was detected in LN specimen only in 2 cases with L858R in PT and LN. The discordance rate major and minor EGFR mutations combined between matched PT and LN specimens was 12% (9/74). Conclusions We observed a high concordance rate of major EGFR mutations between matched LN specimens sampled by EBUS-TBNA and PTs, suggesting that LN samples obtained by EBUS-TBNA from advanced non-squamous NSCLC patients are effective for use in EGFR mutation testing. PMID:27685950

Does Pneumatic Tube System Transport Contribute to Hemolysis in ED Blood Samples?

PubMed Central

Phelan, Michael P.; Reineks, Edmunds Z.; Hustey, Fredric M.; Berriochoa, Jacob P.; Podolsky, Seth R.; Meldon, Stephen; Schold, Jesse D.; Chamberlin, Janelle; Procop, Gary W.

2016-01-01

Introduction Our goal was to determine if the hemolysis among blood samples obtained in an emergency department and then sent to the laboratory in a pneumatic tube system was different from those in samples that were hand-carried. Methods The hemolysis index is measured on all samples submitted for potassium analysis. We queried our hospital laboratory database system (SunQuest®) for potassium results for specimens obtained between January 2014 and July 2014. From facility maintenance records, we identified periods of system downtime, during which specimens were hand-carried to the laboratory. Results During the study period, 15,851 blood specimens were transported via our pneumatic tube system and 92 samples were hand delivered. The proportions of hemolyzed specimens in the two groups were not significantly different (13.6% vs. 13.1% [p=0.90]). Results were consistent when the criterion was limited to gross (3.3% vs 3.3% [p=0.99]) or mild (10.3% vs 9.8% [p=0.88]) hemolysis. The hemolysis rate showed minimal variation during the study period (12.6%–14.6%). Conclusion We found no statistical difference in the percentages of hemolyzed specimens transported by a pneumatic tube system or hand delivered to the laboratory. Certain features of pneumatic tube systems might contribute to hemolysis (e.g., speed, distance, packing material). Since each system is unique in design, we encourage medical facilities to consider whether their method of transport might contribute to hemolysis in samples obtained in the emergency department. PMID:27625719

Does Pneumatic Tube System Transport Contribute to Hemolysis in ED Blood Samples?

PubMed

Phelan, Michael P; Reineks, Edmunds Z; Hustey, Fredric M; Berriochoa, Jacob P; Podolsky, Seth R; Meldon, Stephen; Schold, Jesse D; Chamberlin, Janelle; Procop, Gary W

2016-09-01

Our goal was to determine if the hemolysis among blood samples obtained in an emergency department and then sent to the laboratory in a pneumatic tube system was different from those in samples that were hand-carried. The hemolysis index is measured on all samples submitted for potassium analysis. We queried our hospital laboratory database system (SunQuest(®)) for potassium results for specimens obtained between January 2014 and July 2014. From facility maintenance records, we identified periods of system downtime, during which specimens were hand-carried to the laboratory. During the study period, 15,851 blood specimens were transported via our pneumatic tube system and 92 samples were hand delivered. The proportions of hemolyzed specimens in the two groups were not significantly different (13.6% vs. 13.1% [p=0.90]). Results were consistent when the criterion was limited to gross (3.3% vs 3.3% [p=0.99]) or mild (10.3% vs 9.8% [p=0.88]) hemolysis. The hemolysis rate showed minimal variation during the study period (12.6%-14.6%). We found no statistical difference in the percentages of hemolyzed specimens transported by a pneumatic tube system or hand delivered to the laboratory. Certain features of pneumatic tube systems might contribute to hemolysis (e.g., speed, distance, packing material). Since each system is unique in design, we encourage medical facilities to consider whether their method of transport might contribute to hemolysis in samples obtained in the emergency department.

Specimen rejection in laboratory medicine: Necessary for patient safety?

PubMed Central

Dikmen, Zeliha Gunnur; Pinar, Asli; Akbiyik, Filiz

2015-01-01

Introduction The emergency laboratory in Hacettepe University Hospitals receives specimens from emergency departments (EDs), inpatient services and intensive care units (ICUs). The samples are accepted according to the rejection criteria of the laboratory. In this study, we aimed to evaluate the sample rejection ratios according to the types of pre-preanalytical errors and collection areas. Materials and methods The samples sent to the emergency laboratory were recorded during 12 months between January to December, 2013 in which 453,171 samples were received and 27,067 specimens were rejected. Results Rejection ratios was 2.5% for biochemistry tests, 3.2% for complete blood count (CBC), 9.8% for blood gases, 9.2% for urine analysis, 13.3% for coagulation tests, 12.8% for therapeutic drug monitoring, 3.5% for cardiac markers and 12% for hormone tests. The most frequent rejection reasons were fibrin clots (28%) and inadequate volume (9%) for biochemical tests. Clotted samples (35%) and inadequate volume (13%) were the major causes for coagulation tests, blood gas analyses and CBC. The ratio of rejected specimens was higher in the EDs (40%) compared to ICUs (30%) and inpatient services (28%). The highest rejection ratio was observed in neurology ICU (14%) among the ICUs and internal medicine inpatient service (10%) within inpatient clinics. Conclusions We detected an overall specimen rejection rate of 6% in emergency laboratory. By documentation of rejected samples and periodic training of healthcare personnel, we expect to decrease sample rejection ratios below 2%, improve total quality management of the emergency laboratory and promote patient safety. PMID:26527231

Enzyme-linked immunosorbent assay for detection of pertussis immunoglobulin A in nasopharyngeal secretions as an indicator of recent infection.

PubMed Central

Goodman, Y E; Wort, A J; Jackson, F L

1981-01-01

An enzyme-linked immunosorbent assay was developed for detection of immunoglobulin A (IgA) antibody to Bordetella pertussis (PsIgA) in nasopharyngeal secretions as an indicator of recent infection. Secretion specimens submitted for pertussis culture were examined for PsIgA by this technique. Of 348 specimens tested, B. pertussis was cultured from 57, and PsIgA was detected in 8 culture-positive and 40 culture-negative specimens. The average time between onset of symptoms and specimen collection for the culture-positive, PsIgA-negative specimens was 10 days; for the culture-positive, PsIgA-positive specimens, 15 days; and for the culture-negative, PsIgA-positive specimens, 36 days. Examination of paired samples available from several culture-proven cases demonstrated conversion from a negative PsIgA in the early sample to a positive PsIgA in the follow-up sample. Our results indicate that PsIgA is produced during natural human infection and does not arise as a result of parenteral vaccination. PsIgA usually appears in the nasopharyngeal secretions during the second or third week of illness and persists for at least 3 months. The detection of PsIgA in secretions may be a valuable diagnostic aid in culture-negative patients with pertussis. Images PMID:6259201

Comparative evaluation of 3 microbond strength tests using 4 adhesive systems: Mechanical, finite element, and failure analysis.

