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Sample records for herbarium specimens prospecting

  1. DNA extraction from herbarium specimens.

    Science.gov (United States)

    Drábková, Lenka Záveská

    2014-01-01

    With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).

  2. Foliar Mn accumulation in eastern Australian herbarium specimens: prospecting for ‘new’ Mn hyperaccumulators and potential applications in taxonomy

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    Fernando, Denise R.; Guymer, Gordon; Reeves, Roger D.; Woodrow, Ian E.; Baker, Alan J.; Batianoff, George N.

    2009-01-01

    Background and Aims The analysis of herbarium specimens has previously been used to prospect for ‘new’ hyperaccumulators, while the use of foliar manganese (Mn) concentrations as a taxonomic tool has been suggested. On the basis of their geographic and taxonomic affiliations to known Mn hyperaccumulators, six eastern Australian genera from the Queensland Herbarium collection were sampled for leaf tissue analyses. Methods ICP-OES was used to measure Mn and other elemental concentrations in 47 species within the genera Austromyrtus, Lenwebbia, Gossia (Myrtaceae), Macadamia (Proteaceae), Maytenus and Denhamia (Celastraceae). Key Results The resulting data demonstrated (a) up to seven ‘new’ Mn hyperaccumulators, mostly tropical rainforest species; (b) that one of these ‘new’ Mn hyperaccumulators also had notably elevated foliar Ni concentrations; (c) evidence of an interrelationship between foliar Mn and Al uptake among the Macadamias; (d) considerable variability of Mn hyperaccumulation within Gossia; and (e) the possibility that Maytenus cunninghamii may include subspecies. Conclusions Gossia bamagensis, G. fragrantissima, G. sankowsiorum, G. gonoclada and Maytenus cunninghamii were identified as ‘new’ Mn hyperaccumulators, while Gossia lucida and G. shepherdii are possible ‘new’ Mn hyperaccumulators. Of the three Myrtaceae genera examined, Mn hyperaccumulation appears restricted to Gossia, supporting its recent taxonomic revision. In the context of this present investigation and existing information, a reassesment of the general definition of Mn hyperaccumulation may be warranted. Morphological variation of Maytenus cunninghamii at two extremities was consistent with variation in Mn accumulation, indicating two possible ‘new’ subspecies. Although caution should be exercised in interpreting the data, surveying herbarium specimens by chemical analysis has provided an effective means of assessing foliar Mn accumulation. These findings should be

  3. Extraction of ultrashort DNA molecules from herbarium specimens.

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    Gutaker, Rafal M; Reiter, Ella; Furtwängler, Anja; Schuenemann, Verena J; Burbano, Hernán A

    2017-02-01

    DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.

  4. Herbarium genomics: skimming and plastomics from archival specimens

    NARCIS (Netherlands)

    Bakker, F.T.

    2017-01-01

    Using massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using herbarium DNA have been overcome. For instance, no longer is the degraded nature of most herbarium DNA preventing sequencing (because of blocking effective

  5. How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

    NARCIS (Netherlands)

    Särkinen, T.; Staats, M.; Richardson, J.E.; Cowan, R.S.; Bakker, F.T.

    2012-01-01

    Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance

  6. Going deeper in the automated identification of Herbarium specimens.

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    Carranza-Rojas, Jose; Goeau, Herve; Bonnet, Pierre; Mata-Montero, Erick; Joly, Alexis

    2017-08-11

    Hundreds of herbarium collections have accumulated a valuable heritage and knowledge of plants over several centuries. Recent initiatives started ambitious preservation plans to digitize this information and make it available to botanists and the general public through web portals. However, thousands of sheets are still unidentified at the species level while numerous sheets should be reviewed and updated following more recent taxonomic knowledge. These annotations and revisions require an unrealistic amount of work for botanists to carry out in a reasonable time. Computer vision and machine learning approaches applied to herbarium sheets are promising but are still not well studied compared to automated species identification from leaf scans or pictures of plants in the field. In this work, we propose to study and evaluate the accuracy with which herbarium images can be potentially exploited for species identification with deep learning technology. In addition, we propose to study if the combination of herbarium sheets with photos of plants in the field is relevant in terms of accuracy, and finally, we explore if herbarium images from one region that has one specific flora can be used to do transfer learning to another region with other species; for example, on a region under-represented in terms of collected data. This is, to our knowledge, the first study that uses deep learning to analyze a big dataset with thousands of species from herbaria. Results show the potential of Deep Learning on herbarium species identification, particularly by training and testing across different datasets from different herbaria. This could potentially lead to the creation of a semi, or even fully automated system to help taxonomists and experts with their annotation, classification, and revision works.

  7. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

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    Martijn Staats

    Full Text Available Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes, but at least generating vital comparative genomic data for testing (phylogenetic, demographic and genetic hypotheses, that become increasingly more

  8. Increasing the efficiency of digitization workflows for herbarium specimens

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    Melissa Tulig

    2012-07-01

    Full Text Available The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR of specimen images. With the launch of the National Science Foundation’s new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

  9. Increasing the efficiency of digitization workflows for herbarium specimens.

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    Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers, Barbara M

    2012-01-01

    The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation's new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

  10. CrowdCurio: an online crowdsourcing platform to facilitate climate change studies using herbarium specimens.

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    Willis, Charles G; Law, Edith; Williams, Alex C; Franzone, Brian F; Bernardos, Rebecca; Bruno, Lian; Hopkins, Claire; Schorn, Christian; Weber, Ella; Park, Daniel S; Davis, Charles C

    2017-07-01

    Phenology is a key aspect of plant success. Recent research has demonstrated that herbarium specimens can provide important information on plant phenology. Massive digitization efforts have the potential to greatly expand herbarium-based phenological research, but also pose a serious challenge regarding efficient data collection. Here, we introduce CrowdCurio, a crowdsourcing tool for the collection of phenological data from herbarium specimens. We test its utility by having workers collect phenological data (number of flower buds, open flowers and fruits) from specimens of two common New England (USA) species: Chelidonium majus and Vaccinium angustifolium. We assess the reliability of using nonexpert workers (i.e. Amazon Mechanical Turk) against expert workers. We also use these data to estimate the phenological sensitivity to temperature for both species across multiple phenophases. We found no difference in the data quality of nonexperts and experts. Nonexperts, however, were a more efficient way of collecting more data at lower cost. We also found that phenological sensitivity varied across both species and phenophases. Our study demonstrates the utility of CrowdCurio as a crowdsourcing tool for the collection of phenological data from herbarium specimens. Furthermore, our results highlight the insight gained from collecting large amounts of phenological data to estimate multiple phenophases. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  11. Documenting Reproductive Phenology using Herbarium Specimens: Experiences from the New England Vascular Plants Project

    OpenAIRE

    Sweeney,Patrick; Gilbert,Edward

    2017-01-01

    Herbarium specimens and associated label data are valuable sources of phenological data. They can provide information about the phenological state of the specimen and information about how phenology varies in space and time. In an effort to leverage this tremendous phenological resource, the New England Vascular Plants project (NEVP) has worked over the past few years to create a data set catered to the study of the effects of climate change in New England. This project has focused on capturi...

  12. Dataset of herbarium specimens of threatened vascular plants in Catalonia.

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    Nualart, Neus; Ibáñez, Neus; Luque, Pere; Pedrol, Joan; Vilar, Lluís; Guàrdia, Roser

    2017-01-01

    This data paper describes a specimens' dataset of the Catalonian threatened vascular plants conserved in five public Catalonian herbaria (BC, BCN, HGI, HBIL and MTTE). Catalonia is an administrative region of Spain that includes large autochthon plants diversity and 199 taxa with IUCN threatened categories (EX, EW, RE, CR, EN and VU). This dataset includes 1,618 records collected from 17(th) century to nowadays. For each specimen, the species name, locality indication, collection date, collector, ecology and revision label are recorded. More than 94% of the taxa are represented in the herbaria, which evidence the paper of the botanical collections as an essential source of occurrence data.

  13. Dataset of herbarium specimens of threatened vascular plants in Catalonia

    OpenAIRE

    Neus Nualart; Neus Ibáñez; Pere Luque; Joan Pedrol; Lluís Vilar; Roser Guàrdia

    2017-01-01

    This data paper describes a specimens’ dataset of the Catalonian threatened vascular plants conserved in five public Catalonian herbaria (BC, BCN, HGI, HBIL and MTTE). Catalonia is an administrative region of Spain that includes large autochthon plants diversity and 199 taxa with IUCN threatened categories (EX, EW, RE, CR, EN and VU). This dataset includes 1,618 records collected from 17th century to nowadays. For each specimen, the species name, locality indication, collection date, collecto...

  14. Determining past leaf-out times of New England's deciduous forests from herbarium specimens.

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    Everill, Peter H; Primack, Richard B; Ellwood, Elizabeth R; Melaas, Eli K

    2014-08-01

    • There is great interest in studying leaf-out times of temperate forests because of the importance of leaf-out in controlling ecosystem processes, especially in the face of a changing climate. Remote sensing and modeling, combined with weather records and field observations, are increasing our knowledge of factors affecting variation in leaf-out times. Herbarium specimens represent a potential new source of information to determine whether the variation in leaf-out times observed in recent decades is comparable to longer time frames over past centuries.• Here we introduce the use of herbarium specimens as a method for studying long-term changes in leaf-out times of deciduous trees. We collected historical leaf-out data for the years 1834-2008 from common deciduous trees in New England using 1599 dated herbarium specimens with young leaves.• We found that leaf-out dates are strongly affected by spring temperature, with trees leafing out 2.70 d earlier for each degree C increase in mean April temperature. For each degree C increase in local temperature, trees leafed out 2.06 d earlier. Additionally, the mean response of leaf-out dates across all species and sites over time was 0.4 d earlier per decade. Our results are of comparable magnitude to results from studies using remote sensing and direct field observations.• Across New England, mean leaf-out dates varied geographically in close correspondence with those observed in studies using satellite data. This study demonstrates that herbarium specimens can be a valuable source of data on past leaf-out times of deciduous trees. © 2014 Botanical Society of America, Inc.

  15. Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification.

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    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.

  16. An Account of the Accessioned Specimens in the Jose Vera Santos Memorial Herbarium, University of the Philippines Diliman

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    Sandra L. Yap

    2013-12-01

    Full Text Available The University of the Philippines Herbarium was established in 1908 and originally located in Ermita, Manila. The majority of its pre-war collections were destroyed during World War II, and no formal records of its specimens were preserved. Since then, multiple efforts to restore and improve the Herbarium have been proposed and implemented, most notably its move to the UP Diliman campus. In 1999, the Herbarium was off icially renamed as the Jose Vera Santos Memorial Herbarium after the noted grass expert, who initiated rehabilitation work in the Herbarium after the war. The Herbarium is registered with the international code PUH in the Index Herbariorum, a global directory of public herbaria managed by the New York Botanical Garden. To assess the accessioned (uniquely numbered and recorded collection of the Herbarium, an electronic database of its accessions was created.The Herbarium currently contains 14,648 accessions, 12,681 (86.6% of which were collected in the Philippines. This is comprised of 309 families, 1903 genera, and 4485 distinct species. Thirty-nine type specimens form part of the collection, only one of which is a holotype. On the basis of major plant groups, angiosperms make up 71% of the collection. Unsurprisingly, Family Poaceae has the largest number of specimens at 2,759 accessions. The earliest dated Philippine specimen was collected by E.D. Merrill in 1902, and roughly half of the total accessioned specimens were collected in the 1950s and 1970s. The two most prolif ic collectors were Santos and Leonardo L. Co, with 2,320 and 2,147 specimens, respectively. Luzon is the most well-represented island group with 2,752 specimens collected in Metro Manila alone. At present, PUH Curator James V. LaFrankie is working on the expansion of the collection and upgrading of the herbarium to encourage future educational and research activities.

  17. How to open the treasure chest? Optimising DNA extraction from herbarium specimens.

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    Tiina Särkinen

    Full Text Available Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA, the LEAFY exon 3 (nrDNA, and the trnL((UAA P6 loop (cpDNA. Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10-143 base pairs (bp and the largest fragment the lowest success (10%, rbcL, 670 bp. The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200-300 bp in order to maximise outcomes. Development of shorter barcoding regions, or mini-barcodes within existing ones should be of high importance as only a few options are currently available; this is particularly important if we hope to incorporate the millions of herbarium samples available into barcoding initiatives and other molecular studies.

  18. The use of Optical Character Recognition (OCR in the digitisation of herbarium specimen labels

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    Robyn Drinkwater

    2014-05-01

    Full Text Available At the Royal Botanic Garden Edinburgh (RBGE the use of Optical Character Recognition (OCR to aid the digitisation process has been investigated. This was tested using a herbarium specimen digitisation process with two stages of data entry. Records were initially batch-processed to add data extracted from the OCR text prior to being sorted based on Collector and/or Country. Using images of the specimens, a team of six digitisers then added data to the specimen records. To investigate whether the data from OCR aid the digitisation process, they completed a series of trials which compared the efficiency of data entry between sorted and unsorted batches of specimens. A survey was carried out to explore the opinion of the digitisation staff to the different sorting options. In total 7,200 specimens were processed.When compared to an unsorted, random set of specimens, those which were sorted based on data added from the OCR were quicker to digitise. Of the methods tested here, the most successful in terms of efficiency used a protocol which required entering data into a limited set of fields and where the records were filtered by Collector and Country. The survey and subsequent discussions with the digitisation staff highlighted their preference for working with sorted specimens, in which label layout, locations and handwriting are likely to be similar, and so a familiarity with the Collector or Country is rapidly established.

  19. Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

    DEFF Research Database (Denmark)

    Martin, Michael David; Zimmer, Elizabeth A.; Olsen, Morten Tange

    2014-01-01

    Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have...... expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Towards a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural...... populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed...

  20. Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach

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    Elspeth Haston

    2012-07-01

    Full Text Available Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow.

  1. Recalibrating the Ginkgo Stomatal Index Proxy for Past CO2 with Herbarium Specimens

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    Conde, G. D.; Retallack, G.

    2015-12-01

    The stomatal index of plant cuticles is inversely related to atmospheric CO2 concentrations, as calibrated from greenhouse experiments and herbarium specimens. Such calibration data for Ginkgo biloba are available for the ongoing rise in atmospheric CO2 and for high levels of CO2 anticipated in the future, but lacking for low CO2 levels of preindustrial and glacial ages. The oldest modern specimen that we have been able to obtain consists of leaf fragments collected in 1829 and provided by Arne Anderberg from the Swedish Natural History Museum. The specimen was labeled "Argentina", but also "Hortus Botanicus Augustinus", a garden founded in 1638 in Amsterdam, Netherlands. Ginkgo has a very thin cuticle that is difficult to prepare, but images very similar to cuticular preparation can be obtained by backscatter SEM imagery. We also obtained secondary SEM images of the same areas and counted 13 images with 6,184 cells from five leaf fragments. Our analyses yield a stomatal index of 10.9 ± 0.9 % for an atmospheric CO2 of 286 ppm, as determined by ice core data from Ciais and Sabine for IPCC-2013. This value is lower than from previous calibration curves for this level of CO2 and changes their curvature. With additional late nineteenth, twentieth and twenty-first century leaves, we can improve both the precision and lower limits of the transfer function for atmospheric CO2 from Ginkgo stomatal index last revised in 2009.

  2. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  3. Catalogue of type specimens of fungi and lichens deposited in the Herbarium of the University of Granada (Spain).

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    Vizoso, M Teresa; Quesada, Carmen

    2015-01-01

    A catalogue of types from the Herbarium of the University of Granada has not previously been compiled. As a result, a search of these collections in order to compile digital images for preservation and publication yielded a large number of formerly unrecognized types. This dataset contains the specimen records from the catalogue of the nomenclature types of fungi and lichens in the Herbarium of the University of Granada, Spain. These herbarium specimens are included in the GDA and GDAC collections, acronyms from Index Herbariorum (Thiers 2014). At this time, the type collection of fungi and lichens contains 88 type specimens of 49 nominal taxa, most from Agaricales and the genus Cortinarius, described from the western Mediterranean, mainly Spain, by the following authors: V.Antonin, J.Ballarà, A.Bidaud, G.F.Bills, M.Bon, C.Cano, M.Casares, G.Chevassut, M.Contu, F.Esteve-Raventós, R.Galán, L.Guzmán-Dávalos, R.Henry, E.Horak, R.Mahiques, G.Malençon, P.Moënne-Loccoz, G.Moreno, A.Ortega, F.Palazón, V.N.Suárez.-Santiago, A.Vêzda, J.Vila, and M.Villareal. For each specimen, the locality indication, species name, observation date, collector, type status, related information, associated sequences, other catalogue numbers related to each type, and image URL are recorded. The dataset is associated with an image collection named "Colección de imágenes de los tipos nomenclaturales de hongos, líquenes, musgos y algas incluidos en el Herbario de la Universidad de Granada (GDA y GDAC)" (Vizoso and Quesada 2013) which is housed and accessible at the Global Biodiversity Information Facility in Spain (GBIF.ES) Hosting and Publishing Service "Biodiversity Image Portal of Spanish collections" and is also available at the Herbarium of University of Granada institutional web (Vizoso 2014a, Vizoso 2014b). That image collection contains 113 images, of which 56 correspond to the nomenclature types of 49 taxa (47 fungi, 2 lichens), the rest of the images in this collection

  4. Mercury in air and plant specimens in herbaria: A pilot study at the MAF Herbarium in Madrid (Spain)

    Energy Technology Data Exchange (ETDEWEB)

    Oyarzun, R. [Departamento de Cristalografia y Mineralogia, Facultad de Ciencias Geologicas, Universidad Complutense, 28040 Madrid (Spain)], E-mail: oyarzun@geo.ucm.es; Higueras, P.; Esbri, J.M. [Departamento de Ingenieria Geologica y Minera, Escuela Universitaria Politecnica de Almaden, Universidad de Castilla-La Mancha, Plaza M. Meca 1, 13400 Almaden (Spain); Pizarro, J. [Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense, 28040 Madrid (Spain)

    2007-11-15

    We present data from a study of mercury concentrations in air and plant specimens from the MAF Herbarium in Madrid (Spain). Hg (gas) emissions from old plant collections treated with mercuric chloride (HgCl{sub 2}) in herbaria may pose a health risk for staff working in installations of this type. This is an issue not yet properly addressed. Plants that underwent insecticide treatment with HgCl{sub 2} at the MAF Herbarium until the mid 1970s have persistent high concentrations of Hg in the range 1093-11,967 {mu}g g{sup -1}, whereas untreated specimens are in the range of 1.2-4.3 {mu}g g{sup -1}. The first group induces high concentrations of Hg (gas) in the main herbarium room, with seasonal variations of 404-727 ng m{sup -3} (late winter) and 748-7797 ng m{sup -3} (early summer) (baseline for Hg: 8 ng m{sup -3}). A test survey at another herbarium in Madrid showed even higher concentrations of Hg (gas) above 40,000 ng m{sup -3}. The World Health Organization guidelines for chronic exposure to Hg (gas) are estimated at a maximum of 1000 ng m{sup -3}. While staff was aware of the existence of HgCl{sub 2} treated plants (the plant specimen sheets are labelled as 'poisoned'), they had no knowledge of the presence of high Hg (gas) concentrations in the buildings, a situation that may be relatively common in herbaria.

  5. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects

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    Kentaro eYoshida

    2015-09-01

    Full Text Available The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

  6. A revision of the history of the Colletotrichum acutatum species complex in the Nordic countries based on herbarium specimens.

    Science.gov (United States)

    Sundelin, Thomas; Strømeng, Gunn Mari; Gjærum, Halvor B; Amby, Daniel Buchvaldt; Ørstad, Kari; Jensen, Birgit; Lund, Ole Søgaard; Stensvand, Arne

    2015-08-01

    Herbaria collections containing plants with disease symptoms are highly valuable, and they are often the only way to investigate outbreaks and epidemics from the past as the number of viable isolates in culture collections is often limited. Species belonging to the Colletotrichum acutatum complex infect a range of important crops. As members of the C. acutatum complex are easily confused with other Colletotrichum species, molecular methods are central for the correct identification. We performed molecular analyses on 21 herbaria specimens, displaying anthracnose symptoms, collected in Norway and Denmark before the first confirmed findings of C. acutatum complex members in this region. Sequencing parts of the fungal ITS regions showed that members of the species complex were present in 13 of the 21 specimens collected in different parts of Norway and Denmark between 1948 and 1991, representing seven plant hosts (three cherry species, apple, raspberry and rhododendron). This is the first time herbarium specimens have been used to study these pathogens under Nordic conditions. Differences in the ITS sequences suggest the presence of different genotypes within the complex, indicating a well-established population. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. History and Diversity of Citrus leprosis virus Recorded in Herbarium Specimens.

    Science.gov (United States)

    Hartung, John S; Roy, Avijit; Fu, Shimin; Shao, Jonathan; Schneider, William L; Brlansky, Ronald H

    2015-09-01

    Leprosis refers to two diseases of citrus that present similar necrotic local lesions, often surrounded by chlorotic haloes on citrus. Two distinct viruses are associated with this disease, one that produces particles primarily in the nucleus of infected plant cells (Citrus leprosis virus nuclear type [CiLV-N]; Dichorhavirus) and another type that produces particles in the cytoplasm of infected plant cells (Citrus leprosis virus cytoplasmic type [CiLV-C]; Cilevirus). Both forms are transmitted by Brevipalpid mites and have bipartite, single-stranded, RNA genomes. CiLV-C and CiLV-N are present in South and Central America and as far north as parts of Mexico. Although leprosis disease was originally described from Florida, it disappeared from there in the 1960s. The United States Department of Agriculture-Agricultural Research Service maintains preserved citrus specimens identified at inspection stations 50 or more years ago with symptoms of citrus leprosis. We isolated RNA from these samples and performed degradome sequencing. We obtained nearly full-length genome sequences of both a typical CiLV-C isolate intercepted from Argentina in 1967 and a distinct CiLV-N isolate obtained in Florida in 1948. The latter is a novel form of CiLV-N, not known to exist anywhere in the world today. We have also documented the previously unreported presence of CiLV-N in Mexico in the mid-20th century.

  8. The revision of specimens of the Cladonia pyxidata-chlorophaea group (lichenized Ascomycota from northeastern Poland deposited in the herbarium collections of University in Bialystok

    Directory of Open Access Journals (Sweden)

    Anna Matwiejuk

    2017-01-01

    Full Text Available In northeastern Poland, the chemical variation of the Cladonia chlorophaea-pyxidata group was much neglected, as TLC has not been used in delimitation of species differing in the chemistry. As a great part of herbal material of University in Bialystok from NE Poland was misidentified, I found my studies to be necessary. Based on the collection of 123 specimens deposited in Herbarium of University in Bialystok, nine species of the C. pyxidata-chlorophaea group are reported from NE Poland. The morphology, secondary chemistry, and ecology of examined lichens are presented and the list of localities is provided. The results revealed that C. fimbriata is the most common species in the northeastern Poland, comprising around 33% of the studied specimens. Cladonia conista, C. cryptochlorophaea, and C. merochlorophaea are known only from very few locations. This study shed light on the role of the lichens substances to diagnosis of the species of C. pyxidata-chlorophaea group.

  9. A revision of the history of the Colletotrichum acutatum species complex in the Nordic countries based on herbarium specimens

    DEFF Research Database (Denmark)

    Sundelin, Thomas; Strømeng, Gunn Mari; Gjærum, Halvor B.

    2015-01-01

    and Denmark before the first confirmed findings of C. acutatum complex members in this region. Sequencing parts of the fungal ITS regions showed that members of the species complex were present in 13 of the 21 specimens collected in different parts of Norway and Denmark between 1948 and 1991, representing...

  10. DNA damage in plant herbarium tissue.

    NARCIS (Netherlands)

    Staats, M.; Cuenca, A.; Richardson, J.E.; Ginkel, R.V.; Petersen, G.; Seberg, O.; Bakker, F.T.

    2011-01-01

    Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of

  11. The fern herbarium at the Komarov Botanical Institute, Leningrad

    NARCIS (Netherlands)

    Holttum, R.E.

    1977-01-01

    The Herbarium is arranged according to Christensen’s Index Filicum (1905). I examined all the Old World specimens in Dryopteris and Aspidium, both in the general herbarium and in the separate herbarium for China and Japan. It appears that the genera segregated by Christensen from Dryopteris (e.g.

  12. Type specimens of taxa of Artemisia L. (Asteraceae from Siberia and the Far East kept in the Herbarium of V.L. Komarov Botanical Insitute

    Directory of Open Access Journals (Sweden)

    A. A. Korobkov

    2015-04-01

    Full Text Available Typification of 97 Artemisia (Asteraceae taxa from Siberia and the Far East kept in the Herbarium of V.L. Komarov Botanical Institute was carried out. Holotypes for 39 taxa, lectotypes for 48 taxa, 28 syntypes and 4 isotypes are given.

  13. The Harvard University Herbarium

    NARCIS (Netherlands)

    Howard, Richard A.

    1955-01-01

    During 1954 the Gray Herbarium, the Orchid Herbarium of Oakes Ames, the paleobotanical collections of the Botanical Museum and a portion of the herbarium collections and the library of the Arnold Arboretum were moved into a new building in Cambridge, Massachusetts. This move was the culmination of a

  14. An appreciation of the Rijks Herbarium

    NARCIS (Netherlands)

    Merrill, E.D.

    1931-01-01

    The Netherlands is to be congratulated in having available within its borders such an outstandingly important collection of historical botanical material as that preserved in the Rijks Herbarium at Leiden. To a greater and greater degree the importance of this great assemblage of botanical specimens

  15. Case Study: Brazilian Virtual Herbarium

    Directory of Open Access Journals (Sweden)

    Cameron Neylon

    2017-10-01

    Full Text Available The Brazilian Virtual Herbarium (BVH is a project of the Brazillian Centro de Referência em Informação Ambiental (CRIA that has been running since 2009. The Virtual Herbarium provides an infrastructure that gathers digital records of plant specimens from primary source, mainly in Brazil, and makes them available through a central web portal. The source herbaria have complete control over what data is made through the portal and the data collected by BVH is made fully available. BVH in common with many data infrastructures, faces challenges in retaining funding. Most funding sources are project based and as has been noted elsewhere this creates problems for the sustaining of infrastructures. BVH therefore has an interest in demonstrating the use of the data resources it hosts. Through the OCSDNet project it has strengthened its capacity in this area to develop tools showing its wide usage. Overall the BVH hosts over eight million records (as of October 2017 and received 70 billion data requests in October 2017. Its users are mainly in Brazil but there is also substantial global usage. The primary uses are for research and education. There are a broad range of educational users, including universities but also schools. Through providing a central aggregation and access point BHV provides a data infrastructure that is greater – and more useful – than the sum of its parts.

  16. PRECIS, the Botanical Research Institute herbarium data bank

    Directory of Open Access Journals (Sweden)

    R. E. Magill

    1983-12-01

    Full Text Available PRECIS has been modified to make it more useful to taxonomists. The simplified system contains only specimen-related data, and the resulting decrease in the size of the data bank will make it more efficient to operate and maintain. The methods used to encode herbarium data, the operation of the storage and retrieval system, and several examples of system output, demonstrating the flexibility and versatility of PRECIS and its applications in herbarium curation and taxonomic research are described.

  17. THE SPUNBOND IN HERBARIUM TECHNIQUES

    Directory of Open Access Journals (Sweden)

    A.V. Slavgorodskiy

    2016-06-01

    Full Text Available This article gives information additional to the existing editions about drying and keeping herbarium between the spunbond sheets, the approach not mentioned in Kew’s «The herbarium handbook». The invention was patented: Patent no. 71212, Russian Federation, priority number 2007137443 of 09.10.2007. Spunbond, nonwoven polymeric fabric, allows to introduce technologies which might exclude paper and other moisture absorptive materials from the process of herbarium making. The idea of the new way of drying plants for the herbarium consists in creating thin air linen around the plant in the herbarium press with the use of spunbond. Thanks to the free air access, plants dry very quickly and stay flat at the same time. The plants are dried in the herbarium press with the use of black spunbond, with the density from 60 grams per square meter to 150 grams per square meter, instead of usual newspapers. In 2009-2011 Multi-purpose Herbarium Press was tried out in Central Russia, In the Northern Ural, Northern Africa and France. In all these parts of the world scientists were absolutely satisfied with the results. Spunbond can also be used for keeping the herbarium. It lasts longer and is cheaper than paper. It doesn’t break into small pieces, doesn’t absorb moister from the outside, doesn’t deteriorate because of the sun, and cannot be damaged by insects. The use of spunbond when making herbarium allows to avoid using wood (shelves and cupboards and paper in the rooms where herbariums are kept, because they are kept on metal shelves. This will help to avoid a big number of pests, which is especially a big problem for tropical herbariums.

  18. THE ANALYSIS OF AVAILABLE GIS SERVERS POSSIBILITIES FOR CREATION OF ELECTRONIC HERBARIUM WEB MAPPING SERVICE (ON THE EXAMPLE OF SCIENTIFIC HERBARIUM OF THE BURYAT STATE UNIVERSITY

    Directory of Open Access Journals (Sweden)

    M. V. Tsydypova

    2017-01-01

    Full Text Available An electronic herbarium published on the Internet allows greater access to the data collected by scientific herbarium for a wide range of users, and also provides remote operation from the herbarium materials. This article analyzes the open source software use to create web mapping service of an electronic herbarium. This article describes the requirements for the functionality of the software for creating web mapping service of electronic herbarium. The article gives a brief description and presents comparative characteristics of free web mapping servers MapServer, GeoServer, GeoMixer, QGIS Server, describes their advantages and disadvantages. The adaptation and conversion of an existing electronic database of Herbarium of the Buryat state University from excel format to vector format has been realized.Comparative analysis has shown that all four web mapping servers (MapServer, GeoServer, GeoMixer, QGIS Server have sufficient functionality to create on their basis a web mapping service of electronic herbarium, but with some restrictions on certain parameters. A test version of web mapping service of electronic herbarium of the Buryat State University has been created based on UMN MapServer in conjunction with P.mapper.At the moment, the web mapping service includes the following layers: wms-layer of basic map, vector layer reflecting the place of collection of herbarium specimens and their characteristics, vector layer of districts’ boundaries of the Republic of Buryatia. 

  19. [USJ Herbarium of Costa Rica: history and contributions].

    Science.gov (United States)

    Morales, Carlos O

    2012-12-01

    In 2011 the Herbarium USJ of the University of Costa Rica became 80 years old and came up with 100 000 specimens of all the taxa that traditional botany studies. Data and figures on the history, the founders, and contributions of USJ to the knowledge of Costa Rican flora are summarized.

  20. Herbarium Celebense (CEB and its role in supporting research on plant diversity of Sulawesi

    Directory of Open Access Journals (Sweden)

    RAMADHANIL

    2004-01-01

    Full Text Available Sulawesi is the largest island in Wallacea region and a biogeographically unique area. The island is very rich in endemic species, worldwide known only known from Sulawesi. Nevertheless, scientific knowledge of the plants of Sulawesi is still limited and there is a lack of botanical exploration and publications. In 2000, Tadulako University of Palu with support of the German Research Foundation (DFG, the Universities of Göttingen and Leiden and the Herbarium Bogoriense, has constructed a herbarium, the Herbarium Celebense. The herbarium has been registered in the International Index Herbariorum (New York with the abbreviation CEB. The Herbarium Celebense contains about 3000 plant specimens, especially from Central Sulawesi and mainly spermatophytes and pteridophytes. This article reviews the current knowedge of plant diversity of the Sulawesi and Wallacea bioregion as a basis for the conservation of its rich flora.

  1. The Reimer Diatom Herbarium: An important resource for teaching and research

    Science.gov (United States)

    Rushforth, S.J.; Edlund, M.B.; Spaulding, S.A.; Stoermer, E.F.

    2010-01-01

    The Reimer Diatom Herbarium (ILH) at Iowa Lakeside Laboratory (ILL), a field station of Iowa's state universities, contains 3,280 permanent diatom slides of collections made from prairie potholes, alkaline fens, acid bogs, eutrophic lakes, saline lakes, Pleistocene paleolakes, and Miocene fossil deposits near ILL. The herbarium has a focus on collections made within Dickinson County, a region with an important legacy of study by students and visiting researchers from the US, Canada, and international institutions. The herbarium is well documented by taxon and location catalogues. The taxon card catalogue contains over 2,800 records referencing 67 genera, and the location card catalogue references collection sites from 51 counties in 16 North American states. Curated slides include over 300 species identifications made, or verified, by C.W. Reimer. Most curated slides have diatom specimens identified to species, circled with a diamond objective marker, and indicated on the slide label Six holotypes are included in the herbarium and we present the first light micrograph images of these type specimens. We present documentation of the contents and current condition of the herbarium and report that it is now available to researchers for scientific study. Many of the sites represented in the Reimer Diatom Herbarium are the same locations visited each year by students and visiting researchers at ILL, resulting in an important resource for monitoring environmental change, resolving taxonomic issues, and understanding species distributions in unique habitats.

  2. Are herbarium mosses reliable indicators of historical nitrogen deposition?

    DEFF Research Database (Denmark)

    Nielsen, Tora Finderup; Larsen, Jesper Ruf; Michelsen, Anders

    2017-01-01

    Mosses collected decades ago and stored in herbaria are often used to assess historical nitrogen deposition. This method is effectively based on the assumption that tissue N concentration remains constant during storage. The present study raises serious doubt about the generality of that assumption....... We measured tissue N and C concentrations as well as δ15N, δ13C, Pb and Mg in herbarium and present day samples of seven bryophyte species from six sites across Denmark. While an increase in nitrogen deposition during the last century is well-documented for the study site, we surprisingly found...... foliar N concentration to be higher in historical samples than in modern samples. Based on δ15N values and Pb concentration, we find nitrogen contamination of herbarium specimens during storage to be the most likely cause, possibly in combination with dilution though growth and/or decomposition during...

  3. Herbarium of vascular plants collection of the university of extremadura (Spain).

    Science.gov (United States)

    Espinosa, Marta; López, Josefa

    2013-01-01

    The herbarium of University of Extremadura (UNEX Herbarium) is formed by 36451 specimens of vascular plants whose main origin is the autonomous region of Extremadura (Spain) and Portugal, although it also contains a smaller number of specimens from different places, including the rest of peninsular Spain, the Baleares Islands, the Macaronesian region (Canary Islands, Madeira and Azores), northwest of Africa (Morocco) and Brazil. 98% of the total records are georeferenced. It is an active collection in continuous growth. Its data can be accessed through the GBIF data portal at http://data.gbif.org/datasets/resource/255 and http://www.eweb.unex.es/eweb/botanica/herbario/. This paper describes the specimen associated data set of the UNEX Herbarium, with an objective to disseminate the data contained in a data set with potential users, and promote the multiple uses of the data.

  4. A new herbarium-based method for reconstructing the phenology of plant species across large areas.

    Science.gov (United States)

    Lavoie, Claude; Lachance, Daniel

    2006-04-01

    Phenological data have recently emerged as particularly effective tools for studying the impact of climate change on plants, but long phenological records are rare. The lack of phenological observations can nevertheless be filled by herbarium specimens as long as some correction procedures are applied to take into account the different climatic conditions associated with sampling locations. In this study, we propose a new herbarium-based method for reconstructing the flowering dates of plant species that have been collected across large areas. Coltsfoot (Tussilago farfara L.) specimens from southern Quebec were used to test the method. Flowering dates for coltsfoot herbarium specimens were adjusted according to the date of disappearance of snow cover in the region where they were collected and compared using a reference point (the date of earliest snowmelt). In southern Quebec, coltsfoot blooms earlier at present (15-31 d) than during the first part of the 20th century. This phenomenon is likely associated with the climate warming trends recorded in this region in the last century, especially during the last three decades when the month of April became warmer, thereby favoring very early-flowering cases. The earlier flowering of coltsfoot is, however, only noticeable in large urban areas (Montreal, Quebec City), suggesting a strong urban heat island effect on the flowering of this plant. Herbarium specimens are useful phenological indicators; however, the databases should be carefully examined prior to analysis to detect biases or trends associated with sampling locations.

  5. Scientific user requirements for a herbarium data portal

    Directory of Open Access Journals (Sweden)

    Jorick Vissers

    2017-03-01

    Full Text Available The digitization of herbaria and their online access will greatly facilitate access to plant collections around the world. This will improve the efficiency of taxonomy and help reduce inequalities between scientists. The Botanic Garden Meise, Belgium, is currently digitizing 1.2 million specimens including label data. In this paper we describe the user requirements analysis conducted for a new herbarium web portal. The aim was to identify the required functionality, but also to assist in the prioritization of software development and data acquisition. The Garden conducted the analysis in cooperation with Clockwork, the digital engagement agency of Ordina. Using a series of interactive interviews, potential users were consulted from universities, research institutions, science-policy initiatives and the Botanic Garden Meise. Although digital herbarium data have many potential stakeholders, we focused on the needs of taxonomists, ecologists and historians, who are currently the primary users of the Meise herbarium data portal. The three categories of user have similar needs, all wanted as much specimen data as possible, and for those data, to be interlinked with other digital resources within and outside the Garden. Many users wanted an interactive system that they could comment on, or correct online, particularly if such corrections and annotations could be used to rank the reliability of data. Many requirements depend on the quality of the digitized data associated with each specimen. The essential data fields are the taxonomic name; geographic location; country; collection date; collector name and collection number. Also all researchers valued linkage between biodiversity literature and specimens. Nevertheless, to verify digitized data the researchers still want access to high quality images, even if fully transcribed label information is provided. The only major point of disagreement is the level of access users should have and what they

  6. Scientific user requirements for a herbarium data portal

    Science.gov (United States)

    Vissers, Jorick; den Bosch, Frederik Van; Bogaerts, Ann; Cocquyt, Christine; Degreef, Jérôme; Diagre, Denis; de Haan, Myriam; Smedt, Sofie De; Henry Engledow; Ertz, Damien; Fabri, Régine; Godefroid, Sandrine; Nicole Hanquart; Mergen, Patricia; Ronse, Anne; Sosef, Marc; Stévart, Tariq; Stoffelen, Piet; Vanderhoeven, Sonia; Groom, Quentin

    2017-01-01

    Abstract The digitization of herbaria and their online access will greatly facilitate access to plant collections around the world. This will improve the efficiency of taxonomy and help reduce inequalities between scientists. The Botanic Garden Meise, Belgium, is currently digitizing 1.2 million specimens including label data. In this paper we describe the user requirements analysis conducted for a new herbarium web portal. The aim was to identify the required functionality, but also to assist in the prioritization of software development and data acquisition. The Garden conducted the analysis in cooperation with Clockwork, the digital engagement agency of Ordina. Using a series of interactive interviews, potential users were consulted from universities, research institutions, science-policy initiatives and the Botanic Garden Meise. Although digital herbarium data have many potential stakeholders, we focused on the needs of taxonomists, ecologists and historians, who are currently the primary users of the Meise herbarium data portal. The three categories of user have similar needs, all wanted as much specimen data as possible, and for those data, to be interlinked with other digital resources within and outside the Garden. Many users wanted an interactive system that they could comment on, or correct online, particularly if such corrections and annotations could be used to rank the reliability of data. Many requirements depend on the quality of the digitized data associated with each specimen. The essential data fields are the taxonomic name; geographic location; country; collection date; collector name and collection number. Also all researchers valued linkage between biodiversity literature and specimens. Nevertheless, to verify digitized data the researchers still want access to high quality images, even if fully transcribed label information is provided. The only major point of disagreement is the level of access users should have and what they should be

  7. [Ambrosia, Franseria, Xanthium from the Bonaparte Herbarium].

    Science.gov (United States)

    Déchamp, C; Méon, H

    2003-05-01

    Recently, French Association for Ragweed Study (AFEDA) founders published, in French, a book "Ambrosia, ragweed, biological pollutants". This association was founded in 1982. The authors referred to Bonaparte Herbarium set up in the Université Claude-Bernard Lyon 1. This herbarium is ranking second in France and seventh in the world. There were three aims for this work: to set up, for this herbarium, a complete list of different species of Ambrosia, Franseria and their pollen grains and to study with them Xanthium whose pollen grains look like Ambrosia, to establish a chronological order for Ambrosia that were collected in Europe and in some countries of the New World, to compare some pollen grains of Ambrosia and Xanthium (scanning electronic microscope). Good state plants in spite of about a century of conservation could be selected. They were photographied and some pollens so. The consultation of this herbarium brought a better morphological knowledge of different species of Ambrosia, Franseria and Xanthium, (plants and pollen grains). The authors were able to broadcast this knowledge to scientists and interested public through their book.