PubMed

Campos, Roberto E; Santos Filho, Paulo César F; de O Júnior, Osmir Batista; Ambrosano, Gláucia M B; Pereira, Cristina Alves

2018-01-01

Bond strength (BS) values from in vitro studies are useful when dentists are selecting an adhesive system, but there is no ideal measuring method. The purpose of this in vitro study was to investigate the influence of the evaluation method in the BS between dentin and composite resin. Molars with exposed superficial dentin (N=240) were divided into 3 groups according to the test: microtensile (μTBS), microshear (μSBS), and micropush-out (μPBS). Each one was subdivided into 4 groups according to the adhesive system: total etch, 3- and 2-step; and self-etch, 2- and 1-step). For the μPBS test, a conical cavity was prepared and restored with composite resin. An occlusal slice (1.5 mm in thickness) was obtained from each tooth. For the μSBS test, a composite resin cylinder (1 mm in diameter) was built on the dentin surface of each tooth. For the μTBS test, a 2-increment composite resin cylinder was built on the dentin surface, and beams with a sectional area of 0.5 mm 2 were obtained. Each subgroup was divided into 2 (n=10) as the specimens were tested after 7 days and 1 year of water storage. The specimens were submitted to load, and the failure recorded in units of megapascals. Original BS values from the μTBS and μSBS tests were normalized for the area from μPBS specimens. Original and normalized results were submitted to a 3-way ANOVA (α=.05). The correlation among mechanical results, stress distribution, and failure pattern was investigated. Significant differences (P<.05) were found among the adhesive systems and methods within both the original and normalized data but not between the storage times (P>.05). Within the 7 days of storage, the original BS values from μTBS were significantly higher (P<.001) than those from μPBS and μSBS. After 1 year, μSBS presented significantly lower results (P<.001). However, after the normalization for area, the BS values of the μTBS and μPBS tests were similar, and both were higher (P<.001) than that of μSBS in both storage times. In the μSBS and μTBS specimens, cohesive and adhesive failures were observed, whereas μPBS presented 100% of adhesive failures. The failure modes were compatible with the stress distribution. The storage time did not affect the results, but differences were found among the adhesives and methods. For comparisons of bond strength from tests with different bonding areas, the normalization for area seemed essential. The microshear bond test should not be used for bond strength evaluation, and the microtensile test needs improvement to enable reliable results regarding stress concentration and failure mode. The micropush-out test may be considered more reliable than the microtensile in the bond strength investigation, as demonstrated by the uniform stress concentration and adhesive failure pattern. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Surface sampling concentration and reaction probe

DOEpatents

Van Berkel, Gary J; Elnaggar, Mariam S

2013-07-16

A method of analyzing a chemical composition of a specimen is described. The method can include providing a probe comprising an outer capillary tube and an inner capillary tube disposed co-axially within the outer capillary tube, where the inner and outer capillary tubes define a solvent capillary and a sampling capillary in fluid communication with one another at a distal end of the probe; contacting a target site on a surface of a specimen with a solvent in fluid communication with the probe; maintaining a plug volume proximate a solvent-specimen interface, wherein the plug volume is in fluid communication with the probe; draining plug sampling fluid from the plug volume through the sampling capillary; and analyzing a chemical composition of the plug sampling fluid with an analytical instrument. A system for performing the method is also described.

Characterization of Storage-Induced Red Blood Cell Hemolysis Using Raman Spectroscopy.

PubMed

Gautam, Rekha; Oh, Joo-Yeun; Marques, Marisa B; Dluhy, Richard A; Patel, Rakesh P

2018-06-11

The therapeutic efficacy and safety of stored red blood cells (RBCs) relies on minimal in-bag hemolysis. The accuracy of current methods of measuring hemolysis can suffer as a result of specimen collection and processing artefacts. To test whether Raman spectroscopy could be used to assess hemolysis. RBCs were stored for as long as 42 days. Raman spectra of RBCs were measured before and after washing, and hemolysis was measured in supernatant by visible spectroscopy. Raman spectra indicated increased concentrations of oxyhemoglobin (oxyHb) and methemoglobin (metHb), and decreased membrane fluidity with storage age. Changes in oxyHb and metHb were associated with the intraerythrocytic and extracellular fractions, respectively. Hemolysis increased in a storage age-dependent manner. Changes in Raman bands reflective of oxyHb, metHb, and RBC membranes correlated with hemolysis; the most statistically significant change was an increased intensity of metHb and decreased membrane fluidity. These data suggest that Raman spectroscopy may offer a new label-free modality to assess RBC hemolysis during cold storage.

Temperature and curing time affect composite sorption and solubility

PubMed Central

de CASTRO, Fabrício Luscino Alves; CAMPOS, Bruno Barbosa; BRUNO, Kely Firmino; REGES, Rogério Vieira

2013-01-01

Objective: This study evaluated the effect of temperature and curing time on composite sorption and solubility. Material and Methods: Seventy five specimens (8x2 mm) were prepared using a commercial composite resin (ICE, SDI). Three temperatures (10º C, 25º C and 60º C) and five curing times (5 s, 10 s, 20 s, 40 s and 60 s) were evaluated. The specimens were weighed on an analytical balance three times: A: before storage (M1); B: 7 days after storage (M2); C: 7 days after storage plus 1 day of drying (M3). The storage solution consisted of 75% alcohol/25% water. Sorption and solubility were calculated using these three weights and specimen dimensions. The data were analyzed using the Kruskal-Wallis and Mann-Whitney U Tests (α=5%). Results: The results showed that time, temperature and their interaction influenced the sorption and solubility of the composite (p<0.05). At 60º C, the composite sorption showed an inverse relationship with the curing time (p<0.05). The composite cured for 5 s showed higher sorption for the 40 s or 60 s curing times when compared with all temperatures (p<0.05). Curing times of 20 s and 40 s showed similar sorption data for all temperatures (p>0.05). The 60º C composite temperature led to lower values of sorption for all curing times when compared with the 10º C temperature (p<0.05). The same results were found when comparing 10º C and 25º C (p<0.05), except that the 20 s and 40 s curing times behaved similarly (p>0.05). Solubility was similar at 40 s and 60 s for all temperatures (p>0.05), but was higher at 10º C than at 60º C for all curing times (p<0.05). When the composite was cured at 25º C, similar solubility values were found when comparing the 5 s and 10 s or 20 s and 40 s curing times (p>0.05). Conclusion: In conclusion, higher temperatures or longer curing times led to lower sorption and solubility values for the composite tested; however, this trend was only significant in specific combinations of temperature and curing times. PMID:23739853

Specimen Holder for Analytical Electron Microscopes

NASA Technical Reports Server (NTRS)

Clanton, U. S.; Isaacs, A. M.; Mackinnon, I.

1985-01-01

Reduces spectral contamination by spurious X-ray. Specimen holder made of compressed carbon, securely retains standard electron microscope grid (disk) 3 mm in diameter and absorbs backscattered electrons that otherwise generate spurious X-rays. Since holder inexpensive, dedicated to single specimen when numerous samples examined.

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

PubMed Central

Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, James

2013-01-01

The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders), use of potential immunomodulators, and recent use of antibiotics or probiotics. Subsequent physical examinations excluded individuals based on body mass index (BMI), cutaneous lesions, and oral health. We screened 554 individuals to enroll 300 (149 men and 151 women, mean age 26 yr, mean BMI 24 kg/m2, 20.0% racial minority, and 10.7% Hispanic). We obtained specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women). The study evaluated longitudinal changes in an individual's microbiome by sampling 279 participants twice (mean 212 d after the first sampling; range 30-359 d) and 100 individuals 3 times (mean 72 d after the second sampling; range 30-224 d). This sampling strategy yielded 11,174 primary specimens, from which 12,479 DNA samples were submitted to 4 centers for metagenomic sequencing. Our clinical design and well-defined reference cohort has laid a foundation for microbiome research.—Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., Patel, S., Cutting, M., Madden, T., Hamilton, H., Harris, E., Gevers, D., Simone, G., McInnes, P., Versalovic, J. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. PMID:23165986

Mechanisms of Laser-Induced Dissection and Transport of Histologic Specimens

PubMed Central

Vogel, Alfred; Lorenz, Kathrin; Horneffer, Verena; Hüttmann, Gereon; von Smolinski, Dorthe; Gebert, Andreas

2007-01-01

Rapid contact- and contamination-free procurement of histologic material for proteomic and genomic analysis can be achieved by laser microdissection of the sample of interest followed by laser-induced transport (laser pressure catapulting). The dynamics of laser microdissection and laser pressure catapulting of histologic samples of 80 μm diameter was investigated by means of time-resolved photography. The working mechanism of microdissection was found to be plasma-mediated ablation initiated by linear absorption. Catapulting was driven by plasma formation when tightly focused pulses were used, and by photothermal ablation at the bottom of the sample when defocused pulses producing laser spot diameters larger than 35 μm were used. With focused pulses, driving pressures of several hundred MPa accelerated the specimen to initial velocities of 100–300 m/s before they were rapidly slowed down by air friction. When the laser spot was increased to a size comparable to or larger than the sample diameter, both driving pressure and flight velocity decreased considerably. Based on a characterization of the thermal and optical properties of the histologic specimens and supporting materials used, we calculated the evolution of the heat distribution in the sample. Selected catapulted samples were examined by scanning electron microscopy or analyzed by real-time reverse-transcriptase polymerase chain reaction. We found that catapulting of dissected samples results in little collateral damage when the laser pulses are either tightly focused or when the laser spot size is comparable to the specimen size. By contrast, moderate defocusing with spot sizes up to one-third of the specimen diameter may involve significant heat and ultraviolet exposure. Potential side effects are maximal when samples are catapulted directly from a glass slide without a supporting polymer foil. PMID:17766336

Use of FTA card for dry collection, transportation and storage of cervical cell specimen to detect high-risk HPV.

PubMed

Gustavsson, Inger; Lindell, Monica; Wilander, Erik; Strand, Anders; Gyllensten, Ulf

2009-10-01

The FTA elute micro card, which enable the collection, transport, and archiving of DNA could be an attractive alternative to a liquid based collection system for detection of human papillomavirus (HPV). To develop a method based on the FTA elute micro card for dry collection of cervical epithelial cell samples, suitable for subsequent PCR-based HPV testing. The method was evaluated by a comparison of the DNA collected by cytobrush and the regular FTA elute micro card from 50 cervical cell samples. The method was then used to estimate the DNA amount in 1040 samples applied to the indicating FTA elute micro card. The agreement in HPV positivity between the cytobrush and FTA samples (94%) was excellent (kappa=0.88, 95% CI 0.748-1). All the 1040 samples on the indicating FTA card had sufficient amounts of genomic DNA (>10 copies of a single copy gene) to be suitable for HPV typing. In 53 of the 1040 women the day in the menstrual cycle was noted, and the copy number during follicular phase day 9-13 was found to be statistically significantly lower than for the other three stages in the menstrual cycle (day 4-8, 14, >14) and during menopause. The indicating FTA elute micro card represents a suitable medium for collection of cervical cell samples, although follow-up studies are needed to verify the detection of low frequency HPV types.

Influence of specimen dimensions on ductile-to-brittle transition temperature in Charpy impact test

NASA Astrophysics Data System (ADS)

Rzepa, S.; Bucki, T.; Konopík, P.; Džugan, J.; Rund, M.; Procházka, R.

2017-02-01

This paper discusses the correlation between specimen dimensions and transition temperature. Notch toughness properties of Standard Charpy-V specimens are compared to samples with lower width (7.5 mm, 5 mm, 2.5 mm) and sub-size Charpy specimens with cross section 3×4. In this study transition curves are correlated with lateral ductile part of fracture related ones for 5 considered geometries. Based on the results obtained, correlation procedure for transition temperature determination of full size specimens defined by fracture appearance of sub-sized specimens is proposed.

Forensic Tools to Track and Connect Physical Samples to Related Data

NASA Astrophysics Data System (ADS)

Molineux, A.; Thompson, A. C.; Baumgardner, R. W.

2016-12-01

Identifiers, such as local sample numbers, are critical to successfully connecting physical samples and related data. However, identifiers must be globally unique. The International Geo Sample Number (IGSN) generated when registering the sample in the System for Earth Sample Registration (SESAR) provides a globally unique alphanumeric code associated with basic metadata, related samples and their current physical storage location. When registered samples are published, users can link the figured samples to the basic metadata held at SESAR. The use cases we discuss include plant specimens from a Permian core, Holocene corals and derived powders, and thin sections with SEM stubs. Much of this material is now published. The plant taxonomic study from the core is a digital pdf and samples can be directly linked from the captions to the SESAR record. The study of stable isotopes from the corals is not yet digitally available, but individual samples are accessible. Full data and media records for both studies are located in our database where higher quality images, field notes, and section diagrams may exist. Georeferences permit mapping in current and deep time plate configurations. Several aspects emerged during this study. The first, ensure adequate and consistent details are registered with SESAR. Second, educate and encourage the researcher to obtain IGSNs. Third, publish the archive numbers, assigned prior to publication, alongside the IGSN. This provides access to further data through an Integrated Publishing Toolkit (IPT)/aggregators/or online repository databases, thus placing the initial sample in a much richer context for future studies. Fourth, encourage software developers to customize community software to extract data from a database and use it to register samples in bulk. This would improve workflow and provide a path for registration of large legacy collections.

A cylindrical specimen holder for electron cryo-tomography

PubMed Central

Palmer, Colin M.; Löwe, Jan

2014-01-01

The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the “missing wedge” problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. PMID:24275523

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR STORAGE AND SHIPPING OF SAMPLES (G05)

EPA Science Inventory

The purpose of this SOP is to describe the procedures for storage and shipping of samples. For the NHEXAS project, Harvard School of Public Health/Emory University will collect many different kinds of samples, some of which will require particularly careful storage and shipping ...