  8. Herbarium Areqvipense (HUSA: computerization and representativeness of its collection

    Directory of Open Access Journals (Sweden)

    Italo F. Treviño

    2012-11-01

    Full Text Available Scientific collections and herbaria are essential sources of information and education for researchers and practitioners in biological sciences. The Herbarium Areqvipense (HUSA, registered at Index Herbariorum since 2004, holds one of the most important collections in Peru. In this paper we provide information about the collection, and its representativeness for the Peruvian flora. HUSA has more than 11000 specimens recorded to date, with more than 2300 determined species, consisting mostly of Magnoliophyta and Pteridophyta (ca. 98%, and a smaller proportion of Basidiomycetes, Ascomycetes (fungi and lichens and Bryophyta (mosses. The collection includes specimens from 23 departments of Peru, where the samples belonging to Arequipa have the largest number of individuals collected (3375 accounting for 31% of the collection. Asteraceae and Solanaceae are the most collected with 1571 and 964 specimens, respectively. The majority of geo-referenced specimens came from the tropical wet forest with 15%, followed by the tropical pre-montane wet forest with 8%. We also provide a list of the nomenclatural types and a brief summary of the history and development of HUSA since its creation.

  9. Plants of Mongolia – A Virtual Approach: E-taxonomy, Virtual Herbarium and Digital Key

    Directory of Open Access Journals (Sweden)

    Ulrike Najmi

    2014-12-01

    Full Text Available This work is based on the long-term research experience between Mongolia and Germany, which resulted in extensive plant collections in both countries. One goal is to provide information access via the Internet to the herbarium specimens available in German plant collections. Up to now, 16,403 records (a fi nding of a species documented by images and/or vouchers for 1,533 out of 2879 Mongolian vascular plant species are included in the database. For half of the species described for Mongolia scans of herbarium specimens are available. The plant database is searchable for family, scientifi c name, habitat, growth form as well as distribution, and other parameters such as the red list status or the endemic status.

  10. Insights from natural history collections: analysing the New Zealand macroalgal flora using herbarium data.

    Science.gov (United States)

    Nelson, Wendy A; Dalen, Jennifer; Neill, Kate F

    2013-01-01

    Herbaria and natural history collections (NHC) are critical to the practice of taxonomy and have potential to serve as sources of data for biodiversity and conservation. They are the repositories of vital reference specimens, enabling species to be studied and their distribution in space and time to be documented and analysed, as well as enabling the development of hypotheses about species relationships. The herbarium of the Museum of New Zealand Te Papa Tongarewa (WELT) contains scientifically and historically significant marine macroalgal collections, including type specimens, primarily of New Zealand species, as well as valuable exsiccatae from New Zealand and Australia. The herbarium was initiated in 1865 with the establishment of the Colonial Museum and is the only herbarium in New Zealand where there has been consistent expert taxonomic attention to the macroalgae over the past 50 years. We examined 19,422 records of marine macroalgae from around New Zealand collected over the past 164 years housed in WELT, assessing the records in terms of their spatial and temporal coverage as well as their uniqueness and abundance. The data provided an opportunity to review the state of knowledge of the New Zealand macroalgal flora reflected in the collections at WELT, to examine how knowledge of the macroalgal flora has been built over time in terms of the number of collections and the number of species recognised, and identify where there are gaps in the current collections as far as numbers of specimens per taxon, as well as with respect to geographical and seasonal coverage.

  11. Herbarium of the University of Malaga (Spain: Vascular Plants Collection

    Directory of Open Access Journals (Sweden)

    Jose García Sánchez

    2013-09-01

    Full Text Available The herbarium of University of Málaga (MGC Herbarium is formed by four biological collections. The vascular plants collection (MGC-Cormof is the main collection of the herbarium. MGC-Cormof dataset aims to digitize and publish data associated with over 76.000 specimens deposited in the collection, of which 97.2% of the specimens are identified at species level. Since 2011, the University of Malaga’s Central Research Service (SCAI has been responsible for maintaining the herbariums and the dataset. The collection is growing continuously, with an annual intake of about 1.500 specimens. Nearly 96% of the collection is digitized, by Herbar v3.7.1 software (F. Pando et al. 1996–2011, making over 73.000 specimens accessible through the GBIF network (http://data.gbif.org/datasets/resource/8105/. At present, 247 families and 8.110 taxa, distributed in angiosperms (93.97%, ferns and fern allies (4.89% and gymnosperms (1.14%, constitute the MGC-Cormof collection. The families and genera best represented in the collection are Compositae, Leguminosae, Gramineae, Labiatae, Caryophyllaceae, Teucrium, Silene, Asplenium, Linaria and Quercus. Most of the specimens are from the Western Mediterranean Region, fundamentally Southern Spain (Andalusia: 82% of specimens and Northern Morocco (2.17%. Approximately, 63% of the specimens are georeferenced. The identification of the specimens in the collection has been carried out by the plant biology department at the University of Malaga and plus 40% of the specimens has been reviewed by experts. The MGC-Cormof dataset has been revised by DarwinTest v3.2 tool (Ortega-Maqueda and Pando 2008 before being published in GBIF. The data included in this database are important for conservation works, taxonomy, flora, cartography, phenology, palynology, among others.El Herbario de la Universidad de Málaga (Herbario MGC está constituido por cuatro colecciones biológicas. La colección de plantas vasculares (MGC Cormof es la

  12. The first herbarium botanist in Nairobi | Newton | Journal of East ...

    African Journals Online (AJOL)

    Evelyn R. Napier (1902–1952) established the herbarium of the Coryndon Museum, where she was employed as botanist from 1930 to 1934. She continued contributing to the herbarium collections after her marriage to D.W. Molony in 1935. Several plants that she collected in Kenya were named in her honour as new ...

  13. Prospective evaluation of peritoneal fluid contamination following transabdominal vs. transanal specimen extraction in laparoscopic left-sided colorectal resections.

    Science.gov (United States)

    Costantino, Federico A; Diana, Michele; Wall, James; Leroy, Joel; Mutter, Didier; Marescaux, Jacques

    2012-06-01

    Natural orifice specimen extraction (NOSE) in colorectal surgery prevents the need for an enlarged port site or minilaparotomy to extract the surgical specimen. The downside of this technique may be an increased risk of bacterial contamination of the peritoneal cavity from the external milieu. The aim of this study was to prospectively analyze the peritoneal bacterial contamination in NOSE and non-NOSE laparoscopic colorectal procedures. Consecutive patients operated for sigmoid diverticulitis with laparoscopic approach and transanal extraction of the specimen from January to December 2010 at our university hospital were enrolled. Patients who underwent a laparoscopic sigmoidectomy in the same study period with conventional specimen extraction were used as reference. Peritoneal fluid samples were collected under sterile conditions at the end of the procedure and sent for gram stain as well as anaerobic, aerobic, and fungal cultures. Twenty-nine patients underwent laparoscopic sigmoidectomy for diverticulitis with transanal NOSE, while 9 patients underwent laparoscopic sigmoidectomy with conventional specimen extraction during the same period. The two groups were successfully matched 1:2 (17 NOSE and 9 non-NOSE) according age, sex, ASA, and Charlson comorbidity score. The contamination rate of peritoneal fluid was 100% vs. 88.9% in NOSE and non-NOSE procedures, respectively (P = 0.23). Overall and major complications rates were 27.6% vs. 11.10% (P = 0.41) and 5.08% vs. 11.1% (P = 1) in NOSE vs. non-NOSE procedures, respectively. In the NOSE group there was a statistically significant lower consumption of oral paracetamol (P = 0.007) and of oral tramadol (P = 0.02). Although a higher peritoneal contamination was found in the NOSE procedures, there were no significant differences in clinical outcomes relative to standard approach. Avoiding a minilaparotomy to extract the specimen resulted in a significantly lower postoperative analgesic requirement in the NOSE group.

  14. DNA extraction from frozen field-collected and dehydrated herbarium fungal basidiomata: performance of SDS and CTAB-based methods

    Directory of Open Access Journals (Sweden)

    Rosa Trinidad Guerrero

    2005-11-01

    Full Text Available Extracted DNA from basidiomata of frozen field-collected and herbarium specimens collected in different periods and maintained in a variety of ways was evaluated according to general condition, color, spectral absorbance ratio, final concentration and PCR amplification, using two distinct and most common extraction methods: SDS (Sodium Doecyl Sulphate and CTAB (Cetyl Trimetyl Ammonium Bromide. Most of the frozen fieldcollected basidiomata presented a very good to good DNA condition and no degradation. All the herbarium specimens exhibited poor DNA condition with low molecular weight bands. Practically all the DNA solutions of the samples were colored, and spectral absorbance ratios were considerably variable, with lower values observed in darker ones. All the samples were successfully PCR-amplified. DNA extraction of Herbarium specimens and also specimens with high polysaccharide content was only achievable using the CTAB method. For an all-purpose DNA extraction from field-collected and dehydrated coriaceous and woody basidiomata bearing a high content of secondary metabolites and/or polysaccharides, the CTAB-based method is definitely best the choice of method.

  15. Insights from natural history collections: analysing the New Zealand macroalgal flora using herbarium data

    Directory of Open Access Journals (Sweden)

    Wendy Nelson

    2013-11-01

    Full Text Available Herbaria and natural history collections (NHC are critical to the practice of taxonomy and have potential to serve as sources of data for biodiversity and conservation. They are the repositories of vital reference specimens, enabling species to be studied and their distribution in space and time to be documented and analysed, as well as enabling the development of hypotheses about species relationships. The herbarium of the Museum of New Zealand Te Papa Tongarewa (WELT contains scientifically and historically significant marine macroalgal collections, including type specimens, primarily of New Zealand species, as well as valuable exsiccatae from New Zealand and Australia. The herbarium was initiated in 1865 with the establishment of the Colonial Museum and is the only herbarium in New Zealand where there has been consistent expert taxonomic attention to the macroalgae over the past 50 years. We examined 19,422 records of marine macroalgae from around New Zealand collected over the past 164 years housed in WELT, assessing the records in terms of their spatial and temporal coverage as well as their uniqueness and abundance. The data provided an opportunity to review the state of knowledge of the New Zealand macroalgal flora reflected in the collections at WELT, to examine how knowledge of the macroalgal flora has been built over time in terms of the number of collections and the number of species recognised, and identify where there are gaps in the current collections as far as numbers of specimens per taxon, as well as with respect to geographical and seasonal coverage.

  16. The French Muséum national d'histoire naturelle vascular plant herbarium collection dataset.

    Science.gov (United States)

    Le Bras, Gwenaël; Pignal, Marc; Jeanson, Marc L; Muller, Serge; Aupic, Cécile; Carré, Benoît; Flament, Grégoire; Gaudeul, Myriam; Gonçalves, Claudia; Invernón, Vanessa R; Jabbour, Florian; Lerat, Elodie; Lowry, Porter P; Offroy, Bérangère; Pimparé, Eva Pérez; Poncy, Odile; Rouhan, Germinal; Haevermans, Thomas

    2017-02-14

    We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d'histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.

  17. The US Virtual Herbarium: working with individual herbaria to build a national resource.

    Science.gov (United States)

    Barkworth, Mary E; Murrell, Zack E

    2012-01-01

    The goal of the US Virtual Herbarium (USVH) project is to digitize (database, image, georeference) all specimens in all US herbaria, enabling them to be made available through a single portal. Herbaria house specimens of plants, fungi, and algae, so USVH will offer a rich portrait of biodiversity in the US and in the other countries represented in US herbaria. Equally importantly, working towards this goal will engage people with herbaria and the organisms they house, expanding their appreciation of both the power of biodiversity informatics and the demands that it places on data providers while developing improved communication among those working in and with herbaria. The project is not funded but has strong support among those working in herbaria. It works through regional herbarium networks, some of which existed prior to the USVH project, while others are still in gestation. It differs from most digitization projects in its emphasis on helping those involved with herbaria become part of a national enterprise, an aspect that is seen as critical to creating the resources needed to develop and sustain the project. In this paper, we present some of the lessons we have learned and the difficulties we have encountered during the first few years of the project.

  18. The US Virtual Herbarium: working with individual herbaria to build a national resource

    Science.gov (United States)

    Barkworth, Mary E.; Murrell, Zack E.

    2012-01-01

    Abstract The goal of the US Virtual Herbarium (USVH) project is to digitize (database, image, georeference) all specimens in all US herbaria, enabling them to be made available through a single portal. Herbaria house specimens of plants, fungi, and algae, so USVH will offer a rich portrait of biodiversity in the US and in the other countries represented in US herbaria. Equally importantly, working towards this goal will engage people with herbaria and the organisms they house, expanding their appreciation of both the power of biodiversity informatics and the demands that it places on data providers while developing improved communication among those working in and with herbaria. The project is not funded but has strong support among those working in herbaria. It works through regional herbarium networks, some of which existed prior to the USVH project, while others are still in gestation. It differs from most digitization projects in its emphasis on helping those involved with herbaria become part of a national enterprise, an aspect that is seen as critical to creating the resources needed to develop and sustain the project. In this paper, we present some of the lessons we have learned and the difficulties we have encountered during the first few years of the project. PMID:22859878

  19. Comprehensive analysis of vitreous specimens for uveitis classification: a prospective multicentre observational study.

    Science.gov (United States)

    Maruyama, Kazuichi; Inaba, Tohru; Sugita, Sunao; Ichinohasama, Ryo; Nagata, Kenji; Kinoshita, Shigeru; Mochizuki, Manabu; Nakazawa, Toru

    2017-11-16

    To determine the clinical relevance of vitreous biomarkers in patients with uveitis. Multicentre, prospective, observational study. Uveitis outpatient clinics of two academic medical centres in Japan. This study included 234 eyes of 191 patients with various uveitis aetiologies: definitive sarcoidosis (61 eyes of 46 patients), suspected sarcoidosis (60 eyes of 45 patients), intraocular tumour (34 eyes of 27 patients), viral infection (20 eyes of 18 patients), non-sarcoidosis (16 eyes of 16 patients) and unknown aetiology (43 eyes of 39 patients). Vitreous samples (taken by pars planta vitrectomy) were analysed with flow cytometry, cytology and multiplex PCR analysis. The primary outcome measures were the diagnostic values of various biomarkers (T cells, B cells and pathogen DNA) in vitreous samples. The secondary outcome was visual acuity after vitrectomy. Sarcoidosis showed higher CD4/CD8 or CD4+ measurements than other aetiologies (pvitreous biomarker profiles, especially of infiltrating lymphocytes. Analyses of CD4/CD8 ratio, T-lymphocyte and B-lymphocyte subset, and pathogen DNA in vitreous samples have good safety profiles and high diagnostic value for uveitis classification. UMIN000004980; Pre-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  20. The Myxomycetes in the Rijks-Herbarium at Leyden

    NARCIS (Netherlands)

    Broeksmit, T.

    1925-01-01

    The kindness of Dr. GOETHART has enabled me to investigate all the Myxomycetes (Myxogasteres, Mycetozoa) which are kept in the Rijks-Herbarium at Leyden. Among the older collections I found those of PERSOON, V. HALL, HANKARL, BUSE, JUNGHUHN, WAGNER. Only a little part of these collections remains,

  1. The University of San Carlos Herbarium, Cebu City, The Philippines

    NARCIS (Netherlands)

    Seidenschwarz, F.

    1990-01-01

    The University of San Carlos, Cebu City, (‘USC’) holds a botanical collection which is the fourth largest in size within the Philippines. The three leading herbaria of the Philippines are situated in or close to Manila. The 36 year old USC Herbarium is the only major collection in the Philippines

  2. Herbarium of the university of malaga (Spain): vascular plants collection.

    Science.gov (United States)

    García-Sánchez, José; Cabezudo, Baltasar

    2013-01-01

    The herbarium of University of Málaga (MGC Herbarium) is formed by four biological collections. The vascular plants collection (MGC-Cormof) is the main collection of the herbarium. MGC-Cormof dataset aims to digitize and publish data associated with over 76.000 specimens deposited in the collection, of which 97.2% of the specimens are identified at species level. Since 2011, the University of Malaga's Central Research Service (SCAI) has been responsible for maintaining the herbariums and the dataset. The collection is growing continuously, with an annual intake of about 1.500 specimens. Nearly 96% of the collection is digitized, by Herbar v3.7.1 software (F. Pando et al. 1996-2011), making over 73.000 specimens accessible through the GBIF network (http://data.gbif.org/datasets/resource/8105/). At present, 247 families and 8.110 taxa, distributed in angiosperms (93.97%), ferns and fern allies (4.89%) and gymnosperms (1.14%), constitute the MGC-Cormof collection. The families and genera best represented in the collection are Compositae, Leguminosae, Gramineae, Labiatae, Caryophyllaceae, Teucrium, Silene, Asplenium, Linaria and Quercus. Most of the specimens are from the Western Mediterranean Region, fundamentally Southern Spain (Andalusia: 82% of specimens) and Northern Morocco (2.17%). Approximately, 63% of the specimens are georeferenced. The identification of the specimens in the collection has been carried out by the plant biology department at the University of Malaga and plus 40% of the specimens has been reviewed by experts. The MGC-Cormof dataset has been revised by DarwinTest v3.2 tool (Ortega-Maqueda and Pando 2008) before being published in GBIF. The data included in this database are important for conservation works, taxonomy, flora, cartography, phenology, palynology, among others. El Herbario de la Universidad de Málaga (Herbario MGC) está constituido por cuatro colecciones biológicas. La colección de plantas vasculares (MGC Cormof) es la colecci

  3. Compilation of floristic and herbarium specimen datain Iran: proposal to data structure

    Directory of Open Access Journals (Sweden)

    Majid Sharifi-Tehrani

    2013-09-01

    Full Text Available Floristic databases constitute the second level of plant information systems, after taxonomic-nomenclatural databases. This paper provided the details of data structure and available data resources to develop a floristic database, along with some explanations on taxonomic and floristic databases. Also, this paper proposed the availability and possibility of a shortcut to constructing a national floristic database through uniforming and compilation of dispersed floristic data contained in various botanical centers of Iran. Therefore, Iran could be the second country in SW Asia region to have a national floristic database, and the resulted services can be presented to national scientific community.

  4. The Institute of Biological Sciences Herbarium (PBDH), University of the Philippines Los Baños

    NARCIS (Netherlands)

    Buot, I.E.; Hernaez, B.F.; Tandang, D.N.

    2002-01-01

    With the founding of the Museum of Natural History (MNH) at the University of the Philippines Los Baños (UPLB) the former Department of Botany Herbarium (CAHUP) has been transferred to this. This required the establishment of another herbarium to cater to the increasing need by courses in

  5. A new herbarium-based method for reconstructing the phenology of plant species across large areas

    National Research Council Canada - National Science Library

    Lavoie, Claude; Lachance, Daniel

    2006-01-01

    ... associated with sampling locations. In this study, we propose a new herbarium-based method for reconstructing the flowering dates of plant species that have been collected across large areas. Coltsfoot...

  6. František Nábělek's Iter Turcico-Persicum 1909-1910 - database and digitized herbarium collection.

    Science.gov (United States)

    Kempa, Matúš; Edmondson, John; Lack, Hans Walter; Smatanová, Janka; Marhold, Karol

    2016-01-01

    The Czech botanist František Nábělek (1884-1965) explored the Middle East in 1909-1910, visiting what are now Israel, Palestine, Jordan, Syria, Lebanon, Iraq, Bahrain, Iran and Turkey. He described four new genera, 78 species, 69 varieties and 38 forms of vascular plants, most of these in his work Iter Turcico-Persicum (1923-1929). The main herbarium collection of Iter Turcico-Persicum comprises 4163 collection numbers (some with duplicates), altogether 6465 specimens. It is currently deposited in the herbarium SAV. In addition, some fragments and duplicates are found in B, E, W and WU. The whole collection at SAV was recently digitized and both images and metadata are available via web portal www.nabelek.sav.sk, and through JSTOR Global Plants and the Biological Collection Access Service. Most localities were georeferenced and the web portal provides a mapping facility. Annotation of specimens is available via the AnnoSys facility. For each specimen a CETAF stable identifier is provided enabling the correct reference to the image and metadata.

  7. František Nábělek’s Iter Turcico-Persicum 1909–1910 – database and digitized herbarium collection

    Science.gov (United States)

    Kempa, Matúš; Edmondson, John; Lack, Hans Walter; Smatanová, Janka; Marhold, Karol

    2016-01-01

    Abstract The Czech botanist František Nábělek (1884−1965) explored the Middle East in 1909-1910, visiting what are now Israel, Palestine, Jordan, Syria, Lebanon, Iraq, Bahrain, Iran and Turkey. He described four new genera, 78 species, 69 varieties and 38 forms of vascular plants, most of these in his work Iter Turcico-Persicum (1923−1929). The main herbarium collection of Iter Turcico-Persicum comprises 4163 collection numbers (some with duplicates), altogether 6465 specimens. It is currently deposited in the herbarium SAV. In addition, some fragments and duplicates are found in B, E, W and WU. The whole collection at SAV was recently digitized and both images and metadata are available via web portal www.nabelek.sav.sk, and through JSTOR Global Plants and the Biological Collection Access Service. Most localities were georeferenced and the web portal provides a mapping facility. Annotation of specimens is available via the AnnoSys facility. For each specimen a CETAF stable identifier is provided enabling the correct reference to the image and metadata. PMID:28127245

  8. František Nábělek’s Iter Turcico-Persicum 1909–1910 – database and digitized herbarium collection

    Directory of Open Access Journals (Sweden)

    Matúš Kempa

    2016-12-01

    Full Text Available The Czech botanist František Nábělek (1884−1965 explored the Middle East in 1909-1910, visiting what are now Israel, Palestine, Jordan, Syria, Lebanon, Iraq, Bahrain, Iran and Turkey. He described four new genera, 78 species, 69 varieties and 38 forms of vascular plants, most of these in his work Iter Turcico-Persicum (1923−1929. The main herbarium collection of Iter Turcico-Persicum comprises 4163 collection numbers (some with duplicates, altogether 6465 specimens. It is currently deposited in the herbarium SAV. In addition, some fragments and duplicates are found in B, E, W and WU. The whole collection at SAV was recently digitized and both images and metadata are available via web portal www.nabelek.sav.sk, and through JSTOR Global Plants and the Biological Collection Access Service. Most localities were georeferenced and the web portal provides a mapping facility. Annotation of specimens is available via the AnnoSys facility. For each specimen a CETAF stable identifier is provided enabling the correct reference to the image and metadata.

  9. Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study

    Directory of Open Access Journals (Sweden)

    Samuel Catherine M

    2011-11-01

    Full Text Available Abstract Background Pneumocystis pneumonia (PCP is a major cause of hospitalization and mortality in HIV-infected African children. Microbiologic diagnosis relies predominantly on silver or immunofluorescent staining of a lower respiratory tract (LRT specimens which are difficult to obtain in children. Diagnosis on upper respiratory tract (URT specimens using PCR has been reported useful in adults, but data in children are limited. The main objectives of the study was (1 to compare the diagnostic yield of PCR with immunofluorescence (IF and (2 to investigate the usefulness of upper compared to lower respiratory tract samples for diagnosing PCP in children. Methods Children hospitalised at an academic hospital with suspected PCP were prospectively enrolled. An upper respiratory sample (nasopharyngeal aspirate, NPA and a lower respiratory sample (induced sputum, IS or bronchoalveolar lavage, BAL were submitted for real-time PCR and direct IF for the detection of Pneumocystis jirovecii. A control group of children with viral lower respiratory tract infections were investigated with PCR for PCP. Results 202 children (median age 3.3 [inter-quartile range, IQR 2.2 - 4.6] months were enrolled. The overall detection rate by PCR was higher than by IF [180/349 (52% vs. 26/349 (7% respectively; p Conclusion Real-time PCR is more sensitive than IF for the detection of P. jirovecii in children with PCP. NPA samples may be used for diagnostic purposes when PCR is utilised. Wider implementation of PCR on NPA samples is warranted for diagnosing PCP in children.

  10. Collecting succulent plants for deposition in a herbarium

    CSIR Research Space (South Africa)

    Walters, Michele

    2011-06-01

    Full Text Available A preserved plant specimen is a dried and mounted or pickled voucher that is the botanical world's equivalent to the zoologist's stuffed animals, skins or insect collections that are kept in natural history museums. Plant specimens are housed...

  11. Herbarium collection-based phylogenetics of the ragweeds (Ambrosia, Asteraceae).

    Science.gov (United States)

    Martin, Michael D; Quiroz-Claros, Elva; Brush, Grace S; Zimmer, Elizabeth A

    2017-12-21

    Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea. To resolve undetermined intra-generic relationships within Ambrosia, we used DNA extracted from tissues obtained from seed banks and herbarium collections to generate multi-locus genetic data representing nearly all putative species, including four from South America. We performed Bayesian and Maximum-Likelihood phylogenetic analyses of six chloroplast-genome and two nuclear-genome markers, enabling us to infer monophyly for the genus, resolve major infra-generic species clusters, as well as to resolve open questions about the evolutionary relationships of several Ambrosia species and former members of Franseria. We also provide molecular data supporting the hypothesis that A. sandersonii formed through the hybridization of A. eriocentra and A. salsola. The topology of our chloroplast DNA phylogeny is almost entirely congruent with the most recent molecular work based on chloroplast restriction site variation of a much more limited sampling of 14 North American species of Ambrosia, although our improved sampling of global Ambrosia diversity enables us to draw additional conclusions. As our study is the first direct DNA sequence-based phylogenetic analyses of Ambrosia, we analyze the data in relation to previous taxonomic studies and discuss several instances of chloroplast/nuclear incongruence that leave the precise geographic center of origin of Ambrosia in question. Copyright © 2017. Published by Elsevier Inc.

  12. Herbarium-based studies on taxonomy, biogeography and ecology of Psilochilus (Orchidaceae

    Directory of Open Access Journals (Sweden)

    Marta Kolanowska

    2016-11-01

    Full Text Available Background Psilochilus is a poorly studied orchid genus distributed from southern Mexico to south-eastern Brazil. A taxonomic revision of this Neotropical endemic based on morphological data is presented. Material and Methods Over 170 dried herbarium specimens and flowers preserved in liquid of Psilochilus were analyzed. Morphological variation among examined taxa was described based on multivariate analysis. To evaluate the similarity between niches occupied by various Psilochilus species ecological niche modeling (ENM was applied. Species richness and the distribution patterns of Psilochilus representatives were analyzed based on squares of 5° latitude and longitude while similarities among floras between biogeographical units were measured using the Bray-Curtis index for presence/absence data. Results and Discussion A new species of the P. physurifolius-complex is described based on Central American material. Psilochilus crenatifolius is reduced to the rank of variety as P. macrophyllus var. crenatifolius. A key to 18 accepted Psilochilus species is provided. The illustrations of perianth segments of all recognized taxa are presented. The climatic niches preferred by the particular Psilochilus representatives are well separated based on ecological niche modeling analysis. Their distribution is limited mainly by the isothermality and temperature seasonality. The highest Psilochilus species richness is observed in the North Andean, Panamanian, Brazilian Planalto and Central American biogeographical provinces. A high level of endemism is observed in all those regions as well as Yungas biogeographical province. Most Psilochilus species occur in areas above 800 m of elevation. The populations were most often reported from the tropical rain forest and tropical moist deciduous forest.

  13. Virtual Specimens

    Science.gov (United States)

    de Paor, D. G.

    2009-12-01

    Virtual Field Trips have been around almost as long as the Worldwide Web itself yet virtual explorers do not generally return to their desktops with folders full of virtual hand specimens. Collection of real specimens on fields trips for later analysis in the lab (or at least in the pub) has been an important part of classical field geoscience education and research for generations but concern for the landscape and for preservation of key outcrops from wanton destruction has lead to many restrictions. One of the author’s favorite outcrops was recently vandalized presumably by a geologist who felt the need to bash some of the world’s most spectacular buckle folds with a rock sledge. It is not surprising, therefore, that geologists sometimes leave fragile localities out of field trip itineraries. Once analyzed, most specimens repose in drawers or bins, never to be seen again. Some end up in teaching collections but recent pedagogical research shows that undergraduate students have difficulty relating specimens both to their collection location and ultimate provenance in the lithosphere. Virtual specimens can be created using 3D modeling software and imported into virtual globes such as Google Earth (GE) where, they may be linked to virtual field trip stops or restored to their source localities on the paleo-globe. Sensitive localities may be protected by placemark approximation. The GE application program interface (API) has a distinct advantage over the stand-alone GE application when it comes to viewing and manipulating virtual specimens. When instances of the virtual globe are embedded in web pages using the GE plug-in, Collada models of specimens can be manipulated with javascript controls residing in the enclosing HTML, permitting specimens to be magnified, rotated in 3D, and sliced. Associated analytical data may be linked into javascript and localities for comparison at various points on the globe referenced by ‘fetching’ KML. Virtual specimens open up

  14. Specimen Preparation

    Science.gov (United States)

    Williams, David B.; Carter, C. Barry

    Specimen preparation is a very broad subject; there are books devoted to this topic alone. The intention here is to summarize the techniques, suggest routes that you might follow, and above all to emphasize that there are many ways to produce a TEM specimen; the one you choose will depend on the information you need, time constraints, availability of equipment, your skill, and the material. So we’ll concentrate on the ‘principles of cooking,’ but won’t try to list all the possible ‘recipes.’ One important point to bear in mind is that your technique must not affect what you see or measure, or if it does, then you must know how. Specimen preparation artifacts may be interesting but they are not usually what you want to study. Incidentally, we’ll make ‘specimens’ from the ‘sample’ we’re investigating so we’ll look at ‘TEM specimens,’ but sometimes we, and everyone else, will interchange the two words.

  15. The Cebu State College of Science and Technology, College of Agriculture Herbarium, Lahug, Cebu City, The Philippines

    NARCIS (Netherlands)

    Bout, I.E.

    1992-01-01

    Recognizing the vital role that a herbarium plays in instruction, research, and public service, the Cebu State College of Science and Technology College of Agriculture (CSCSTCA) in Lahug, Cebu City, the Philippines, founded a herbarium in June 1987. It is a very humble scientific project of the

  16. Typification of taxa of subfamily Silenoideae (Caryophyllaceae Juss. from Siberia and Russian Far East based on materials kept in the Herbarium of the Komarov Botanical Institute (LE

    Directory of Open Access Journals (Sweden)

    G. A. Lazkov

    2016-06-01

    Full Text Available Data on type material of previously not typified taxa of the subfamily Silenoideae (Caryophyllaceae Juss., kept in the Herbarium of the Komarov Botanical Institute (LE are summarized in the paper. All relevant taxa including eight species (or subsequently accepted as species: Gastrolychnis violascens Tolm., Gypsophila stricta Bunge, Heterochroa petraea Bunge, Lychnis ajanensis var. villosula Trautv. [L. villosula (Trautv. Gorschk.], L. fulgens var. wilfordi Regel [L. wilfordi (Regel Maxim.], L. tristis Bunge, Melandrium olgae Maxim., Silene melandriiformis Maxim., five varieties (Melandrium affine var. Intermedium Tolm., Silene repens var. pratensis Kom., S. repens var. alpina Kom., S. repens var. angustifolia Turcz., S. repens var. latifolia Turcz., and one form (Silene repens f. densa Kom. are lectotypified.Key words: Caryophyllaceae, Silenoideae, type specimens, typification, Komarov Botanical Institute (LE, Siberia, Far East. 

  17. Diagnostic approaches for paediatric tuberculosis by use of different specimen types, culture methods, and PCR: a prospective case-control study.

    Science.gov (United States)

    Oberhelman, Richard A; Soto-Castellares, Giselle; Gilman, Robert H; Caviedes, Luz; Castillo, Maria E; Kolevic, Lenka; Del Pino, Trinidad; Saito, Mayuko; Salazar-Lindo, Eduardo; Negron, Eduardo; Montenegro, Sonia; Laguna-Torres, V Alberto; Moore, David A J; Evans, Carlton A

    2010-09-01

    The diagnosis of pulmonary tuberculosis presents challenges in children because symptoms are non-specific, specimens are difficult to obtain, and cultures and smears of Mycobacterium tuberculosis are often negative. We assessed new diagnostic approaches for tuberculosis in children in a resource-poor country. Children with symptoms suggestive of pulmonary tuberculosis (cases) were enrolled from August, 2002, to January, 2007, at two hospitals in Lima, Peru. Age-matched and sex-matched healthy controls were enrolled from a low-income shanty town community in south Lima. Cases were grouped into moderate-risk and high-risk categories by Stegen-Toledo score. Two specimens of each type (gastric-aspirate, nasopharyngeal-aspirate, and stool specimens) taken from each case were examined for M tuberculosis by auramine smear microscopy, broth culture by microscopic-observation drug-susceptibility (MODS) technique, standard culture on Lowenstein-Jensen medium, and heminested IS6110 PCR. Specimens from controls consisted of one nasopharyngeal-aspirate and two stool samples, examined with the same techniques. This study is registered with ClinicalTrials.gov, number NCT00054769. 218 cases and 238 controls were enrolled. 22 (10%) cases had at least one positive M tuberculosis culture (from gastric aspirate in 22 cases, nasopharyngeal aspirate in 12 cases, and stool in four cases). Laboratory confirmation of tuberculosis was more frequent in cases at high risk for tuberculosis (21 [14.1%] of 149 cases with complete specimen collection were culture positive) than in cases at moderate risk for tuberculosis (one [1.6%] of 61). MODS was more sensitive than Lowenstein-Jensen culture, diagnosing 20 (90.9%) of 22 patients compared with 13 (59.1%) of 22 patients (p=0.015), and M tuberculosis isolation by MODS was faster than by Lowenstein-Jensen culture (mean 10 days, IQR 8-11, vs 25 days, 20-30; p=0.0001). All 22 culture-confirmed cases had at least one culture-positive gastric

  18. Clinical Evaluation of the Cepheid Xpert® TV Assay for detection of Trichomonas vaginalis with Prospectively Collected Female and Male Specimens.

    Science.gov (United States)

    Schwebke, Jane R; Gaydos, C A; Davis, T; Marrazzo, J; Furgerson, D; Taylor, S N; Smith, B; Bachmann, L H; Ackerman, R; Spurrell, T; Ferris, D; Burnham, C A; Reno, H; Lebed, J; Eisenberg, D; Kerndt, P; Philip, S; Jordan, J; Quigley, N

    2017-11-22

    Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and acquisition/transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA-cleared in the United States for detection of Trichomonas vaginalis (TV) in specimens from both women and men. This current study reports the results of a multicenter study recently conducted using the Xpert TV Assay to test specimens from both men and women. On-demand results were available in as little as 40 minutes for positive specimens. A total of 1867 women and 4791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV Assay was compared to a patient infected status (PIS) derived from results of InPouch TV broth culture and Aptima NAAT for TV. Diagnostic sensitivity and specificity of the Xpert TV Assay for the combined female specimens (urines, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 - 100% and 99.4 - 99.9%, respectively. For male urines, diagnostic sensitivity and specificity was 97.2% and 99.9% respectively, compared to a PIS derived from results of broth culture for TV and bi-directional gene sequencing of the amplicons. Excellent performance characteristics were seen using both female and male specimens. The ease of using the Xpert TV Assay should result in opportunities for enhanced screening for TV in both men and women and hopefully improved control of this infection. Copyright © 2017 Schwebke et al.

  19. Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal

    Directory of Open Access Journals (Sweden)

    Nico Franz

    2016-09-01

    the Euler/X logic reasoning toolkit to provide comprehensive genus- to variety-level concept alignments for at least 10 major flora treatments with highest relevance to SERNEC. The visualizations and estimated > 1 billion inferred concept-to-concept relations will effectively drive specimen data integration in the transformed portal. (3 We will expand Symbiota's taxonomy and occurrence schemas and related user interfaces to support the new concept data, including novel batch and map-based specimen determination modules, with easy output options in Darwin Core Archive format. (4 Through combinations of the new technology, enlisted taxonomic expertise, and SERNEC's large image resources, we will upgrade minimally 80% of all SERNEC specimen identifications from names to the narrowest suitable TCLs, or add "uncertainty" flags to specimens needing further study. (5 We will utilize the novel tools and data to demonstrate how controlling for the taxonomic variable in 12 use cases variously drives the outcomes of evolutionary, ecological, and conservation-based research hypotheses. Broader impacts. Our project is focused on just one herbarium network, but the potential impact is as wide as Darwin Core or even comparative biology. We believe that trust in networked biodiversity data depends on open and dynamic system designs, allowing expert access and resolution of multiple conflicting views that reflect the complex realities of ongoing taxonomic research. Taking well over 1 million SERNEC records from name- to TCL-resolution will show that "big" specimen data can pass the credibility threshold needed to validate the substantive data mobilization investment. We will mentor one postdoctoral researcher (UNC, two Ph.D. students (ASU, UIUC, and at least 15 undergraduate students (ASU. Each of our workshops will capacitate 10-15 SERNEC experts, who in turn can recruit colleagues and students at their home collections. We will incorporate the project theme and use cases into

  20. New Taxa of Solenostoma and Plectocolea and Other Taxonomic Novelties Based on Study of Collections in the New York Botanical Garden Herbarium

    Directory of Open Access Journals (Sweden)

    Bakalin Vadim A.

    2013-07-01

    Full Text Available Six new taxa are described based on study of Jungermannia s.l. collections in herbarium NY. Solenostoma costaricanum Bakalin, sp. nov. is related to S. crassulum (Nees & Mont. Steph., from which it differs in plant size, the presence of ventral stolons, perianth shape, spore and elater size. Plectocolea subbalfourii Bakalin, sp. nov. is related to Solenostoma (Plectocolea balfourii (Váňa Váňa, Hentschel & J. Heinrichs, from which it differs in rhizoid features and size of perigynium and midleaf cells. Solenostoma rubrum var. underwoodii Bakalin, var. nov., based on Nardia macounii Underwood, nom. nud., differs from var. rubrum in coloration and leaf structure features. Plectocolea yunnanensis Bakalin, sp. nov., belonging to the ‘Plectocolea truncata’ group, differs from related species in leaf structure and rhizoid features. Solenostoma gracillimum subsp. camiguinense Bakalin, subsp. nov. differs from the typical variety in perianth and leaf structure features. Solenostoma inundatum var. grandirete Bakalin, var. nov. differs from the typical variety in leaf structure. Additionally, it was found that the type specimen of Plectocolea micrantha Mitt. is paroicous, not dioicous. Critical study of type specimens of Jungermannia marcescens Mitt. and J. sanguinolentha Griff. showed that these taxa are not conspecific, and the new combination Solenostoma marcescens (Mitt. Bakalin, comb. nov. is proposed.

  1. Effects of UV-B radiation on leaf hair traits of invasive plants-Combining historical herbarium records with novel remote sensing data.

    Directory of Open Access Journals (Sweden)

    Tomáš Václavík

    Full Text Available Ultraviolet-B (UV-B radiation is a key but under-researched environmental factor that initiates diverse responses in plants, potentially affecting their distribution. To date, only a few macroecological studies have examined adaptations of plant species to different levels of UV-B. Here, we combined herbarium specimens of Hieracium pilosella L. and Echium vulgare L. with a novel UV-B dataset to examine differences in leaf hair traits between the plants' native and alien ranges. We analysed scans of 336 herbarium specimens using standardized measurements of leaf area, hair density (both species and hair length (H. pilosella only. While accounting for other bioclimatic variables (i.e. temperature, precipitation and effects of herbivory, we examined whether UV-B exposure explains the variability and geographical distribution of these traits in the native (Northern Hemisphere vs. the alien (Southern Hemisphere range. UV-B explained the largest proportion of the variability and geographical distribution of hair length in H. pilosella (relative influence 67.1%, and hair density in E. vulgare (66.2%. Corresponding with higher UV-B, foliar hairs were 25% longer for H. pilosella and 25% denser for E. vulgare in records from the Southern as compared to those from the Northern Hemisphere. However, focusing on each hemisphere separately or controlling for its effect in a regression analysis, we found no apparent influence of UV-B radiation on hair traits. Thus, our findings did not confirm previous experimental studies which suggested that foliar hairs may respond to higher UV-B intensities, presumably offering protection against detrimental levels of radiation. We cannot rule out UV-B radiation as a possible driver because UV-B radiation was the only considered variable that differed substantially between the hemispheres, while bioclimatic conditions (e.g. temperature, precipitation and other considered variables (herbivory damage, collection date were at

  2. Prospective evaluation of a high multiplexing real-time polymerase chain reaction array for the rapid identification and characterization of bacteria causative of nosocomial pneumonia from clinical specimens: a proof-of-concept study.