Detection and genotyping of rubella virus from exanthematous patients suspected of having measles using reverse transcription-PCR.

PubMed

Yasui, Yoshihiro; Mori, Yoshio; Adachi, Hirokazu; Kobayashi, Shinichi; Yamashita, Teruo; Minagawa, Hiroko

2014-01-01

Between July 2012 and March 2013, a total of 133 clinical specimens from 47 patients suspected of having measles were collected for virological surveillance in Aichi Prefecture, Japan. Facing the rubella epidemic, the reverse transcription (RT)-PCR protocol for measles virus (MeV) was modified to simultaneously detect rubella virus (RUBV) in these clinical specimens. As a result, 30 specimens from 15 patients were positive for RUBV and 8 specimens from 3 patients were positive for MeV. The RUBV genotype analysis for the samples from 13 patients revealed 12 samples as 2B and 1 sample as 1E. The results provided additional evidence for the difficulty in the diagnosis of exanthematous diseases based on clinical manifestations alone and the necessity of virological diagnosis to maintain the accuracy of case-based surveillance. Furthermore, the results indicated that the modified RT-PCR protocol could be useful as a routine procedure to simultaneously detect MeV and RUBV in clinical specimens of patients suspected of having exanthematous disease caused by these viruses.

76 FR 24862 - Proposed Information Collection; Comment Request; Protocol for Access to Tissue Specimen Samples...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-03

... Collection; Comment Request; Protocol for Access to Tissue Specimen Samples From the National Marine Mammal Tissue Bank AGENCY: National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice... National Marine Mammal Tissue Bank (NMMTB) was established by the National Marine Fisheries Service (NMFS...

16 CFR 303.21 - Marking of samples, swatches, or specimens and products sold therefrom.

Code of Federal Regulations, 2012 CFR

2012-01-01

... and products sold therefrom. 303.21 Section 303.21 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULES AND REGULATIONS UNDER THE TEXTILE FIBER PRODUCTS IDENTIFICATION ACT § 303.21 Marking of samples, swatches, or specimens and products sold therefrom. (a) Where...

16 CFR 303.21 - Marking of samples, swatches, or specimens and products sold therefrom.

Code of Federal Regulations, 2013 CFR

2013-01-01

... and products sold therefrom. 303.21 Section 303.21 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULES AND REGULATIONS UNDER THE TEXTILE FIBER PRODUCTS IDENTIFICATION ACT § 303.21 Marking of samples, swatches, or specimens and products sold therefrom. (a) Where...

16 CFR 303.21 - Marking of samples, swatches, or specimens and products sold therefrom.

Code of Federal Regulations, 2010 CFR

2010-01-01

... and products sold therefrom. 303.21 Section 303.21 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULES AND REGULATIONS UNDER THE TEXTILE FIBER PRODUCTS IDENTIFICATION ACT § 303.21 Marking of samples, swatches, or specimens and products sold therefrom. (a) Where...

16 CFR 303.21 - Marking of samples, swatches, or specimens and products sold therefrom.

Code of Federal Regulations, 2014 CFR

2014-01-01

... and products sold therefrom. 303.21 Section 303.21 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULES AND REGULATIONS UNDER THE TEXTILE FIBER PRODUCTS IDENTIFICATION ACT § 303.21 Marking of samples, swatches, or specimens and products sold therefrom. (a) Where...

16 CFR 303.21 - Marking of samples, swatches, or specimens and products sold therefrom.

Code of Federal Regulations, 2011 CFR

2011-01-01

... and products sold therefrom. 303.21 Section 303.21 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULES AND REGULATIONS UNDER THE TEXTILE FIBER PRODUCTS IDENTIFICATION ACT § 303.21 Marking of samples, swatches, or specimens and products sold therefrom. (a) Where...

Calibrated photostimulated luminescence is an effective approach to identify irradiated orange during storage

NASA Astrophysics Data System (ADS)

Jo, Yunhee; Sanyal, Bhaskar; Chung, Namhyeok; Lee, Hyun-Gyu; Park, Yunji; Park, Hae-Jun; Kwon, Joong-Ho

2015-06-01

Photostimulated luminescence (PSL) has been employed as a fast screening method for various irradiated foods. In this study the potential use of PSL was evaluated to identify oranges irradiated with gamma ray, electron beam and X-ray (0-2 kGy) and stored under different conditions for 6 weeks. The effects of light conditions (natural light, artificial light, and dark) and storage temperatures (4 and 20 °C) on PSL photon counts (PCs) during post-irradiation periods were studied. Non-irradiated samples always showed negative values of PCs, while irradiated oranges exhibited intermediate results after first PSL measurements. However, the irradiated samples had much higher PCs. The PCs of all the samples declined as the storage time increased. Calibrated second PSL measurements showed PSL ratio <10 for the irradiated samples after 3 weeks of irradiation confirming their irradiation status in all the storage conditions. Calibrated PSL and sample storage in dark at 4 °C were found out to be most suitable approaches to identify irradiated oranges during storage.

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation)

PubMed Central

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-01-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists. PMID:25336760

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation).

PubMed

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-08-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists.

Armored RNA as Virus Surrogate in a Real-Time Reverse Transcriptase PCR Assay Proficiency Panel

PubMed Central

Hietala, S. K.; Crossley, B. M.

2006-01-01

In recent years testing responsibilities for high-consequence pathogens have been expanded from national reference laboratories into networks of local and regional laboratories in order to support enhanced disease surveillance and to test for surge capacity. This movement of testing of select agents and high-consequence pathogens beyond reference laboratories introduces a critical need for standardized, noninfectious surrogates of disease agents for use as training and proficiency test samples. In this study, reverse transcription-PCR assay RNA targets were developed and packaged as armored RNA for use as a noninfectious, quantifiable synthetic substitute for four high-consequence animal pathogens: classical swine fever virus; foot-and-mouth disease virus; vesicular stomatitis virus, New Jersey serogroup; and vesicular stomatitis virus, Indiana serogroup. Armored RNA spiked into oral swab fluid specimens mimicked virus-positive clinical material through all stages of the reverse transcription-PCR testing process, including RNA recovery by four different commercial extraction procedures, reverse transcription, PCR amplification, and real-time detection at target concentrations consistent with the dynamic ranges of the existing real-time PCR assays. The armored RNA concentrations spiked into the oral swab fluid specimens were stable under storage conditions selected to approximate the extremes of time and temperature expected for shipping and handling of proficiency panel samples, including 24 h at 37°C and 2 weeks at temperatures ranging from ambient room temperature to −70°C. The analytic test performance, including the reproducibility over the dynamic range of the assays, indicates that armored RNA can provide a noninfectious, quantifiable, and stable virus surrogate for specific assay training and proficiency test purposes. PMID:16390950

Microtensile bond strength of eleven contemporary adhesives to enamel.