    Science.gov (United States)

    Roisin, S; Huang, T-D; de Mendonça, R; Nonhoff, C; Bogaerts, P; Hites, M; Delaere, B; Hamels, S; de Longueville, F; Glupczynski, Y; Denis, O

    2017-09-27

    The purpose of this study was evaluation of the VAPChip assay based on the "Rapid-Array-PCR-technology" which targets 13 respiratory pathogens and 24 β-lactam resistance genes directly on respiratory clinical specimens. The first step included analysis of 45 respiratory specimens in order to calibrate and determine the threshold for target genes. The second prospective step involved 85 respiratory samples from patients suspected of nosocomial pneumonia collected in two academic hospitals over an 8-month period. Results of the VAPChip assay were compared to routine methods. The first step showed a large proportion of positive signals for H. influenzae and/or S. pneumoniae. For identification, discrepancies were observed in seven samples. Thresholds were adapted and two probes were re-designed to create a new version of the cartridge. In the second phase, sensitivity and specificity of the VAPchip for bacterial identification were 72.9% and 99.1%, respectively. Seventy (82%) pathogens were correctly identified by both methods. Nine pathogens detected by the VAPChip were culture negative and 26 pathogens identified by culture were VAPChip negative. For resistance mechanisms, 11 probes were positive without identification of pathogens with an antimicrobial-susceptibility testing compatible by culture. However, the patient's recent microbiological history was able to explain most of these positive signals. The VAPChip assay simultaneously detects different pathogens and resistance mechanisms directly from clinical samples. This system seems very promising but the extraction process needs to be automated for routine implementation. This kind of rapid point-of-care automated platform permitting a syndromic approach will be the future challenge in the management of infectious diseases.

  3. Fungal monitoring of the indoor air of the Museo de La Plata Herbarium, Argentina.

    Science.gov (United States)

    Mallo, Andrea C; Elíades, Lorena A; Nitiu, Daniela S; Saparrat, Mario C N

    Biological agents, such as fungal spores in the air in places where scientific collections are stored, can attack and deteriorate them. The aim of this study was to gather information on the indoor air quality of the Herbarium of Vascular Plants of the Museo de Ciencias Naturales de La Plata, Argentina, in relation to fungal propagules and inert particles. This study was made using a volumetric system and two complementary sampling methods: (1) a non-viable method for direct evaluation, and (2) a viable method by culture for viable fungal propagules. The non-viable method led to ten spore morphotypes being found from related fungal sources. A total of 4401.88spores/m3 and 32135.18 inert suspended particles/m3 were recorded. The viable method led to the finding of nine fungal taxa as viable spores that mostly belonged to anamorphic forms of Ascomycota, although the pigmented yeast Rhodotorula F.C. Harrison (Basidiomycota) was also found. A total count of 40,500fungal CFU/m3 air was estimated for all the sites sampled. Both the non-viable and viable sampling methods were necessary to monitor the bio-aerosol load in the La Plata Herbarium. The indoor air of this institution seems to be reasonably adequate for the conservation of vascular plants due to the low indoor/outdoor index, low concentrations of air spores, and/or lack of indicators of moisture problems. Copyright © 2016 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

  4. Urine culture - catheterized specimen

    Science.gov (United States)

    Culture - urine - catheterized specimen; Urine culture - catheterization; Catheterized urine specimen culture ... International Clinical Practice Guidelines from the Infectious Diseases Society of America. Clin Infect Dis . 2010;50(5): ...

  5. A one-year prospective study on the antibiotic resistance of E. coli strains isolated in urinary specimens of children hospitalized at the University Pediatric Medical Center in Novi Sad, Serbia.

    Science.gov (United States)

    Jakovljević, E; Ilić, K; Jelesić, Z; Konstantinidis, G

    2013-12-01

    Urinary tract infections (UTIs), the most common serious bacterial infections in children, are frequently caused by Escherichia coli. The purpose of this study was to investigate E. coli resistance/multidrug resistance to antibiotics most frequently used for UTIs. Children 0-18 years of age, hospitalized at the University Pediatric Hospital in Novi Sad, Serbia, were included in a 1-year observational prospective study. The microbiological analysis was performed using the standard Kirby-Bauer disk diffusion method. The results were analyzed using WHONET 5.4 software. E. coli was isolated from 61.7 % of positive urine specimens. In general, higher average E. coli antibiotic resistance was found in infants and toddlers compared to children and adolescents (33.4 vs. 25.0 %) (p 93.1 %), amikacin (86.3 %), quinolones (>75.0 %), and penems (>96.6 %). The prevalence of multiresistant E. coli strains was significantly higher in infants and toddlers (72.3 vs. 36.8 %) (p < 0.0001). E. coli, a common cause of UTIs in children admitted to pediatric hospitals, is highly resistant/multidrug-resistant to commonly used antibiotics. Higher average resistance is found in infants and toddlers than in children and adolescents, as well as in boys compared to girls. These findings are important for the regional empiric therapy of UTIs and call for actions to decrease E. coli antibiotic resistance.

  6. Phylogenetic analyses of Podaxis specimens from Southern Africa reveal hidden diversity and new insights into associations with termites.

    Science.gov (United States)

    Conlon, Benjamin H; de Beer, Z Wilhelm; De Fine Licht, Henrik H; Aanen, Duur K; Poulsen, Michael

    2016-09-01

    Although frequently found on mounds of the grass-cutting termite genus Trinervitermes, virtually nothing is known about the natural history of the fungal genus Podaxis (Agaricaceae) nor why it associates with termite mounds. More than 40 species of this secotioid genus have been described since Linnaeus characterised the first species in 1771. However, taxonomic confusion arose when most of these species were reduced to synonymy with Podaxis pistillaris in 1933. Although a few more species have since been described, the vast majority of specimens worldwide are still treated as P. pistillaris. Using 45 fresh and herbarium specimens from Southern Africa, four from North America and one each from Ethiopia, and Kenya, we constructed the first comprehensive phylogeny of the genus. Four of the genotyped specimens were more than 100 y old. With the exception of the type specimen of Podaxis rugospora, all herbarium specimens were labelled as P. pistillaris or Podaxis sp. However, our data shows that the genus contains at least five well-supported clades with significant inter-clade differences in spore length, width and wall thickness, and fruiting body length, supporting that clades likely represent distinct Podaxis species. Certain clades consistently associate with termites while others appear entirely free-living. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. Controlled Environment Specimen Transfer

    DEFF Research Database (Denmark)

    Damsgaard, Christian Danvad; Zandbergen, Henny W.; Hansen, Thomas Willum

    2014-01-01

    an environmental transmission electron microscope to an in situ X-ray diffractometer through a dedicated transmission electron microscope specimen transfer holder, capable of sealing the specimen in a gaseous environment at elevated temperatures. Two catalyst material systems have been investigated; Cu/ZnO/Al2O3...... transferred in a reactive environment to the environmental transmission electron microscope where further analysis on the local scale were conducted. The Co/Al2O3 catalyst was reduced in the environmental microscope and successfully kept reduced outside the microscope in a reactive environment. The in situ......Specimen transfer under controlled environment conditions, such as temperature, pressure, and gas composition, is necessary to conduct successive complementary in situ characterization of materials sensitive to ambient conditions. The in situ transfer concept is introduced by linking...

  8. Genomics and museum specimens.

    Science.gov (United States)

    Nachman, Michael W

    2013-12-01

    Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years. © 2013 John Wiley & Sons Ltd.

  9. 37 CFR 2.59 - Filing substitute specimen(s).

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Filing substitute specimen(s). 2.59 Section 2.59 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES Drawing § 2.59 Filing substitute specimen(s). (a...

  10. Biaxial Creep Specimen Fabrication

    Energy Technology Data Exchange (ETDEWEB)

    JL Bump; RF Luther

    2006-02-09

    This report documents the results of the weld development and abbreviated weld qualification efforts performed by Pacific Northwest National Laboratory (PNNL) for refractory metal and superalloy biaxial creep specimens. Biaxial creep specimens were to be assembled, electron beam welded, laser-seal welded, and pressurized at PNNL for both in-pile (JOYO reactor, O-arai, Japan) and out-of-pile creep testing. The objective of this test campaign was to evaluate the creep behavior of primary cladding and structural alloys under consideration for the Prometheus space reactor. PNNL successfully developed electron beam weld parameters for six of these materials prior to the termination of the Naval Reactors program effort to deliver a space reactor for Project Prometheus. These materials were FS-85, ASTAR-811C, T-111, Alloy 617, Haynes 230, and Nirnonic PE16. Early termination of the NR space program precluded the development of laser welding parameters for post-pressurization seal weldments.

  11. Vulnerability of oak-dominated forests in West Virginia to invasive exotic plants: temporal and spatial patterns of nine exotic species using herbarium records and land classification data

    Science.gov (United States)

    Cynthia D. Huebner

    2003-01-01

    Are oak-dominated forests immune to invasive exotic plants? Herbarium and land classification data were used to evaluate the extent of spread of nine invasive exotic plants and to relate their distributions to remotely-sensed land use types in West Virginia. Collector-defined habitats indicated that the most common habitat was roadsides, but seven of the nine species...

  12. An annotated index to species and intraspecific taxa of boletes (Mycota: Boletales: Boletaceae) in the Clinton herbarium of the Buffalo Society of Natural Sciences

    Science.gov (United States)

    Ernst E. Both; Beatriz. Ortiz-Santana

    2012-01-01

    The Bolete Collection of the Clinton Herbarium (BUF) was started in 1968 by the senior author at the suggestion of then museum director Fred T. Hall. Collecting continued for the next forty years, resulting in some 3,500 collections representing 210 species of boletes. While the bulk of the collections are from the northeastern states, collections from adjacent states...

  13. Long-term herbarium data reveal the decline of a temperate-water algae at its southern range

    Science.gov (United States)

    Riera, Rodrigo; Sangil, Carlos; Sansón, Marta

    2015-11-01

    Distributional shifts of marine species have recently received attention as a result of increasing man-induced pressures on coastal ecosystems and global climate change (i.e. ocean warming). The southernmost geographical limit of the fucoid Fucus guiryi is the Canarian archipelago (Northeastern Atlantic Ocean) where this species is currently forming scarce and low-dense populations. Studies on long-term herbarium data revealed the decrease in size of morphological features (length and width of thallus and receptacles), and recent surveys confirmed the sharp decline, or even extinction, of F. guiryi from most sites previously documented. The increase of mean seawater surface temperature consistently matches the regression of populations of F. guiryi. Other environmental variables, such as wave exposure, cloud cover and chlorophyll-a concentration, contributed to explain local-scale spatial variability detected in Canarian populations.

  14. NASA Biological Specimen Repository

    Science.gov (United States)

    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.

  15. Documenting biogeographical patterns of African timber species using herbarium records: a conservation perspective based on native trees from Angola.

    Science.gov (United States)

    Romeiras, Maria M; Figueira, Rui; Duarte, Maria Cristina; Beja, Pedro; Darbyshire, Iain

    2014-01-01

    In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to

  16. Breast specimen shrinkage following formalin fixation

    Directory of Open Access Journals (Sweden)

    Horn CL

    2014-02-01

    Full Text Available Christopher L Horn, Christopher Naugler Department of Pathology and Laboratory Medicine, University of Calgary, and Calgary Laboratory Services, Calgary, AB, Canada Abstract: Accurate measurement of primary breast tumors and subsequent surgical margin assessment is critical for pathology reporting and resulting patient therapy. Anecdotal observations from pathology laboratory staff indicate possible shrinkage of breast cancer specimens due to the formalin fixation process. As a result, we conducted a prospective study to investigate the possible shrinkage effects of formalin fixation on breast cancer specimens. The results revealed no significant changes in tumor size, but there were significant changes in the distance to all surgical resection margins from the unfixed to fixed state. This shrinkage effect could interfere with the accuracy of determining distance to margin assessment and tumor-free margin assessment. Thus, changes in these measurements due to the formalin fixation process have the potential to alter treatment options for the patient. Keywords: breast margins, formalin, shrinkage, cancer

  17. Information available within the PRECIS data bank of the National Herbarium, Pretoria, with examples of uses to which it may be put

    Directory of Open Access Journals (Sweden)

    J. W Morris

    1981-12-01

    Full Text Available The contents of the computerized information storage and retrieval system (PRECIS of the National Herbarium, Pretoria (PRE are described at length mainly by means of frequency histograms of descriptor codes. The frequency distributions found are discussed in the light of the history of the herbarium, the geography of the area and the habits of plant collectors. Two uses of PRECIS are illustrated by example. Firstly, the flowering phenology of  Eragrostis capensis, Themeda triandra and Heteropogon contortus is plotted and, secondly, the route followed by Dinter in South West Africa/Namibia from December 1933 until March 1935 is described. It is concluded that the system should be o f particular use in revisionary studies, regional floras and biogeographic research.

  18. Janka hardness using nonstandard specimens

    Science.gov (United States)

    David W. Green; Marshall Begel; William Nelson

    2006-01-01

    Janka hardness determined on 1.5- by 3.5-in. specimens (2×4s) was found to be equivalent to that determined using the 2- by 2-in. specimen specified in ASTM D 143. Data are presented on the relationship between Janka hardness and the strength of clear wood. Analysis of historical data determined using standard specimens indicated no difference between side hardness...

  19. Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes.

    Science.gov (United States)

    Sánchez Barreiro, Fátima; Vieira, Filipe G; Martin, Michael D; Haile, James; Gilbert, M Thomas P; Wales, Nathan

    2017-03-01

    Population genetic studies of nonmodel organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich for RRL loci (Restriction Enzyme-Associated Loci baits, or REALbaits). Starting with genotyping-by-sequencing (GBS) data generated on modern common ragweed (Ambrosia artemisiifolia L.) specimens, we designed 20 000 RNA probes to target well-characterized genomic loci in herbarium voucher specimens dating from 1835 to 1913. Compared to shotgun sequencing, we observed enrichment of the targeted loci at 19- to 151-fold. Using our GBS capture pipeline on a data set of 38 herbarium samples, we discovered 22 813 SNPs, providing sufficient genomic resolution to distinguish geographic populations. For these samples, we found that dilution of REALbaits to 10% of their original concentration still yielded sufficient data for downstream analyses and that a sequencing depth of ~7m reads was sufficient to characterize most loci without wasting sequencing capacity. In addition, we observed that targeted loci had highly variable rates of success, which we primarily attribute to similarity between loci, a trait that ultimately interferes with unambiguous read mapping. Our findings can help researchers design capture experiments for RRL loci, thereby providing an efficient means to integrate samples with degraded DNA into existing RRL data sets. © 2016 John Wiley & Sons Ltd.

  20. The role of K-ras gene mutation analysis in EUS-guided FNA cytology specimens for the differential diagnosis of pancreatic solid masses: a meta-analysis of prospective studies.

    Science.gov (United States)

    Fuccio, Lorenzo; Hassan, Cesare; Laterza, Liboria; Correale, Loredana; Pagano, Nico; Bocus, Paolo; Fabbri, Carlo; Maimone, Antonella; Cennamo, Vincenzo; Repici, Alessandro; Costamagna, Guido; Bazzoli, Franco; Larghi, Alberto

    2013-10-01

    Differential diagnosis of pancreatic solid masses with EUS-guided FNA (EUS-FNA) is still challenging in about 15% of cases. Mutation of the K-ras gene is present in over 75% of pancreatic adenocarcinomas (PADC). To assess the accuracy of K-ras gene mutation analysis for diagnosing PADC. We systematically searched the electronic databases for relevant studies published. Data from selected studies underwent meta-analysis by use of a bivariate model providing a pooled value for sensitivity, specificity, diagnostic odds ratio, and summary receiver operating characteristic curve. Meta-analysis of 8 prospective studies. Total of 931 patients undergoing EUS-FNA for diagnosis of pancreatic solid masses. K-ras mutation analysis. Diagnostic accuracy of K-ras mutation analysis and of combined diagnostic strategy by using EUS-FNA and K-ras mutation analysis in the diagnosis of PADC. The pooled sensitivity of EUS-FNA for the differential diagnosis of PADC was 80.6%, and the specificity was 97%. Estimated sensitivity and specificity were 76.8% and 93.3% for K-ras gene analysis, respectively, and 88.7% and 92% for combined EUS-FNA plus K-ras mutation analysis. Overall, K-ras mutation testing applied to cases that were inconclusive by EUS-FNA reduced the false-negative rate by 55.6%, with a false-positive rate of 10.7%. Not repeating EUS-FNA in cases in which mutation testing of the K-ras gene is inconclusive would reduce the repeat-biopsy rate from 12.5% to 6.8%. Small number of studies and between-study heterogeneity. K-ras mutation analysis can be useful in the diagnostic work-up of pancreatic masses, in particular when tissue obtained by EUS-FNA is insufficient, and the diagnosis inconclusive. Copyright © 2013 American Society for Gastrointestinal Endoscopy. Published by Mosby, Inc. All rights reserved.

  1. Histopathologic Analysis of Pancreaticoduodenectomy Specimen

    Directory of Open Access Journals (Sweden)

    Ramesh Dhakhwa

    2016-12-01

    Conclusions: Pancreaticoduodenectomy specimen requires thorough histopathological evaluation. Pathologists should also be aware of possibility of a benign diagnosis in PD specimens which have been resected presuming malignancy based on clinical judgement and radiological data. Keywords: histopathologic evaluation, pancreaticoduodenectomy, periampullary carcinoma. | PubMed

  2. 2003 Dead Bald Eagle Specimen

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The specimen report states the Bald Eagle was found along the side of the I-95 by a motorist who contacted Santee National Wildlife Refuge. The Bald Eagle was taken...

  3. Durkheim’s herbarium

    DEFF Research Database (Denmark)

    Thomassen, Bjørn

    2017-01-01

    This introductory article situates Arnold van Gennep’s review of Émile Durkheim’s The elementary forms of the religious life. It does so by relating the review to van Gennep’s much-neglected endeavor to establish methodological foundations for the emerging social sciences in the early twentieth...... century, in open contrast to Durkheim and the Durkhemian school of anthropology and sociology. It also contextualizes the review by revisiting earlier publications where van Gennep decisively went up against Durkheim’s approach to religion and society. The article finally suggests that Arnold van Gennep...

  4. Specimen Collection and Submission Manual

    Science.gov (United States)

    2016-06-01

    local, approved medical treatment facility collection procedures. Superficial wounds and abscesses Sterile swab Follow local, approved medical...Tests May Include: West Nile virus (WNV), Eastern equine encephalitis virus, Venezuelan equine encephalitis virus, yellow fever virus, dengue virus... Wound Botulism Acceptable Specimens Required Volume/Comments Toxin Assay (T) or Culture (C) Performed Serum (priority sample type) 5 ml (less

  5. Itinerary and specimen list of M.A. Pocock’s botanical collecting expedition in Zambia and Angola in 1925

    Directory of Open Access Journals (Sweden)

    M. G. Balarin

    1999-12-01

    Full Text Available Mary Agard Pocock, bom in Rondebosch in 1886, and best known as an algologist, was also a ‘trailblazer' in the biological exploration o f Angola. She, and the ethnologist Dorothea Bleek, undertook a scientific expedition which started at Livingstone, Zambia, and ended at Lobito Bay, Angola, during the dry season, from April to October 1925.During the journey Mary Pocock collected ±  1  000 specimens in the Zambesian region o f endemism  (II.  as delineated by White (1983 o f which 12 were considered to be  species novae. Many o f the specimens were painted by Mary. Some original paintings are housed in the Selmar Schonland Herbarium, Grahamstown (GRA. She also kept detailed diaries o f her route past villages and through the different vegetation types. Collecting locations, with specimen numbers relating to her collection in the Zambesian region, are indicated. An alphabetical list o f all the species collected by Mary Pocock during this exploration has been compiled

  6. Innovation for reducing blood culture contamination: initial specimen diversion technique.

    Science.gov (United States)

    Patton, Richard G; Schmitt, Timothy

    2010-12-01

    We hypothesized that diversion of the first milliliter of venipuncture blood-the initial specimen diversion technique (ISDT)-would eliminate incompletely sterilized fragments of skin from the culture specimen and significantly reduce our blood culture contamination rate (R). We studied our hypothesis prospectively beginning with our control culture (C) definition: one venipuncture with two sequentially obtained specimens, 10 ml each, the first specimen (M1) for aerobic and the second (M2) for anaerobic media. The test ISDT culture (D) was identical, with the exception that each was preceded by diverting a 1-ml sample (DS) from the same venipuncture. During the first of two sequential 9-month periods, we captured D versus C data (n=3,733), where DMXR and CMXR are R for D and C specimens. Our hypothesis predicted DS would divert soiled skin fragments from DM1, and therefore, CM1R would be significantly greater than DM1R. This was confirmed by CM1R (30/1,061 [2.8%]) less DM1R (37/2,672 [1.4%]; P=0.005), which equals 1.4%. For the second 9-month follow-up period, data were compiled for all cultures (n=4,143), where ADMXR is R for all (A) diversion specimens, enabling comparison to test ISDT. Our hypothesis predicted no significant differences for test ISDT versus all ISDT. This was confirmed by DM1R (37/2,672 [1.4%]) versus ADM1R (42/4,143 [1.0%]; P=0.17) and DM2R (21/2,672 [0.80%]) versus ADM2R (39/4,143 [0.94%]; P=0.50). We conclude that our hypothesis is valid: venipuncture needles soil blood culture specimens with unsterilized skin fragments and increase R, and ISDT significantly reduces R from venipuncture-obtained blood culture specimens.

  7. Heavy-section fracture toughness screening specimen

    Science.gov (United States)

    Shannon, J. L., Jr.; Brown, W. F., Jr.; Donald, J. K.

    1977-01-01

    The reported study has the objective to fix the proportions and limits of application of a double-edge-notch specimen with one of the notches tipped with a fatigue crack (DENC). Details regarding the DENC specimen are discussed, taking into account specimen length, notch length, specimen width and thickness, and the loading pins. The influence of specimen width and thickness on the crack strenght and apparent plane-strain fracture toughness of the specimen has been determined for eight alloys. It is concluded that the DENC specimen shows promise for screening alloys with reference to their plane-strain fracture toughness in sections up to 1 in.

  8. Optimizing specimen processing for ancient soft tissue specimens.

    Science.gov (United States)

    Prats-Muñoz, G; Malgosa, A; Isidro, A; Galtés, I

    2015-05-01

    Despite many reports concerning processing of ancient soft tissues, scant attention has been paid to optimizing procedures for processing soft tissues that have been altered by taphonomic processes. To determine the best procedures, we investigated the rehydration solution, time of exposure to the solutions, fixative solution and exposure to heat. Processes were evaluated based on the minimum section thickness, degree of tissue fragmentation, definition of tissue architecture and penetration of stains. We found that in desiccated samples, tissue architecture was optimized by using Ruffer's solution for rehydration and Schaffer's solution as fixative, because these tissues require water restoration within the tissues due to their compacted character. Heating enhanced penetration of dyes in these specimens, which improved diagnosis. Saponified tissues that had suffered extensive decomposition were more labile and required slow water uptake. The best histological sections were obtained using Sandison's solution followed by fixation with formaldehyde and avoiding heat. To obtain the best results with paleohistological specimens, the procedure must be determined by the condition of the sample and by accounting for the nature of its damage.

  9. Factors affecting the risk of blood bank specimen hemolysis.

    Science.gov (United States)

    Tanabe, Paula; Kyriacou, Demetrios N; Garland, Franklyn; Kyriacou, Demetrious

    2003-08-01

    To evaluate simultaneously several possible risk factors for blood bank specimen hemolysis. This was a prospective cohort study of emergency department and labor and delivery patients to estimate the effect of various factors on the risk of blood bank specimen hemolysis. Study variables included patient demographics, type and gauge of needle or catheter, anatomic location of venipuncture, and patient care area. Hemolysis was determined by blood bank laboratory technicians. Cox proportional hazards multivariate regression modeling was performed to estimate the adjusted relative risks for hemolysis. Of the 605 subjects with complete data, 194 (32.1%) subjects had blood specimens drawn directly with a steel needle, and 411 (69.1%) had specimens drawn through a Vialon (BD Medical Systems, Inc., Sandy, UT) intravenous (IV) angiocatheter. The overall risk of hemolysis for all was 7%, 10% for Vialon IV angiocatheters and 1.5% for steel needles. In the multivariate analysis, the factors most closely associated with hemolysis were the use of Vialon IV catheters and sampling from an anatomic site other than the antecubital area. Blood bank specimens drawn from Vialon IV catheters (particularly smaller gauge catheters) and from veins outside the antecubital area are at significantly increased risk to hemolyze.

  10. The status of the name Alysium holtingii C. Agardh, a red alga described from Brazil, and a depiction of the type specimen

    Directory of Open Access Journals (Sweden)

    Michael J. Wynne

    2008-06-01

    Full Text Available The type specimen of the red alga Alysium holtingii C. Agardh, described from Brazil, is located in the Lund Herbarium, and it is depicted for the first time in a publication. It is taxonomically identical to Dichotomaria obtusata (J. Ellis and Solander Lamarck and thus can be treated as a later taxonomic synonym. Alysium is regarded as congeneric with Dichotomaria.O espécime tipo da alga vermelha Alysium holtingii C. Agardh, descrito para o Brasil, está localizado no Herbário Lund, e é aqui apresentado. Ele é taxonomicamente idêntico a Dichotomaria obtusata (J. Ellis e Solander Lamarck e portanto deve ser tratado como um sinônimo taxonômico posterior. Alysium é considerado como congenérico com Dichotomaria.

  11. Measurements and Counts for Notacanthidae Specimens

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Taxonomic data were collected for specimens of deep-sea spiny eels (Notacanthidae) from the Hawaiian Ridge by Bruce C. Mundy. Specimens were collected off the north...

  12. Rate of occult specimen provenance complications in routine clinical practice.

    Science.gov (United States)

    Pfeifer, John D; Liu, Jingxia

    2013-01-01

    Occult specimen provenance complications (SPCs), which occur when there is an absence of any direct or indirect indication that a specimen switch or contamination may have occurred, constitute a significant patient safety and medical-legal problem because they can lead to misdiagnosis. However, the rate at which occult SPCs occur is unknown because, by definition, this category of errors is not identified by standard laboratory practices. In this study, we evaluated a data set comprising almost 13,000 prostate biopsies that were prospectively tested for specimen provenance errors as part of routine clinical practice. The frequency of occult type 1 errors (a complete transposition between patients) and type 2 errors (contamination of the patient's tissue with 1 or more unrelated patients) was 0.26% and 0.67%, respectively; every urology practice setting and surgical pathology laboratory type with a representative sample size experienced at least 1 type 1 and 1 type 2 error during the study period. Overall, the mean frequency of SPCs across practice settings was 0.22% for type 1 errors and 1.69% for type 2 errors. The type 1 rate showed no correlation with a surgical pathology laboratory setting or urologic practice group setting; the type 2 rate correlated solely with a surgical pathology laboratory setting. The occult SPC rate in this limited data set provides an estimate of the scope of the problem of potential misdiagnosis as a result of occult specimen provenance errors in routine clinical practice.

  13. [The German Environmental Specimen Bank].

    Science.gov (United States)

    Schröter-Kermani, Christa; Gies, Andreas; Kolossa-Gehring, Marike

    2016-03-01

    The main objective of the German Environmental Specimen Bank (ESB) is the long-term storage of environmental and human samples under stable deep-freeze conditions for future research. The ESB is unique in providing a continuous historical record of environmental and human exposure to chemicals in Germany. ESB was started parallel to the development of the first German Chemicals Legislation in the late 1970s. In 1979, the ESB test operation began. After the Chemicals Law came into force in 1982, the ESB was established as a permanent facility in 1985. With the new European Chemicals Legislation, REACH, in 2007 responsibility for the safety of commercial chemicals and risk assessment was assigned to the industry. Since then, the ESB has become even more important in verifying the self-assessment of the industry, in evaluating the effectiveness of regulations, thus ensuring the protection of humans and the environment against adverse effects caused by exposure to chemicals. These objectives are pursued by the regular monitoring of contaminations and the assessment of temporal trends. Demonstrating the necessity of deriving exposure reduction measures, ESB results serve as key information for policy-makers. Information on preventing exposure to chemicals is available to the general public and to the public health services. The ESB is thus an important monitoring instrument of the Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety. The Federal Environment Agency operates the ESB based on its own concepts, heads the scientific data evaluation and transfers results into the environmental policy arena and to the general public.

  14. 36 CFR 2.5 - Research specimens.

    Science.gov (United States)

    2010-07-01

    ... Federal agency for the purpose of research, baseline inventories, monitoring, impact analysis, group study... if removal of the specimen would result in damage to other natural or cultural resources, affect... available to the public and reports and publications resulting from a research specimen collection permit...

  15. 36 CFR 1002.5 - Research specimens.

    Science.gov (United States)

    2010-07-01

    ... of research, baseline inventories, monitoring, impact analysis, group study, or museum display when... of the specimen would result in damage to other natural or cultural resources, affect adversely... specimens will be made available to the public and reports and publications resulting from a research...

  16. Fatigue Specimens for Sheet and Plate Material

    NARCIS (Netherlands)

    Schijve, J.

    1998-01-01

    The usefulness of simple sheet and plate specimens is discussed for various experimental research purposes. Specimens should be representative as much as possible for the conditions of fatigue problems in practice, which is more difficult to achieve for the fatigue crack initiation phase than for

  17. 37 CFR 2.56 - Specimens.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Specimens. 2.56 Section 2.56 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE RULES OF PRACTICE IN TRADEMARK CASES Drawing § 2.56 Specimens. (a) An application under section 1(a) of...

  18. Machining technique prevents undercutting in tensile specimens

    Science.gov (United States)

    Moscater, R. E.; Royster, D. M.

    1968-01-01

    Machining technique prevents undercutting at the test section in tensile specimens when machining the four corners of the reduced section. Made with a gradual taper in the test section, the width of the center of the tensile specimen is less than the width at the four corners of the reduced section.

  19. Recent advances on Charpy specimen reconstitution techniques

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Arnaldo H.P.; Lobo, Raquel M.; Miranda, Carlos Alexandre J., E-mail: aandrade@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-07-01

    Charpy specimen reconstitution is widely used around the world as a tool to enhance or supplement surveillance programs of nuclear reactor pressure vessels. The reconstitution technique consists in the incorporation of a small piece from a previously tested specimen into a compound specimen, allowing to increase the number of tests. This is especially important if the available materials is restricted and fracture mechanics parameter have to be determined. The reconstitution technique must fulfill some demands, among them tests results like the original standard specimens and the loaded material of the insert must not be influenced by the welding and machining procedure. It is known that reconstitution of Charpy specimens may affect the impact energy in a consequence of the constraint of plastic deformation by the hardened weldment and HAZ. This paper reviews some recent advances of the reconstitution technique and its applications. (author)

  20. Catálogo de tipos de algas depositados en el Herbario Nacional de Plantas Celulares (BA del Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Argentina Catalogue of algae types deposited in the National Cryptogamic Herbarium (BA of the Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Argentina

    Directory of Open Access Journals (Sweden)

    Andrea Coradeghini

    2011-12-01

    Full Text Available El Herbario Nacional de Plantas Celulares (BA alberga 50.000 especímenes, de los cuales 9.000 son ejemplares de algas marinas y continentales. El catálogo consta de 11 tipos argentinos y 20 tipos del exterior: Australia y Brasil. Cinco de los tipos argentinos fueron depositados por la Lic. Carmen Pujals quién se desempeñó como investigadora de este Museo. El trabajo incluye la lista de nombres ordenados alfabéticamente, sus autores, fecha y cita original seguido por la categoría del tipo, país, provincia, localidad, fecha y datos del colector. De existir una Exsiccata se señalan nombre y número de la misma, número de BA y las observaciones y notas consideradas relevantes. En el caso que corresponde se anota sinonimia y autores.The National Cryptogamic Herbarium (BA contains 50.000 specimens, of which 9.000 are continental and marine algae. The catalogue consists of 11 argentine types and 20 foreign types from Australia and Brazil. Five of the argentine types were deposited by Lic. Carmen Pujals, a former researcher at the Museum. The paper includes the alphabetically ordered list of names, their authors, date and original citation, followed by the type category, country, province, city, date and collector number and original citation. If there is an Exsiccata the name, number, number of BA, observations and relevant notes are reported. When necessary, synonymy and authors are given.

  1. An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

    Science.gov (United States)

    Eminaga, O; Semjonow, A; Oezguer, E; Herden, J; Akbarov, I; Tok, A; Engelmann, U; Wille, S

    2014-01-01

    The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

  2. Evaluation of irradiated coating material specimens

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yong Jin; Nam, Seok Woo; Cho, Lee Moon [RCS Korea Co., Ltd., Seoul (Korea, Republic of)

    2007-12-15

    Evaluation result of irradiated coating material specimens - Coating material specimens radiated Gamma Energy(Co 60) in air condition. - Evaluation conditions was above 1 X 10{sup 4} Gy/hr, and radiated TID 2.0 X 10{sup 6} Gy. - The radiated coating material specimens, No Checking, Cracking, Flaking, Delamination, Peeling and Blistering. - Coating system at the Kori no. 1 and APR 1400 Nuclear power plant, evaluation of irradiated coating materials is in accordance with owner's requirement(2.0 X 10{sup 6} Gy)

  3. A Biaxial Fatigue Specimen for Uniaxial Loading

    OpenAIRE

    Bellett, Daniel; Morel, Franck; Morel, Anne; Lebrun, Jean-Lou

    2011-01-01

    International audience; The aim of this paper is to present a novel un-notched fatigue test specimen in which a biaxial stress state is achieved using a uniaxial loading condition. This allows the problem of multi-axial fatigue to be studied using relatively common one-axis servo-hydraulic testing machines. In addition the specimen presented here is very compact and can be made using a small volume of material (100x40x4.5mm). For this specimen, the degree of biaxiality, defined by the paramet...

  4. CPS Trawl Life History Specimen Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Individual specimens measured (weight in grams and length in mm) and sexed from mainly targeted species caught during SWFSC-FRD fishery independent trawl surveys of...

  5. Diagnostic quality of percutaneous fine-needle aspirates and laparoscopic biopsy specimens of the liver in rabbits (Oryctolagus cuniculus).

    Science.gov (United States)

    Proença, Laila M; Camus, Melinda; Nemeth, Nicole; Sharma, Ajay; Stelmach, Dainna; Mayer, Jörg; Divers, Stephen J

    2015-02-01

    To evaluate diagnostic quality of liver percutaneous ultrasound-guided fine-needle aspirates and laparoscopic biopsy specimens of rabbits (Oryctolagus cuniculus). Prospective descriptive study. 7 healthy adult rabbits. 3 to 5 liver fine-needle aspirates were obtained with a 22-gauge needle under ultrasound guidance in anesthetized rabbits. Liver biopsy specimens were also obtained with 1.7-mm (n = 2) or 3.0-mm (1) biopsy forceps by direct laparoscopic observation. Fine-needle aspirates were cytologically evaluated on a scale from 0 (suboptimal specimen) to 3 (optimal specimen) for cellularity, cell distribution, cell preservation, cell morphology, and blood contamination. Biopsy specimens were histologically evaluated on a scale from 0 (optimal specimen) to 5 (suboptimal specimen) for artifactual changes; numbers of portal triads and central veins were quantified. Aspirates were moderately to highly cellular (mean, 2.54) with good cell distribution (mean, 2.56), good cell preservation (mean, 2.20), and moderate blood contamination (mean, 1.04). The 1.7-mm biopsy specimens had a mean score of 1.3 for artifactual changes and contained a mean of 0.6 portal triads and 1.6 central veins/biopsy specimen. The 3.0-mm liver biopsy specimens had a mean score of 2.7 for artifactual changes, with a mean of 4.0 portal triads and 4.14 central veins/biopsy specimen. All but one 3.0-mm liver biopsy specimen had ≥ 1 portal triad suitable for histologic evaluation, and all had ≥ 1 central vein; in contrast, only half of the 1.7-mm liver biopsy specimens had a discernible portal triad or central vein. For histologic evaluation, advantages of obtaining 3.0-mm liver biopsy specimens, compared with 1.7-mm liver biopsy specimens or fine-needle aspirates, should be considered in rabbits with suspected liver disease.

  6. Morphometric analysis of one anatomic scoliotic specimen.

    Science.gov (United States)

    Parent, Stefan; Labelle, Hubert; Mitulescu, Anca; Latimer, Bruce; Skalli, Wafa; Lavaste, François; de Guise, Jacques

    2002-01-01

    Idiopathic scoliosis is a 3-D deformation affecting the position of the spine in space. The regional deformity has been studied extensively but the local changes have not been widely investigated and this being mainly due to the rarity of anatomical specimens. The objective of this study was to identify a deformation pattern for idiopathic scoliosis. We thus studied one complete scoliotic specimen using a digitizing protocol developed by our research group. The anatomical specimen was selected from the Hamann-Todd Osteology Collection at the Cleveland Natural History Museum, which contains over 1,300 skeletons. We were also able to match this scoliotic specimen with one normal specimen for age, sex, race, height and weight. Each vertebra was measured by taking approximately 200 points on each surface. Parameters for each vertebra were then calculated from these sets of points. Each scoliotic vertebra was then compared with a corresponding normal vertebra of the matched specimen. We present the first findings of these measurements, which show pedicle and posterior elements changes that are thought to be secondary to the scoliotic deformation.

  7. Morphometric analysis of anatomic scoliotic specimens.

    Science.gov (United States)

    Parent, Stefan; Labelle, Hubert; Skalli, Wafa; Latimer, Bruce; de Guise, Jacques

    2002-11-01

    Morphometric analysis of anatomic scoliotic specimens. The objective of this study was to identify a typical deformation pattern for thoracic and lumbar vertebrae in idiopathic scoliosis. Idiopathic scoliosis is a three-dimensional deformity affecting the orientation and position of the spine in space. The regional deformity has been studied extensively, but most of the knowledge we currently have regarding the local deformity is the result of isolated observations made on rare scoliotic specimens with severe deformities. Thirty scoliotic specimens from two major osteologic sources were studied using a three-dimensional digitizing protocol developed by our research group creating a precise three-dimensional reconstruction of the vertebrae. Parameters were then calculated for each vertebra from these reconstructions. Every scoliotic specimen was then matched with a normal specimen to provide for a representative control group. A total of 984 vertebrae (472 scoliotic and 512 normal vertebrae) were measured, creating the largest database of normal and scoliotic vertebral specimens. A characteristic deformity pattern was identified consisting of progressive vertebral wedging, decreased pedicle width on the concave side of the curve, and articular facet surface varying greatly with all findings increasingly more important toward the apex of the curve and as curve severity increased. All findings were statistically significant with P< 0.05. These results are of critical importance for the understanding of the local and regional deformity and in understanding curve progression. Our results also advocate caution in the use of pedicle screws in the thoracic spine, especially on the concave side of the curve.

  8. Closeout of JOYO-1 Specimen Fabrication Efforts

    Energy Technology Data Exchange (ETDEWEB)

    ME Petrichek; JL Bump; RF Luther

    2005-10-31

    Fabrication was well under way for the JOYO biaxial creep and tensile specimens when the NR Space program was canceled. Tubes of FS-85, ASTAR-811C, and T-111 for biaxial creep specimens had been drawn at True Tube (Paso Robles, CA), while tubes of Mo-47.5 Re were being drawn at Rhenium Alloys (Cleveland, OH). The Mo-47.5 Re tubes are now approximately 95% complete. Their fabrication and the quantities produced will be documented at a later date. End cap material for FS-85, ASTAR-811C, and T-111 had been swaged at Pittsburgh Materials Technology, Inc. (PMTI) (Large, PA) and machined at Vangura (Clairton, PA). Cutting of tubes, pickling, annealing, and laser engraving were in process at PMTI. Several biaxial creep specimen sets of FS-85, ASTAR-811C, and T-111 had already been sent to Pacific Northwest National Laboratory (PNNL) for weld development. In addition, tensile specimens of FS-85, ASTAR-811C, T-111, and Mo-47.5 Re had been machined at Kin-Tech (North Huntington, PA). Actual machining of the other specimen types had not been initiated. Flowcharts 1-3 detail the major processing steps each piece of material has experienced. A more detailed description of processing will be provided in a separate document [B-MT(SRME)-51]. Table 1 lists the in-process materials and finished specimens. Also included are current metallurgical condition of these materials and specimens. The available chemical analyses for these alloys at various points in the process are provided in Table 2.