PubMed

Inoue, Satoshi; Vargas, Marcos A; Abe, Yasuhiko; Yoshida, Yasuhiro; Lambrechts, Paul; Vanherle, Guido; Sano, Hidehiko; Van Meerbeek, Bart

2003-10-01

To compare the microtensile bond strength (microTBS) to enamel of 10 contemporary adhesives, including three one-step self-etch systems, four two-step self-etch systems and three two-step total-etch systems, with that of a conventional three-step total-etch adhesive. Resin composite (Z100, 3M) was bonded to flat, #600-grit wet-sanded enamel surfaces of 18 extracted human third molars using the adhesives strictly according to the respective manufacturer's instructions. After storage overnight in 37 degrees C water, the bonded specimens were sectioned into 2-4 thin slabs of approximately 1 mm thickness and 2.5 mm width. They were then trimmed into an hourglass shape with an interface area of approximately 1 mm2, and subsequently subjected to microTBS-testing with a cross-head speed of 1 mm/minute. The microTBS to enamel varied from 3.2 MPa for the experimental one-step self-etch adhesive PQ/Universal (self-etch) to 43.9 MPa for the two-step total-etch adhesive Scotchbond 1. When compared with the conventional three-step total-etch adhesive OptiBond FL, the bond strengths of most adhesives with simplified application procedures were not significantly different, except for two one-step self-etch adhesives, experimental PQ/Universal (self-etch) and One-up Bond F, that showed lower bond strengths. Specimen failures during sample preparation were recorded for the latter adhesives as well.

Breast cancer: determining the genetic profile from ultrasound-guided percutaneous biopsy specimens obtained during the diagnostic workups.

PubMed

López Ruiz, J A; Zabalza Estévez, I; Mieza Arana, J A

2016-01-01

To evaluate the possibility of determining the genetic profile of primary malignant tumors of the breast from specimens obtained by ultrasound-guided percutaneous biopsies during the diagnostic imaging workup. This is a retrospective study in 13 consecutive patients diagnosed with invasive breast cancer by B-mode ultrasound-guided 12 G core needle biopsy. After clinical indication, the pathologist decided whether the paraffin block specimens seemed suitable (on the basis of tumor size, validity of the sample, and percentage of tumor cells) before sending them for genetic analysis with the MammaPrint® platform. The size of the tumors on ultrasound ranged from 0.6cm to 5cm. In 11 patients the preserved specimen was considered valid and suitable for use in determining the genetic profile. In 1 patient (with a 1cm tumor) the pathologist decided that it was necessary to repeat the core biopsy to obtain additional samples. In 1 patient (with a 5cm tumor) the specimen was not considered valid by the genetic laboratory. The percentage of tumor cells in the samples ranged from 60% to 70%. In 11/13 cases (84.62%) it was possible to do the genetic analysis on the previously diagnosed samples. In most cases, regardless of tumor size, it is possible to obtain the genetic profile from tissue specimens obtained with ultrasound-guided 12 G core biopsy preserved in paraffin blocks. Copyright © 2015 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

Genetic utility of natural history museum specimens: endangered fairy shrimp (Branchiopoda, Anostraca)

PubMed Central

Wall, Adam R.; Campo, Daniel; Wetzer, Regina

2014-01-01

Abstract We examined the potential utility of museum specimens as a source for genetic analysis of fairy shrimp. Because of loss of their vernal pool habitat, some fairy shrimp (including Branchinecta sandiegonensis and Branchinecta lynchi) are listed as threatened or endangered in Southern California by the United States Fish and Wildlife Service. Management of those species requires extensive population genetics studies and the resolution of important genetic complexity (e.g. possible hybridization between endangered and non-endangered species). Regulations mandating deposition of specimens of listed species have resulted in thousands of specimens accessioned into the Natural History Museum of Los Angeles County that have been preserved in a variety of solutions. We subsampled those specimens, as well as other Anostraca with known collection and preservation histories, to test their potential for genetic analysis by attempting DNA extraction and amplification for mt16SrDNA. Fixation and preservation in not denatured ethanol had a far greater sequencing success rate than other (and unknown) fixatives and preservatives. To maximize scientific value we recommend field preservation in 95% not denatured ethanol (or, if pure ethanol is unavailable, high-proof drinking spirits, e.g. Everclear™, or 151 proof white rum), followed by storage in 95% not denatured ethanol. PMID:25561827

Stability of Chronic Hepatitis-Related Parameters in Serum Samples After Long-Term Storage.

PubMed

Yu, Rentao; Dan, Yunjie; Xiang, Xiaomei; Zhou, Yi; Kuang, Xuemei; Yang, Ge; Tang, Yulan; Liu, Mingdong; Kong, Weilong; Tan, Wenting; Deng, Guohong

2017-06-01

Serum samples are widely used in clinical research, but a comprehensive research of the stability of parameters relevant to chronic hepatitis and the effect of a relatively long-term (up to 10 years) storage on the stability have rarely been studied. To investigate the stability of chronic hepatitis-related parameters in serum samples after long-term storage. The storage stability of common clinical parameters such as total bile acid (TBA), total bilirubin (TBIL), potassium, cholesterol, and protein parameters such as alanine aminotransferase (ALT), creatine kinase (CK), γ-glutamyltransferase (GGT), albumin, high-density lipoprotein (HDL) and also hepatitis B virus (HBV) DNA, hepatitis C virus (HCV) RNA, hepatitis B surface antigen (HBsAg), and chemokine (C-X-C motif) ligand 10 (CXCL10) were tested in serum samples after storing at -20°C or -70°C for 1, 2, 3, 7, 8, and 10 years. Levels of TBA, TBIL, and protein parameters such as ALT, CK, GGT, HDL, and HBsAg decreased significantly, but levels of potassium and cholesterol increased significantly after long-term storage, whereas blood glucose and triglycerides were stable during storage. HBV DNA remained stable at -70°C but changed at -20°C, whereas HCV RNA was stable after 1-, 2-, and 3-year storage. CXCL10 was still detectable after 8-year storage. Low temperatures (-70°C/80°C) are necessary for storage of serum samples in chronic hepatitis B research after long-term storage.

Factors affecting genotyping success in giant panda fecal samples.

PubMed

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong; Zhang, He-Min

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH -20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at -20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates ( P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

Factors affecting genotyping success in giant panda fecal samples

PubMed Central

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies. PMID:28560107

Comparison of sampling methods for the detection of human rhinovirus RNA.