  9. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

    Science.gov (United States)

    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.

  10. Human tissue thickness measurements from excised sleeve gastrectomy specimens.

    Science.gov (United States)

    Rawlins, Logan; Rawlins, Melissa P; Teel, Donovan

    2014-03-01

    Little basic science data exists regarding the thickness of transected stomach as the limits of smaller gastric sleeves are created closer to the lesser curvature in laparoscopic sleeve gastrectomy (SG). We sought to determine the tissue thickness trends along the staple line and examine what factors might predispose to thicker tissue. This was a single-center, single-surgeon nonrandomized prospective study of patients undergoing SG. Excised SG specimens, with patient consent, underwent tissue measurement at multiple predetermined locations and at the midpoint of each fired staple cartridge. After 9 months, ending in July 2012, we met our goal enrollment of 50 gastric sleeve specimens. Most of the patients were female (80 %) and white (92.5 %). Average age was 42 years (range, 19-60 years), and average body mass index (BMI) was 49 kg/m(2) (range, 34-82 kg/m(2)). Tissue thickness was significantly different (p 50 kg/m(2)) and gender (male) are associated with increased tissue thickness, but only in the antrum. Surgeons should consider using a thicker staple load, such as black, when these factors are present. Also, significant changes in tissue thickness at the fourth and fifth staple fires suggest stepwise alteration in staple cartridge color selection.

  11. Einige Ericaceen des Leidener Herbariums

    NARCIS (Netherlands)

    Smith, J.J.

    1916-01-01

    Frutex, ramulis validiusculis, rigidis, vix tortilibus, plus minusve obtuso-trigonis vel subteretibus, glabris. Folia alterna, breviter petiolata, oblongo-ovata, sensim acuminata, angusta obtuse callosoapiculata, basi rotundata et brevissime in petiolum contracta, densius crenato-serrata, dentibus

  12. The Value of Agricultural Voucher Specimens

    OpenAIRE

    Barkworth, Mary; Wolf, Paul; Kinosian,Sylvia; Dyreson,Curtis; Pearse,Will; Brandt, Benjamin; Cobb, Neil

    2017-01-01

    Voucher specimens are the ultimate raw data of biodiversity studies because they document the interpretation of the names used in papers and reports resulting from such studies. The value of voucher specimens is increased by making their records web-accessible but they can be further enhanced by linking them to other online resources, particularly if the links are birectional.  In this presentation, we discuss the potential benefits of such links for a group of agricultural significance, the ...

  13. Forgotten forests - issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study

    Science.gov (United States)

    2011-01-01

    Background South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. Results Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Conclusions Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be

  14. Forgotten forests--issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study.

    Science.gov (United States)

    Särkinen, Tiina; Iganci, João R V; Linares-Palomino, Reynaldo; Simon, Marcelo F; Prado, Darién E

    2011-11-24

    South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be particularly useful for mapping

  15. Rehydration of forensically important larval Diptera specimens.

    Science.gov (United States)

    Sanford, Michelle R; Pechal, Jennifer L; Tomberlin, Jeffery K

    2011-01-01

    Established procedures for collecting and preserving evidence are essential for all forensic disciplines to be accepted in court and by the forensic community at large. Entomological evidence, such as Diptera larvae, are primarily preserved in ethanol, which can evaporate over time, resulting in the dehydration of specimens. In this study, methods used for rehydrating specimens were compared. The changes in larval specimens with respect to larval length and weight for three forensically important blow fly (Diptera: Calliphoridae) species in North America were quantified. Phormia regina (Meigen), Cochliomyia macellaria (F.), and Chrysomya rufifacies (Macquart) third-instar larvae were collected from various decomposing animals and preserved with three preservation methods (80% ethanol, 70% isopropyl alcohol, and hot-water kill then 80% ethanol). Preservative solutions were allowed to evaporate. Rehydration was attempted with either of the following: 80% ethanol, commercial trisodium phosphate substitute solution, or 0.5% trisodium phosphate solution. All three methods partially restored weight and length of specimens recorded before preservation. Analysis of variance results indicated that effects of preservation, rehydration treatment, and collection animal were different in each species. The interaction between preservative method and rehydration treatment had a significant effect on both P. regina and C. macellaria larval length and weight. In addition, there was a significant interaction effect of collection animal on larval C. macellaria measurements. No significant effect was observed in C. rufifacies larval length or weight among the preservatives or treatments. These methods could be used to establish a standard operating procedure for dealing with dehydrated larval specimens in forensic investigations.

  16. Improved compliance with the World Health Organization Surgical Safety Checklist is associated with reduced surgical specimen labelling errors.

    Science.gov (United States)

    Martis, Walston R; Hannam, Jacqueline A; Lee, Tracey; Merry, Alan F; Mitchell, Simon J

    2016-09-09

    A new approach to administering the surgical safety checklist (SSC) at our institution using wall-mounted charts for each SSC domain coupled with migrated leadership among operating room (OR) sub-teams, led to improved compliance with the Sign Out domain. Since surgical specimens are reviewed at Sign Out, we aimed to quantify any related change in surgical specimen labelling errors. Prospectively maintained error logs for surgical specimens sent to pathology were examined for the six months before and after introduction of the new SSC administration paradigm. We recorded errors made in the labelling or completion of the specimen pot and on the specimen laboratory request form. Total error rates were calculated from the number of errors divided by total number of specimens. Rates from the two periods were compared using a chi square test. There were 19 errors in 4,760 specimens (rate 3.99/1,000) and eight errors in 5,065 specimens (rate 1.58/1,000) before and after the change in SSC administration paradigm (P=0.0225). Improved compliance with administering the Sign Out domain of the SSC can reduce surgical specimen errors. This finding provides further evidence that OR teams should optimise compliance with the SSC.

  17. Standard guide for preparation of metallographic specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2011-01-01

    1.1 The primary objective of metallographic examinations is to reveal the constituents and structure of metals and their alloys by means of a light optical or scanning electron microscope. In special cases, the objective of the examination may require the development of less detail than in other cases but, under nearly all conditions, the proper selection and preparation of the specimen is of major importance. Because of the diversity in available equipment and the wide variety of problems encountered, the following text presents for the guidance of the metallographer only those practices which experience has shown are generally satisfactory; it cannot and does not describe the variations in technique required to solve individual specimen preparation problems. Note 1—For a more extensive description of various metallographic techniques, refer to Samuels, L. E., Metallographic Polishing by Mechanical Methods, American Society for Metals (ASM) Metals Park, OH, 3rd Ed., 1982; Petzow, G., Metallographic Etchin...

  18. Damage modeling in Small Punch Test specimens

    DEFF Research Database (Denmark)

    Martínez Pañeda, Emilio; Cuesta, I.I.; Peñuelas, I.

    2016-01-01

    Ductile damage modeling within the Small Punch Test (SPT) is extensively investigated. The capabilities ofthe SPT to reliably estimate fracture and damage properties are thoroughly discussed and emphasis isplaced on the use of notched specimens. First, different notch profiles are analyzed....... Furthermore,Gurson-Tvergaard-Needleman model predictions from a top-down approach are employed to gain insightinto the mechanisms governing crack initiation and subsequent propagation in small punch experiments.An accurate assessment of micromechanical toughness parameters from the SPT...

  19. A Review of Sleeve Gastrectomy Specimen Histopathology.

    Science.gov (United States)

    Kinsinger, Luke A; Garber, James C; Whipple, Oliver

    2016-11-01

    With the increasing popularity of sleeve gastrectomy, many stomach specimens are being evaluated. Understanding the significance and treatment for unexpected pathology is important. This study examines the incidence of relevant histopathology of sleeve gastrectomy specimens. It evaluates previous data for each histopathology and provides recommendations for treatment. In this study, a retrospective review was performed for 241 patients who underwent sleeve gastrectomy from 2009 to 2014 at a single institution. Of the specimens, 122 had no significant histopathology, 91 had gastritis, 13 had lymphoid aggregates, 5 had hyperplasia, 3 had intestinal metaplasia, 3 had gastrointestinal stromal tumors (GISTs), and 3 had gastric polyps. Of the GISTs all had a low mitotic rate and the size of the tumor ranged from 1.5 to 4.5 cm. The findings of metaplasia may be a marker for increased risk of malignancy and may require additional surveillance. The findings of GIST may warrant interval imaging to survey for recurrence, though the likelihood of recurrence for the tumors in this study is less than 2 per cent based on previous studies.

  20. 10 CFR 26.113 - Splitting the urine specimen.

    Science.gov (United States)

    2010-01-01

    ... splitting of the urine specimen and to maintain visual contact with both specimen bottles until the custody... 10 Energy 1 2010-01-01 2010-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy... Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

  1. Specimen loading list for the varying temperature experiment

    Energy Technology Data Exchange (ETDEWEB)

    Qualls, A.L.; Sitterson, R.G. [Oak Ridge National Lab., TN (United States)

    1998-09-01

    The varying temperature experiment HFIR-RB-13J has been assembled and inserted in the reactor. Approximately 5300 specimens were cleaned, inspected, matched, and loaded into four specimen holders. A listing of each specimen loaded into the steady temperature holder, its position in the capsule, and the identification of the corresponding specimen loaded into the varying temperature holder is presented in this report.

  2. HMSRP Hawaiian Monk Seal Specimen Data (includes physical specimens, collection information, status, storage locations, and laboratory results associated with individual specimens)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set includes physical specimens, paper logs and Freezerworks database of all logged information on specimens collected from Hawaiian monk seals since 1975....

  3. Additions to the type collection of Cruciferae Juss. (Brassicaceae Burnett) of Siberia and Russian Far East kept in Herbarium of V. L. Komarov Botanical Institute (LE)

    OpenAIRE

    V. I. Dorofeyev

    2017-01-01

    A complete set of the type specimens of Cruciferae (Brassicaceae) of Siberia and Far East stored in the Komarov Botanical Institute of Russian Academy of Sciences was investigated. Previously uncounted samples of 130 taxa from 23 genera have been identified. Lectotypification of 119 taxa is done in the paper. Most valuable contribution into the study of Siberian and the Far Eastern Cruciferae biodiversity was made by the works of N. A. Busch (genera Arabis, Draba, Erysimum, Nasturtium), E. Re...

  4. Maternal screening for hypothyroidism and thyroiditis using filter paper specimens.

    Science.gov (United States)

    Foley, T P; Henry, J J; Hofman, L F; Thomas, R D; Sanfilippo, J S; Naylor, E W

    2013-11-01

    Hypothyroidism and autoimmune thyroiditis are more prevalent than previously considered in women during pregnancy and the postpartum, and are associated with adverse effects on the mother and her fetus. We determined the efficacy and accuracy of screening women for primary hypothyroidism and autoimmune thyroiditis by testing TSH and two thyroid antibodies (TAb): thyroperoxidase antibodies (TPOAb) and thyroglobulin antibodies (TgAb), in eluates of filter paper specimens collected during early pregnancy and the postpartum. We enrolled 494 first-trimester pregnant women with no exclusion criteria into a prospective study to detect primary hypothyroidism and autoimmune thyroiditis. Finger stick blood was applied to filter paper, dried in room air, eluted, and promptly tested for TSH and TAb. A total of 178 of the pregnant women (36%) were tested in the early postpartum. Women with abnormal results had confirmatory serum tests. It was found that 91 pregnant women (18.4%) and 43 postpartum women (24.2%) had abnormal TSH values (>4.0 mU/L) and/or positive TAb; 140 pregnant women (28.3%) had TSH values >2.5 mU/L. All subjects with TSH values >4.0 mU/L tested positive for TAb. Eighteen women (3.6%) who tested normal during pregnancy tested abnormal in the postpartum. This study confirms that TSH and TPOAb measured in eluates of blood-spotted filter paper specimens are excellent screening tests to detect primary hypothyroidism and autoimmune thyroiditis in pregnant and postpartum women. Results are very comparable to serum data in this population published in the literature.

  5. Multicenter Evaluation of the Xpert Norovirus Assay for Detection of Norovirus Genogroups I and II in Fecal Specimens

    Science.gov (United States)

    Gonzalez, Mark D.; Langley, L. Claire; Faron, Matthew L.; Maier, Melanie; Templeton, Kate; Walker, Kimberly; Popowitch, Elena B.; Miller, Melissa B.; Rao, Arundhati; Liebert, Uwe G.; Ledeboer, Nathan A.; Vinjé, Jan

    2015-01-01

    Norovirus is the most common cause of sporadic gastroenteritis and outbreaks worldwide. The rapid identification of norovirus has important implications for infection prevention measures and may reduce the need for additional diagnostic testing. The Xpert Norovirus assay recently received FDA clearance for the detection and differentiation of norovirus genogroups I and II (GI and GII), which account for the vast majority of infections. In this study, we evaluated the performance of the Xpert Norovirus assay with both fresh, prospectively collected (n = 914) and frozen, archived (n = 489) fecal specimens. A Centers for Disease Control and Prevention (CDC) composite reference method was used as the gold standard for comparison. For both prospective and frozen specimens, the Xpert Norovirus assay showed positive percent agreement (PPA) and negative percent agreement (NPA) values of 98.3% and 98.1% for GI and of 99.4% and 98.2% for GII, respectively. Norovirus prevalence in the prospective specimens (collected from March to May of 2014) was 9.9% (n = 90), with the majority of positives caused by genogroup II (82%, n = 74). The positive predictive value (PPV) of the Xpert Norovirus assay was 75% for GI-positive specimens, whereas it was 86.5% for GII-positive specimens. The negative predictive values (NPV) for GI and GII were 100% and 99.9%, respectively. PMID:26560532

  6. Evaluation of Fluorotype MTB for detection of Mycobacterium tuberculosis complex DNA in clinical specimens from a low-incidence country.

    Science.gov (United States)

    Hofmann-Thiel, Sabine; Hoffmann, Harald

    2014-02-05

    With Fluorotype MTB (FT MTB, HAIN Lifesciences, Germany) a new semi-automated assay for detection of M. tuberculosis complex (MTBC) in clinical specimens has been introduced. In a prospective study, we evaluated the diagnostic performance of FT MTB in a routine diagnostic setting in a low-incidence country. A total of 1039 respiratory specimens received for routine mycobacteriology diagnostics were analysed by FT MTB. Results were compared to those of culture, microscopy and clinical diagnosis. 61 specimens were excluded from further analysis due to bacterial contamination of cultures. FT MTB detected 52 of 59 TB specimens (45 culture-positive with MTBC, 7 with clinical diagnosis of TB). With 902 of 912 non-TB specimens (884 culture-negative, 18 with growth of non-tuberculous mycobacteria) FT MTB was negative; discrepant positive FT MTB results were found with 10 specimens. Overall sensitivity, specificity, positive and negative predictive values were 88.1%, 98.9%, 83.8% and 99.2%. Sensitivity rates for smear-positive and smear-negative TB specimens were 100% and 56.3%, respectively. Seven of 978 samples (0.7%) yielded invalid FT MTB results. FT MTB is a new accurate, half automated assay for rapidly diagnosing TB and suitable for larger series of samples. Performance characteristics were found to be similar to those of other commercial NAATs. Its sensitivity in paucibacillary, smear-negative specimens and its utility for TB diagnostics in high-incidence settings needs to be addressed in further studies.

  7. Histological evaluation of 400 cholecystectomy specimens

    Directory of Open Access Journals (Sweden)

    H Kumar

    2015-09-01

    Full Text Available Background: A majority of gallbladder specimens show changes associated with chronic cholecystitis; however few harbour a highly lethal carcinoma. This study was conducted to review the significant histopathological findings encountered in gallbladder specimens received in our laboratory.Materials and Methods: Four hundred cholecystectomy specimens were studied over a period of five years (May, 2002 to April, 2007 received at department of pathology, Kasturba Medical College, Mangalore, India. Results: Gallstones and associated diseases were more common in women in the 4th to 5th decade as compared to men with M: F ratio of 1:1.33. Maximum number of patients (28.25% being 41 to 50 years old. Histopathologically, the most common diagnosis was chronic cholecystitis (66.75%, followed by chronic active cholecystitis (20.25%, acute cholecystitis (6%, gangrenous cholecystitis (2.25%,xanthogranulomatous cholecystitis (0.50%, empyema (1%, mucocele (0.25%, choledochal cyst (0.25%, adenocarcinoma gallbladder (1.25% and  normal  gallbladders (1%.Conclusion: All lesions were found more frequently in women except chronic active cholecystitis. Gallstones were present in (80.25% cases, and significantly associated with various lesions (P value 0.009. Pigment stones were most common, followed by cholesterol stones and mixed stones. Adequate  sectioning  is  mandatory  in  all  cases  to  assess  epithelial changes arising from cholelithiasis and chronic cholecystitis as it has been known to progress to malignancy in some cases.

  8. Wildlife specimen collection, preservation, and shipment

    Science.gov (United States)

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

    2015-01-01

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

  9. Muscle degeneration in inguinal hernia specimens.

    Science.gov (United States)

    Amato, G; Agrusa, A; Romano, G; Salamone, G; Gulotta, G; Silvestri, F; Bussani, R

    2012-06-01

    There are few articles in the literature reporting the histological changes of groin structures affected by inguinal hernia. A deeper knowledge of this matter could represent an important step forward in the identification of the causes of hernia protrusion. This study aimed to recognise the pathological modifications of muscular structures in autopsy specimens excised from tissues surrounding the hernia orifice. Inguinal hernia was identified in 30 autopsied cadavers, which presented different varieties of hernia, including indirect, direct and mixed. Tissue specimens were resected for histological study from structures of the inguinal area surrounding the hernia opening, following a standardised procedure. The histological examination was focussed on the detection of structural changes in the muscle tissues. The results were compared with biopsy specimens resected from corresponding sites of the inguinal region in a control group of 15 fresh cadavers without hernia. Significant modification of the muscular arrangement of the inguinal area was recognized. Pathological alterations such as atrophy, hyaline and fibrotic degeneration, as well as fatty dystrophy of the myocytes were detected. These findings were observed consistently in the context of multistructural damage also involving vessels and nerves. In cadavers with hernia these alterations were always present independent of hernia type. No comparable damage was found in control cadavers without hernia. The high degree of degenerative changes in the muscle fibres in the inguinal area involved in hernia protrusion described in this report seems to be consistent with chronic compressive damage. These alterations could embody one important factor among the multifactorial sources of hernia genesis. Conjectures concerning its impact on the physiology and biodynamics of the inguinal region are made. The relationship between the depicted degenerative injuries and the genesis of inguinal hernia is also a focus of

  10. Fabrication and testing of composite ring specimens

    Science.gov (United States)

    Liber, T.; Daniel, I. M.; Labedz, R.; Niiro, T.

    1979-01-01

    The tooling and techniques used in the fabrication of composite laminate tubes of any desired ply orientation and stacking sequence are described along with techniques for cutting ring specimens under internal pressure. The method consists of laying up the tube on a central circular mandrel, and by means of internal pressure, expanding the prepreg tube against the cavity wall of an external mold tool, which forms the geometric curing envelope for the tube. Tube quality is assessed by laminate wall thickness measurement, by hoop strength measurement on rings cut from the ends of the tube, and by ultrasonic inspection.

  11. Development of fatigue life evaluation method using small specimen

    Science.gov (United States)

    Nogami, Shuhei; Nishimura, Arata; Wakai, Eichi; Tanigawa, Hiroyasu; Itoh, Takamoto; Hasegawa, Akira

    2013-10-01

    For developing the fatigue life evaluation method using small specimen, the effect of specimen size and shape on the fatigue life of the reduced activation ferritic/martensitic steels (F82H-IEA, F82H-BA07 and JLF-1) was investigated by the fatigue test at room temperature in air using round-bar and hourglass specimens with various specimen sizes (test section diameter: 0.85-10 mm). The round-bar specimen showed no specimen size and no specimen shape effects on the fatigue life, whereas the hourglass specimen showed no specimen size effect and obvious specimen shape effect on it. The shorter fatigue life of the hourglass specimen observed under low strain ranges could be attributed to the shorter micro-crack initiation life induced by the stress concentration dependent on the specimen shape. On the basis of this study, the small round-bar specimen was an acceptable candidate for evaluating the fatigue life using small specimen.

  12. Flexor tendon specimens in organ cultures.

    Science.gov (United States)

    Rank, F; Eiken, O; Bergenholtz, A; Lundborg, G; Erkel, L J

    1980-01-01

    The healing process of sectioned and subsequently sutured rabbit tendon segments was studied over a period of 3 weeks, using an organ culture technique. In one series, the tendon specimens were exposed to a chemically defined culture medium for nutrition. In two control series, the specimens were kept in the synovial cavity of the knee joint for varying periods of time, before being transferred to the culture medium. The tendons remained viable in the medium. The superficial tendon cells demonstrated the morphological characteristics of fibroblasts, but cellular fibroplasia could not be detected. The two control series subjected to synovia prior to transfer into the culture medium showed superficial repair similar to the findings in previous studies on healing capacity of tendon nourished by synovia. The investigation supports the hypothesis that superficial tendon cells are fibroblasts with a potential for repair and that synovia is an efficient nutrient medium. Thus, the beneficial effects on repair exercised by the tendon sheath function should be utilized in flexor tendon surgery.

  13. Automated clinical annotation of tissue bank specimens.

    Science.gov (United States)

    Gilbertson, John R; Gupta, Rajnish; Nie, Yimin; Patel, Ashokkumar A; Becich, Michael J

    2004-01-01

    Modern, molecular bio-medicine is driving a growing demand for extensively annotated tissue bank specimens. With careful clinical, pathologic and outcomes annotation, samples can be better matched to the research question at hand and experimental results better understood and verified. However, the difficulty and expense of detailed specimen annotation is well beyond the capability of most banks and has made access to well documented tissue a major limitation in medical re-search. In this context, we have implemented automated annotation of banked tissue by integrating data from three clinical systems--the cancer registry, the pathology LIS and the tissue bank inventory system--through a classical data warehouse environment. The project required modification of clinical systems, development of methods to identify patients between and map data elements across systems and the creation of de-identified data in data marts for use by researchers. The result has been much more extensive and accurate initial tissue annotation with less effort in the tissue bank, as well as dynamic ongoing annotation as the cancer registry follows patients over time.

  14. 46 CFR 4.06-40 - Specimen handling and shipping.

    Science.gov (United States)

    2010-10-01

    ... qualified to conduct tests on such specimens. A proper chain of custody must be maintained for each specimen... collection procedures of § 16.113 of this chapter and the chain of custody requirements of 49 CFR part 40...

  15. High Temperature Fatigue Life Evaluation Using Small Specimen

    National Research Council Canada - National Science Library

    NOGAMI, Shuhei; HISAKA, Chiaki; FUJIWARA, Masaharu; WAKAI, Eichi; HASEGAWA, Akira

    2017-01-01

    For developing the high temperature fatigue life evaluation method using small specimen, the effect of specimen size and test environment on the high temperature fatigue life of the reduced activation...

  16. Elastic-plastic analysis of the SS-3 tensile specimen

    Energy Technology Data Exchange (ETDEWEB)

    Majumdar, S. [Argonne National Lab., IL (United States)

    1998-09-01

    Tensile tests of most irradiated specimens of vanadium alloys are conducted using the miniature SS-3 specimen which is not ASTM approved. Detailed elastic-plastic finite element analysis of the specimen was conducted to show that, as long as the ultimate to yield strength ratio is less than or equal to 1.25 (which is satisfied by many irradiated materials), the stress-plastic strain curve obtained by using such a specimen is representative of the true material behavior.

  17. ORIGINAL ARTICLES Validity of oral mucosal transudate specimens ...

    African Journals Online (AJOL)

    samples, with DBS as the gold-standard specimen. Results. Paired DBS and OMT specimens were .... within 24 hours signified complete elution. Positive and negative control specimens provided by the ... Using the DBS as the gold standard test, HIV prevalence was 3.2% overall. Prevalence was highest in the 6 - 8-year ...

  18. Difference between actual vs. pathology prostate weight in TURP and radical robotic-assisted prostatectomy specimen

    Directory of Open Access Journals (Sweden)

    Szilveszter Lukacs

    2014-12-01

    Full Text Available Introduction To investigate and highlight the effect of formaldehyde induced weight reduction in transurethral resection of prostate (TURP and radical robotically-assisted prostatectomy (RALP specimen as a result of standard chemical fixation. Materials and Methods 51 patients were recruited from January 2013 to June 2013 who either underwent a TURP (n=26 or RALP (n=25. Data was collected prospectively by the operating surgeon who measured the native, unfixed histology specimen directly after operation. The specimens were fixed in 10% Formaldehyde Solution BP and sent to the pathology laboratory where after sufficient fixation period was re-weighed. Results Overall mean age 64.78 years, TURP mean age 68.31 years RALP mean age 61.12years. We found that the overall prostatic specimen (n=51 weight loss after fixation was a mean of 11.20% (3.78 grams (p≤0.0001. Subgroup analysis of the native TURP chips mean weight was 16.15 grams and formalin treated mean weight was 14.00 grams (p≤0.0001. Therefore, TURP chips had a mean of 13.32 % (2.15 grams weight loss during chemical fixation. RALP subgroup unfixed specimen mean weight was 52.08 grams and formalin treated mean weight was 42.60 grams (p≤0.0001, a 19.32 % (9.48grams mean weight reduction. Conclusion It has not been known that prostatic chips and whole human radical prostatectomy specimen undergo a significant weight reduction. The practical significance of the accurate prostate weight in patient management may be limited, however, it is agreed that this should be recorded correctly, as data is potential interest for research purposes and vital for precise documentation.

  19. Structure of wet specimens in electron microscopy. Improved environmental chambers make it possible to examine wet specimens easily.

    Science.gov (United States)

    Parsons, D F

    1974-11-01

    Several recent technological advances have increased the practicality and usefulness of the technique of electron microscopy of wet objects. (i) There have been gains in the effective penetration of high-voltage microscopes, scanning transmission microscopes, and high-voltage scanning microscopes. The extra effective penetration gives more scope for obtaining good images through film windows, gas, and liquid layers. (ii) Improved methods of obtaining contrast are available (especially dark field and inelastic filtering) that often make it possible to obtain sufficient contrast with wet unstained objects. (iii) Improved environmental chamber design makes it possible to insert and examine wet specimens as easily as dry specimens. The ultimate achievable resolution for wet objects in an environmental chamber will gradually become clear experimentally. Resolution is mainly a function of gas path, liquid and wet specimen thickness, specimen stage stability, acceleration voltage, and image mode (fixed or scanning beam) (13). Much depends on the development of the technique for controlling the thickness of extraneous water film around wet objects or the technique for depositing wet objects onto dry, hydrophobic support films. Although some loss of resolution due to water or gas scattering will always occur, an effective gain is anticipated in preserving the shape of individual molecules and preventing the partial collapse that usually occurs on drying or negative staining. The most basic question for biological electron microscopy is probably whether any living functions of cells can be observed so that the capabilities of the phase contrast and interference light microscopes can be extended. Investigators are now rapidly approaching a final answer to this question. The two limiting factors are (i) maintaining cell motility in spread cells immersed in thin layers of media and (ii) reducing beam radiation damage to an acceptable level. The use of sensitive emulsions and

  20. Apparatus and method for magnetically processing a specimen

    Science.gov (United States)

    Ludtka, Gerard M; Ludtka, Gail M; Wilgen, John B; Kisner, Roger A; Jaramillo, Roger A

    2013-09-03

    An apparatus for magnetically processing a specimen that couples high field strength magnetic fields with the magnetocaloric effect includes a high field strength magnet capable of generating a magnetic field of at least 1 Tesla and a magnetocaloric insert disposed within a bore of the high field strength magnet. A method for magnetically processing a specimen includes positioning a specimen adjacent to a magnetocaloric insert within a bore of a magnet and applying a high field strength magnetic field of at least 1 Tesla to the specimen and to the magnetocaloric insert. The temperature of the specimen changes during the application of the high field strength magnetic field due to the magnetocaloric effect.

  1. Evaluation of hybrid composite materials in cylindrical specimen geometries

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1976-01-01

    Static and fatigue properties of three composite materials and hybrids were examined. The materials investigated were graphite/epoxy, S-glass/epoxy, PRD-49 (Kevlar 49)/epoxy, and hybrids in angle-ply configurations. A new type of edgeless cylindrical specimen was developed. It is a flattened tube with two flat sides connected by curved sections and it is handled much like the standard flat coupon. Special specimen fabrication, tabbing, and tab region reinforcing techniques were developed. Axial modulus, Poisson's ratio, strength, and ultimate strain were obtained under static loading from flattened tube specimens of nine laminate configurations. In the case of graphite/epoxy the tubular specimens appeared to yield somewhat higher strength and ultimate strain values than flat specimens. Tensile fatigue tests were conducted with all nine types of specimens and S-N curves obtained. Specimens surviving 10 million cycles of tensile loading were subsequently tested statically to failure to determine residual properties.

  2. Gradient field microscopy of unstained specimens

    Science.gov (United States)

    Kim, Taewoo; Sridharan, Shamira; Popescu, Gabriel

    2012-01-01

    We present a phase derivative microscopy technique referred to as gradient field microscopy (GFM), which provides the first-order derivatives of the phase associated with an optical field passing through a transparent specimen. GFM utilizes spatial light modulation at the Fourier plane of a bright field microscope to optically obtain the derivatives of the phase and increase the contrast of the final image. The controllable spatial modulation pattern allows us to obtain both one component of the field gradient (derivative along one direction) and the gradient intensity, which offers some advantages over the regular differential interference contrast (DIC) microscopy. Most importantly, unlike DIC, GFM does not use polarizing optics and, thus, it is applicable to birefringent samples. We demonstrate these features of GFM with studies of static and dynamic biological cells (HeLa cells and red blood cells). We show that GFM is capable of qualitatively providing information about cell membrane fluctuations. Specifically, we captured the disappearance of the bending mode of fluctuations in osmotically swollen red blood cells. PMID:22418558

  3. Nerve degeneration in inguinal hernia specimens.

    Science.gov (United States)

    Amato, G; Ober, E; Romano, G; Salamone, G; Agrusa, A; Gulotta, G; Bussani, R

    2011-02-01

    The histological study of the herniated inguinal area is rare in the literature. This report is focused on the detection of structural changes of the nerves within tissues bordering the inguinal hernia of cadavers. Their physiopathological consequences are hypothesized. Primary inguinal hernia was diagnosed in 30 fresh cadavers. Tissue specimens from the inguinal region close to and around the hernia opening were excised for histological examination. A control of the data was achieved through tissue samples excised from equivalent sites of the inguinal region in 15 cadavers without hernia. The detected nerves in the inguinal area demonstrated pathological changes such as fibrotic degeneration, atrophy, and fatty dystrophy of the axons. The thickening of the perineural sheath was constantly seen. These findings were consistently present, independent of the hernia type. The detected nerve alterations lead us to imagine a worsening, or even the cessation, of the nervous impulse to the muscles, leading to atrophy and weakening of the abdominal wall. This could represent one of the multifactorial causes of hernia genesis.

  4. Limited flow cytometry panels on bone marrow specimens reduce costs and predict negative cytogenetics.

    Science.gov (United States)

    Hoffmann, Douglas G; Kim, Burton H

    2014-01-01

    To determine the clinical and financial impact and predictive value of a limited flow cytometry strategy in the evaluation of bone marrow specimens. Consecutive bone marrow cases (n = 1,242) were reviewed following the independent, prospective application of two flow cytometry protocols: a limited marker strategy and a multimarker strategy. Combined morphologic and flow cytometry findings were also compared with cytogenetic results. A limited flow cytometry strategy did not have a negative impact on disease detection and resulted in reduced utilization and cost. In addition, negative combined morphology and flow cytometry had a 98.4% predictive value for negative cytogenetics (P flow cytometric and cytogenetic studies on these samples.

  5. Evaluation of composite flattened tubular specimen. [fatigue tests

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1978-01-01

    Flattened tubular specimens of graphite/epoxy, S-glass/epoxy, Kevlar-49/epoxy, and graphite/S-glass/epoxy hybrid materials were evaluated under static and cyclic uniaxial tensile loading and compared directly with flat coupon data of the same materials generated under corresponding loading conditions. Additional development for the refinement of the flattened specimen configuration and fabrication was required. Statically tested graphite/epoxy, S-glass/epoxy, and Kevlar 49/epoxy flattened tube specimens exhibit somewhat higher average strengths than their corresponding flat coupons. Flattened tube specimens of the graphite/S-glass/epoxy hybrid and the graphite/epoxy flattened tube specimens failed in parasitic modes with consequential lower strength than the corresponding flat coupons. Fatigue tested flattened tube specimens failed in parasitic modes resulting in lower fatigue strengths than the corresponding flat coupons.

  6. "Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment.

    Directory of Open Access Journals (Sweden)

    John J Farrell

    Full Text Available PCR coupled with electrospray ionization mass spectrometry (ESI-MS is a diagnostic approach that has demonstrated the capacity to detect pathogenic organisms from culture negative clinical samples after antibiotic treatment has been initiated. [1] We describe the application of PCR/ESI-MS for detection of bacteria in original patient specimens that were obtained after administration of antibiotic treatment in an open investigation analysis.We prospectively identified cases of suspected bacterial infection in which cultures were not obtained until after the initiation of antimicrobial treatment. PCR/ESI-MS was performed on 76 clinical specimens that were submitted for conventional microbiology testing from 47 patients receiving antimicrobial treatment.In our series, 72% (55/76 of cultures obtained following initiation of antimicrobial treatment were non-diagnostic (45 negative cultures; and 10 respiratory specimens with normal flora (5, yeast (4, or coagulase-negative staphylococcus (1. PCR/ESR-MS detected organisms in 83% (39/47 of cases and 76% (58/76 of the specimens. Bacterial pathogens were detected by PCR/ESI-MS in 60% (27/45 of the specimens in which cultures were negative. Notably, in two cases of relapse of prosthetic knee infections in patients on chronic suppressive antibiotics, the previous organism was not recovered in tissue cultures taken during extraction of the infected knee prostheses, but was detected by PCR/ESI-MS.Molecular methods that rely on nucleic acid amplification may offer a unique advantage in the detection of pathogens collected after initiation of antimicrobial treatment and may provide an opportunity to target antimicrobial therapy and "salvage" both individual treatment regimens as well as, in select cases, institutional antimicrobial stewardship efforts.

  7. Prestress losses evaluation in prestressed concrete prismatic specimens

    OpenAIRE

    CARO FORERO, LIBARDO ANDRÉS; Martí Vargas, José Rocío; Serna Ros, Pedro

    2013-01-01

    This paper presents an experimental research work to evaluate prestress losses in pretensioned prestressed concrete. An experimental program including variables such as concrete mix design, specimen cross-section size and concrete age at the prestress transfer was carried out. Several pretensioned prestressed concrete prismatic specimens were made and tested using the ECADA+ test method, based on measuring prestressing reinforcement force. In addition, specimens were instrumented to obtain th...

  8. Fracture mechanics characterisation of medium-size adhesive joint specimens

    DEFF Research Database (Denmark)

    Sørensen, Bent F.; Jacobsen, T.K.

    2004-01-01

    Medium-size specimens (adhesive layer were tested in four point bending to determine their load carrying capacity. Specimens having different thickness were tested. Except for onespecimen, the cracking occurred as cracking...... along the adhesive layer; initially cracking occurred along the adhesive/laminate interface, but after some crack extension the cracking took place inside the laminate (for one specimen the later part of thecracking occurred unstably along the adhesive/ laminate interface). Crack bridging by fibres...

  9. Specimen Provenance Testing Identifies Contamination That Affects Molecular Prognostic Assay Results in Prostate Cancer Biopsy Specimens.

    Science.gov (United States)

    Wojno, Lathem; Minutella, Caitlyn; Moylan, Donald; Bush, Arla; Wojno, Kirk

    2018-02-21

    To determine if tissue contamination in histologic specimens can significantly affect the results of prognostic molecular markers that are routinely used as confirmatory tests to safely assign appropriate candidates to prostate cancer active surveillance protocols. This study evaluates 2,134 cases from a single, large urology practice that were successfully tested for DNA specimen provenance verification using short tandem repeat analysis for the presence of a significant level of contaminating DNA. After removal of the contamination, five of the samples were retested, and the results of the molecular diagnostic test were compared. 49 of the 2,134 cases (2.3%) sent for DNA provenance analysis were found to possess significant levels of contamination. Of these 49 cases, seven of them were resent for a repeat molecular diagnostic test after being decontaminated. Five of these prostate cancer specimens had sufficient tissue and RNA to give a more accurate cell cycle progression (CCP) score. The average absolute change in these patient's CCP scores was 0.48, with a low of a 0.1-unit and a high of a 1.0-unit difference. These changes in CCP scores are significant enough to cause meaningful alterations in a patient's calculated 10-year mortality rate, as defined by their combined risk score (CRS). DNA contamination in unstained tissue sections sent for prognostic prostate cancer molecular diagnostic testing occurs on 2.3% of cases, and can be of a magnitude that affects the results and subsequent clinical decision of appropriateness for active surveillance. Copyright © 2018. Published by Elsevier Inc.

  10. A freeze-fracture replication apparatus for biological specimens.

    Science.gov (United States)

    Stolinski, C

    1975-08-01

    A freeze-fracture apparatus of original design has been constructed which can be fitted onto a standard vacuum evaporator unit. In it, cell suspensions and organized tissue may be processed by inserting a sample into a cylindrical holder. By leaving a small part of the tissue protruding from the holder, pre-selected and aligned portions of the specimen can subsequently be revealed by fracture under vacuum. After rapid freezing, the specimen remains firmly attached to the inner wall of the sample holder, preventing its possible loss during fracturing. A mechanism, in the form of a double-sided converging wedge, which is operated from outside the vacuum chamber, is used to produce a fracture in the specimen. The device gently induces a fracture in the desired part of the tissue and lifts the protruding part of the specimen out of the way. In this way, reasonably flat fracture faces are produced for subsequent replication. As the fracturing mechanism comes into contact only with the outer edges of the specimen, damage and contamination liable to occur when the entire specimen is traversed by a blade, is avoided. In addition the specimen stage is surrounded by a cold metal shroud which acts as an efficient trap for contaminants. In this way, favourable vacuum conditions are produced in the vicinity of the specimen. Such effective enclosing of the specimen also facilitates controlled sublimation of the sample.

  11. Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

    Science.gov (United States)

    Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

    2016-10-01

    Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Analysis of off-axis tension test of wood specimens

    Science.gov (United States)

    Jen Y. Liu

    2002-01-01

    This paper presents a stress analysis of the off-axis tension test of clear wood specimens based on orthotropic elasticity theory. The effects of Poisson's ratio and shear coupling coefficient on stress distribution are analyzed in detail. The analysis also provides a theoretical foundation for the selection of a 10° grain angle in wood specimens for the...

  13. stomach contents of a specimen of proteles cristatus from angola

    African Journals Online (AJOL)

    north of Sa da Bandeira, Angola (at about 140. SO' Sjl3° 35' E). The skin and skull were deposited in the Alexander McGregor Memorial Museum. Kimberley, Cape (Collectors No. 276a). The stomach contents of this specimen are detailed in. Table I. The habitat where the specimen was obtained was degraded ...

  14. Design Analysis of the Mixed Mode Bending Sandwich Specimen

    DEFF Research Database (Denmark)

    Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

    2010-01-01

    . The analysis facilitates selection of the appropriate geometry for the MMB sandwich specimen to promote debond failure. An experimental study is performed using MMB sandwich specimens with a H100 PVC foam core and E-glass–polyester faces. The results reveal that debond propagation is successfully achieved...

  15. A Debonded Sandwich Specimen Under Mixed Mode Bending (MMB)

    DEFF Research Database (Denmark)

    Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

    2008-01-01

    for the MMB specimen were derived from a superposition analysis. An experimental verification of the methodology proposed was performed using MMB sandwich specimens with H100 PVC foam core and E-glass/polyester non-crimp quadro-axial [0/45/90/-45]s DBLT-850 faces. Different mixed mode loadings were applied...