PubMed

Waris, Matti; Österback, Riikka; Lahti, Elina; Vuorinen, Tytti; Ruuskanen, Olli; Peltola, Ville

2013-09-01

Obtaining a nasal swab (NS) from a child for human rhinovirus (HRV) RNA detection is simple and well tolerated even for repeated sampling, but only few studies have compared them qualitatively and quantitatively with other sampling methods. Real-time PCR was used to study the stability of HRV genomes in swabs, and to compare different swabs and induced sputum specimens with nasopharyngeal aspirates (NPAs). Replicate swabs in a dry test tube were stored at room temperature or mailed to the laboratory before freezing, and compared to freshly frozen specimens. To compare sampling methods, paediatric patients had NPA, NS and throat swab collected. In paired sputum and NPA specimens, viral load was correlated to the amount of β-actin mRNA. Specimens were stable at room temperature for at least 4 days and survived mailing without loss of HRV detectability. As compared to NPA, NS had an equal diagnostic sensitivity, with no significant quantitative difference using flocked nylon swabs and a 2.2-fold drop in the average copy number using cotton swabs. The diagnostic sensitivity of cotton swab-collected throat specimens was 97%, with a 26-fold lower mean copy number. Sputum specimens had higher HRV RNA (2.3-fold) and β-actin mRNA (1.6-fold) copy numbers than NPAs, but there was a poor correlation between HRV RNA and β-actin mRNA. HRV remains well detectable by PCR in specimens mailed to the laboratory. The diagnostic efficacy of NPA can be obtained with NS, quantitative comparison and patient comfort favouring flocked nylon-tipped over cotton-tipped swabs. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of asphalt rejuvenator on thermal and mechanical properties on oxidized hot mixed asphalt pavements

NASA Astrophysics Data System (ADS)

Farace, Nicholas A.; Buttlar, William G.; Reis, Henrique

2016-04-01

The utilization of asphalt rejuvenator, and its effectiveness for restoring thermal and mechanical properties was investigated via Disk-shaped Compact Tension (DC(T)) and acoustic emission (AE) testing for determining mechanical properties and embrittlement temperatures of the mixtures. During the DC(T) testing the fracture energies and peak loads were used to measure the resistance of the rejuvenated asphalt to low temperature cracking. The AE testing monitored the acoustic emission activity while the specimens were cooled from room temperature to -40 °C to estimate the temperature at which thermal cracking began (i.e. the embrittlement temperature). First, a baseline response was obtained by obtaining the mechanical and thermal response of virgin HMA samples and HMA samples that had been exposed to oxidative aging for 36 hours at 135°C. The results showed the virgin samples had much higher peak loads and fracture energies than the 36 hours aged samples. Acoustic Emission showed similar results with the virgin samples having embrittlement temperatures 10 °C cooler than the 36 hours aged specimens. Then, overaged for 36 hours specimens were treated different amounts of rejuvenator (10%, 15%, and 20% by weight of binder content) and left to dwell for increased amount of time periods varying from one to eight weeks. It was observed that the AE results showed an improvement of embrittlement temperature with increasing with the dwell times. The 8 weeks specimens had cooler embrittlement temperatures than the virgin specimens. Finally, the low temperature effects on fracture energy and peak load of the rejuvenated asphalt was investigated. Rejuvenator was applied (10% by weight of binder) to specimens aged 36 hours at 135 °C, and the dwell time was varied from 1 to 4 weeks. The results showed that the peak loads were restored to levels of the virgin specimens, and the fracture energies improved to levels beyond that of the virgin specimens. The results also showed a general trend of improvement for the AE testing of the embrittlement temperature.

Effect of high pressure treatment on microbiological quality of Indian white prawn (Fenneropenaeus indicus) during chilled storage.

PubMed

Ginson, J; Panda, Satyen Kumar; Bindu, J; Kamalakanth, C K; Srinivasa Gopal, T K

2015-04-01

High pressure treatment of 250 MPa for 6 min at 25 °C was applied to headless Indian white prawn (Fenneropenaeus indicus) to evaluate changes in microbiological characteristics of the species during chilled storage. Changes in load of mesophilic bacteria, psychrotrophic bacteria, proteolytic bacteria, Enterobacteriaceae, Pseudomonas spp., H2S producing bacteria, lactic acid bacteria, Brochothrix thermosphacta and yeast & mold were estimated in pressurized and un-pressurized samples during chilled storage. All microbes were reduced significantly after high pressure treatment and there was significant difference in microbial quality of control and high pressure treated samples in the entire duration of chilled storage (p < 0.05). There was delay in the growth of Enterobacteriaceae and H2S producing bacteria up to 6th and 9th day of storage, respectively in high pressure treated samples. In high pressure treated sample, no lag phase (λ) was observed for psychrotrophic bacteria, H2S producing bacteria, B. thermosphacta, Pseudomonas spp. and lactic acid bacteria; however, other bacteria showed a reduced lag phase during chilled storage. Kinetic parameter such as specific growth rate (μmax) in high pressure treated samples was significantly reduced in most of the bacterial groups except for psychrotrophic bacteria, Enterobacteriaceae and lactic acid bacteria. Mesophilic bacterial count of control samples crossed the marginal limit of acceptability on 12th day and unacceptable limit on 18th day of storage, whereas high pressure treated samples never breached the acceptability limit during entire duration of chilled storage. The present study indicated that application of high pressure processing can be used to improve microbial quality of Indian white prawn and extend the chilled storage life. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization.

PubMed

Botling, Johan; Micke, Patrick

2011-01-01

Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.

Significance of isolated reactive treponemal chemiluminescence immunoassay results.

PubMed

Hunter, Michael G; Robertson, Peter W; Post, Jeffrey J

2013-05-01

Isolated reactive serum treponemal chemiluminescence immunoassay (CIA) specimens cause clinical uncertainty. Sera were screened by CIA, and reactive samples underwent reflex testing with rapid plasma reagin (RPR), Treponema pallidum particle agglutination (TPPA), and fluorescent treponemal antibody absorption (FTA Abs) assays. Samples reactive only on the CIA were deemed "isolated" reactive CIA samples. We undertook detailed review of a subset of subjects with isolated reactive CIA specimens. Of 28 261 specimens, 1171 (4.1%) were reactive on CIA, of which 133 (11.3%) had isolated CIA reactivity. Most subjects (66 of 82 [80.5%]) with isolated reactive CIA specimens were from high-prevalence populations. We found evidence of CIA, TPPA, and FTA Abs seroreversion. The median chemiluminescent signal-to-cutoff ratio was similar for isolated reactive CIA sera and sera that were reactive on either FTA Abs or TPPA assays (2.19 vs 2.32; P = .15) but lower than for sera reactive on both FTA Abs and TPPA assays (12.37; P < .001) or for sera reactive on RPR assays (25.53; P < .001). A total of 11 of 20 patients (55%) with an isolated reactive CIA specimen who underwent medical record review had previous or subsequent evidence of syphilis infection. Isolated reactive CIA specimens may represent true T. pallidum infection and may be found after seroreversion of traditional treponemal assays.

Serotype distribution of Streptococcus mutans a pathogen of dental caries in cardiovascular specimens from Japanese patients.