  16. Validity of oral mucosal transudate specimens for HIV testing using ...

    African Journals Online (AJOL)

    The overall sensitivity of OMT specimens for HIV testing in children using ELISA was low. Stratifying the analysis by sector showed that OMT samples are good specimens for HIV testing. It is important to note that factors such as the low HIV prevalence in our study population, quality of the OMT, diet and oral hygiene could ...

  17. 16 CFR Figures 3 and 4 to Subpart... - Test Specimens

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test Specimens 3 Figures 3 and 4 to Subpart... REGULATIONS SAFETY STANDARD FOR ARCHITECTURAL GLAZING MATERIALS The Standard Pt. 1201, Subpt. A, Figs. 3, 4 Figures 3 and 4 to Subpart A of Part 1201—Test Specimens EC03OC91.006 ...

  18. Progress towards an optimal specimen support for electron cryomicroscopy.

    Science.gov (United States)

    Russo, Christopher J; Passmore, Lori A

    2016-04-01

    The physical principles of electron-specimen interaction govern the design of specimen supports for electron cryomicroscopy (cryo-EM). Supports are constructed to suspend biological samples within the vacuum of the electron microscope in a way that maximises image contrast. Although the problem of specimen motion during imaging has been known since cryo-EM was first developed, the role of the support in this movement has only been recently identified. Here we review the key technological advances in specimen supports for cryo-EM. This includes the use of graphene as a surface for the adsorption of proteins and the design of an ultrastable, all-gold substrate that reduces the motion of molecules during electron irradiation. We discuss the implications of these and other recent improvements in specimen supports on resolution, and place them in the context of important developments in structure determination by cryo-EM. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Tensile strength of various nylon PA6 specimen modes

    Science.gov (United States)

    Raz, Karel; Zahalka, Martin

    2017-05-01

    This article explores the influence of production technique on the strength of nylon parts. Identical specimens were manufactured by various techniques. The material of specimens was nylon PA6. 3D printing and injection molding were used, with various orientations of printed layers, and various orientations of specimens in the working space of the 3D printer. The variants are described in detail. A special mold was used for the injection molding process in order to make specimens with and without a weld line. The effect of this weld line was evaluated. All specimens were tested using the standard tensile test configuration. The strength was compared. It was found that the same plastic material has very different mechanical properties depending on the production process.

  20. Shape optimization of shear fracture specimen considering plastic anisotropy

    Science.gov (United States)

    Zhang, S.; Yoon, J. W.; Lee, S.; Lou, Y.

    2017-10-01

    It is important to fabricate fracture specimens with minimum variation of triaxiality in order to characterize the failure behaviors experimentally. Fracture in ductile materials is usually calibrated by uniaxial tensile, shear and plane strain tests. However, it is often observed that triaxiality for shear specimen changes severely during shear fracture test. The nonlinearity of triaxiality is most critical for shear test. In this study, a simple in-plane shear specimen is optimized by minimizing the variation of stress triaxiality in the shear zone. In the optimization, the Hill48 and Yld2000-2d criteria are employed to model the anisotropic plastic deformation of an aluminum alloy of 6k21. The evolution of the stress triaxiality of the optimized shear specimen is compared with that of the initial design of the shear specimen. The comparison reveals that the stress triaxiality changes much less for the optimized shear specimen than the evolution of the stress triaxiality with the original design of the shear specimen.

  1. Effect of specimen size on work-of-fracture measurements.

    Science.gov (United States)

    Rogers, L L; Moyle, D D

    1988-01-01

    It has been suggested that work-of-fracture, which quantifies the ability of a material to resist fracture, is dependent on specimen size. This experiment compared work-of-fracture, calculated as energy per unit area, for different specimen sizes of Plexiglas, bovine tibial bone and aluminum. Three different geometrically similar cross sections were tested for each material for a total of 54 specimens. Work-of-fracture was measured by loading a notched beam (triangular cross section) in three-point bending at a constant deformation rate. The energy necessary to cause fracture was measured from a load-deformation curve. Specimen fracture area was determined using macrophotography. Atomic absorption spectrophotometry was used to determine weight percent calcium of bone specimens and quantitative light microscopy was used to determine fractional void area. Analysis of variance showed no effect of specimen size on work-of-fracture for aluminum or Plexiglas specimens (p greater than 0.05). A significant difference was found, however, between the large (area = 11.7 +/- 1.9 mm2) and small (area = 3.48 +/- 0.68 mm2) bone specimens and between the medium (area = 5.89 +/- 0.69 mm2) and small (area = 3.48 +/- 0.68 mm2) bone specimens. No correlation was found between work-of-fracture and either calcium content (r2 = 0.128) or fractional void area (r2 = 0.0713). The mean work-of-fracture values found are as follows: aluminum, 59.8 +/- 13.7 kJ m-2; Plexiglas, 0.620 +/- 0.074 kJ m-2; bone (area 5.89 +/- 0.69 mm2-11.7 +/- 1.9 mm2), 9.72 +/- 1.93 kJ m-2 and bone (area 3.48 +/- 0.68 mm2), 5.48 +/- 1.79 kJ m-2.

  2. Final Report: Posttest Analysis of Omega II Optical Specimens

    Energy Technology Data Exchange (ETDEWEB)

    Newlander, C D; Fisher, J H

    2007-01-30

    Preliminary posttest analyses have been completed on optical specimens exposed during the Omega II test series conducted on 14 July 2006. The Omega Facility, located at the Laboratory for Laser Energetics (LLE) at the University of Rochester was used to produce X-ray environments through the interaction of intense pulsed laser radiation upon germanium-loaded silica aerogels. The optical specimen testing was supported by GH Systems through experiment design, pre- and post-test analyses, specimen acquisition, and overall technical experience. The test specimens were fabricated and characterized by Surface Optics Corporation (SOC), San Diego, CA and were simple protected gold coatings on silica substrates. Six test specimens were exposed, five filtered with thin beryllium foil filters, and one unfiltered which was exposed directly to the raw environment. The experimental objectives were: (1) demonstrate that tests of optical specimens could be performed at the Omega facility; (2) evaluate the use and survivability of beryllium foil filters as a function of thickness; (3) obtain damage data on optical specimens which ranged from no damage to damage; (4) correlate existing thermal response models with the damage data; (5) evaluate the use of the direct raw environment upon the specimen response and the ability/desirability to conduct sensitive optical specimen tests using the raw environment; and (6) initiate the development of a protocol for performing optical coatings/mirror tests. This report documents the activities performed by GH Systems in evaluating and using the environments provided by LLNL, the PUFFTFT analyses performed using those environments, and the calculated results compared to the observed and measured posttest data.

  3. Fabrication and testing of prestressed composite rotor blade spar specimens

    Science.gov (United States)

    Gleich, D.

    1974-01-01

    Prestressed composite spar specimens were fabricated and evaluated by crack propagation and ballistic penetration tests. The crack propagation tests on flawed specimens showed that the prestressed composite spar construction significantly suppresses crack growth. Damage from three high velocity 30 caliber projectile hits was confined to three small holes in the ballistic test specimen. No fragmentation or crack propagation was observed indicating good ballistic damage resistance. Rotor attachment approaches and improved structural performance configurations were identified. Design theory was verified by tests. The prestressed composite spar configuration consisted of a compressively prestressed high strength ARDEFORM 301 stainless steel liner overwrapped with pretensioned S-994 fiberglass.

  4. Small Specimen Data from a High Temperature HFIR Irradiation Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Burchell, Timothy D [ORNL; McDuffee, Joel Lee [ORNL; Thoms, Kenneth R [ORNL

    2014-01-01

    The HTV capsule is a High Flux Isotope Reactor (HFIR) target-rod capsule designed to operate at very high temperatures. The graphite containing section of the capsule (in core) is approximately 18 inches (457.2 mm) long and is separated into eight temperature zones. The specimen diameters within each zone are set to achieve the desired gas gap and hence design temperature (900 C, 1200 C or 1500 C). The capsule has five zones containing 0.400 inch (10.16 mm) diameter specimens, two zones containing 0.350 inch (8.89 mm) diameter specimens and one zone containing 0.300 inch (7.62 mm) diameter specimens. The zones have been distributed within the experiment to optimize the gamma heating from the HFIR core as well as minimize the axial heat flow in the capsule. Consequently, there are two 900 C zones, three 1200 C zones, and three 1500 C zones within the HTV capsule. Each zone contains nine specimens 0.210 0.002 inches (5.334 mm) in length. The capsule will be irradiated to a peak dose of 3.17 displacements per atom. The HTV specimens include samples of the following graphite grades: SGL Carbon s NBG-17 and NBG-18, GrafTech s PCEA, Toyo Tanso s IG-110, Mersen s 2114 and the reference grade H-451 (SGL Carbon). As part of the pre-irradiation program the specimens were characterized using ASTM Standards C559 for bulk density, and ASTM C769 for approximate Young s modulus from the sonic velocity. The probe frequency used for the determination of time of flight of the ultrasonic signal was 2.25 MHz. Marked volume (specimen diameter) effects were noted for both bulk density (increased with increasing specimen volume or diameter) and Dynamic Young s modulus (decreased with increasing specimen volume or diameter). These trends are extended by adding the property vs. diameter data for unirradiated AGC-1 creep specimens (nominally 12.5 mm-diameter x 25.4 mm-length). The relatively large reduction in Dynamic Young s Modulus was surprising given the trend for increasing density

  5. Post-deformation examination of specimens subjected to SCC testing

    Energy Technology Data Exchange (ETDEWEB)

    Gussev, Maxim N. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Field, Kevin G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Busby, Jeremy T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Leonard, Keith J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-01

    This report details the results of post-radiation and post-deformation characterizations performed during FY 2015–FY 2016 on a subset of specimens that had previously been irradiated at high displacement per atom (dpa) damage doses. The specimens, made of commercial austenitic stainless steels and alloys, were subjected to stress-corrosion cracking tests (constant extension rate testing and crack growth testing) at the University of Michigan under conditions typical of nuclear power plants. After testing, the specimens were returned to Oak Ridge National Laboratory (ORNL) for further analysis and evaluation.

  6. Edgeless composite laminate specimen for static and fatigue testing

    Science.gov (United States)

    Liber, T.; Daniel, I. M.

    1978-01-01

    The influence of edge effects on the tensile properties of angle-ply laminate composites can be eliminated by using edgeless (round tubular) specimens. However, uniaxial tests with such specimens, static and fatigue, have been generally unsuccessful because of the differential Poisson effect between the test section and the grips. An edgeless cylindrical specimen, developed to circumvent these difficulties, is examined in the present paper. It is a flattened tube consisting of two flat sides connected by curved sections. It can be handled much like the standard flat coupon. The flat ends of the specimen are provided with crossplied fiberglass gripping tabs, the same as used for flat test coupons. As part of the tabbing, the hollow ends must be plugged with inserts to prevent crushing of the ends. A special insert design was developed to minimize detrimental Poisson effects ordinarily introduced by inserts.

  7. Replacement/Refurbishment of JSC/NASA POD Specimens

    Science.gov (United States)

    Castner, Willard L.

    2010-01-01

    The NASA Special NDE certification process requires demonstration of NDE capability by test per NASA-STD-5009. This test is performed with fatigue cracked specimens containing very small cracks. The certification test results are usually based on binomial statistics and must meet a 90/95 Probability of Detection (POD). The assumption is that fatigue cracks are tightly closed, difficult to detect, and inspectors and processes passing such a test are well qualified for inspecting NASA fracture critical hardware. The JSC NDE laboratory has what may be the largest inventory that exists of such fatigue cracked NDE demonstration specimens. These specimens were produced by the hundreds in the late 1980s and early 1990s. None have been produced since that time and the condition and usability of the specimens are questionable.

  8. Description of Specimens in the Marine Mammal Osteology Reference Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NMFS Alaska Fisheries Science Center National Marine Mammal Laboratory (NMML) Marine Mammal Osteology Collection consists of approximately 2500 specimens (skulls...

  9. North Mississippi Refuges Complex Dragonfly Vouchered Specimens 2005

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report contains a list of dragonflies and photographs of them collected in 2005 from the refuge complex. These were verified by Steve Krotzer and specimens retained...

  10. Control of Contamination in Psittacosis Specimens by Antibiotics

    Science.gov (United States)

    Lewis, Vester J.; Engelman, Helen M.

    1971-01-01

    Diluent containing a combination of vancomycin, kanamycin, and streptomycin is shown to be more effective than diluent previously used for isolating Chlamydia psittaci from bird tissue specimens. PMID:4940879

  11. Specimen thickness effect on elastic-plastic constraint parameter A

    National Research Council Canada - National Science Library

    GP Nikishkov; YuG Matvienko

    2015-01-01

    .... Distributions of the J-integral and constraint parameter A along the crack front for varying specimen thickness and crack depth are determined for edge cracked plate, center cracked plate, three...

  12. A general mixed mode fracture mechanics test specimen: The DCB-specimen loaded with uneven bending moments

    DEFF Research Database (Denmark)

    Sørensen, Bent F.; Jørgensen, K.; Jacobsen, T.K.

    2004-01-01

    glass-fibre laminates was studied. The mixed mode fracture resistance increased with increasing crack length due to fibre bridging, eventually reaching asteady-state level (R-curve behaviour). The steady-state fracture toughness level increased with increasing tangential crack opening displacement.......A mixed mode specimen is proposed for fracture mechanics characterisation of adhesive joints, laminates and multilayers. The specimen is a double cantilever beam specimen loaded with uneven bending moments at the two free beams. By varying the ratiobetween the two applied moments, the full mode...

  13. Improved PID control for triaxial testing liquefied specimen

    DEFF Research Database (Denmark)

    Sabaliauskas, Tomas; Ibsen, Lars Bo

    Using a frictionless triaxial apparatus, sand specimens can be tested at relatively high axial strains, even while liquefying. However, liquefying specimens have extremely nonlinear stiffness, thus standard PID control does not perform well. To maintain control over applied loads, the PID...... controller was modified to adapt to disturbed soil states. The proposed methods expand the scope of testing towards options which are otherwise inaccessible by triaxial testing....

  14. Section planes of snow specimens visualized with sudan black B

    OpenAIRE

    ハチクボ, アキヒロ; アラカワ, ハヤト; ニシダ; フクザワ, タクヤ; アキタヤ, エイジ; Akihiro, HACHIKUBO; Hayato, Arakawa; Kenlo, Nishida; Takuya, Fukuzawa; Eizi, AKITAYA

    2000-01-01

    A technique for preparing section planes of snow specimens dyed with sudan black B was introduced. After the pour space of a snow specimen is filled with aniline and frozen solid, a section plane is microtomed and rubbed with sudan black B powder for contrast enhancement. Compared with previous methods, this technique was simple and provided high-contrast images and reduction of noise on a section plane.

  15. Fe-based magnetic shape memory alloy-sheet specimen

    Science.gov (United States)

    Kanada, Tsugunori; Enokizono, Masato

    1999-05-01

    We contrived a new composite functional alloy which is compatible for both magnetization and the shape memory effect (SME). A FeMnSiCr alloy, one of the shape memory alloys (SMA) has strong magnetization in addition to SME after heating in air. It is because the specimen is composed of a ferromagnetic iron oxide Fe 3O 4 (magnetite) surface layer, the inside being SMA. The measurements were carried out on a sheet specimen.

  16. Progress Report on Alloy 617 Notched Specimen Testing

    Energy Technology Data Exchange (ETDEWEB)

    McMurtrey, Michael David [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wright, Richard Neil [Idaho National Lab. (INL), Idaho Falls, ID (United States); Lillo, Thomas Martin [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-08-01

    Creep behavior of Alloy 617 has been extensively characterized to support the development of a draft Code Case to qualify Alloy 617 in Section III division 5 of the ASME Boiler and Pressure Vessel Code. This will allow use of Alloy 617 in construction of nuclear reactor components at elevated temperatures and longer periods of time (up to 950°C and 100,000 hours). Prior to actual use, additional concerns not considered in the ASME code need to be addressed. Code Cases are based largely on uniaxial testing of smooth gage specimens. In service conditions, components will generally be under multi axial loading. There is also the concern of the behavior at discontinuities, such as threaded components. To address the concerns of multi axial creep behavior and at geometric discontinuities, notched specimens have been designed to create conditions representative of the states that service components experience. Two general notch geometries have been used for these series of tests: U notch and V notch specimens. The notches produce a tri axial stress state, though not uniform across the specimen. Characterization of the creep behavior of the U notch specimens and the creep rupture behavior of the V notch specimens provides a good approximation of the behavior expected of actual components. Preliminary testing and analysis have been completed and are reported in this document. This includes results from V notch specimens tested at 900°C and 800°C. Failure occurred in the smooth gage section of the specimen rather than at the root of the notch, though some damage was present at the root of the notch, where initial stress was highest. This indicates notch strengthening behavior in this material at these temperatures.

  17. Stress Analysis of a Secondary-Bending Specimen

    Science.gov (United States)

    1993-11-01

    Control Office Ansett Airlines of Australia, Library 0 Qantas Airways Limited Hawker de Havilland Aust Pty Ltd, Victoria, Library Hawker de Havilland...elements are also used to restrict the movement 0 of linked nodes, however, in a limited way. They enable the adjacent components to separate and slide but...sketch of the specimen for clarity. The presence of the SPATE signal outside the boundary of the specimen is due to limitations in the depth of field of

  18. Biaxial Testing of 2195 Aluminum Lithium Alloy Using Cruciform Specimens

    Science.gov (United States)

    Johnston, W. M.; Pollock, W. D.; Dawicke, D. S.; Wagner, John A. (Technical Monitor)

    2002-01-01

    A cruciform biaxial test specimen was used to test the effect of biaxial load on the yield of aluminum-lithium alloy 2195. Fifteen cruciform specimens were tested from 2 thicknesses of 2195-T8 plate, 0.45 in. and 1.75 in. These results were compared to the results from uniaxial tensile tests of the same alloy, and cruciform biaxial tests of aluminum alloy 2219-T87.

  19. Intraoperative specimen radiography in patients with nonpalpable malignant breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Schmachtenberg, C.; Engelken, F.; Fischer, T.; Bick, U.; Poellinger, A.; Fallenberg, E.M. [Charite, Berlin (Germany). Radiology

    2012-07-15

    Purpose: Specimen mammography of nonpalpable wire-localized breast lesions is the standard in breast-conserving surgery. The aim of this study was to evaluate the reliability of intraoperative 2-view specimen mammography in different cancer types. Materials and Methods: After ethics approval, 3 readers retrospectively evaluated margins on 266 2-view specimen radiographs. They determined the closest margin and the orientation. The results were correlated with the histopathology (intra-class correlation coefficient [ICC] and contingency coefficient [CC]) and compared (Wilcoxon test). Results: Invasive ductal carcinoma (IDC) with ductal carcinoma in situ (DCIS) was present in 115 (43 %), IDC in 75 (28 %), invasive lobular carcinoma (ILC) in 57 (22 %) and rare cancers (CA) in 19 specimens (7 %). The sensitivity/specificity and positive/negative predictive value (P/NPV) of specimen mammography were 0.50/0.86 and 0.86/0.50 for CA, 0.42/0.68 and 0.48/0.63 for IDC, 0.36/0.81 and 0.69/0.51 for ILC, and 0.22/0.78 and 0.68/0.32 for IDC+DCIS. Readers correctly identified the orientation of the closest margin in at least one view in an average of 149 specimens (56 %). CCs were between 0.680 (IDC) and 0.912 (CA), suggesting a moderate correlation between radiographic and histological orientation. The correlations were worse for the radiographic and histological distances, with ICC ranging from 0.238 (ILC) to 0.475 (CA). The Wilcoxon test revealed overestimation of the radiographic margins compared to the histological ones for DCIS. Conclusion: Our results suggest that specimen radiography has relatively good overall specificity and good PPV, while the sensitivity and NPV are low for DCIS. A negative result on specimen radiography does not rule out histologically involved margins. (orig.)

  20. Specimen Sample Preservation for Cell and Tissue Cultures

    Science.gov (United States)

    Meeker, Gabrielle; Ronzana, Karolyn; Schibner, Karen; Evans, Robert

    1996-01-01

    The era of the International Space Station with its longer duration missions will pose unique challenges to microgravity life sciences research. The Space Station Biological Research Project (SSBRP) is responsible for addressing these challenges and defining the science requirements necessary to conduct life science research on-board the International Space Station. Space Station will support a wide range of cell and tissue culture experiments for durations of 1 to 30 days. Space Shuttle flights to bring experimental samples back to Earth for analyses will only occur every 90 days. Therefore, samples may have to be retained for periods up to 60 days. This presents a new challenge in fresh specimen sample storage for cell biology. Fresh specimen samples are defined as samples that are preserved by means other than fixation and cryopreservation. The challenge of long-term storage of fresh specimen samples includes the need to suspend or inhibit proliferation and metabolism pending return to Earth-based laboratories. With this challenge being unique to space research, there have not been any ground based studies performed to address this issue. It was decided hy SSBRP that experiment support studies to address the following issues were needed: Fixative Solution Management; Media Storage Conditions; Fresh Specimen Sample Storage of Mammalian Cell/Tissue Cultures; Fresh Specimen Sample Storage of Plant Cell/Tissue Cultures; Fresh Specimen Sample Storage of Aquatic Cell/Tissue Cultures; and Fresh Specimen Sample Storage of Microbial Cell/Tissue Cultures. The objective of these studies was to derive a set of conditions and recommendations that can be used in a long duration microgravity environment such as Space Station that will permit extended storage of cell and tissue culture specimens in a state consistent with zero or minimal growth, while at the same time maintaining their stability and viability.

  1. Failed PCR of Ganoderma type specimens affects nomenclature.

    Science.gov (United States)

    Paterson, R R M; Lima, N

    2015-06-01

    The nomenclature of Ganoderma used as a Chinese medicine is debated. A group of researchers could not amplify the DNA of type specimens and concluded the DNA was degraded irreparably. New topotypes were used as the type specimens which was premature. The use of internal amplification controls is recommended to determine if other factors were involved as alternative explanations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Specimen aspect ratio and light transmission in photoactive dental resins.

    Science.gov (United States)

    Hadis, Mohammed A; Shortall, Adrian C; Palin, William M

    2012-11-01

    To test the influence of specimen dimensions on light transmission and shrinkage strain properties of curing dental resins. Photocurable resin specimens (Bis-GMA/TEGDMA) with aspect ratios (AR) of 2 (4mm×2mm); 4 (4mm×1mm and 8mm×2mm); 8 (8mm×1mm); 12 (AR: 12mm×1mm); and 24 (12mm×0.5mm) were light cured. Light transmission and shrinkage-strain data were recorded throughout, and upper and lower surface hardness measurements were performed following cure. Light transmission was significantly affected by the specimen aspect ratio even at similar thicknesses (presin without photoinitiator, the lowest AR specimens showed a relative increase in transmission above 100% throughout curing, which was caused by specimen constraint. The extent of lower surface cure (as assessed by increasing hardness) was principally affected by cavity height and decreased for thicker specimens (presin-based restorations through depth. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  3. HER2 testing on core needle biopsy specimens from primary breast cancers: interobserver reproducibility and concordance with surgically resected specimens

    Directory of Open Access Journals (Sweden)

    Yamamoto Sohei

    2010-10-01

    Full Text Available Abstract Background Accurate evaluation of human epidermal growth factor receptor type-2 (HER2 status based on core needle biopsy (CNB specimens is mandatory for identification of patients with primary breast cancer who will benefit from primary systemic therapy with trastuzumab. The aim of the present study was to validate the application of HER2 testing with CNB specimens from primary breast cancers in terms of interobserver reproducibility and comparison with surgically resected specimens. Methods A total of 100 pairs of archival formalin-fixed paraffin-embedded CNB and surgically resected specimens of invasive breast carcinomas were cut into sections. All 100 paired sections were subjected to HER2 testing by immunohistochemistry (IHC and 27 paired sections were subjected to that by fluorescence in situ hybridization (FISH, the results being evaluated by three and two observers, respectively. Interobserver agreement levels in terms of judgment and the concordance of consensus scores between CNB samples and the corresponding surgically resected specimens were estimated as the percentage agreement and κ statistic. Results In CNB specimens, the percentage interobserver agreement of HER2 scoring by IHC was 76% (κ = 0.71 for 3 × 3 categories (0-1+ versus 2+ versus 3+ and 90% (κ = 0.80 for 2 × 2 categories (0-2+ versus 3+. These levels were close to the corresponding ones for the surgically resected specimens: 80% (κ = 0.77 for 3 × 3 categories and 92% (κ = 0.88 for 2 × 2 categories. Concordance of consensus for HER2 scores determined by IHC between CNB and the corresponding surgical specimens was 87% (κ = 0.77 for 3 × 3 categories, and 94% (κ = 0.83 for 2 × 2 categories. Among the 13 tumors showing discordance in the mean IHC scores between the CNB and surgical specimens, the results of consensus for FISH results were concordant in 11. The rate of successful FISH analysis and the FISH positivity rate in cases with a HER2 IHC score of

  4. Induced Polarization Responses of the Specimen with Sulfide Ore Minerals

    Science.gov (United States)

    Park, S.; Sung, N. H.

    2012-04-01

    Basic data of the physical properties of the rocks is required to effectively interpret geologic structures and mineralized zones in study areas from the geophysical data in the field of subsurface investigations and mineral resources explorations. In this study, the spectral induced polarization (SIP) measurement system in the laboratory was constructed to obtain the IP characteristics of the specimen with sulfide ore minerals. The SIP measurement system consists of lab transmitter for electrical current transmission, and GDP-32 for current receiver. The SIP system employs 14 steps of frequencies from 0.123 to 1,024 Hz, and uses copper sulfate solution as an electrolyte. The SIP data for system verification was acquired using a measurement system of parallel circuit with fixed resistance and condenser. This measured data was in good agreement with Cole-Cole model data. First of all, the experiment on the SIP response was conducted in the laboratory with the mixture of glass beads and pyrite powders for ore grade assessment using characteristics of IP response of the rocks. The results show that the phase difference of IP response to the frequency is nearly proportional to the weight content of pyrite, and that the dominant frequency of the IP response varies with the size of the pyrite powder. Subsequently, the specimens used for SIP measurement are slate and limestone which were taken from drilling cores and outcrops of skarn ore deposits. All specimens are cylindrical in shape, with a diameter of 5 cm and a length of 10 cm. When measuring SIP of water-saturated specimens, the specimen surface is kept dry, tap water is put into the bottom of sample holder and a lid is closed. It is drawn that the SIP characteristics of the rocks show the phase difference depends on the amount of the sulfide minerals. The phase difference did not occur with frequencies applied in the absence of sulfide minerals in the rock specimens. On the contrary, the rock specimens containing

  5. Microwave applications to rock specimen drying in laboratory

    Science.gov (United States)

    Park, Jihwan; Park, Hyeong-Dong

    2014-05-01

    Microwave heating is the process in which electromagnetic wave with 300 MHz - 300 GHz heats dielectric material. Although in the beginning microwave was mainly used in food industry to cook or heat the food, it soon became clear that microwave had a large potential for other applications. It was thus introduced in geological fields of investigation like mineral processing, oil sand and oil shale extraction, soil remediation, waste treatment. However, the drying techniques using microwave was rarely treated in geology field. According to the ISRM suggested methods, experimental rock specimens in laboratory test were dried in 105°C oven for a period of at least 24 hours. In this method, hot air transmits heats to material by means of thermal conduction, and the heat was transferred from the surface to the inside of the rock specimens. The thermal gradient and moisture gradient can deteriorate the specimens, and energy can be wasted in bulk heating the specimens. The aim of our study was to compare physical property, microstructural property, and energy efficiency between microwave drying method and conventional oven drying method, and to suggest new method for rock drying. Granite, basalt, and sandstone were selected as specimens and were made in cylinder shape with 54 mm diameter. To compare two different methods, one set of saturated specimens were dried in 105°C conventional oven and the other set of saturated specimens were dried in microwave oven. After dried, the specimens were cooled and saturated in 20°C water 48 hours. The saturation-drying were repeated 50 cycles, and the physical property and microstructural property were measured every 10 cycles. Absorption and elastic wave velocity were measured to investigate the change of physical property, and microscope image and X-ray computed tomography image were obtained to investigate the change of microstructural property of rock specimens. The electricity consumption of conventional oven and microwave oven

  6. Design optimization of cruciform specimens for biaxial fatigue loading

    Directory of Open Access Journals (Sweden)

    R. Baptista

    2014-10-01

    Full Text Available In order to correctly assess the biaxial fatigue material properties one must experimentally test different load conditions and stress levels. With the rise of new in-plane biaxial fatigue testing machines, using smaller and more efficient electrical motors, instead of the conventional hydraulic machines, it is necessary to reduce the specimen size and to ensure that the specimen geometry is appropriated for the load capacity installed. At the present time there are no standard specimen’s geometries and the indications on literature how to design an efficient test specimen are insufficient. The main goal of this paper is to present the methodology on how to obtain an optimal cruciform specimen geometry, with thickness reduction in the gauge area, appropriated for fatigue crack initiation, as a function of the base material sheet thickness used to build the specimen. The geometry is optimized for maximum stress using several parameters, ensuring that in the gauge area the stress is uniform and maximum with two limit phase shift loading conditions. Therefore the fatigue damage will always initiate on the center of the specimen, avoiding failure outside this region. Using the Renard Series of preferred numbers for the base material sheet thickness as a reference, the reaming geometry parameters are optimized using a derivative-free methodology, called direct multi search (DMS method. The final optimal geometry as a function of the base material sheet thickness is proposed, as a guide line for cruciform specimens design, and as a possible contribution for a future standard on in-plane biaxial fatigue tests.

  7. 3D volume reconstruction from serial breast specimen radiographs for mapping between histology and 3D whole specimen imaging.

    Science.gov (United States)

    Mertzanidou, Thomy; Hipwell, John H; Reis, Sara; Hawkes, David J; Ehteshami Bejnordi, Babak; Dalmis, Mehmet; Vreemann, Suzan; Platel, Bram; van der Laak, Jeroen; Karssemeijer, Nico; Hermsen, Meyke; Bult, Peter; Mann, Ritse

    2017-03-01

    In breast imaging, radiological in vivo images, such as x-ray mammography and magnetic resonance imaging (MRI), are used for tumor detection, diagnosis, and size determination. After excision, the specimen is typically sliced into slabs and a small subset is sampled. Histopathological imaging of the stained samples is used as the gold standard for characterization of the tumor microenvironment. A 3D volume reconstruction of the whole specimen from the 2D slabs could facilitate bridging the gap between histology and in vivo radiological imaging. This task is challenging, however, due to the large deformation that the breast tissue undergoes after surgery and the significant undersampling of the specimen obtained in histology. In this work, we present a method to reconstruct a coherent 3D volume from 2D digital radiographs of the specimen slabs. To reconstruct a 3D breast specimen volume, we propose the use of multiple target neighboring slices, when deforming each 2D slab radiograph in the volume, rather than performing pairwise registrations. The algorithm combines neighborhood slice information with free-form deformations, which enables a flexible, nonlinear deformation to be computed subject to the constraint that a coherent 3D volume is obtained. The neighborhood information provides adequate constraints, without the need for any additional regularization terms. The volume reconstruction algorithm is validated on clinical mastectomy samples using a quantitative assessment of the volume reconstruction smoothness and a comparison with a whole specimen 3D image acquired for validation before slicing. Additionally, a target registration error of 5 mm (comparable to the specimen slab thickness of 4 mm) was obtained for five cases. The error was computed using manual annotations from four observers as gold standard, with interobserver variability of 3.4 mm. Finally, we illustrate how the reconstructed volumes can be used to map histology images to a 3D specimen

  8. AGC-2 Specimen Post Irradiation Data Package Report

    Energy Technology Data Exchange (ETDEWEB)

    Windes, William Enoch [Idaho National Lab. (INL), Idaho Falls, ID (United States); Swank, W. David [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rohrbaugh, David T. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cottle, David L. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-08-01

    This report documents results of the post-irradiation examination material property testing of the creep, control, and piggyback specimens from the irradiation creep capsule Advanced Graphite Creep (AGC)-2 are reported. This is the second of a series of six irradiation test trains planned as part of the AGC experiment to fully characterize the neutron irradiation effects and radiation creep behavior of current nuclear graphite grades. The AGC-2 capsule was irradiated in the Idaho National Laboratory Advanced Test Reactor at a nominal temperature of 600°C and to a peak dose of 5 dpa (displacements per atom). One-half of the creep specimens were subjected to mechanical stresses (an applied stress of either 13.8, 17.2, or 20.7 MPa) to induce irradiation creep. All post-irradiation testing and measurement results are reported with the exception of the irradiation mechanical strength testing, which is the last destructive testing stage of the irradiation testing program. Material property tests were conducted on specimens from 15 nuclear graphite grades using a similar loading configuration as the first AGC capsule (AGC-1) to provide easy comparison between the two capsules. However, AGC-2 contained an increased number of specimens (i.e., 487 total specimens irradiated) and replaced specimens of the minor grade 2020 with the newer grade 2114. The data reported include specimen dimensions for both stressed and unstressed specimens to establish the irradiation creep rates, mass and volume data necessary to derive density, elastic constants (Young’s modulus, shear modulus, and Poisson’s ratio) from ultrasonic time-of-flight velocity measurements, Young’s modulus from the fundamental frequency of vibration, electrical resistivity, and thermal diffusivity and thermal expansion data from 100–500°C. No data outliers were determined after all measurements were completed. A brief statistical analysis was performed on the irradiated data and a limited comparison between

  9. Standard Guide for Reconstitution of Irradiated Charpy-Sized Specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2007-01-01

    1.1 This guide covers procedures for the reconstitution of ferritic pressure boundary steels used in nuclear power plant applications, Type A Charpy (Test Methods E 23) specimens and specimens suitable for testing in three point bending in accordance with Test Methods E 1921 or E 1820. Materials from irradiation programs (principally broken specimens) are reconstituted by welding end tabs of similar material onto remachined specimen sections that were unaffected by the initial test. Guidelines are given for the selection of suitable specimen halves and end tab materials, for dimensional control, and for avoidance of overheating the notch area. A comprehensive overview of the reconstitution methodologies can be found in Ref (1). 1.2 The values stated in SI units are to be regarded as the standard. The values given in parentheses are for information only. This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard...

  10. Small specimen technique for assessing mechanical properties of metallic components

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, Raquel M.; Andrade, Arnaldo H.P.; Morcelli, Aparecido E., E-mail: rmlobo@ipen.br, E-mail: morcelliae@gmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-11-01

    Small Punch Test (SPT) is one of the most promising techniques of small specimen test, which was originally applied in testing of irradiated materials in nuclear engineering. Then it was introduced to other fields as an almost nondestructive method to measure the local mechanical properties that are difficult to be obtained using conventional mechanical tests. Most studies to date are focused on metallic materials, although SPT applications are recently spreading to other materials. The small punch test (SPT) employs small-sized specimens (for example, samples measuring 8 mm in diameter and 0.5 mm thick). The specimen is firmly clamped between two circular dies and is bi-axially strained until failure into a circular hole using a hemispherical punch. The 'load-punch displacement' record can be used to estimate the yield strength, the ultimate tensile strength, the tensile elongation, and the temperature of the ductile-to-brittle transition. Recently, some researchers are working on the use of miniature notched or pre-cracked specimens (denoted as p-SPT) to validate its geometry and dimensions for obtaining the fracture properties of metallic materials. In a first approach, the technique makes it possible to convert primary experimental data into conventional mechanical properties of a massive specimen. In this paper a comprehensive review of the different STP applications is presented with the aim of clarifying its usefulness. (author)

  11. Digital staining of pathological tissue specimens using spectral transmittance

    Science.gov (United States)

    Bautista, Pinky A.; Abe, Tokiya; Yamaguchi, Masahiro; Yagi, Yukako; Ohyama, Nagaaki

    2005-04-01

    Staining of tissue specimens is a classical procedure in pathological diagnosis to enhance the contrast between tissue components such that identification and classification of these components can be easily performed. In this paper, a framework for digital staining of pathological specimens using the information derived from the L-band spectral transmittance of various pathological tissue components is introduced, particularly the transformation of a Hematoxylin and Eosin (HE) stained specimen to its Masson-Trichrome (MT) stained counterpart. The digital staining framework involves the classification of tissue components, which are highlighted when the specimen is actually stained with MT stain, e.g. fibrosis, from the HE-stained image; and the linear mapping between specific sets of HE and MT stained transmittance spectra through pseudo-inverse procedure to produce the LxL transformation matrices that will be used to transform the HE stained transmittance to its equivalent MT stained transmittance configuration. To generate the digitally stained image, the decisions of multiple quadratic classifiers are pooled to form the weighting factors for the transformation matrices. Initial results of our experiments on liver specimens show the viability of multispectral imaging (MSI) for the implementation of digital staining in the pathological context.

  12. Xanthogranulomatous appendicitis in interval appendectomy specimens of children

    Directory of Open Access Journals (Sweden)

    Yusuf Hakan Çavuşoğlu

    2016-05-01

    Full Text Available Xanthogranulomatous inflammation is common in interval appendectomy specimens in adults, but it is unusual in children. Histopathologic specimens of interval appendectomy, within an 8-year period, were reevaluated to assess the true incidence. A computer search of the hospital database of all appendectomies was performed between January 2008 and June 2015 to identify all interval appendectomy cases. A total of 2694 patients underwent appendectomies. Of these, 13 were interval appendectomies. After pathologic evaluation, 2 (15.4% of the specimens were reported as xanthogranulomatous appendicitis (XA. Histopathologic examination of these interval appendectomy specimens, granulomas (59%, xanthogranulomatous inflammation (36% and Crohn-like changes (50% were common in adults. However, XA is a particularly rare clinical entity among children. Two cases of XA were reported in children in the English literature. One was a 12-year old boy that underwent interval appendectomy 6 weeks after an episode of acute appendicitis. The other was an 11-year old boy with acute (non-interval appendicitis, but the complete blood count was suggestive of an acute suppurative inflammation. These two cases are the 3rd and 4th cases of XA reported in children in the English literature, and both were managed by interval appendectomy. Thus, XA may be encountered in interval appendectomy specimens and association with IBD has to be ruled out.

  13. The effect of specimen and flaw dimensions on fracture toughness

    Energy Technology Data Exchange (ETDEWEB)

    Nevalainen, M.J. [VTT Manufacturing Technology, Espoo (Finland)

    1997-06-01

    The effect of the specimen size and geometry on fracture toughness has been investigated both by experimental tests and computational analyses. The methods for constraint description, namely T-stress, Q-parameter and Small-Scale Yielding Correction (SSYC) have been compared and applied for various geometries. A statistical treatment for the specimen thickness effect on cleavage fracture toughness has been investigated. Elliptical surface cracks were compared with straight-thickness cracks and a method for crack shape correction was presented. Based on the results, the differences in apparent fracture toughness values obtained from various specimen configurations can be better understood and taken into account. 64 refs. The thesis includes also four previous publications by author.

  14. Positivity of Demodex spp. in biopsy specimens of nevi.

    Science.gov (United States)

    Serpil, S; Ulku, K; Cemil, C; Nasuhi Engin, A; Sezai, S; Meryem, I

    2009-04-01

    Melanocytic skin tumors are caused by nevus cells, epidermal melanocytes and dermal melanocytes. The aim of the study was to detect the positivity of Demodex spp. in biopsy specimens of skin diagnosed as nevus. In this retrospective study, the specimens obtained from 110 patients diagnosed with nevus and stained by hematoxylin & eosin (H&E) method were assessed for Demodex. Statistical analysis was done using independent sample t test, Pearson Chi-square and Yates' adjusted Chi-square test. For statistics, p < 0.05 was considered significant. Consequently, 43 (39.1%) out of 110 specimens were detected to have Demodex spp. Demodex colonization augmented in nevi can be explained by the possible affinity of the parasite to the melanin pigment.

  15. Determining mechanical behavior of solid materials using miniature specimens

    Science.gov (United States)

    Manahan, M.P.; Argon, A.S.; Harling, O.K.

    1986-02-04

    A Miniaturized Bend Test (MBT) capable of extracting and determining mechanical behavior information from specimens only so large as to have at least a volume or smallest dimension sufficient to satisfy continuum behavior in all directions is disclosed. The mechanical behavior of the material is determined from the measurements taken during the bending of the specimen and is processed according to the principles of linear or nonlinear material mechanics or both. In a preferred embodiment the determination is carried out by a code which is constructed according to the finite element method, and the specimen used for the determinations is a miniature disk simply supported for central loading at the axis on the center of the disk. 51 figs.

  16. Friction Compensation in the Upsetting of Cylindrical Test Specimens

    DEFF Research Database (Denmark)

    Christiansen, Peter; Martins, P. A. F.; Bay, Niels Oluf

    2016-01-01

    . The methodology is based on minimizing the errorbetween the average surface pressure obtained from the experimental measurements of the force and displacement and thatobtained from the slab method of analysis of metal plasticity.Three different friction models based on Coulomb friction, the constant friction......This manuscript presents a combined numerical andexperimental methodology for determining the stress-straincurve of metallic materials from the measurements of forceand displacement obtained in the axial compression of cylindrical test specimens with friction between the specimens and the platens...... model or combined friction models are utilized .Experimental results obtained from cylindrical and Rastegaev test specimens with different lubricants combined with the experimental determination of friction by means of ring compression tests allows compensating the effect of friction...

  17. T*{sub {epsilon}} integral analysis of fracture specimens

    Energy Technology Data Exchange (ETDEWEB)

    Omori, Y.; Ma, L.; Kobayashi, A.S. [Univ. of Washington, Seattle, WA (United States)] [and others

    1996-12-31

    T*{sub {epsilon}} integral values associated with stable crack growth in thin 2024-T3 aluminum compact (CT) specimens and A606 HSLA steel single edge notched (SEN) specimens were determined directly from the crack tip displacement field obtained by moire interferometry. Stable crack growth in the SEN specimen was also simulated by an elastic-plastic finite element (FE) model which was driven by the experimentally determined boundary conditions. T*{sub {epsilon}} obtained experimentally and by FE were in reasonable agreements with each other. Unlike the vanishing J integrals with crack extension, T*{sub {epsilon}} reached steady state values with stable crack growth. Thus, for a given integration contour, {Gamma}{sub {epsilon}}, near the crack tip, T*{sub {epsilon}} can be used as a stable crack growth as well as a ductile fracture criteria.

  18. Specimen edge effects on bending fatigue of carburized steel

    Science.gov (United States)

    Cohen, R. E.; Matlock, D. K.; Krauss, G.

    1992-10-01

    The effects of specimen geometry on the fatigue behavior of SAE 4320 steel carburized at 927 °C were evaluated with two sets of cantilever bend specimens, one set machined with square edges and one set machined with round edges. The specimens with square edges exhibited a 13% lower fatigue limit. In comparison to the rounded samples, the lower fatigue limit in the square-edged samples was attributed to the presence of a higher volume fraction of retained austenite in the sample corners and a lower surface residual compressive stress. As a result of the differences in residual stress, preferential crack initiation sites existed in the square-edged samples at a location approximately 200 to 900 ώm from the square edge. The implications of this study on laboratory analyses of the bending fatigue performance of carburized gear steels are discussed.

  19. Thick Concrete Specimen Construction, Testing, and Preliminary Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Clayton, Dwight A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hoegh, Kyle [Univ. of Minnesota, Minneapolis, MN (United States); Khazanovich, Lev [Univ. of Minnesota, Minneapolis, MN (United States)

    2015-03-01

    The purpose of the U.S. Department of Energy Office of Nuclear Energy’s Light Water Reactor Sustainability (LWRS) Program is to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the operating lifetimes of nuclear power plants (NPPs) beyond 60 years. Since many important safety structures in an NPP are constructed of concrete, inspection techniques must be developed and tested to evaluate the internal condition. In-service containment structures generally do not allow for the destructive measures necessary to validate the accuracy of these inspection techniques. This creates a need for comparative testing of the various nondestructive evaluation (NDE) measurement techniques on concrete specimens with known material properties, voids, internal microstructure flaws, and reinforcement locations. A preliminary report detailed some of the challenges associated with thick reinforced concrete sections and prioritized conceptual designs of specimens that could be fabricated to represent NPP concrete structures for using in NDE evaluation comparisons. This led to the construction of the concrete specimen presented in this report, which has sufficient reinforcement density and cross-sectional size to represent an NPP containment wall. Details on how a suitably thick concrete specimen was constructed are presented, including the construction materials, final nominal design schematic, as well as formwork and rigging required to safely meet the desired dimensions of the concrete structure. The report also details the type and methods of forming the concrete specimen as well as information on how the rebar and simulated defects were embedded. Details on how the resulting specimen was transported, safely anchored, and marked to allow access for systematic comparative NDE testing of defects in a representative NPP containment wall concrete specimen are also given. Data collection using the MIRA Ultrasonic NDE equipment and

  20. Strip specimen tests for pipeline materials and girth welds

    Energy Technology Data Exchange (ETDEWEB)

    Mohr, William C. [Edison Welding Institute (EWI), Columbus, Ohio (United States)

    2009-07-01

    Strip specimen testing of pipeline materials has been widely applied as a method of getting data relevant to the performance of pipelines under axial direction loading. Comparisons of strip specimen against smaller standard tests (round tensile bar, fracture toughness specimens, polished round bars) and against full-scale or large-scale testing will be explored. Data from early-generation pipe welds from the 1920's to the 1940's to the most recent materials for offshore reeled pipe will be used for examples. Strip samples can provide full thickness information to take account of varying material properties or imperfection distribution through the thickness. Strip samples can also accommodate measurement of effects of the original surface finish or weld surface shape. Strip samples have more design flexibility than standard tests, but must be designed to limit stress concentrations and effects of local bending. (author)

  1. Improved Diagnosis of Prosthetic Joint Infection by Culturing Periprosthetic Tissue Specimens in Blood Culture Bottles

    Science.gov (United States)

    Peel, Trisha N.; Dylla, Brenda L.; Hughes, John G.; Lynch, David T.; Greenwood-Quaintance, Kerryl E.; Cheng, Allen C.; Mandrekar, Jayawant N.

    2016-01-01

    ABSTRACT Despite known low sensitivity, culture of periprosthetic tissue specimens on agars and in broths is routine. Culture of periprosthetic tissue samples in blood culture bottles (BCBs) is potentially more convenient, but it has been evaluated in a limited way and has not been widely adopted. The aim of this study was to compare the sensitivity and specificity of inoculation of periprosthetic tissue specimens into blood culture bottles with standard agar and thioglycolate broth culture, applying Bayesian latent class modeling (LCM) in addition to applying the Infectious Diseases Society of America (IDSA) criteria for prosthetic joint infection. This prospective cohort study was conducted over a 9-month period (August 2013 to April 2014) at the Mayo Clinic, Rochester, MN, and included all consecutive patients undergoing revision arthroplasty. Overall, 369 subjects were studied; 117 (32%) met IDSA criteria for prosthetic joint infection, and 82% had late chronic infection. Applying LCM, inoculation of tissues into BCBs was associated with a 47% improvement in sensitivity compared to the sensitivity of conventional agar and broth cultures (92.1 versus 62.6%, respectively); this magnitude of change was similar when IDSA criteria were applied (60.7 versus 44.4%, respectively; P = 0.003). The time to microorganism detection was shorter with BCBs than with standard media (P culture in blood culture bottles is more sensitive than and as specific as agar and thioglycolate broth cultures and yields results faster. PMID:26733067

  2. Occurrence of biflavones in leaves of Caesalpinia pyramidalis specimens

    Directory of Open Access Journals (Sweden)

    Marcus V. Bahia

    2010-01-01

    Full Text Available The chloroform partition of methanol extract of leaves of Caesalpinia pyramidalis was submitted to different chromatographic procedures which afforded besides agathisflavone and taxifolin, the minor biflavones loniflavone, amentoflavone, 5'- hydroxyamentoflavone and podocarpusflavone A. The structures of the compounds were established on the basis of NMR and MS data analysis. Besides, the content of biflavones of different specimens of C. pyramidalis, which are collected in different habitats of the Brazilian semi-arid region, was determinated by LC-APCI-MS analysis. These analysis demonstrated that only the specimens harvested in Bahia state showed collectively the presence of agathisflavone, amentoflavone, sequoiaflavone and podocarpusflavone A.

  3. Study of cavities in a creep crack growth test specimen

    OpenAIRE

    Jazaeri, H; Bouchard, P. J.; Hutchings, M. T.; Mamun, A. A.; Heenan, R K

    2016-01-01

    Small Angle Neutron Scattering (SANS) and Scanning Electron Microscopy (SEM) have been used to determine the degree of cavitation damage, of length scale 5-300 nm, associated with a creep crack grown in a compact tension specimen cut from a Type 316H stainless steel weldment. The specimen was supplied by EDF Energy as part of an extensive study of creep crack growth in the heat affected zone of reactor components. The creep crack propagates along a line 1.5 mm away from, and parallel to, the ...

  4. Apparatus for Testing Flat Specimens of Thermal Insulation

    Science.gov (United States)

    Fesmire, James E.; Augustynowicz, Stanislaw D.

    2005-01-01

    An apparatus has been developed to implement an improved method of testing flat-plate specimens of thermal-insulation materials for cryogenic application. The method includes testing under realistic use conditions that could include vacuum and mechanical loading at a pressure up to 70 psi (=0.48 MPa). The apparatus can accommodate a rigid or flexible specimen having thickness up to 1.25 in. (=3.2 cm) and diameters between 6 and 10 in. (about 15.2 and 25.4 cm, respectively). Typical test conditions include boundary temperatures between 77 K and 373 K and vacuum/interstitial gas filling at a pressure between 10(exp -6) torr (=1.3 x 10(exp -4) Pa) and 760 torr (atmospheric pressure =0.1 MPa). The interstitial gas could be N2, He, CO2, or any other suitable gas to which the insulation is expected to be exposed in use. Relative to prior apparatuses and testing methods, this apparatus and the testing method that it implements offer advantages of relative simplicity and ease of use. The basic principle of operation of the apparatus is that of boil-off calorimetry, using liquid nitrogen or any other suitable liquid that boils at a desired temperature below ambient temperature. Comparative rates of flow of heat through the thicknesses of the specimens (heat-leak rates) and apparent-thermal-conductivity values are obtained from tests of specimens. Absolute values of heat-leak rates and apparent thermal conductivities are computed from a combination of (1) the aforementioned comparative values and (2) calibration factors obtained by testing reference specimens of materials that have known thermal-insulation properties. The apparatus includes a full complement of temperature sensors, a vacuum pump and chamber, a monitoring and control system, and tools and fixtures that enable rapid and reliable installation and removal of specimens. A specimen is installed at the bottom of the vacuum chamber, and a cold-mass assembly that includes a tank is lowered into position above and

  5. Comparison of gross anatomy test scores using traditional specimens vs. QuickTime Virtual Reality animated specimens

    Science.gov (United States)

    Maza, Paul Sadiri

    In recent years, technological advances such as computers have been employed in teaching gross anatomy at all levels of education, even in professional schools such as medical and veterinary medical colleges. Benefits of computer based instructional tools for gross anatomy include the convenience of not having to physically view or dissect a cadaver. Anatomy educators debate over the advantages versus the disadvantages of computer based resources for gross anatomy instruction. Many studies, case reports, and editorials argue for the increased use of computer based anatomy educational tools, while others discuss the necessity of dissection for various reasons important in learning anatomy, such as a three-dimensional physical view of the specimen, physical handling of tissues, interactions with fellow students during dissection, and differences between specific specimens. While many articles deal with gross anatomy education using computers, there seems to be a lack of studies investigating the use of computer based resources as an assessment tool for gross anatomy, specifically using the Apple application QuickTime Virtual Reality (QTVR). This study investigated the use of QTVR movie modules to assess if using computer based QTVR movie module assessments were equal in quality to actual physical specimen examinations. A gross anatomy course in the College of Veterinary Medicine at Cornell University was used as a source of anatomy students and gross anatomy examinations. Two groups were compared, one group taking gross anatomy examinations in a traditional manner, by viewing actual physical specimens and answering questions based on those specimens. The other group took the same examinations using the same specimens, but the specimens were viewed as simulated three-dimensional objects in a QTVR movie module. Sample group means for the assessments were compared. A survey was also administered asking students' perceptions of quality and user-friendliness of the QTVR

  6. Characterization of Two Historic Smallpox Specimens from a Czech Museum

    Czech Academy of Sciences Publication Activity Database

    Pajer, P.; Dresler, J.; Kabickova, H.; Píša, L.; Aganov, P.; Fucik, K.; Elleder, Daniel; Hron, Tomáš; Kuželka, V.; Velemínský, P.; Klimentová, J.; Fučíková, A.; Pejchal, J.; Hrabáková, Rita; Beneš, V.; Rausch, T.; Dundr, P.; Pilin, A.; Čabala, R.; Hubálek, Martin; Stříbrný, J.; Antwerpen, M.H.; Meyer, H.

    2017-01-01

    Roč. 9, č. 8 (2017), č. článku 200. ISSN 1999-4915 Institutional support: RVO:68378050 ; RVO:67985904 ; RVO:61388963 Keywords : smallpox * variola virus * evolution * next generation suquencing * historic specimen * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.465, year: 2016

  7. 21 CFR 864.3250 - Specimen transport and storage container.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 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...

  8. Pathologic diagnoses of appendectomy specimens: a 10-year review.

    African Journals Online (AJOL)

    A retrospective study was performed to see the pattern of histopathologic diagnoses in appendectomy specimens, their demographics, and the rate of negative appendectomy. Materials and methods: Records of resected appendices with a clinical diagnosis of acute appendicitis submitted to histopathology department of ...

  9. Effect of erodent particles on the erosion of metal specimens

    Energy Technology Data Exchange (ETDEWEB)

    Razzaque, M. Mahbubur, E-mail: mmrazzaque@me.buet.ac.bd; Alam, M. Khorshed; Khan, M. Ishak, E-mail: ishak.buet@gmail.com [Department of Mechanical Engineering Bangladesh University of Engineering and Technology (BUET), Dhaka (Bangladesh)

    2016-07-12

    This paper presents the experimental results of the measurement of erosion rate of carbon steel specimens in sand water slurry system in a slurry pot tester. Sylhet sand has been sieved to get three sizes of erodent particles; namely, less than 250 micron, 250 to 590 micron and 590 to 1190 micron. Experiments are done with three sand concentrations (10%, 15% and 20%). The rate of erosion of the carbon steel specimens is measured as the loss of weight per unit surface area per unit time under the dynamic action of solid particles. The eroded surfaces of the specimens are examined using Scanning Electron Microscopy (SEM) to visualize the impact of the slurry of various conditions. It is seen that irrespective of the particle size the rate of erosion increases with the increase of slurry concentration. This increment of erosion rate at high concentration is high for large particles. High erosion rate is observed in case of large sand particles. In case of small and fine particles erosion rate is small because of low impact energy as well as the wastage of energy to overcome the hindrance of the finer particles before striking on the specimen surface.

  10. Comparison of three methods of collecting nasal specimens for ...

    African Journals Online (AJOL)

    Background: Nasopharyngeal aspiration (NPA) is used widely in the collection of nasal specimens for respiratory virus diagnosis. The method has limitations in relation to technical expertise, patient anxiety, and apparatus dependence. Nasal washing (NW) offers an alternative approach. Objective: To identify the merits of ...

  11. Isolation of Proteus mirabilis from Clinical Urogenital Specimens: A ...

    African Journals Online (AJOL)

    This retrospective study was designed to ascertain the epidemiological sources and antibiotic susceptibility patterns of Proteus mirabilis strains recovered from urogenital specimens in Jos University Teaching Hospital; (JUTH) over a five year period (Janurary 2000 – December 2004). Information on epidemiological and ...

  12. Need for appropriate specimen for microbiology diagnosis of chronic osteomyelitis

    Directory of Open Access Journals (Sweden)

    Lakshmi Vemu

    2018-01-01

    CONCLUSION: As per our data, the culture yield from wound swabs was low or contaminated with normal skin flora, as compared to the biopsy or tissue specimen. Hence, an appropriate sampling of the infected bone using recommended protocols is highly essential for improving microbiological yield and the outcome of COM.

  13. 50 CFR 31.12 - Sale of wildlife specimens.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Sale of wildlife specimens. 31.12 Section 31.12 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE INTERIOR (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM WILDLIFE SPECIES MANAGEMENT Terms and Conditions of Wildlife...

  14. Natural Selection: Finding Specimens in a Natural History Collection

    NARCIS (Netherlands)

    Erp, M. van; Bosch, A.P.J. van den; Hunt, S.; Meij, M. van der; Dekker, R.; Lendvai, P.

    2011-01-01

    The natural history domain is rich in information. For hundreds of years, biodiversity researchers have collected specimens and samples, and meticulously recorded the how, what, and where of these objects of research. To retrace this information, however, deep knowledge of the collection and

  15. Is routine histopathology of tonsil specimen necessary? | Adoga ...

    African Journals Online (AJOL)

    Background: Tonsillar diseases are common in paediatric and adult otolaryngological practice. These diseases require tonsillectomy. Specimens are subjected to histopathology routinely in my institution for fear of infections and tumour without consideration for risk factors. The financial burden is on the patients and waste ...

  16. Cell-based quantification of molecular biomarkers in histopathology specimens.

    Science.gov (United States)

    Al-Kofahi, Yousef; Lassoued, Wiem; Grama, Kedar; Nath, Sumit K; Zhu, Jianliang; Oueslati, Ridha; Feldman, Michael; Lee, William M F; Roysam, Badrinath

    2011-07-01

    To investigate the use of a computer-assisted technology for objective, cell-based quantification of molecular biomarkers in specified cell types in histopathology specimens, with the aim of advancing current visual estimation and pixel-level (rather than cell-based) quantification methods. Tissue specimens were multiplex-immunostained to reveal cell structures, cell type markers, and analytes, and imaged with multispectral microscopy. The image data were processed with novel software that automatically delineates and types each cell in the field, measures morphological features, and quantifies analytes in different subcellular compartments of specified cells.The methodology was validated with the use of cell blocks composed of differentially labelled cultured cells mixed in known proportions, and evaluated on human breast carcinoma specimens for quantifying human epidermal growth factor receptor 2, estrogen receptor, progesterone receptor, Ki67, phospho-extracellular signal-related kinase, and phospho-S6. Automated cell-level analyses closely matched human assessments, but, predictably, differed from pixel-level analyses of the same images. Our method reveals the type, distribution, morphology and biomarker state of each cell in the field, and allows multiple biomarkers to be quantified over specified cell types, regardless of their abundance. It is ideal for studying specimens from patients in clinical trials of targeted therapeutic agents, for investigating minority stromal cell subpopulations, and for phenotypic characterization to personalize therapy and prognosis. © 2011 Blackwell Publishing Limited.

  17. 21 CFR 58.51 - Specimen and data storage facilities.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Specimen and data storage facilities. 58.51 Section 58.51 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL... storage facilities. Space shall be provided for archives, limited to access by authorized personnel only...

  18. Biochemical modulation in male specimens of Channa punctatus ...

    African Journals Online (AJOL)

    admin

    Biochemical modulation in male specimens of Channa punctatus (Bloch) under different habitats and seasons. C. P. Singh1, R. N. Ram2, Mohd. Danish2* and .... were analyzed using titrimetric method. (APHA, 1992) and temperature, pH, total dissolved solids and conductivity were measured using electronic digital meter.

  19. Automatic grinding apparatus to control uniform specimen thicknesses

    Science.gov (United States)

    Bryner, J.S.

    1981-01-07

    This invention is directed to a new and improved grinding apparatus comprisng: (1) a movable grinding surface; (2) a specimen holder; (3) a dislacing means for moving the holder and/or grinding surface toward one another; and (4) at least three means for limiting displacement of the holder to the grinding surface.

  20. Letter to the editor The number of urine specimens for ...

    African Journals Online (AJOL)

    contents/approach-to-the-adult-with-asymptomatic- bacteriuria. Letter to the editor. The number of urine specimens for bacteriological examination in women. Ertugrul Guclu, Tuba Damar, Oguz Karabay. 1. Department of Infectious Diseases and Clinical Microbiology, Sakarya University Faculty of Medicine, Sakarya, Turkey.

  1. Observation of Intralaminar Cracking in the Edge Crack Torsion Specimen

    Science.gov (United States)

    Czabaj, Michael W.; Ratcliffe, James G.; Davidson, Barry D.

    2013-01-01

    The edge crack torsion (ECT) test is evaluated to determine its suitability for measuring fracture toughness associated with mode III delamination growth onset. A series of ECT specimens with preimplanted inserts with different lengths is tested and examined using nondestructive and destructive techniques. Ultrasonic inspection of all tested specimens reveals that delamination growth occurs at one interface ply beneath the intended midplane interface. Sectioning and optical microscopy suggest that the observed delamination growth results from coalescence of angled intralaminar matrix cracks that form and extend across the midplane plies. The relative orientation of these cracks is approximately 45 deg with respect to the midplane, suggesting their formation is caused by resolved principal tensile stresses arising due to the global mode-III shear loading. Examination of ECT specimens tested to loads below the level corresponding to delamination growth onset reveals that initiation of intralaminar cracking approximately coincides with the onset of nonlinearity in the specimen's force-displacement response. The existence of intralaminar cracking prior to delamination growth onset and the resulting delamination extension at an unintended interface render the ECT test, in its current form, unsuitable for characterization of mode III delamination growth onset. The broader implications of the mechanisms observed in this study are also discussed with respect to the current understanding of shear-driven delamination in tape-laminate composites.

  2. Pathological findings in reduction mammoplasty specimens: A South ...

    African Journals Online (AJOL)

    The increased prevalence of carcinoma of the breast in these women suggests that they may ultimately develop ... Pathological findings in reduction mammoplasty specimens: A South African perspective .... Indeed, 'The primary intent of mammoplasty is cosmetic, but it is a medical procedure, taking place in a medical ...

  3. Fracture Mechanics Analysis of a Modified TSD Specimen

    DEFF Research Database (Denmark)

    Berggreen, Christian; Carlsson, Leif A.

    2008-01-01

    The Tilted Sandwich Debond (TSD) specimen has been recognized as a viable candidate for characterization of the face/core fracture resistance. Analysis, however, shows that the range of phase angles that can be realized by altering the tilt angle is quite limited. A parametric study however shows...

  4. Resistance to freezing and thawing of mortar specimens made from ...

    Indian Academy of Sciences (India)

    Resistance to freezing and thawing of mortar specimens made from sulphoaluminate–belite cement (M–SAB) is compared with that of mortars made from portland cement (M–PC). The results suggest that larger median radius of the pores and total porosity of M–SAB compared to those of M–PC are primarily caused by the ...

  5. Dimensioning of dog bone specimens and numerical analysis of the ...

    African Journals Online (AJOL)

    The effects of different fillet radii, clamp area dimensions, and pinhole loading through a hole located in the clamp area of a dog bone specimen were investigated using the Finite Element Analysis (FEA) software Abaqus. Changes in the fillet radius were shown to have little effect on the distribution and magnitude of the von ...

  6. Pathological findings in reduction mammoplasty specimens: A South ...

    African Journals Online (AJOL)

    Background: Preoperative, intraoperative and follow-up guidelines for managing occult carcinoma in reduction mammoplasty specimens are scant. Methods: We retrospectively analysed the records and pathology reports of 200 patients who had undergone reduction mammoplasty at two major public hospitals in ...

  7. Preservation of tissue specimens during transport to mycobacteriology laboratories.

    Science.gov (United States)

    Richards, W D; Wright, H S

    1983-01-01

    Chloramine-T and sodium borate solutions were evaluated for their effectiveness in preserving Mycobacterium bovis and controlling the growth of non-mycobacterial contaminants on tissue specimens during transport to laboratories. The number of culturable M. bovis cells in suspension was reduced by 5.1 log10 upon exposure to chloramine-T solution and by less than 1 log10 upon exposure to sodium borate solution for 7 days. Reinoculation of laboratory media (because of overgrowth by non-mycobacterial contaminants) was required for 52.6% of 190 routine bovine tissue specimens shipped refrigerated in chloramine-T solution and for 6.1% of 520 specimens shipped unrefrigerated in sodium borate solution. M. bovis was isolated from bovine tissue stored in sodium borate solution at 23 degrees C for 17 weeks and at 4 degrees C for 25 weeks. Unrefrigerated sodium borate solution has been used successfully to ship tissue specimens to our laboratory for the past 11 years. PMID:6341397

  8. specimens of patients with bloody diarrhoea in Mwanza, Tanzania

    African Journals Online (AJOL)

    Bacteriological cultures were done at the National Institute for Medical Research laboratory. .... Mwanza for culture. For optimal isolation ofS/rigc/lo and Salmonella species three different media and an enrichment medium were used. Stool specimens were inoculated .... antibiotics, the establishment of hygienic measures.

  9. Polyps in the gastrointestinal tract: discrepancy between endoscopic forceps biopsies and resected specimens.

    Science.gov (United States)

    Sung, Hye Young; Cheung, Dae Young; Cho, Se-Hyun; Kim, Jin Il; Park, Soo-Heon; Han, Joon-Yeol; Park, Gyeong Sin; Kim, Jae Kwang; Chung, In-Sik

    2009-02-01

    An endoscopic forceps biopsy (EFB) carries the risk of missing the neoplastic foci within a polyp as only a small portion of the lesion is sampled using this technique. Accordingly, the histological examination of specimens obtained by an EFB is of limited accuracy and patient management based on the histological findings is controversial. The aim of this prospective study was to determine the diagnostic concordance between an EFB and resected tissues of gastric and colon polyps. Between January 2006 and October 2007, 1312 gastrointestinal polyps from 896 patients were resected in our hospital. Patients with polyps of epithelial origin of at least 8 mm in diameter and not associated with polyposis syndromes were included in the study. Polyps of nonepithelial origin were excluded. One thousand two hundred and sixty-four polyps of epithelial origin [gastric polyps (n=268) and colon polyps (n=996)] obtained from 813 patients met the inclusion criteria. All patients underwent an EFB and resection of the polyp by endoscopic mucosal resection and endoscopic submucosal dissection. Multiple polyps existed in 31.6% of the patients. The pathological diagnoses of resected gastric polyps were as follows: adenomas with low-grade dysplasia, 46 (17.2%); adenomas with high-grade dysplasia, 42 (15.7%); hyperplastic polyps, 126 (47.0%); chronic inflammatory polyps, 29 (10.8%); and adenocarcinomas, 25 (9.3%). The discrepancy rate between an EFB and the pathology of the resected gastric polyps was 39.2% (the Kendall's tau-b and the kappa coefficient for agreement between the EFB and resected specimens of gastric polyps were 0.577 and 0.472, respectively; P value polyp and the concordance rate was observed. The pathological diagnoses of the resected colon polyps were as follows: adenomas with low-grade dysplasia, 559 (56.1%); adenomas with high-grade dysplasia, 229 (23.0%); hyperplastic polyps, 44 (4.4%); adenocarcinomas, 53 (5.3%); and inflammatory polyps, 111 (11.1%). The discrepancy

  10. Comparison of molecular diagnostic methods for the detection of Acanthamoeba spp. from clinical specimens submitted for keratitis.

    Science.gov (United States)

    Khairnar, Krishna; Tamber, Gurdip S; Ralevski, Filip; Pillai, Dylan R

    2011-08-01

    Acanthamoeba spp. are responsible for a significant annual number of keratitis (AK) cases leading to vision-threatening disease worldwide. Current methods rely on direct examination of specimens by microscopy and/or culture. The former lacks sensitivity and the latter suffers from a poor turnaround time. We undertook a comparison of all published molecular methods, evaluating performance characteristics such as analytical sensitivity, specificity, limit of detection (LOD), reproducibility, accuracy, and cost of test. The study population comprised 128 patients. Eligible specimens were tested prospectively between April 2007 and May 2010 by microscopy and/or culture. Eleven different specimen types were used including corneal scrapings (51.5%), corneal swab (17.9%), and contact lens material (10.9%). Results of 2 published gel-based polymerase chain reaction (PCR) and 2 published real-time quantitative (Q) PCR methods were compared in a blinded manner to direct microscopic examination and/or culture for the detection of Acanthamoeba in clinical specimens. QPCR (Riviere method) had the highest sensitivity at 89.3%, excellent accuracy using ROC analysis (AUC ∼0.90), lowest LOD down to 0.1 organism per microliter, and superior linear correlation with parasite density (R(2) = 0.9965) when compared with microscopy, culture, and other molecular methods. Phylogenetic analysis using a sequence-based typing method revealed that clinical isolates in this population with AK were genetically distinct from granulomatous amebic encephalitis or environmental isolates. The QPCR method was more expensive ($14.80) than traditional methods such as culture ($2.50) or microscopy ($2.50). However, 13 culture- and microscopy-negative specimens were positive by QPCR during the study period, suggesting that detection using QPCR may result in reduced complications and health care costs associated with misdiagnosed AK. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Psychophysiology of prospective memory.

    Science.gov (United States)

    Rothen, Nicolas; Meier, Beat

    2014-01-01

    Prospective memory involves the self-initiated retrieval of an intention upon an appropriate retrieval cue. Cue identification can be considered as an orienting reaction and may thus trigger a psychophysiological response. Here we present two experiments in which skin conductance responses (SCRs) elicited by prospective memory cues were compared to SCRs elicited by aversive stimuli to test whether a single prospective memory cue triggers a similar SCR as an aversive stimulus. In Experiment 2 we also assessed whether cue specificity had a differential influence on prospective memory performance and on SCRs. We found that detecting a single prospective memory cue is as likely to elicit a SCR as an aversive stimulus. Missed prospective memory cues also elicited SCRs. On a behavioural level, specific intentions led to better prospective memory performance. However, on a psychophysiological level specificity had no influence. More generally, the results indicate reliable SCRs for prospective memory cues and point to psychophysiological measures as valuable approach, which offers a new way to study one-off prospective memory tasks. Moreover, the findings are consistent with a theory that posits multiple prospective memory retrieval stages.

  12. SHOULD EVERY APPENDECECTOMY SPECIMEN BE SUBJECTED TO HISTOPATHOLOGICAL EXAMINATION? A RETROSPECTIVE STUDY OF HISTOLOGICAL FINDINGS IN APPENDICECTOMY SPECIMENS

    Directory of Open Access Journals (Sweden)

    Shahanuma Shaik

    2017-12-01

    Full Text Available BACKGROUND Appendicitis is one of the commonest surgical emergencies with a lifetime risk of 7-8%. The appendicectomy specimens operated upon clinically-suspected appendicitis often appear normal on gross examination, but histopathological evaluation may reveal a diverse underlying pathology. Therefore, for accurate diagnosis, histopathological examination of all appendicectomy specimens is mandatory. MATERIALS AND METHODS A retrospective study of 175 appendicectomy cases operated over a period of two years. The clinical data and histopathological reports were reviewed and various histopathological findings are categorised. RESULTS Out of the total 175 appendicectomies, 155 emergency appendicectomy cases were included in the study, while 20 cases of incidental appendicectomy were excluded. The peak incidence was found in the 2nd and 3rd decades with male predominance. Among the 155 specimens, 96.8% had histological features of appendicitis and 1.9% were normal appendix. The unusual histopathological findings were Carcinoid tumour and Enterobius vermicularis. CONCLUSION The definitive diagnoses of appendicitis as well as the unusual incidental findings that were missed intraoperatively are established by histopathological examination. The study supports the histological examination of all resected appendicectomy specimens.

  13. Clinical Evaluation and Cost Analysis of Great Basin Shiga Toxin Direct Molecular Assay for Detection of Shiga Toxin-Producing Escherichia coli in Diarrheal Stool Specimens.

    Science.gov (United States)

    Faron, Matthew L; Ledeboer, Nathan A; Connolly, Jessica; Granato, Paul A; Alkins, Brenda R; Dien Bard, Jennifer; Daly, Judy A; Young, Stephen; Buchan, Blake W

    2017-02-01

    The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxin-producing Escherichia coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin (stx 1 and stx 2 ), as well as the E. coli serotype O:157-specific marker rfbE, are simultaneously detected within 2 h. ST Direct was evaluated using 1,084 prospectively collected preserved stool specimens across five clinical centers. An additional 55 retrospectively collected, frozen specimens were included to increase the number of positive specimens evaluated. Results were compared to results from routine culture and an enzyme immunoassay (EIA) specific for the recovery and identification of STEC. ST Direct was found to be 93.2% sensitive and 99.3% specific for detection of stx 1 and stx 2 and 95.7% sensitive and 99.3% specific for detection of E. coli serotype O:157. All specimens with false-positive results were found to contain stx 1 or stx 2 or were found to be positive for serotype O:157 when analyzed using alternative molecular methods. All 4 false-negative stx 1 or stx 2 results were reported for frozen, retrospectively tested specimens. In all cases, the specimens tested positive for stx by an alternative FDA-cleared nucleic acid amplification test (NAAT) but were negative for stx 1 and stx 2 following nucleic acid sequence analysis. Based on these data, culture and EIA-based methods for detection of STEC are only 33% sensitive compared to molecular tests. A retrospective cost analysis demonstrated 59% of the cost of routine stool culture to be attributable to the identification of STEC. Taken together, these data suggest that ST Direct may provide a cost-effective, rapid molecular alternative to routine culture for the identification of STEC in preserved stool specimens. Copyright © 2017 American Society for Microbiology.

  14. Vacuum sealing and cooling as methods to preserve surgical specimens

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Engvad, Birte; Nielsen, Ole

    2011-01-01

    Recently, vacuum-based preservation of surgical specimens has been proposed as a safe alternative to formalin fixation at the surgical theater. The method seems feasible from a practical point of view, but no systematic study has examined the effect of vacuum sealing alone with respect to tissue...... preservation. In this study, we therefore subjected tissue samples from 5 different organs to treatments with and without vacuum sealing and cooling at 4°C to study the effect of vacuum sealing of surgical specimens with respect to tissue preservation and compare it with the effect of cooling. No preserving...... effect of vacuum sealing was observed with respect to cellular morphology, detection of immunohistochemical epitopes, or RNA integrity. In contrast, storage at 4°C was shown to preserve tissue to a higher degree than storage at room temperature for all included endpoints, independently of whether...

  15. Study of Biological Pigments by Single Specimen Derivative Spectrophotometry

    Science.gov (United States)

    Goldstein, Jack M.

    1970-01-01

    The single specimen derivative (SSD) method provides an absolute absorption spectrum of a substance in the absence of a suitable reference. Both a reference and a measuring monochromatic beam pass through a single sample, and the specimen itself acts as its own reference. The two monochromatic beams maintain a fixed wavelength difference upon scanning, and the difference in absorbance of the two beams is determined. Thus, the resulting spectrum represents the first derivative of the conventional type absorption spectrum. Tissues and cell fractions have been examined at room and liquid N2 temperature and chromophoric molecules such as the mitochondrial cytochromes and blood pigments have been detectable in low concentrations. In the case of isolated cellular components, the observed effects of substrates and inhibitors confirm similar studies by conventional spectrophotometry. The extension of the SSD concept to the microscopic level has permitted the study of the tissue compartmentalization and function of cytochromes and other pigments within layered tissue. PMID:4392452

  16. Safety analysis report for Hot-Cell irradiated specimen cask

    Energy Technology Data Exchange (ETDEWEB)

    Ku, J. H.; Lee, J. C.; Seo, K. S.; Lee, D. W. [Korea Atomic Energy Research Institute, Taejon (Korea)

    1999-03-01

    For the examination of spent fuels and radioactive materials by using scanning electron microscope, a irradiated specimen cask is needed to transport the specimen from the hot-cell to the shielded glove box in which the scanning electron microscope is installed. This cask should be easy to handle and transport, has safe to maintain the shielding safety of operators as well as the thermal and structural integrities under prescribed load conditions by the regulations as requirements. Also the cask should be assured that docked perfectly maintaining shielding integrity with the interfaces of hot-cell and shield glove box. Accordingly, the main features of cask were analyzed with functional capabilities, and the integrities of cask under required load conditions were evaluated. Therefore, it was verified that the cask is suitable to use at the outside transport as well as Post Irradiated Examination Facility in KAERI. 9 refs., 50 figs., 14 tabs. (Author)

  17. Photorealistic Modeling of the Growth of Filamentous Specimens

    Science.gov (United States)

    Sedlář, Jiří; Flusser, Jan; Sedlářová, Michaela

    2007-12-01

    We present a new method for modeling the development of settled specimens with filamentous growth patterns, such as fungi and oomycetes. In phytopathology, the growth parameters of such microorganisms are frequently examined. Their development is documented repeatedly, in a defined time sequence, leaving the growth pattern incomplete. This restriction can be overcome by reconstructing the missing images from the images acquired at consecutive observation sessions. Image warping is a convenient tool for such purposes. In the proposed method, the parameters of the geometric transformation are estimated by means of the growth tracking based on the morphological skeleton. The result is a sequence of photorealistic artificial images that show the development of the specimen within the interval between observations.

  18. Photorealistic Modeling of the Growth of Filamentous Specimens

    Directory of Open Access Journals (Sweden)

    Michaela Sedlářová

    2008-02-01

    Full Text Available We present a new method for modeling the development of settled specimens with filamentous growth patterns, such as fungi and oomycetes. In phytopathology, the growth parameters of such microorganisms are frequently examined. Their development is documented repeatedly, in a defined time sequence, leaving the growth pattern incomplete. This restriction can be overcome by reconstructing the missing images from the images acquired at consecutive observation sessions. Image warping is a convenient tool for such purposes. In the proposed method, the parameters of the geometric transformation are estimated by means of the growth tracking based on the morphological skeleton. The result is a sequence of photorealistic artificial images that show the development of the specimen within the interval between observations.

  19. Preparation And Analysis Of Specimens Of Ablative Materials

    Science.gov (United States)

    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.

  20. Design and Realization of Geographic Information System for Plant Specimens

    Directory of Open Access Journals (Sweden)

    Zhenran Gao

    2016-03-01

    Full Text Available The thesis research work is based on adopting the combination of theory and technology research. For the unique characteristics of bambusoideae in yunnan province, analyses the characteristics, value and the present situation of resources of bambusoideae plant resources in yunnan province. According to the system requirements of the specimen of bambusoideae in Yunnan province, by Microsoft. Net framework platform, a collection of Web services and ASP.NET technology, based on the data of Microsoft SQL Server2008 and ADO.NET technology support, selecting desktop GIS Arc GIS platform (Arc GIS Desktop and server (Arc GIS Server as a system of GIS secondary development of GIS, and using developed tools of Microsoft Visual Studio 2010 Visual, Finally, the information system of plant specimen which based on GIS integration development of bambusoideae is finished .

  1. Innovations in macroscopic evaluation of pancreatic specimens and radiologic correlation

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    Charikleia Triantopoulou

    2016-01-01

    Full Text Available The purpose of this study was to evaluate the feasibility of a novel dissection technique of surgical specimens in different cases of pancreatic tumors and provide a radiologic pathologic correlation. In our hospital, that is a referral center for pancreatic diseases, the macroscopic evaluation of the pancreatectomy specimens is performed by the pathologists using the axial slicing technique (instead of the traditional procedure with longitudinal opening of the main pancreatic and/or common bile duct and slicing along the plane defined by both ducts. The specimen is sliced in an axial plane that is perpendicular to the longitudinal axis of the descending duodenum. The procedure results in a large number of thin slices (3–4 mm. This plane is identical to that of CT or MRI and correlation between pathology and imaging is straightforward. We studied 70 cases of suspected different solid and cystic pancreatic tumors and we correlated the tumor size and location, the structure—consistency (areas of necrosis—hemorrhage—fibrosis—inflammation, the degree of vessels’ infiltration, the size of pancreatic and common bile duct and the distance from resection margins. Missed findings by imaging or pitfalls were recorded and we tried to explain all discrepancies between radiology evaluation and the histopathological findings. Radiologic-pathologic correlation is extremely important, adding crucial information on imaging limitations and enabling quality assessment of surgical specimens. The deep knowledge of different pancreatic tumors’ consistency and way of extension helps to improve radiologists’ diagnostic accuracy and minimize the radiological-surgical mismatching, preventing patients from unnecessary surgery.

  2. Solution Preserves Nucleic Acids in Body-Fluid Specimens

    Science.gov (United States)

    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.