PubMed

Nakano, Kazuhiko; Nemoto, Hirotoshi; Nomura, Ryota; Homma, Hiromi; Yoshioka, Hideo; Shudo, Yasuhiro; Hata, Hiroki; Toda, Koichi; Taniguchi, Kazuhiro; Amano, Atsuo; Ooshima, Takashi

2007-04-01

The involvement of oral bacteria in the pathogenesis of cardiovascular disease has been studied, with Streptococcus mutans, a pathogen of dental caries, detected in cardiovascular lesions at a high frequency. However, no information is available regarding the properties of S. mutans detected in those lesions. Heart valve specimens were collected from 52 patients and atheromatous plaque specimens from 50 patients, all of whom underwent cardiovascular operations, and dental plaque specimens were taken from 41 of those subjects prior to surgery. Furthermore, saliva samples were taken from 73 sets of healthy mothers (n=73) and their healthy children (n=78). Bacterial DNA was extracted from all specimens, then analysed by PCR with S. mutans-specific and serotype-specific primer sets. The detection rates of S. mutans in the heart valve and atheromatous plaque specimens were 63 and 64 %, respectively. Non-c serotypes were identified with a significantly higher frequency in both cardiovascular and dental plaque samples from the subjects who underwent surgery as compared to serotype c, which was detected in 70-75 % of the samples from the healthy subjects. The serotype distribution in cardiovascular patients was significantly different from that in healthy subjects, suggesting that S. mutans serotype may be related to cardiovascular disease.

Detection of methaemoglobinaemia and its application in 'poppers' abuse: maintaining the right balance between reduction and autooxidation during storage.

PubMed

Domingo, Olwen; Stöver, Andreas; Roider, Gabriele; Graw, Matthias

2017-03-01

In our study, we analysed the effect of a variety of storage conditions on the methaemoglobin (MetHb) content of blood samples obtained from altogether 110 deceased subjects with diverse causes of death, including three 'poppers'-related fatalities. The obtained results were compared to data from blood samples of six living, healthy subjects. Results obtained from the spectrophotometric measurement of blood MetHb content suggest that storage at room temperature (RT) and storage at -20 °C result in either highly fluctuating values, as was the case for the RT samples, or values much higher than the initial MetHb concentrations when stored at -20 °C. Blood samples at 4 °C showed more stable MetHb levels, which, however, increased with up to 4 % of the initial value after only 3 weeks of storage. These factors pose a problem in forensic toxicology, especially in nitrite abuse cases, where the involvement of such substance abuse is often unknown at the time of blood sampling and thus often requires longer storage times. Nevertheless, even after the storage of blood samples over several months at 4 and -20 °C, 'poppers' cases still show a significantly higher MetHb concentration as compared to non-'poppers' samples that were stored for the same time period under identical conditions.

Changes in the enzymatic activity of soil samples upon their storage

NASA Astrophysics Data System (ADS)

Dadenko, E. V.; Kazeev, K. Sh.; Kolesnikov, S. I.; Val'Kov, V. F.

2009-12-01

The influence of the duration and conditions of storage of soil samples on the activity of soil enzymes (catalase, β-fructofuranosidase, and dehydrogenase) was studied for the main soils of southern Russia (different subtypes of chernozems, chestnut soils, brown forest soils, gray forest soils, solonetzes, and solonchaks). The following soil storage conditions were tested: (1) the air-dry state at room temperature, (2) the airdry state at a low positive (in a refrigerator, +4°C) temperature, (3) naturally moist samples at a low positive temperature, and (4) naturally moist samples at a negative (in a freezer, -5°C) temperature. It was found that the sample storing caused significant changes in the enzymatic activities, which depended on the soil type, the land use, the type of enzyme, and the duration and conditions of the sample storage. In the course of the storage, the changes in the enzymatic activity had a nonlinear character. The maximum changes were observed in the initial period (up to 12 weeks). Then, a very gradual decrease in the activity of the studied enzymes was observed. Upon the long-term (>12 weeks) storage under the different conditions, the difference in the activities of the soil enzymes became less pronounced. The storage of soil samples in the air-dried state at room temperature can be recommended for mass investigations.

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

PubMed

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.

Simultaneous quantitation of sphingoid bases by UPLC-ESI-MS/MS with identical 13C-encoded internal standards.

PubMed

Mirzaian, M; Wisse, P; Ferraz, M J; Marques, A R A; Gaspar, P; Oussoren, S V; Kytidou, K; Codée, J D C; van der Marel, G; Overkleeft, H S; Aerts, J M

2017-03-01

Free sphingoid bases (lysosphingolipids) of primary storage sphingolipids are increased in tissues and plasma of several sphingolipidoses. As shown earlier by us, sphingoid bases can be accurately quantified using UPLC-ESI-MS/MS, particularly in combination with identical 13 C-encoded internal standards. The feasibility of simultaneous quantitation of sphingoid bases in plasma specimens spiked with a mixture of such standards is here described. The sensitivity and linearity of detection is excellent for all examined sphingoid bases (sphingosine, sphinganine, hexosyl-sphingosine (glucosylsphingosine), hexosyl 2 -sphingosine (lactosylsphingosine), hexosyl 3 -sphingosine (globotriaosylsphingosine), phosphorylcholine-sphingosine) in the relevant concentration range and the measurements show very acceptable intra- and inter-assay variation (<10% average). Plasma samples of a series of male and female Gaucher Disease and Fabry Disease patients were analyzed with the multiplex assay. The obtained data compare well to those earlier determined for plasma globotriaosylsphingosine and glucosylsphingosine in GD and FD patients. The same approach can be also applied to measure sphingolipids in the same sample. Following extraction of sphingolipids from the same sample these can be converted to sphingoid bases by microwave exposure and subsequently quantified using 13 C-encoded internal standards. Copyright © 2017 Elsevier B.V. All rights reserved.

Algae viability over time in a ballast water sample

NASA Astrophysics Data System (ADS)

Gollasch, Stephan; David, Matej

2018-03-01

The biology of vessels' ballast water needs to be analysed for several reasons, one of these being performance tests of ballast water management systems. This analysis includes a viability assessment of phytoplankton. To overcome logistical problems to get algae sample processing gear on board of a vessel to document algae viability, samples may be transported to land-based laboratories. Concerns were raised how the storage conditions of the sample may impact algae viability over time and what the most appropriate storage conditions were. Here we answer these questions with a long-term algae viability study with daily sample analysis using Pulse-Amplitude Modulated (PAM) fluorometry. The sample was analysed over 79 days. We tested different storage conditions: fridge and room temperature with and without light. It seems that during the first two weeks of the experiment the viability remains almost unchanged with a slight downwards trend. In the continuing period, before the sample was split, a slightly stronger downwards viability trend was observed, which occurred at a similar rate towards the end of the experiment. After the sample was split, the strongest viability reduction was measured for the sample stored without light at room temperature. We concluded that the storage conditions, especially regarding temperature and light exposure, have a stronger impact on algae viability compared to the storage duration and that inappropriate storage conditions reduce algal viability. A sample storage time of up to two weeks in a dark and cool environment has little influence on the organism viability. This indicates that a two week time duration between sample taking on board a vessel and the viability measurement in a land-based laboratory may not be very critical.