  3. Evaluation of miniature tensile specimen fabrication techniques and performance

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, M.L. [Pacific Northwest Lab., Richland, WA (United States); Blotter, M.A.; Edwards, D.J. [Missouri Univ., Rolla, MO (United States)

    1992-01-01

    The confident application of miniature tensile specimens requires adequate control over their fabrication and is facilitated by automated test and analysis techniques. Three fabrication processes -- punching, chemical, milling, and electrical discharge machining (EDM) -- were recently evaluated, leading to the replacement of the previously used punching technique with a wire EDM technique. The automated data acquisition system was upgraded, and an interactive data analysis program was developed.

  4. Enteropathogenic bacteria isolated from specimens of patients with diarrhea

    OpenAIRE

    Salary M

    1997-01-01

    Acute infectious gastroenteritis is one of the most common infectious diseases of humans in the world. Diarrheal disease still ranks very high as a major cause of illness and death especially in developing nations. This study has been carried out to investigate enteropathogenic bacteria isolated from 2517 specimens of patients with diarrhea. The results obtained are as follow: Salmonella typhimurium: 6 cases 3.1 percent, Salmonella havana: 5 cases 2.6 percent, Shigella dysenteriae: 12 cases 6...

  5. Museum specimen data predict crop damage by tropical rodents

    OpenAIRE

    Sánchez-Cordero, Víctor; Martínez-Meyer, Enrique

    2000-01-01

    Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rod...

  6. The management of incidental findings of reduction mammoplasty specimens

    OpenAIRE

    Goodwin, Jessica T.; DeCroff, Chantelle; Dauway, Emilia; Sybenga, Amelia; Mahabir, Raman C

    2013-01-01

    Reduction mammoplasty is one of the most commonly performed procedures in plastic surgery. Occasionally, there are findings reported by pathologists that are unfamiliar to the treating surgeon. The aim of the present study was to determine the types of pathologies encountered in reduction mammoplasty specimens. From this list of diagnoses, a best practice guideline for management will be organized to better assist plastic surgeons in the management of patients with incidental findings on path...

  7. NEW TRIASSIC ASTEROIDEA (ECHINODERMATA SPECIMENS AND THEIR EVOLUTIONARY SIGNIFICANCE

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    DANIEL B. BLAKE

    2017-04-01

    Full Text Available The Paleozoic-Mesozoic transition saw the disappearance of asteroid stem groups and the ascent of the crown group, but late Paleozoic and Triassic asteroids are rare and transition events are poorly documented. Three new Middle and Late Triassic specimens augment existing data; included are a specimen of Trichasteropsis weissmanni from Germany, a specimen of Trichasteropsis? sp. indet. from Italy, and a possible member of the extant Poraniidae from Slovenia. Presence of a small ossicle at the interbrachial midline and adjacent to the marginal series of the new T. weissmanni specimen is consistent with similar expressions not only of other trichasteropsids but also occurrence of two interbrachial ossicles in Paleozoic, stem-group asterozoans; presence is in turn consistent with a hypothesis of derivation of the axillary/odontophore coupling from two ossicles rather than direct derivation of the crown-group odontophore from a single stem-group axillary. Morphology of Trichasteropsis? sp. indet., including, for example, the evenly-tapering arms are reminiscent of those of diverse crown-group asteroids whereas the enlarged distal arms of T. weissmanni are unique, the morphology of T? sp. indet. thereby potentially indicative of a plesiomorphic, stemward positioning within the Trichasteropsiidae. The range of the Poraniidae is tentatively extended to the Carnian. Similarities shared by the Poraniidae and the Trichasteropsiidae suggest stemward positioning within crown-group diversification; however, known Triassic fossils do not appear closely related to extant taxa identified in recent molecular studies as basal within the crown-group. A temperate climate is suggested as preferred by the Triassic asteroids rather than a tropical, warmer one.

  8. Histopathological Study of Uterine and Cervical Lesions in Hysterectomy Specimens.

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    Dr.Varsha Dhuliya

    2016-12-01

    Full Text Available Background: The adult nulliparous uterus is a hollow, pear shaped organ that weights 40-80 grams. It is divided into the Cervix and Corpus. The uterus being a vital reproductive and hormone-responsive organ, is subjected to a variety of physiological changes and benign and malignant disorders. Hysterectomy is the most common major gynecological procedure in the world. It can be done through either abdominal or vaginal route. Aims and objectives: The present study was aimed at detailed histopathological evaluation of all lesion of hysterectomy specimen Material and methods: This was a retrospective study of the gross and histopathological findings of uterus and cervix in 150 hysterectomy specimens received in the pathology department, B. J. Medical college, Ahmedabad during the period from July to December 2015.The hysterectomy specimens received were fixed in 10% formalin for 24 hours, were examined grossly and necessary sections were obtained. The tissue pieces were then processed in automated tissue processor , well labeled paraffin blocks were made. Sections were cut with the help of microtome and were stained routinely by Hematoxylin & Eosin stain and special stains wherever necessary. Sections were examined with the help of light microscopy. Results: Peak age group of hysterectomy was 41-50 years. Most common pathology found was uterine leiomyomas in 55 cases and next to it was adenomyosis. In cervix most common finding was chronic cervicitis in 116 cases. Conclusion: Most common benign lesion in uterus is leiomyoma followed by adenomyosis and in cervix it is chronic cervicitis in hysterectomy specimens received in our department.

  9. Instrumented Impact Testing: Influence of Machine Variables and Specimen Position

    Energy Technology Data Exchange (ETDEWEB)

    Lucon, E.; McCowan, C. N.; Santoyo, R. A.

    2008-09-15

    An investigation has been conducted on the influence of impact machine variables and specimen positioning on characteristic forces and absorbed energies from instrumented Charpy tests. Brittle and ductile fracture behavior has been investigated by testing NIST reference samples of low, high and super-high energy levels. Test machine variables included tightness of foundation, anvil and striker bolts, and the position of the center of percussion with respect to the center of strike. For specimen positioning, we tested samples which had been moved away or sideways with respect to the anvils. In order to assess the influence of the various factors, we compared mean values in the reference (unaltered) and altered conditions; for machine variables, t-test analyses were also performed in order to evaluate the statistical significance of the observed differences. Our results indicate that the only circumstance which resulted in variations larger than 5 percent for both brittle and ductile specimens is when the sample is not in contact with the anvils. These findings should be taken into account in future revisions of instrumented Charpy test standards.

  10. Banking Brain Tumor Specimens Using a University Core Facility.

    Science.gov (United States)

    Bregy, Amade; Papadimitriou, Kyriakos; Faber, David A; Shah, Ashish H; Gomez, Carmen R; Komotar, Ricardo J; Egea, Sophie C

    2015-08-01

    Within the past three decades, the significance of banking human cancer tissue for the advancement of cancer research has grown exponentially. The purpose of this article is to detail our experience in collecting brain tumor specimens in collaboration with the University of Miami/Sylvester Tissue Bank Core Facility (UM-TBCF), to ensure the availability of high-quality samples of central nervous system tumor tissue for research. Successful tissue collection begins with obtaining informed consent from patients following institutional IRB and federal HIPAA guidelines, and it needs a well-trained professional staff and continued maintenance of high ethical standards and record keeping. Since starting in 2011, we have successfully banked 225 brain tumor specimens for research. Thus far, the most common tumor histology identified among those specimens has been glioblastoma (22.1%), followed by meningioma (18.1%). The majority of patients were White, non-Hispanics accounting for 45.1% of the patient population; Hispanic/Latinos accounted for 23%, and Black/African Americans accounted for 14%, which represent the particular population of the State of Florida according to the 2010 census data. The most common tumors found in each subgroup were as follows: Black/African American, glioblastoma and meningioma; Hispanic, metastasis and glioblastoma; White, glioblastoma and meningioma. The UM-TBCF is a valuable repository, offering high-quality tumor samples from a unique patient population.

  11. Processing and Quality Evaluation of Additive Manufacturing Monolayer Specimens

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    Christiane Wendt

    2016-01-01

    Full Text Available Although its importance has increased significantly, Additive Manufacturing is not yet a fully accepted industrial manufacturing process for load-carrying parts. The future success of the process group depends on its standardization. This work proposes a methodology for the design, manufacturing, and quality evaluation of specimens manufactured by Fused Layer Modeling that are composed of only one layer (so-called monolayers. The processing methodology and properties of monolayers have not been studied systematically yet. A first systematic design of monolayers for mechanical testing is presented. Rectangular and circular monolayers adapted to the loads of tensile and compression testing are manufactured using different trajectory strategies. Frequently occurring macro- and microgeometrical defects are evaluated and categorized in order to optimize the part quality. This work also studies the effect of some manufacturing parameters such as the gap between print head and machine bed, trajectory strategy, bed leveling, and temperatures on part quality. The most suitable specimens are tested mechanically in tensile or compression tests. In the case of study, tensile strength values are only 8.6% lower than the values for reference tests on the unextruded filament. However, the properties deviate more strongly for compression tests which may be due to the selected specimen geometry.

  12. Antarctic environmental specimen bank. A tool for chemical monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Soggia, F.; Dalla Riva, S.; Abelmoschi, M.L.; Frache, R. [Genoa Univ., Genoa (Italy). Dipt. di Chimica e Chimica Industriale

    2000-02-01

    The work illustrates the project on Antarctic Environmental Specimen Bank (BCAA), which is an integral part of the Italian project on the micropollutants chemistry (sector on chemical contamination of the Italian Antarctic Research program, PNRA), begun in 1994 when the BCAA was installed in the department of chemistry and industrial chemistry (Genoa University, Italy). Its objective underlines an emphasis on environmental chemistry and the establishment of baselines similar to the approaches followed by the other environmental specimen banks, begun at the end of Sixties with the aim of long-term storage of representative environmental specimens in order to study the presence and the evolution of dangerous substances, but focus on the chemical characterization of samples. [Italian] Il lavoro illustra le finalita' del Progetto su una Banca Campioni Ambientali Antartici (BCAA), che e' parte integrante del progetto Chmica dei microinquinannti del Settore Contaminazione chimica del Programma Nazionale di ricerche in Antartide (ONRA), nata nel 1994 presso il dipartimento di chimicia e chimica industriale dell'universita' di Genova. A differenza di altri progetti internazionali che enfatizzano gli aspetti biologici, ecologici e medici, il progetto BCAA enfatizza la chimica ambientale.

  13. Frequency of adenomyosis in hysterectomy specimens performed for benign indications

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    bulent cakmak

    2012-09-01

    Results: Adenomyosis frequency was determined as 11.7% (17 of 149 patients received for the elavuation for this study. There was no statistically significance in terms of ages among the cases with or without adenomyosis (49.4+/-8.3 vs 50.5+/-9.7 (p>0.05. Similarly there was no statistically significance between two groups in the number of pregnancy and parous (p>0.05. Adenomyosis was determined as 13.2% in hysterectomy specimens performed for leiomyoma and again it was determined as 17.8% in hysterectomy specimens performed for refracter menorrhagia. There was no statistically significance between two indication groups for the sake of being determined of adenomyosis hystopathologically in hysterectomy specimens (p>0.05. Conclusion: Adenomyosis can be seen in patients with leiomyoma and menorrhagia. So the possibility of adenomyosis detection should not be forgotten when the treatment is planned for the cases with leiomyoma and menorrhagia. [J Contemp Med 2012; 2(3.000: 158-161

  14. Lessons learned from the comparative study between renal mass biopsy and the analysis of the surgical specimen.

    Science.gov (United States)

    Domínguez-Esteban, M; Villacampa-Aubá, F; Garcia-Muñóz, H; Tejido Sánchez, A; Romero Otero, J; de la Rosa Kehrmann, F

    2014-12-01

    The role of renal mass (RM) biopsy is currently under discussion. As a result of the progressive increase in the incidental diagnosis of RMs (which have a higher percentage of benignity and well-differentiated cancers), new approaches have emerged such as observation, especially with elderly patients or those with significant comorbidity. RM biopsy (RMB) should provide sufficient information for making this decision, but so far this has not been the case. We examine our prospective series of in-bench RMBs after surgery and compare them with the anatomy of the removed specimen. We obtained (prospectively, in-bench and with a 16-gauge needle) 4 biopsies of RMs operated on in our department from October 2008 to December 2009. These RMs were analyzed by 2 uropathologists and compared with the results of the specimen. We analyzed 188 biopsies (47 RMs); 12.75% were "not valid". The ability of biopsy to diagnose malignancy or benignity was 100%, and the coincidence in the histological type was 95%. The success in determining the tumor grade was 100% when the cancer was low-grade and 62% when high-grade. None of the analyzed data (necrosis, size, etc.) influenced the results in a statistically significant manner. RMB with a 16-G needle enables the differentiation between malignancy and benignity in 100% of cases, with a very similar diagnostic accuracy in the tumor type. Tumor grade is still the pending issue with renal mass biopsy. Copyright © 2014 AEU. Published by Elsevier Espana. All rights reserved.

  15. The Venice specimen of Ouranosaurus nigeriensis (Dinosauria, Ornithopoda

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    Filippo Bertozzo

    2017-06-01

    Full Text Available Ouranosaurus nigeriensis is an iconic African dinosaur taxon that has been described on the basis of two nearly complete skeletons from the Lower Cretaceous Gadoufaoua locality of the Ténéré desert in Niger. The entire holotype and a few bones attributed to the paratype formed the basis of the original description by Taquet (1976. A mounted skeleton that appears to correspond to O. nigeriensis has been on public display since 1975, exhibited at the Natural History Museum of Venice. It was never explicitly reported whether the Venice specimen represents a paratype and therefore, the second nearly complete skeleton reported in literature or a third unreported skeleton. The purpose of this paper is to disentangle the complex history of the various skeletal remains that have been attributed to Ouranosaurus nigeriensis (aided by an unpublished field map of the paratype and to describe in detail the osteology of the Venice skeleton. The latter includes the paratype material (found in 1970 and collected in 1972, with the exception of the left femur, the right coracoid and one manus ungual phalanx I, which were replaced with plaster copies, and (possibly other manus phalanges. Some other elements (e.g., the first two chevrons, the right femur, the right tibia, two dorsal vertebrae and some pelvic bones were likely added from other individual/s. The vertebral column of the paratype was articulated and provides a better reference for the vertebral count of this taxon than the holotype. Several anatomical differences are observed between the holotype and the Venice specimen. Most of them can be ascribed to intraspecific variability (individual or ontogenetic, but some are probably caused by mistakes in the preparation or assemblage of the skeletal elements in both specimens. The body length of the Venice skeleton is about 90% the linear size of the holotype. Osteohistological analysis (the first for this taxon of some long bones, a rib and a dorsal

  16. Evaluation of the Behavior of Technova Corporation Rod-Stiffened Stitched Compression Specimens

    Science.gov (United States)

    Jegley, Dawn C.

    2013-01-01

    Under Space Act Agreement 1347 between NASA and Technova Corporation, Technova designed and fabricated two carbon-epoxy crippling specimens and NASA loaded them to failure in axial compression. Each specimen contained a pultruded rod stiffener which was held to the specimen skin with through-the-thickness stitches. One of these specimens was designed to be nominally the same as pultruded rod stitched specimens fabricated by Boeing under previous programs. In the other specimen, the rod was prestressed in a Technova manufacturing process to increase its ability to carrying compressive loading. Experimental results demonstrated that the specimen without prestressing carried approximately the same load as the similar Boeing specimens and that the specimen with prestressing carried significantly more load than the specimen without prestressing.

  17. Influence of gross specimen sampling on the incidence of incidental prostatic carcinoma in cystoprostatectomy specimens of patients with bladder carcinoma

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    Jernej Mlakar

    2016-05-01

    Full Text Available 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.

  18. Improved Diagnosis of Prosthetic Joint Infection by Culturing Periprosthetic Tissue Specimens in Blood Culture Bottles

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    Trisha N. Peel

    2016-01-01

    Full Text Available Despite known low sensitivity, culture of periprosthetic tissue specimens on agars and in broths is routine. Culture of periprosthetic tissue samples in blood culture bottles (BCBs is potentially more convenient, but it has been evaluated in a limited way and has not been widely adopted. The aim of this study was to compare the sensitivity and specificity of inoculation of periprosthetic tissue specimens into blood culture bottles with standard agar and thioglycolate broth culture, applying Bayesian latent class modeling (LCM in addition to applying the Infectious Diseases Society of America (IDSA criteria for prosthetic joint infection. This prospective cohort study was conducted over a 9-month period (August 2013 to April 2014 at the Mayo Clinic, Rochester, MN, and included all consecutive patients undergoing revision arthroplasty. Overall, 369 subjects were studied; 117 (32% met IDSA criteria for prosthetic joint infection, and 82% had late chronic infection. Applying LCM, inoculation of tissues into BCBs was associated with a 47% improvement in sensitivity compared to the sensitivity of conventional agar and broth cultures (92.1 versus 62.6%, respectively; this magnitude of change was similar when IDSA criteria were applied (60.7 versus 44.4%, respectively; P = 0.003. The time to microorganism detection was shorter with BCBs than with standard media (P < 0.0001, with aerobic and anaerobic BCBs yielding positive results within a median of 21 and 23 h, respectively. Results of our study demonstrate that the semiautomated method of periprosthetic tissue culture in blood culture bottles is more sensitive than and as specific as agar and thioglycolate broth cultures and yields results faster.

  19. Improved Diagnosis of Prosthetic Joint Infection by Culturing Periprosthetic Tissue Specimens in Blood Culture Bottles.

    Science.gov (United States)

    Peel, Trisha N; Dylla, Brenda L; Hughes, John G; Lynch, David T; Greenwood-Quaintance, Kerryl E; Cheng, Allen C; Mandrekar, Jayawant N; Patel, Robin

    2016-01-05

    Despite known low sensitivity, culture of periprosthetic tissue specimens on agars and in broths is routine. Culture of periprosthetic tissue samples in blood culture bottles (BCBs) is potentially more convenient, but it has been evaluated in a limited way and has not been widely adopted. The aim of this study was to compare the sensitivity and specificity of inoculation of periprosthetic tissue specimens into blood culture bottles with standard agar and thioglycolate broth culture, applying Bayesian latent class modeling (LCM) in addition to applying the Infectious Diseases Society of America (IDSA) criteria for prosthetic joint infection. This prospective cohort study was conducted over a 9-month period (August 2013 to April 2014) at the Mayo Clinic, Rochester, MN, and included all consecutive patients undergoing revision arthroplasty. Overall, 369 subjects were studied; 117 (32%) met IDSA criteria for prosthetic joint infection, and 82% had late chronic infection. Applying LCM, inoculation of tissues into BCBs was associated with a 47% improvement in sensitivity compared to the sensitivity of conventional agar and broth cultures (92.1 versus 62.6%, respectively); this magnitude of change was similar when IDSA criteria were applied (60.7 versus 44.4%, respectively; P = 0.003). The time to microorganism detection was shorter with BCBs than with standard media (P tissue culture in blood culture bottles is more sensitive than and as specific as agar and thioglycolate broth cultures and yields results faster. Prosthetic joint infections are a devastating complication of arthroplasty surgery. Despite this, current microbiological techniques to detect and diagnose infections are imperfect. This study examined a new approach to diagnosing infections, through the inoculation of tissue samples from around the prosthetic joint into blood culture bottles. This study demonstrated that, compared to current laboratory practices, this new technique increased the detection of

  20. Histopathology findings in patients presenting with menorrhagia: A study of 100 hysterectomy specimen

    Directory of Open Access Journals (Sweden)

    Nilima G Sawke

    2015-01-01

    Full Text Available Background: Menorrhagia, by definition, is heavy cyclical blood loss in excess of 80 ml/month of menstrual period lasting longer than 7 days. There are many possible causes of heavy menstrual bleeding which include hormonal imbalance, fibroids, miscarriage or ectopic pregnancy, nonhormonal intrauterine device, adenomyosis, pelvic inflammatory disease, and rarely uterine, ovarian, or cervical cancer. Treatment depends on the causes of the menorrhagia. Hysterectomy is one of the several surgical procedures as definitive treatment. Objective: To determine the histopathologic spectrum of lesions associated with menorrhagia in different age groups. Study Design: This prospective descriptive study was conducted at the Department of Pathology, People′s College of Medical Sciences and Research Centre, Bhopal. During the study period, 100 hysterectomy specimens were taken which were performed for the treatment of menorrhagia. Patients with menorrhagia in the age group of 30-50 years were selected after detailed history and fulfilling the inclusion criteria. Result: In our study, it was observed that maximum number of cases were in the age group of 41-50 years (n = 35 followed by the age group of 31-40 (n = 30. Out of 100 cases, 31% cases (n = 31 showed adenomyosis followed by leiomyomas 25% (n = 25, endometrial hyperplasia 23% (n = 23, and endometrial polyp 4% (n = 4. 11% cases (n = 11 showed dual pathology consisting of both adenomyosis and endometrial hyperplasia and 6% cases (n = 6 of leiomyoma with adenomyosis. Conclusion: Uterine adenomyosis and leiomyoma are the most common benign conditions found in hysterectomy specimens with peak incidence at 31-50 years. Patients having menorrhagia above 40 years should be screened for any endometrial pathology. Histopathology is mandatory for confirming diagnosis and the key to effective therapy and optimal outcome.

  1. Prediction of carotid plaque characteristics using non-gated MR imaging: correlation with endarterectomy specimens.

    Science.gov (United States)

    Narumi, S; Sasaki, M; Ohba, H; Ogasawara, K; Kobayashi, M; Hitomi, J; Mori, K; Ohura, K; Yamaguchi, M; Kudo, K; Terayama, Y

    2013-01-01

    Electrocardiographic gating, commonly used in MR carotid plaque imaging, can negatively affect intraplaque contrast if the TR is inappropriate. The present study aimed to determine whether a non-gated technique with appropriate TRs can accurately evaluate intraplaque characteristics in specimens excised by CEA. We prospectively examined 40 consecutive patients who underwent CEA (59-82 years of age) by using a 1.5T scanner. Axial T1WI with a TR of 500 ms and PDWI and T2WI with a TR of 3000 ms with a self-navigated rotating-blade scan instead of cardiac gating were obtained. Signal intensities of the plaque and adjacent muscle were measured, and the CR on T1WI, PDWI, and T2WI as well as the gray-scale median on US were correlated with the pathologic findings of the CEA specimens. On T1WI, the CRs of the carotid plaques differed significantly among groups in which the main components were histologically confirmed as fibrous tissue, lipid/necrosis, and hemorrhage (0.54-1.17, 1.16-1.53, and 1.40-2.29, respectively). The sensitivity and specificity for discriminating lipid/necrosis/hemorrhage from fibrous tissue were 96% and 100%, respectively. On T2WI, the CRs of plaques with lipid/necrosis were significantly higher than those of other groups, but the CRs on PDWI and the gray-scale median on US were not significantly different among the groups. Non-gated MR plaque imaging, particularly T1WI, can readily predict the intraplaque main components of the carotid artery with high sensitivity and specificity.

  2. Multicenter Clinical Evaluation of the Luminex Aries Flu A/B & RSV Assay for Pediatric and Adult Respiratory Tract Specimens

    Science.gov (United States)

    Mahony, James; Buller, Richard S.; Manji, Ryhana; Dunbar, Sherry; Walker, Kimberly; Rao, Arundhati

    2017-01-01

    ABSTRACT Influenza A and B viruses and respiratory syncytial virus (RSV) are three common viruses implicated in seasonal respiratory tract infections and are a major cause of morbidity and mortality in adults and children worldwide. In recent years, an increasing number of commercial molecular tests have become available to diagnose respiratory viral infections. The Luminex Aries Flu A/B & RSV assay is a fully automated sample-to-answer molecular diagnostic assay for the detection of influenza A, influenza B, and RSV. The clinical performance of the Aries Flu A/B & RSV assay was prospectively evaluated in comparison to that of the Luminex xTAG respiratory viral panel (RVP) at four North American clinical institutions over a 2-year period. Of the 2,479 eligible nasopharyngeal swab specimens included in the prospective study, 2,371 gave concordant results between the assays. One hundred eight specimens generated results that were discordant with those from the xTAG RVP and were further analyzed by bidirectional sequencing. Final clinical sensitivity values of the Aries Flu A/B & RSV assay were 98.1% for influenza A virus, 98.0% for influenza B virus, and 97.7% for RSV. Final clinical specificities for all three pathogens ranged from 98.6% to 99.8%. Due to the low prevalence of influenza B, an additional 40 banked influenza B-positive specimens were tested at the participating clinical laboratories and were all accurately detected by the Aries Flu A/B & RSV assay. This study demonstrates that the Aries Flu A/B & RSV assay is a suitable method for rapid and accurate identification of these causative pathogens in respiratory infections. PMID:28539342

  3. Generation of voxelized breast phantoms from surgical mastectomy specimens.

    Science.gov (United States)

    O'Connor, J Michael; Das, Mini; Dider, Clay S; Mahd, Mufeed; Glick, Stephen J

    2013-04-01

    In the research and development of dedicated tomographic breast imaging systems, digital breast object models, also known as digital phantoms, are useful tools. While various digital breast phantoms do exist, the purpose of this study was to develop a realistic high-resolution model suitable for simulating three-dimensional (3D) breast imaging modalities. The primary goal was to design a model capable of producing simulations with realistic breast tissue structure. The methodology for generating an ensemble of digital breast phantoms was based on imaging surgical mastectomy specimens using a benchtop, cone-beam computed tomography system. This approach allowed low-noise, high-resolution projection views of the mastectomy specimens at each angular position. Reconstructions of these projection sets were processed using correction techniques and diffusion filtering prior to segmentation into breast tissue types in order to generate phantoms. Eight compressed digital phantoms and 20 uncompressed phantoms from which an additional 96 pseudocompressed digital phantoms with voxel dimensions of 0.2 mm(3) were generated. Two distinct tissue classification models were used in forming breast phantoms. The binary model classified each tissue voxel as either adipose or fibroglandular. A multivalue scaled model classified each tissue voxel as percentage of adipose tissue (range 1%-99%). Power spectral analysis was performed to compare simulated reconstructions using the breast phantoms to the original breast specimen reconstruction, and fits were observed to be similar. The digital breast phantoms developed herein provide a high-resolution anthropomorphic model of the 3D uncompressed and compressed breast that are suitable for use in evaluating and optimizing tomographic breast imaging modalities. The authors believe that other research groups might find the phantoms useful, and therefore they offer to make them available for wider use.

  4. Optimal z-axis scanning parameters for gynecologic cytology specimens.

    Science.gov (United States)

    Donnelly, Amber D; Mukherjee, Maheswari S; Lyden, Elizabeth R; Bridge, Julia A; Lele, Subodh M; Wright, Najia; McGaughey, Mary F; Culberson, Alicia M; Horn, Adam J; Wedel, Whitney R; Radio, Stanley J

    2013-01-01

    The use of virtual microscopy (VM) in clinical cytology has been limited due to the inability to focus through three dimensional (3D) cell clusters with a single focal plane (2D images). Limited information exists regarding the optimal scanning parameters for 3D scanning. The purpose of this study was to determine the optimal number of the focal plane levels and the optimal scanning interval to digitize gynecological (GYN) specimens prepared on SurePath™ glass slides while maintaining a manageable file size. The iScanCoreo Au scanner (Ventana, AZ, USA) was used to digitize 192 SurePath™ glass slides at three focal plane levels at 1 μ interval. The digitized virtual images (VI) were annotated using BioImagene's Image Viewer. Five participants interpreted the VI and recorded the focal plane level at which they felt confident and later interpreted the corresponding glass slide specimens using light microscopy (LM). The participants completed a survey about their experiences. Inter-rater agreement and concordance between the VI and the glass slide specimens were evaluated. This study determined an overall high intra-rater diagnostic concordance between glass and VI (89-97%), however, the inter-rater agreement for all cases was higher for LM (94%) compared with VM (82%). Survey results indicate participants found low grade dysplasia and koilocytes easy to diagnose using three focal plane levels, the image enhancement tool was useful and focusing through the cells helped with interpretation; however, the participants found VI with hyperchromatic crowded groups challenging to interpret. Participants reported they prefer using LM over VM. This study supports using three focal plane levels and 1 μ interval to expand the use of VM in GYN cytology. Future improvements in technology and appropriate training should make this format a more preferable and practical option in clinical cytology.

  5. Optimal z-axis scanning parameters for gynecologic cytology specimens

    Directory of Open Access Journals (Sweden)

    Amber D Donnelly

    2013-01-01

    Full Text Available Background: The use of virtual microscopy (VM in clinical cytology has been limited due to the inability to focus through three dimensional (3D cell clusters with a single focal plane (2D images. Limited information exists regarding the optimal scanning parameters for 3D scanning. Aims: The purpose of this study was to determine the optimal number of the focal plane levels and the optimal scanning interval to digitize gynecological (GYN specimens prepared on SurePath™ glass slides while maintaining a manageable file size. Subjects and Methods: The iScanCoreo Au scanner (Ventana, AZ, USA was used to digitize 192 SurePath™ glass slides at three focal plane levels at 1 μ interval. The digitized virtual images (VI were annotated using BioImagene′s Image Viewer. Five participants interpreted the VI and recorded the focal plane level at which they felt confident and later interpreted the corresponding glass slide specimens using light microscopy (LM. The participants completed a survey about their experiences. Inter-rater agreement and concordance between the VI and the glass slide specimens were evaluated. Results: This study determined an overall high intra-rater diagnostic concordance between glass and VI (89-97%, however, the inter-rater agreement for all cases was higher for LM (94% compared with VM (82%. Survey results indicate participants found low grade dysplasia and koilocytes easy to diagnose using three focal plane levels, the image enhancement tool was useful and focusing through the cells helped with interpretation; however, the participants found VI with hyperchromatic crowded groups challenging to interpret. Participants reported they prefer using LM over VM. This study supports using three focal plane levels and 1 μ interval to expand the use of VM in GYN cytology. Conclusion: Future improvements in technology and appropriate training should make this format a more preferable and practical option in clinical cytology.

  6. A Century of Shope Papillomavirus in Museum Rabbit Specimens.

    Science.gov (United States)

    Escudero Duch, Clara; Williams, Richard A J; Timm, Robert M; Perez-Tris, Javier; Benitez, Laura

    2015-01-01

    Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansas and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco-Mexico's first-and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), pre-dating Shope's first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though

  7. Effective electromagnetic forces in thin sheet metal specimen

    Directory of Open Access Journals (Sweden)

    Langstädtler L.

    2015-01-01

    Full Text Available Electromagnetic forming is mainly investigated for the macro world as the body forces in this high speed process are decreasing with the volume of the specimen. For micro metal sheets different effects are observed which make an analysis of the acting forces more difficult. Hence, the validity of process simulations for electromagnetic forming is still limited. In this research the effective electromagnetic force on thin EN AW-1050A (Al99.5 sheet metals is investigated by varying the loading energy EC, the ration sR between sheet thickness and skin depth, the sheets width b and the distance dC between passive tool and sheet metal.

  8. Experimental Determination of Stress Intensity in a Cracked Cylindrical Specimen,

    Science.gov (United States)

    1980-05-01

    CRACKED CYLINDRICAL SPEC IMEN 7 ABSTRACT The range of stress intensity at the tip of a fatigue crack is the major factor controlling the crack growth...of this report will be similarly clesiied): The range of stress intensity at the tip of a fatigue crack is the major factor controlling the crack...EXPERIMENTAL STRESS INTENSITY CALIBRATION 3 3. EXPERIMENTAL DETAILS 4 3.1 Specimen Geometries 4 3.2 Material 5 3.3 Fatigue Loading 5 3.4 Crack Length

  9. Fecal specimens preparation methods for PCR diagnosis of human taeniosis

    Directory of Open Access Journals (Sweden)

    Nunes Cáris Maroni

    2006-01-01

    Full Text Available Sample preparation and DNA extraction protocols for DNA amplification by PCR, which can be applied in human fecal samples for taeniasis diagnosis, are described. DNA extracted from fecal specimens with phenol/chloroform/isoamilic alcohol and DNAzol® reagent had to be first purified to generate fragments of 170 pb and 600 pb by HDP2-PCR. This purification step was not necessary with the use of QIAmp DNA stool mini kit®. Best DNA extraction results were achieved after eggs disruption with glass beads, either with phenol/chloroform/isoamilic alcohol, DNAzol® reagent or QIAmp DNA stool mini kit®.

  10. Museum specimen data predict crop damage by tropical rodents.

    Science.gov (United States)

    Sánchez-Cordero, V; Martínez-Meyer, E

    2000-06-20

    Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rodent species for seven of nine crops. Museum collections may thus provide important baseline information for designing land-use and agricultural pest-management programs.

  11. [Candida dubliniensis in clinical specimens and possibilities for identification].

    Science.gov (United States)

    Mahelová, M; Růžička, F

    2014-06-01

    The species Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans, the most common yeast species isolated from clinical specimens. This is a considerable complication for the detection and identification of Candida dubliniensis from clinical specimens. The lack of data on the incidence of C. dubliniensis in the Czech Republic was the motivation behind the efforts to detect this pathogen in specimens analyzed at the Institute for Microbiology, Faculty of Medicine Masaryk University and St. Anne's Faculty Hospital in Brno. Another aim was to test the reliability of the culture methods used. Altogether 2260 yeast isolates initially identified as C. albicans were analysed. To differentiate C. dubliniensis from C. albicans, four phenotypic methods were used: colour-based differentiation on CHROMagar Candida medium, culture on medium with 6.5% of NaCl, growth at 42 °C, and colony characteristics on Staib agar. To verify the results, the Bichro-Dubli Fumouze latex agglutination test and species-specific polymerase chain reactions (PCR) were used. Using phenotypic methods, latex agglutination, and PCR, 50 (2.2%) strains from the study set were assigned to C. dubliniensis. Most (31) C. dubliniensis isolates were recovered from the respiratory tract and the remaining others were three urine isolates, four stool isolates, one central venous catheter isolate, and one blood isolate. With the exception of colour-based differentiation on CHROMagar Candida medium showing a specificity of 85.5%, all the culture methods used have a high sensitivity and a high specificity. Identification of C. dubliniensis as C. albicans was confirmed in various clinical specimens, most often from the upper respiratory tract. The colour-based differentiation of C. dubliniensis from C. albicans on chromogenic CHROMagar Candida medium can only be recommended as a screening test for the differentiation of C. dubliniensis from other species of the genus Candida

  12. Specimen Collection for Induced Pluripotent Stem Cell Research: Harmonizing the Approach to Informed Consent

    Science.gov (United States)

    Lowenthal, Justin; Lipnick, Scott; Rao, Mahendra

    2012-01-01

    Induced pluripotent stem cells (iPSCs) have elicited excitement in both the scientific and ethics communities for their potential to advance basic and translational research. They have been hailed as an alternative to derivation from embryos that provides a virtually unlimited source of pluripotent stem cells for research and therapeutic applications. However, research with iPSCs is ethically complex, uniquely encompassing the concerns associated with genomics, immortalized cell lines, transplantation, human reproduction, and biobanking. Prospective donation of tissue specimens for iPSC research thus requires an approach to informed consent that is constructed for this context. Even in the nascent stages of this field, approaches to informed consent have been variable in ways that threaten the simultaneous goals of protecting donors and safeguarding future research and translation, and investigators are seeking guidance. We address this need by providing concrete recommendations for informed consent that balance the perspectives of a variety of stakeholders. Our work combines analysis of consent form language collected from investigators worldwide with a conceptual balancing of normative ethical concerns, policy precedents, and scientific realities. Our framework asks people to consent prospectively to a broad umbrella of foreseeable research, including future therapeutic applications, with recontact possible in limited circumstances. We argue that the long-term goals of regenerative medicine, interest in sharing iPSC lines, and uncertain landscape of future research all would be served by a framework of ongoing communication with donors. Our approach balances the goals of iPSC and regenerative medicine researchers with the interests of individual research participants. PMID:23197820

  13. Review of forensically important entomological specimens collected from human cadavers in Malaysia (2005-2010).

    Science.gov (United States)

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Azirun, Mohd Sofian

    2013-07-01

    Forensic entomological specimens collected from human decedents during crime scene investigations in Malaysia in the past 6 years (2005-2010) are reviewed. A total of 80 cases were recorded and 93 specimens were collected. From these specimens, 10 species of cyclorrphagic flies were identified, consisting of Chrysomya rufifacies (Macquart) -38 specimens (40.86%), Chrysomya megacephala (Fabricius) -36 specimens (38.70%), Chrysomya villeneuvi (Patton) -2 specimens (2.15%), Chrysomya nigripes (Aubertin) -2 specimens (2.15%), Chrysomya pinguis (Walker) -1 specimen (1.08%), Hermetia illucens (Linnaeus) -1 specimen (1.08%), Hemipyrellia liguriens (Wiedemann) -5 specimens (5.37%), Synthesiomyia nudiseta (Wulp) -1 specimen (1.08%), Megaselia scalaris (Loew)-1 specimen (1.08%) and Sarcophaga ruficornis (Fabricius) -4 specimens (4.30%). In two specimens (2.15%), the maggots were not identifiable. Ch. megacephala and Ch. rufifacies were the commonest species found in human decedents from three different ecological habitats. S. nudiseta is an uncommon species found only on human cadavers from indoors. A total of 75 cases (93.75%) had a single fly infestation and 5 cases (6.25%) had double fly infestation. In conclusion, although large numbers of fly species were found on human decedents, the predominant species are still those of Chrysomya. Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  14. Electron microscopy by specimen design: application to strain measurements.

    Science.gov (United States)

    Cherkashin, Nikolay; Denneulin, Thibaud; Hÿtch, Martin J

    2017-09-29

    A bewildering number of techniques have been developed for transmission electron microscopy (TEM), involving the use of ever more complex combinations of lens configurations, apertures and detector geometries. In parallel, the developments in the field of ion beam instruments have modernized sample preparation and enabled the preparation of various types of materials. However, the desired final specimen geometry is always almost the same: a thin foil of uniform thickness. Here we will show that judicious design of specimen geometry can make all the difference and that experiments can be carried out on the most basic electron microscope and in the usual imaging modes. We propose two sample preparation methods that allow the formation of controlled moiré patterns for general monocrystalline structures in cross-section and at specific sites. We developed moiré image treatment algorithms using an absolute correction of projection lens distortions of a TEM that allows strain measurements and mapping with a nanometer resolution and 10-4 precision. Imaging and diffraction techniques in other fields may in turn benefit from this technique in perspective.

  15. Characterization of some biological specimens using TEM and SEM

    Science.gov (United States)

    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.

  16. Usual interstitial pneumonia: histologic study of biopsy and explant specimens.

    Science.gov (United States)

    Katzenstein, Anna-Luise A; Zisman, David A; Litzky, Leslie A; Nguyen, Binh T; Kotloff, Robert M

    2002-12-01

    The pathologic findings in biopsy and subsequent explant specimens from 20 patients with usual interstitial pneumonia (UIP) were reviewed to refine histologic criteria for diagnosis, to identify factors that may confound diagnosis, and to assess the relationship of UIP and nonspecific interstitial pneumonia (NSIP). One case of NSIP was also identified and included for comparison. Surgical biopsies from 15 of the 20 UIP cases were diagnosed as UIP, whereas 5 showed only nondiagnostic changes. An important new observation is that areas resembling nonspecific interstitial pneumonia (NSIP-like areas) are present in the majority of UIP cases in both biopsy and explant specimens, and they are extensive in some. Ten of the 15 UIP biopsies were considered straightforward, with typical patchy interstitial fibrosis, honeycomb change, and fibroblast foci. Five cases were considered difficult because of prominent NSIP-like areas in two, extensive honeycomb change in one, superimposed diffuse alveolar damage in one, and superimposed bronchiolitis obliterans-organizing pneumonia in one. The most helpful feature for diagnosing UIP in difficult cases was the presence of a distinct patchwork appearance to the characteristic uneven or variegated parenchymal involvement along with evidence of architectural derangement. No explant showing UIP was preceded by biopsy findings of NSIP, and the one NSIP case appeared similar at biopsy and explant. NSIP or NSIP-like areas and UIP may reflect different mechanisms of fibrosis related either to different severity of injury or to different injuries.