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.

PubMed

Hill, Cian J; Brown, Jillian R M; Lynch, Denise B; Jeffery, Ian B; Ryan, C Anthony; Ross, R Paul; Stanton, Catherine; O'Toole, Paul W

2016-05-10

Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p < 0.001). When the microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p < 0.001) means that any alteration in the infant datasets has a proportionally larger effect. The commercial storage vials appear to be suitable for high diversity microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is unavoidable, a consistent storage regime should be used. We would recommend extraction ideally within the first week of storage.

Temperature fluctuations during deep temperature cryopreservation reduce PBMC recovery, viability and T-cell function.

PubMed

Germann, Anja; Oh, Young-Joo; Schmidt, Tomm; Schön, Uwe; Zimmermann, Heiko; von Briesen, Hagen

2013-10-01

The ability to analyze cryopreserved peripheral blood mononuclear cell (PBMC) from biobanks for antigen-specific immunity is necessary to evaluate response to immune-based therapies. To ensure comparable assay results, collaborative research in multicenter trials needs reliable and reproducible cryopreservation that maintains cell viability and functionality. A standardized cryopreservation procedure is comprised of not only sample collection, preparation and freezing but also low temperature storage in liquid nitrogen without any temperature fluctuations, to avoid cell damage. Therefore, we have developed a storage approach to minimize suboptimal storage conditions in order to maximize cell viability, recovery and T-cell functionality. We compared the influence of repeated temperature fluctuations on cell health from sample storage, sample sorting and removal in comparison to sample storage without temperature rises. We found that cyclical temperature shifts during low temperature storage reduce cell viability, recovery and immune response against specific-antigens. We showed that samples handled under a protective hood system, to avoid or minimize such repeated temperature rises, have comparable cell viability and cell recovery rates to samples stored without any temperature fluctuations. Also T-cell functionality could be considerably increased with the use of the protective hood system compared to sample handling without such a protection system. This data suggests that the impact of temperature fluctuation on cell integrity should be carefully considered in future clinical vaccine trials and consideration should be given to optimal sample storage conditions. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR COLLECTION, STORAGE AND SHIPMENT OF URINE SAMPLES FOR SELECTED METALS AND PESTICIDES (UA-F-20.1)

EPA Science Inventory

The purpose of this SOP is to guide the collection, storage, and shipment of urine samples collected for the NHEXAS Arizona project. This SOP provides a brief description of sample, collection, preservation, storage, shipping, and custody procedures. This procedure was followed ...

HPV Testing from Dried Urine Spots as a Tool for Cervical Cancer Screening in Low-Income Countries.

PubMed

Frati, Elena Rosanna; Martinelli, Marianna; Fasoli, Ester; Colzani, Daniela; Bianchi, Silvia; Binda, Sandro; Olivani, Pierfranco; Tanzi, Elisabetta

2015-01-01

Nowadays, several screening strategies are available to prevent cervical cancer, but inadequate resources, sociocultural barriers, and sampling issues impede their success in low-income countries. To overcome these issues, this study aimed to evaluate the performance of human papillomavirus (HPV) testing from dried urine spots (DUS). Eighty-eight urine samples (including 56 HPV DNA positive specimens) were spotted on filter paper, dried, and stored in paper-bags. HPV DNA was detected from the DUS after 1 week and 4 weeks of storage using a polymerase chain reaction (PCR) assay. The sensitivity, specificity, and concordance of the DUS-based HPV test were evaluated by comparing the results with those of HPV testing on fresh urine samples as the gold standard. The sensitivity of the test was 98.21% (95% CI: 90.56-99.68) for DUS stored for 1 week and 96.42% (95% CI: 87.88-99.01) for DUS stored for 4 weeks. The specificity was 100% (95% CI: 89.28-100) at both time points. The concordance between DUS and fresh urine HPV testing was "almost perfect" using the κ statistic. These preliminary data suggest that a DUS-based assay could bypass sociocultural barriers and sampling issues and therefore could be a suitable, effective tool for epidemiological surveillance and screening programs, especially in low-income countries.

HPV Testing from Dried Urine Spots as a Tool for Cervical Cancer Screening in Low-Income Countries

PubMed Central

Olivani, Pierfranco

2015-01-01

Nowadays, several screening strategies are available to prevent cervical cancer, but inadequate resources, sociocultural barriers, and sampling issues impede their success in low-income countries. To overcome these issues, this study aimed to evaluate the performance of human papillomavirus (HPV) testing from dried urine spots (DUS). Eighty-eight urine samples (including 56 HPV DNA positive specimens) were spotted on filter paper, dried, and stored in paper-bags. HPV DNA was detected from the DUS after 1 week and 4 weeks of storage using a polymerase chain reaction (PCR) assay. The sensitivity, specificity, and concordance of the DUS-based HPV test were evaluated by comparing the results with those of HPV testing on fresh urine samples as the gold standard. The sensitivity of the test was 98.21% (95% CI: 90.56–99.68) for DUS stored for 1 week and 96.42% (95% CI: 87.88–99.01) for DUS stored for 4 weeks. The specificity was 100% (95% CI: 89.28–100) at both time points. The concordance between DUS and fresh urine HPV testing was “almost perfect” using the κ statistic. These preliminary data suggest that a DUS-based assay could bypass sociocultural barriers and sampling issues and therefore could be a suitable, effective tool for epidemiological surveillance and screening programs, especially in low-income countries. PMID:26180790

Packaging Considerations for Biopreservation

PubMed Central

Woods, Erik J.; Thirumala, Sreedhar

2011-01-01

Summary The packaging system chosen for biopreservation is critical for many reasons. An ideal biopreservation container system must provide for closure integrity, sample stability and ready access to the preserved material. This means the system needs to be hermetically sealed to ensure integrity of the specimen is maintained throughout processing, storage and distribution; the system must remain stable over long periods of time as many biobanked samples may be stored indefinitely; and functionally closed access systems must be used to avoid contamination upon sample withdraw. This study reviews the suitability of a new commercially available vial configuration container utilizing blood bag style closure and access systems that can be hermetically sealed and remain stable through cryopreservation and biobanking procedures. This vial based systems allow for current good manufacturing/tissue practice (cGTP) requirements during processing of samples and may provide the benefit of ease of delivery by a care giver. In this study, the CellSeal® closed system cryovial was evaluated and compared to standard screw cap vials. The CellSeal system was evaluated for durability, closure integrity through transportation and maintenance of functional viability of a cryopreserved mesenchymal stem cell model. The results of this initial proof-of-concept study indicated that the CellSeal vials are highly suitable for biopreservation and biobanking, and provide a suitable container system for clinical and commercial cell therapy products frozen in small volumes. PMID:21566715

A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

PubMed Central

Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

2013-01-01

An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659