  17. Correlations between Standard and Miniaturised Charpy-V Specimens

    Energy Technology Data Exchange (ETDEWEB)

    Lucon, E.; Van Walle, E.; Fabry, A.; Puzzolante, J.-L.; Verstrepen, A.; Vosch, R.; Van de Velde, L

    1998-12-01

    A total of 565 instrumented impact tests (232 performed on full-size and 333 on sub-size Charpy-V specimens) have been analysed in order to derive meaningful assumptions on the correlations existing between test results obtained on specimens of different size. Nine materials (pressure vessel steels) have been considered, in both as-received and irradiated state, for a total of 19 conditions examined. For the analysis of data, conventional as well novel approaches have been investigated; former ones, based on a review of the existing literature, include predictions of USE values by the use of normalization factors (NF), shifts of index temperatures related to energy/lateral expansion/shear fracture levels, and a combination of both approaches (scaling and shifting of energy curves). More original and recent proposals have also been verified, available in the literature but also proposed by SCK-CEN in the frame of enhanced surveillance of nuclear reactor pressure vessels. Conclusions have been drawn regarding the applicability and reliability of these methodologies, and recommendations have been given for future developments of the activities on this topic.

  18. Thermal diffusivity measurement of ring specimens by infrared thermography

    Science.gov (United States)

    Ferrarini, G.; Bison, P.; Bortolin, A.; Cadelano, G.; Rossi, S.

    2017-05-01

    The thermal diffusivity of solid materials is usually measured with the well-known flash method. In the traditional setup, the tested specimens have the shape of a small disc. However, several industrial applications need to test different typologies of samples. This work is focused on ring specimens, that are widely used as joints or sealants in various applications. The goal is investigating the possibilities and limitations of the flash method, applying minimum adjustments to the traditional experimental setup. A preliminary numerical study is conducted with the creation of a finite element model. Firstly, the model is checked with the standard case of a full disk. Then the simulation investigates the case of an aluminum oxide ring, that is taken as the reference case to determine the reliability of the proposed technique. After the simulation, an experimental measurement is performed on the aluminum oxide ring reference case. Several samples are tested and useful information on the practical feasibility of the experimental setup are collected. The obtained thermal diffusivity values fall into the expected range for the material, confirming the validity of the suggested method.

  19. Toxicological Analysis of Exhumed Specimens: A Challenge for Toxicologists

    Directory of Open Access Journals (Sweden)

    Muhammad Taimoor Chaudhary

    2016-06-01

    Full Text Available The objective of this work is to describe the type of biological samples submitted for toxicological analysis after exhumation. Forensic toxicologists receive a variety of biological samples, but exhumed biological specimens with varying degrees of putrefaction pose a greater challenge for analysis. Usually, immunoassay and colorimetric screening are the first line approach for toxicological analysis. Suitable samples can be selected for direct analysis using chromatographic techniques with a mass spectrometer, providing reliable results. The authors report two case studies where exhumed specimens were submitted for the determination of possible intoxication. The deceased were severely injured and remained hospitalized for more than 24 hours before death. Their corpses were exhumed for chemical analysis. For the toxicological analysis, selected samples were analyzed by immunoassay and a gas chromatograph mass spectrometer (GC/MS with electron impact ionization. Although the samples were negative for drugs of abuse (benzodiazepines and opiates, by immunoassay, midazolam (benzodiazepine was detected in putrefied material using GC/MS, thus indicating the hospitalization before death.

  20. Stabilizing specimens for routine ammonia testing in the clinical laboratory.

    Science.gov (United States)

    Gifford, Jessica L; Nguyen, William N T; de Koning, Lawrence; Seiden-Long, Isolde

    2017-12-16

    In vitro deamination generates ammonia in freshly collected blood specimens. To prevent this, samples for ammonia testing are usually collected on ice and run rapidly (e.g., within 1h). We developed a method to stabilize specimens for ammonia analysis. Following plasma separation, 500μmol/l cycloserine or a combination of 2mmol/l sodium borate with 5mmol/l l-serine were added to sample pools with normal or increased concentrations of ALT and/or GGT to inhibit deamination; and/or residual platelets were removed via centrifugation. Sample pools were then incubated at room temperature or 4°C. Untreated sample pools were also incubated at -80°C. Ammonia was measured at 0, 1, 2, 4, 8, 16, and 24h. When incubated at 4°C without treatment, sample pools with enzymes within their reference limit had an increase of 0.5μmol/l/h, whereas sample pools with ALT and/or GGT activity above their upper reference limit had an increase of 3.6μmol/l/h (p12h. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Simplified, Accurate Method for Antibiotic Assay of Clinical Specimens

    Science.gov (United States)

    Bennett, John V.; Brodie, Jean L.; Benner, Ernest J.; Kirby, William M. M.

    1966-01-01

    Large glass plates are used for this modified agar-well diffusion assay method, allowing up to 81 replications on a single plate. With a specially designed agar punch, it is possible to prepare the small agar wells very quickly. The saving in serum resulting from fewer replications of standards with the large plates, and the small volume of the agar wells, makes it economically feasible to use pooled human serum for the standard antibiotic solutions. Methods are described for preparing the standard solutions, and for providing controls for the deterioration of standards and unknowns. Procedures for preparing and maintaining the commonly used assay organisms are presented. Serum specimens are tested directly rather than diluting them to a narrow range of antibiotic concentrations. This is possible because of a procedure for calculations that recognizes the curvilinear relationship between zone sizes and antibiotic concentrations. Adaptation of this method to a number of the commonly used antibiotics is described. With this method, it has been possible to test large numbers of clinical specimens in a minimal time, and with accuracy consistently better than 10%. Images Fig. 1 PMID:4959982

  2. Characterization of Two Historic Smallpox Specimens from a Czech Museum.

    Science.gov (United States)

    Pajer, Petr; Dresler, Jiri; Kabíckova, Hana; Písa, Libor; Aganov, Pavel; Fucik, Karel; Elleder, Daniel; Hron, Tomas; Kuzelka, Vitezslav; Velemínsky, Petr; Klimentova, Jana; Fucikova, Alena; Pejchal, Jaroslav; Hrabakova, Rita; Benes, Vladimir; Rausch, Tobias; Dundr, Pavel; Pilin, Alexander; Cabala, Radomir; Hubalek, Martin; Stríbrny, Jan; Antwerpen, Markus H; Meyer, Hermann

    2017-07-27

    Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees. Here, we determined two complete variola virus genomes from human tissues kept in a museum in Prague dating back 60 and 160 years, respectively. Moreover, mass spectrometry-based proteomic, chemical, and microscopic examinations were performed. The 60-year-old specimen was most likely an importation from India, a country with endemic smallpox at that time. The genome of the 160-year-old specimen is related to clade 2 West African and variola minor strains. This sequence likely represents a new endemic European variant of variola virus circulating in the midst of the 19th century in Europe.

  3. Immunohistochemistry of Programmed Cell Death in Archival Human Pathology Specimens

    Directory of Open Access Journals (Sweden)

    Takami Matsuyama

    2012-05-01

    Full Text Available Immunohistochemistry (IHC for detecting key signal molecules involved in programmed cell death (PCD in archival human pathology specimens is fairly well established. Detection of cleaved caspase-3 in lymphocytes in rheumatoid arthritis (RA and gastric surface foveolar glandular epithelia but not in synoviocytes in RA, gastric fundic glandular epithelia, or nasal NK/T-cell lymphoma (NKTCL cells suggests anti-apoptotic mechanisms in cell differentiation and in oncogenesis such as the induction of survivin. Enzymatically pretreated and ultra-super sensitive detection of beclin-1 in synoviocytes in RA and gastric fundic glandular epithelia suggests enhanced autophagy. The deposition of beclin-1 in fibrinoid necrosis in RA and expression of beclin-1 in detached gastric fundic glandular cells suggest that enhanced autophagy undergoes autophagic cell death (ACD. NKTCL exhibited enhanced autophagy through LC3 labeling and showed densely LC3 labeled cell-debris in regions of peculiar necrosis without deposition of beclin-1, indicating massive ACD in NKTCL and the alternative pathway enhancing autophagy following autophagic vesicle nucleation. Autophagy progression was monitored by labeling aggregated mitochondria and cathepsin D. The cell-debris in massive ACD in NKTCL were positive for 8-hydroxydeoxyguanosine, suggesting DNA oxidation occurred in ACD. Immunohistochemical autophagy and PCD analysis in archival human pathology specimens may offer new insights into autophagy in humans.

  4. Constitutive Modeling and Numerical Simulation of Frp Confined Concrete Specimens

    Directory of Open Access Journals (Sweden)

    Smitha Gopinath

    2014-09-01

    Full Text Available Fiber-reinforced polymer (FRP composites are generally used for the seismic retrofit of concrete members to enhance their strength and ductility. In the present work, the confining effect of Carbon Fiber-Reinforced Polymer (CFRP composite layers has been investigated by numerical simulation. The numerical simulation has been carried out using nonlinear finite element analysis (FEA to predict the response behaviour of CFRP-wrapped concrete cylinders. The nonlinear behaviour of concrete in compression and the linear elastic behaviour of CFRP has been modeled using an appropriate constitutive relationship. A cohesive model has been developed for modeling the interface between the concrete and CFRP. The interaction and damage failure criteria between the concrete to the cohesive element and the cohesive element to the CFRP has also been accounted for in the modeling. The response behaviour of the wrapped concrete specimen has been compared with the proposed interface model and with a perfectly bonded condition. The results obtained from the present study showed good agreement with the experimental load-displacement response and the failure pattern in the literature. Further, a sensitivity analysis has been carried out to study the effect of the number of layers of CFRP on the concrete specimens. It has been observed that wrapping with two layers was found to be the optimum, beyond which the response becomes flexible but with a higher load-carrying capacity

  5. Constitutive Modeling and Numerical Simulation of Frp Confined Concrete Specimens

    Science.gov (United States)

    Smitha, Gopinath; Ramachandramurthy, Avadhanam; Nagesh, Ranganatha Iyer; Shahulhameed, Eduvammal Kunhimoideen

    2014-09-01

    Fiber-reinforced polymer (FRP) composites are generally used for the seismic retrofit of concrete members to enhance their strength and ductility. In the present work, the confining effect of Carbon Fiber-Reinforced Polymer (CFRP) composite layers has been investigated by numerical simulation. The numerical simulation has been carried out using nonlinear finite element analysis (FEA) to predict the response behaviour of CFRP-wrapped concrete cylinders. The nonlinear behaviour of concrete in compression and the linear elastic behaviour of CFRP has been modeled using an appropriate constitutive relationship. A cohesive model has been developed for modeling the interface between the concrete and CFRP. The interaction and damage failure criteria between the concrete to the cohesive element and the cohesive element to the CFRP has also been accounted for in the modeling. The response behaviour of the wrapped concrete specimen has been compared with the proposed interface model and with a perfectly bonded condition. The results obtained from the present study showed good agreement with the experimental load-displacement response and the failure pattern in the literature. Further, a sensitivity analysis has been carried out to study the effect of the number of layers of CFRP on the concrete specimens. It has been observed that wrapping with two layers was found to be the optimum, beyond which the response becomes flexible but with a higher load-carrying capacity

  6. Identities of Microbacterium spp. encountered in human clinical specimens.

    Science.gov (United States)

    Gneiding, Kathrina; Frodl, Reinhard; Funke, Guido

    2008-11-01

    In the present study, 50 strains of yellow-pigmented gram-positive rods that had been isolated from human clinical specimens and collected over a 5-year period were further characterized by phenotypic and molecular genetic methods. All 50 strains belonged to the genus Microbacterium, and together they represented 18 different species. Microbacterium oxydans (n = 11), M. paraoxydans (n = 9), and M. foliorum (n = 7) represented more than half of the strains included in the present study. The isolation of strains belonging to M. hydrocarbonoxydans (n = 2), M. esteraromaticum (n = 1), M. oleivorans (n = 1), M. phyllosphaerae (n = 1), and M. thalassium (n = 1) from humans is reported for the first time. Microbacterium sp. strain VKM Ac-1389 (n = 1) and the previously uncultured Microbacterium sp. clone YJQ-29 (n = 1) probably represent new species. Comprehensive antimicrobial susceptibility data are given for the 50 Microbacterium isolates. This study is, so far, the largest on Microbacterium spp. encountered in human clinical specimens and outlines the heterogeneity of clinical Microbacterium strains.

  7. Clinicopathologic features of incidental prostatic adenocarcinoma in radical cystoprostatectomy specimens

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    Vuruskan Hakan

    2011-07-01

    Full Text Available Abstract Background The aim of this study is to review all features of incidentally discovered prostate adenocarcinoma in patients undergoing radical cystoprostatectomy for bladder cancer. Methods The medical charts of 300 male patients who underwent radical cystoprostatectomy for bladder cancer between 1997 and 2005 were retrospectively reviewed. The mean age of the patients was 62 (range 51-75 years. Results Prostate adenocarcinoma was present in 60 (20% of 300 specimens. All were acinar adenocarcinoma. Of these, 40 (66.7% were located in peripheral zone, 20 (33.3% had pT2a tumor, 12 (20% had pT2b tumor, 22(36.7% had pT2c and, 6 (10% had pT3a tumor. Gleason score was 6 or less in 48 (80% patients. Surgical margins were negative in 54 (90% patients, and tumor volume was less than 0.5 cc in 23 (38.3% patients. Of the 60 incidentally detected cases of prostate adenocarcinoma 40 (66.7% were considered clinically significant. Conclusion Incidentally detected prostate adenocarcinoma is frequently observed in radical cystoprostatectomy specimens. The majority are clinically significant.

  8. Where are primary type specimens of new mite species deposited?

    Science.gov (United States)

    Liu, Jian-Feng; Wei, Xiao-Ying; Li, Guang-Yun; Zhang, Zhi-Qiang

    2017-12-08

    A list of type depositories of new mite species published in two journals (Systematic & Applied Acarology and Zootaxa) during the last five years (2012-2016) is presented in this paper. The 1370 new species are deposited unevenly among 134 collections. The top collection is the Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia (145 species), which alone accounts for 10% of the total new species, and the top ten collections accounted for 48% of the total. The average number of new species per collection is 10 and over three quarters of the collections are below the average. Just over half (51%) of the collections are in Europe. However, overall there were still more new species deposited in collections in developing counties (741) than developed countries (629). The top country for type depositories of new mite species for each continent is: Russia (199 species) for Europe, Brazil (134 species) for South America, Iran (133 species) for Asia, Australia (87 species) for Oceania, USA (80 species) for North America and South Africa (36 species) for Africa. The top European collections hold type specimens mostly of foreign origin, whereas those of South America, Asia, Africa and Australasia hold type specimens mostly originating from their own countries.

  9. The management of incidental findings of reduction mammoplasty specimens.

    Science.gov (United States)

    Goodwin, Jessica T; Decroff, Chantelle; Dauway, Emilia; Sybenga, Amelia; Mahabir, Raman C

    2013-01-01

    Reduction mammoplasty is one of the most commonly performed procedures in plastic surgery. Occasionally, there are findings reported by pathologists that are unfamiliar to the treating surgeon. The aim of the present study was to determine the types of pathologies encountered in reduction mammoplasty specimens. From this list of diagnoses, a best practice guideline for management will be organized to better assist plastic surgeons in the management of patients with incidental findings on pathology reports. A total of 441 pathology reports from patients who underwent bilateral or unilateral reduction mammoplasty in the past three years were identified. A list of 21 different pathologies was generated from the pathology reports, along with supplemental data from recent texts and articles. Occult carcinomas were encountered in two cases (0.45%) and high-risk lesions were found in three cases (0.68%) at the authors' institution. An algorithm was then constructed to organize the pathologies according to risk of malignancy and assign them to a management guideline. There are many different lesions encountered incidentally in reduction mammoplasty specimens that may or may not confer some cancer risk. It is important for plastic surgeons to know which lesions need closer follow-up to provide the best care for their patients.

  10. The management of incidental findings of reduction mammoplasty specimens

    Science.gov (United States)

    Goodwin, Jessica T; DeCroff, Chantelle; Dauway, Emilia; Sybenga, Amelia; Mahabir, Raman C

    2013-01-01

    Reduction mammoplasty is one of the most commonly performed procedures in plastic surgery. Occasionally, there are findings reported by pathologists that are unfamiliar to the treating surgeon. The aim of the present study was to determine the types of pathologies encountered in reduction mammoplasty specimens. From this list of diagnoses, a best practice guideline for management will be organized to better assist plastic surgeons in the management of patients with incidental findings on pathology reports. A total of 441 pathology reports from patients who underwent bilateral or unilateral reduction mammoplasty in the past three years were identified. A list of 21 different pathologies was generated from the pathology reports, along with supplemental data from recent texts and articles. Occult carcinomas were encountered in two cases (0.45%) and high-risk lesions were found in three cases (0.68%) at the authors’ institution. An algorithm was then constructed to organize the pathologies according to risk of malignancy and assign them to a management guideline. There are many different lesions encountered incidentally in reduction mammoplasty specimens that may or may not confer some cancer risk. It is important for plastic surgeons to know which lesions need closer follow-up to provide the best care for their patients. PMID:24497763

  11. Improving ED specimen TAT using Lean Six Sigma.

    Science.gov (United States)

    Sanders, Janet H; Karr, Tedd

    2015-01-01

    Lean and Six Sigma are continuous improvement methodologies that have garnered international fame for improving manufacturing and service processes. Increasingly these methodologies are demonstrating their power to also improve healthcare processes. The purpose of this paper is to discuss a case study for the application of Lean and Six Sigma tools in the reduction of turnaround time (TAT) for Emergency Department (ED) specimens. This application of the scientific methodologies uncovered opportunities to improve the entire ED to lab system for the specimens. This case study provides details on the completion of a Lean Six Sigma project in a 1,000 bed tertiary care teaching hospital. Six Sigma's Define, Measure, Analyze, Improve, and Control methodology is very similar to good medical practice: first, relevant information is obtained and assembled; second, a careful and thorough diagnosis is completed; third, a treatment is proposed and implemented; and fourth, checks are made to determine if the treatment was effective. Lean's primary goal is to do more with less work and waste. The Lean methodology was used to identify and eliminate waste through rapid implementation of change. The initial focus of this project was the reduction of turn-around-times for ED specimens. However, the results led to better processes for both the internal and external customers of this and other processes. The project results included: a 50 percent decrease in vials used for testing, a 50 percent decrease in unused or extra specimens, a 90 percent decrease in ED specimens without orders, a 30 percent decrease in complete blood count analysis (CBCA) Median TAT, a 50 percent decrease in CBCA TAT Variation, a 10 percent decrease in Troponin TAT Variation, a 18.2 percent decrease in URPN TAT Variation, and a 2-5 minute decrease in ED registered nurses rainbow draw time. This case study demonstrated how the quantitative power of Six Sigma and the speed of Lean worked in harmony to improve

  12. Effect of specimen size on the fracture toughness of V-4Cr-4Ti

    Energy Technology Data Exchange (ETDEWEB)

    Kurtz, R.J.; Jones, R.H. [Pacific Northwest National Laboratory, Richland, WA (United States); Li, Huaxin

    1996-04-01

    J-R curves were generated using the single specimen unload-compliance technique on four specimens of V-4Cr-4Ti to determine the effect of specimen dimensions on the fracture behavior. Ductile crack initiation and growth was observed in the 6.35 mm thick specimens but not in the 12.70 mm thick specimens. The J-R curves determined from these tests were not valid per ASTM validity criteria so quantitative measures of the resistance to ductile crack initiation and growth were not obtained. These data suggests that standard fracture toughness tests were performed with small-scale DCT specimens may also not be valid.

  13. The specimen adequacy and Atypical Squamous Cell frequency: conventional versus liquid-based cytology pap smears

    Directory of Open Access Journals (Sweden)

    Izadi Mood N

    2009-03-01

    Full Text Available "nBackground: The papanicolaou (pap smear has been used to screen cervical cancer since 1940. Recently, a number of new technologies have been developed to improve the detection of cervical cancer and its precursors. However, there is substantial controversy about whether the new tests offer meaningful advantages over the conventional pap smear. Ideally, these new tests will increase the early detection of meaningful pap smear abnormalities, reduce the number of unsatisfactory smears and provide fewer ambiguous results. "nMethods: In this prospective study the result of Liquid- based cytology smears (Liquid prep method compared with conventional pap smears in terms of adequacy and ASC diagnosis in 289 patients in pathology department of mirza kochak khan hospital (Tehran, 2005- 2006. The smears were interpreted based on Bethesda system 2001. "nResults: In conventional pap smear method, the number of occasions of unsatisfactory smear was 24(5%. In Liquid- based cytology method 66(22.8% smears were unsatisfactory, In which difference between unsatisfactory groups were statistically significant (p<0.05, Also ASC diagnosis in conventional method 5(1.8% as compared with Liquid- based cytology 6(2.1%, was not statistically significant (p>0.05. "nConclusions: There was no significant difference between two methods in term of ASC diagnosis but in conventional method adequacy of specimen was significantly better as compared with this Liquid- based cytology method.

  14. A Century of Shope Papillomavirus in Museum Rabbit Specimens.

    Directory of Open Access Journals (Sweden)

    Clara Escudero Duch

    Full Text Available Sylvilagus floridanus Papillomavirus (SfPV causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus from Kansas and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8% than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco-Mexico's first-and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915, pre-dating Shope's first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species

  15. [Future of gynecological exfoliative cytology specimen, the Pap test].

    Science.gov (United States)

    Nieminen, Pekka; Timonen, Tuomo

    2014-01-01

    Screenings of cervical cancer in Finland by using the Pap test have decreased the incidence of the disease by approx. 80%. Automation-assisted cytology and liquid-based Pap test have improved the technical quality of cytological examination. The HPV test allows the prevention of more cancers and its negative predictive value is crucially better than that of the Pap test. Its problem is the modest specificity in young age groups. When the HPV-vaccinated age groups reach the screening age, the HPV test should be adopted as the first-line screening test in all age groups. The Pap test will continue to have an important role as a further investigation and diagnostic specimen.

  16. Fracture properties of concrete specimens made from alkali activated binders

    Science.gov (United States)

    Šimonová, Hana; Kucharczyková, Barbara; Topolář, Libor; Bílek, Vlastimil, Jr.; Keršner, Zbyněk

    2017-09-01

    The aim of this paper is to quantify crack initiation and other fracture properties - effective fracture toughness and specific fracture energy - of two types of concrete with an alkali activated binder. The beam specimens with a stress concentrator were tested in a three-point bending test after 28, 90, and 365 days of maturing. Records of fracture tests in the form of load versus deflection (P-d) diagrams were evaluated using effective crack model and work-of-fracture method and load versus mouth crack opening displacement (P-CMOD) diagrams were evaluated using the Double-K fracture model. The initiation of cracks during the fracture tests for all ages was also monitored by the acoustic emission method. The higher value of monitored mechanical fracture parameters of concrete with alkali activated blast furnace slag were achieved with substitution blast furnace slag by low calcium fly ash in comparison with substitution by cement kiln dust.

  17. Condition For Strain-Hardening In Ecc Uniaxial Test Specimen

    DEFF Research Database (Denmark)

    Dick-Nielsen, Lars; Stang, Henrik; Poulsen, Peter Noe

    2006-01-01

    This paper discusses the adequateness of the steady state flat crack criterion for crack propagation in Engineered Cementitious Composites. The investigation is performed by use of a semi-analytical model as well as a Finite Element Model. The simulations are for one crack propagating in finite...... and infinite sheets under uniaxial tension. The crack is assumed to be cohesive and the cohesive law applied takes into account fiber as well as mortar properties. It is shown that the maximum crack opening observed during crack propagation in various test specimen geometries is small, 20 m and also small...... compared to typical deformations at peak bridging stress. The requirement of a minimum complementary energy for the fiber bridging curve is found not to be relevant in the aim of controlling the crack opening during crack propagation....

  18. Standard practice for preparing, cleaning, and evaluating corrosion test specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2003-01-01

    1.1 This practice covers suggested procedures for preparing bare, solid metal specimens for tests, for removing corrosion products after the test has been completed, and for evaluating the corrosion damage that has occurred. Emphasis is placed on procedures related to the evaluation of corrosion by mass loss and pitting measurements. (Warning—In many cases the corrosion product on the reactive metals titanium and zirconium is a hard and tightly bonded oxide that defies removal by chemical or ordinary mechanical means. In many such cases, corrosion rates are established by mass gain rather than mass loss.) 1.2 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use. For specific precautionary statements, see 1 and 7.2.

  19. Mini-tensile specimen application for sheets characterization

    Science.gov (United States)

    Džugan, J.; Rund, M.; Prantl, A.; Konopík, P.

    2017-02-01

    There are many cases when there is a shortage of the experimental material for detailed analysis and then small size specimens techniques becomes essential. The current paper deals with investigations of mini-tensile tests (MTT) application to metal sheets characterization. In the case of metal sheets assessment the most common are tensile tests for Lankford parameters and strain hardening determination. As most of the processes are not quasi-static and constant strain rate processes, thus assessment of strain rate hardening is also crucial part of the characterization. Previously developed and verified testing procedure of M-TTs for bulk materials is applied here for steel sheet made of DC01 characterization. Tests under quasi-static and dynamic loading conditions are carried out in order to describe above mentioned properties at room temperature. Accurate strain measurement is carried out with digital image correlation systems and results obtained with M-TTs are going to be confronted with standard size specimens’ results.

  20. Salvia divinorum: toxicological aspects and analysis in human biological specimens.

    Science.gov (United States)

    Margalho, Cláudia; Corte-Real, Francisco; López-Rivadulla, Manuel; Gallardo, Eugenia

    2016-07-01

    The identification and quantitation of the main psychoactive component of Salvia divinorum (salvinorin A) in biological specimens are crucial in forensic and clinical toxicology. Despite all the efforts made, its uncontrolled abuse has increased quickly, exposing its users' health to serious risks both in the short and long term. The use of alternative biological matrices in toxicological analyzes can be advantageous as complementary postmortem samples, or in situations when neither blood nor urine can be collected; they may be useful tools in those determinations, providing important information about prior exposure. The aim of this article is to present a brief summary of legal aspects of Salvia divinorum and salvinorin A, including the methods used for the determination of the latter in biological matrices.

  1. Accuracy analysis of point cloud modeling for evaluating concrete specimens

    Science.gov (United States)

    D'Amico, Nicolas; Yu, Tzuyang

    2017-04-01

    Photogrammetric methods such as structure from motion (SFM) have the capability to acquire accurate information about geometric features, surface cracks, and mechanical properties of specimens and structures in civil engineering. Conventional approaches to verify the accuracy in photogrammetric models usually require the use of other optical techniques such as LiDAR. In this paper, geometric accuracy of photogrammetric modeling is investigated by studying the effects of number of photos, radius of curvature, and point cloud density (PCD) on estimated lengths, areas, volumes, and different stress states of concrete cylinders and panels. Four plain concrete cylinders and two plain mortar panels were used for the study. A commercially available mobile phone camera was used in collecting all photographs. Agisoft PhotoScan software was applied in photogrammetric modeling of all concrete specimens. From our results, it was found that the increase of number of photos does not necessarily improve the geometric accuracy of point cloud models (PCM). It was also found that the effect of radius of curvature is not significant when compared with the ones of number of photos and PCD. A PCD threshold of 15.7194 pts/cm3 is proposed to construct reliable and accurate PCM for condition assessment. At this PCD threshold, all errors for estimating lengths, areas, and volumes were less than 5%. Finally, from the study of mechanical property of a plain concrete cylinder, we have found that the increase of stress level inside the concrete cylinder can be captured by the increase of radial strain in its PCM.

  2. Ultimate Strength Prediction of Carbon/Epoxy Tensile Specimens from Acoustic Emission Data

    National Research Council Canada - National Science Library

    V. Arumugam R. Naren Shankar B. T.N. Sridhar A. Joseph Stanley

    2010-01-01

    .... 21 tensile specimens (ASTM D3039 standard) were cut from the cross ply laminates. 16 specimens were subjected to impact load from three different heights using a Fractovis Plus drop impact tester...

  3. Routine histopathology for carcinoma in cholecystectomy specimens not evidence based: a systematic review

    NARCIS (Netherlands)

    Swank, Hilko A.; Mulder, Irene M.; Hop, Wim C.; van de Vijver, Marc J.; Lange, Johan F.; Bemelman, Willem A.

    2013-01-01

    Routine histopathological examination of gallbladder specimens is mainly performed to identify unexpected gallbladder carcinoma (GBC). This systematic review assesses the prevalence and characteristics of GBC in cholecystectomy specimens. PubMed, EMBASE, Web of Science, and the Cochrane Library were

  4. USE OF ROUND BAR SPECIMEN IN FRACTURE TOUGHNESS TEST OF METALLIC MATERIALS

    OpenAIRE

    NEELAKANTHA V LONDE,; DR. T.JAYARAJU; DR. P.R.SADANANDA RAO

    2010-01-01

    The fracture toughness of high strength metallic materials is determined by standard test methods like ASTM E 399, ASTM E-1820 using standard specimen geometries such as Compact tension (CT) or Single edge notched bend (SENB) specimens. This paper explains a simple test methodology based on fracture mechanics approach usingcircumferentially cracked round bar (CCRB) specimen. Specimen preparation and fatigue precracking is quite simple, consuming less material and machining time. This CCRB, be...

  5. Specimen Machining for the Study of the Effect of Swelling on CGR in PWR Environment.

    Energy Technology Data Exchange (ETDEWEB)

    Teysseyre, Sebastien Paul [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-06-01

    This report describes the preparation of ten specimens to be used for the study of the effect of swelling on the propagation of irradiation assisted stress corrosion cracking cracks. Four compact tension specimens, four microscopy plates and two tensile specimens were machined from a AISI 304 material that was irradiated up to 33 dpa. The specimens had been machined such as to represent the behavior of materials with 3.7%swelling and <2% swelling.

  6. TENSILE PROPERTIES OF JPCA AND JFMS IRRADIATED IN JMTR BY MEANS OF MINIATURIZED SPECIMEN TESTING

    OpenAIRE

    Akira, Kohyama; Kazushi, Hamada; Hideki, Matsui; Department of Materials Science, The University of Tokyo; Institute for Materials Research, Tohoku University

    1991-01-01

    In the research and development of miniaturized specimen technology, consideration of specimen size effect is the key issue. In this work, tensile tests were studied with variations of specimen size around the standard mini-tensile specimen in the Japanese fusion materials program. The materials used were JPCA (modified 316 SS) and JFMS (modified 10Cr-2Mo dual phase steel). Microstructure has been controlled to clarify the effect of grain size for the former and the effect of ferrite/martensi...

  7. Consideration of Correction Method for Compressive Strength of Core Specimen Within Deformed Bar

    OpenAIRE

    大塚, 秀三; 中田, 善久; 大木, 崇輔

    2013-01-01

    In rare occasions, there is core specimen that cut off deformed bar in structural concrete. However, there is not the correction method for compressive strength of core specimen within deformed bar that corresponds to the current concrete. This study proposed a simple correction method for compressive strength of core specimen within deformed bar, regardless of type of cement.

  8. 10 CFR 26.117 - Preparing urine specimens for storage and shipping.

    Science.gov (United States)

    2010-01-01

    ... collector shall complete the custody-and-control form(s) and shall certify proper completion of the collection. (f) The specimens and chain-of-custody forms must be packaged for transfer to the HHS-certified... and sign a statement on the custody-and-control form certifying that the specimen(s) identified as...

  9. 10 CFR 26.115 - Collecting a urine specimen under direct observation.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Collecting a urine specimen under direct observation. 26... for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for... specimen under direct observation, the collector shall obtain the agreement of the FFD program manager or...

  10. Application of the ThinPrep Imaging System in Urine Cytology A Prospective Study

    NARCIS (Netherlands)

    van Hemel, Bettien M.; Haarsma, Jolanda G.; Ruitenbeek, Teus; Groen, Henk; Suurmeijer, Albert J. H.

    BACKGROUND In this prospective study, for the first time, the authors compared the accuracy of reading urine specimens using the ThinPrep Imager System (TIS) with the accuracy of conventional screening for the detection of abnormal urine cells. METHODS ThinPrep slides were made from 1455 urine

  11. Catalog of insect type specimens preserved at the Kunming Institute of Zoology, Chinese Academy of Science with corrections of some specimens.

    Science.gov (United States)

    Li, Kai-Qin; Wang, Yun-Zhen; Dong, Da-Zhi; Zhang, Li-Kun

    2015-09-18

    This article presents a list of insect types preserved in Kunming Natural History Museum of Zoology (KNHMZ). As of March, 2015, 3 412 type specimens belonging to 266 species/subspecies of 37 families in 9 orders (Odonata, Isoptera, Mantodea, Orthoptera, Hemiptera, Coleoptera, Diptera, Hymenoptera and Lepidoptera) are included. Information corrections of some specimens are provided in this article.

  12. Adherence of Streptococcus mutans on lithium disilicate porcelain specimens.

    Science.gov (United States)

    Vo, Diane T; Arola, Dwayne; Romberg, Elaine; Driscoll, Carl F; Jabra-Rizk, Mary Ann; Masri, Radi

    2015-11-01

    Streptococcus mutans can adhere at restored tooth margins to cause recurrent caries. Limited information about surface quality and bacterial adherence is available for lithium disilicate ceramic materials. The purpose of this in vitro study was to investigate how bacterial adherence is influenced by commercially available preparations of lithium disilicate ceramic materials. Seventeen rectangular specimens (10×10×4 mm) were fabricated for each type of lithium disilicate material: pressed (Press), milled (CAD), fluorapatite layered (ZirPress/Ceram), and glazed (Ceram Glaze). The surface roughness of each specimen was assessed before incubation with wild-type S mutans for 48 hours at 37°C with Brain Heart Infusion broth media under anaerobic conditions. Adherent bacteria were sonicated, diluted, and plated in triplicate for quantification using the plate count method to assay for colony forming units (CFUs) as an indication of bacterial viability. Statistical analysis was performed with SPSS using an analysis of variance (ANOVA) followed by the Tukey Honestly Significant Difference (HSD) test (α=.05). The Pearson r was used to evaluate the correlation between surface roughness and adherence. The surface roughness of Ceram Glaze (1.32 ±0.19 μm) was significantly the highest, followed by ZirPress/Ceram (0.71 ±0.09 μm), which was significantly rougher than the Press (0.11 ±0.02 μm) and CAD (0.10 ±0.02 μm) groups, which were not significantly different from each other. (F=513.898, P<.001). CFUs (cells/mL) of S mutans were also significantly the highest for Ceram Glaze (61.82 ±13.76), followed by ZirPress/Ceram (28.53 ±2.40), which had significantly higher adherence than CAD (12.86 ±1.70) and Press (6.62 ±2.74), which were not significantly different from each other. (F= 201.721, P<.001). A strong positive association was found between bacterial count and surface roughness (r=.95, P<.001). The surface roughness of differently prepared lithium disilicate

  13. Small specimen test technology and methodology of IFMIF/EVEDA and the further subjects

    Science.gov (United States)

    Wakai, E.; Nogami, S.; Kasada, R.; Kimura, A.; Kurishita, H.; Saito, M.; Ito, Y.; Takada, F.; Nakamura, K.; Molla, J.; Garin, P.

    2011-10-01

    About one thousands of small size specimens will be irradiated in the High Flux Test Module (HFTM) with a limited irradiation volume of 0.5 l in the International Fusion Materials Irradiation Facility (IFMIF). It is necessary to verify that the experimental data of these small specimens mechanical characterization can be safely extrapolated to standard specimen data, enabling a sound dimensioning of DEMO reactor. The program of small specimen test technique (SSTT) in IFMIF/EVEDA (Engineering Validation and Engineering Design Activity) phase for fatigue, fracture toughness and crack growth measurement is summarized, and recent progress and some analysis of the experiments for small size specimens have been shown.

  14. Standard practice for making and using precracked double beam stress corrosion specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2000-01-01

    1.1 This practice covers procedures for fabricating, preparing, and using precracked double beam stress corrosion test specimens. This specimen configuration was formerly designated the double cantilever beam (DCB) specimen. Guidelines are given for methods of exposure and inspection. 1.2 The precracked double beam specimen, as described in this practice, is applicable for evaluation of a wide variety of metals exposed to corrosive environments. It is particularly suited to evaluation of products having a highly directional grain structure, such as rolled plate, forgings, and extrusions, when stressed in the short transverse direction. 1.3 The precracked double beam specimen may be stressed in constant displacement by bolt or wedge loading or in constant load by use of proof rings or dead weight loading. The precracked double beam specimen is amenable to exposure to aqueous or other liquid solutions by specimen immersion or by periodic dropwise addition of solution to the crack tip, or exposure to the atmos...

  15. Comparison between dog-bone and Gaussian specimens for size effect evaluation in gigacycle fatigue

    Directory of Open Access Journals (Sweden)

    A. Tridello

    2013-10-01

    Full Text Available Gigacycle fatigue properties of materials are strongly affected by the specimen risk volume (volume of material subjected to a stress amplitude larger than the 90% of the maximum stress. Gigacycle fatigue tests, performed with ultrasonic fatigue testing machines, are commonly carried out by using hourglass shaped specimens with a small risk volume. The adoption of traditional dog-bone specimens allows for increasing the risk volume, even if the increment is quite limited. In order to obtain larger risk volumes, a new specimen shape is proposed (Gaussian specimen. The dog-bone and the Gaussian specimens are compared through Finite Element Analyses and the numerical results are validated experimentally by means of strain gages measurements. The range of applicability of the two different specimens in terms of available risk volume and stress concentration effects due to the cross section variation is determined.

  16. Hand-assisted laparoscopic nephrectomy as a minimally invasive option in the treatment of large renal specimens

    Directory of Open Access Journals (Sweden)

    M. Tobias-Machado

    2005-12-01

    Full Text Available INTRODUCTION: We describe our experience with hand-assisted laparoscopy (HAL as an option for the treatment of large renal specimens. MATERIALS AND METHODS: Between March 2000 and August 2004, 13 patients candidate to nephrectomies due to benign renal conditions with kidneys larger than 20 cm were included in a prospective protocol. Unilateral nephrectomy was performed in cases of hydronephrosis (6 patients or giant pyonephrosis (4 patients. Bilateral nephrectomy was performed in 3 patients with adult polycystic kidney disease (APKD with low back pain refractory to clinical treatment previous to kidney transplant. The technique included the introduction of 2 to 3 10 mm ports, manual incision to allow enough space for the surgeon's wrist without a commercial device to keep the pneumoperitoneum. The kidney was empty, preferably extracorporeally, enough to be removed through manual incision. We have assessed operative times, transfusions, complications, conversions, hospital stay and convalescence. RESULTS: The patients mean age (9 women and 4 men was 58 years. Mean operating time was 120 ± 10 min (hydronephrosis, 160 ± 28 min (pyonephrosis and 190 ± 13 min (bilateral surgery for APKD. There was a need for a conversion in 1 case and another patient needed a transfusion due to a lesion in the renal vein; 2 patients had minor complications. CONCLUSION: HAL surgery is a minimally invasive alternative in the treatment of large renal specimens, with or without significant inflammation.

  17. Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens.

    Science.gov (United States)

    Goubran, Maged; Crukley, Cathie; de Ribaupierre, Sandrine; Peters, Terence M; Khan, Ali R

    2013-12-01

    Intractable or drug-resistant epilepsy occurs in up to 30% of epilepsy patients, with many of these patients undergoing surgical excision of the affected brain region to achieve seizure control. Recent magnetic resonance imaging (MRI) sequences and analysis techniques have the potential to detect abnormalities not identified with diagnostic MRI protocols. Prospective studies involving pre-operative imaging and collection of surgically-resected tissue provide a unique opportunity for verification and tuning of these image analysis techniques, since direct comparison can be made against histopathology, and can lead to better prediction of surgical outcomes and potentially less invasive procedures. To carry out MRI and histology comparison, spatial correspondence between the MR images and the histology images must be found. Towards this goal, a novel pipeline is presented here for bringing ex-vivo MRI of surgically-resected temporal lobe specimens and digital histology into spatial correspondence. The sparsely-sectioned histology images represent a challenge for 3D reconstruction which we address with a combined 3D and 2D registration algorithm that alternates between slice-based and volume-based registration with the ex-vivo MRI. We evaluated our registration method on specimens resected from patients undergoing anterior temporal lobectomy (N=7) and found our method to have a mean target registration error of 0.76±0.66 and 0.98±0.60 mm for hippocampal and neocortical specimens respectively. This work allows for the spatially-local comparison of histology with post-operative MRI and paves the way for eventual correlation with pre-operative MRI image analysis techniques. © 2013.

  18. Particle size analysis of amalgam powder and handpiece generated specimens.

    Science.gov (United States)

    Drummond, J L; Hathorn, R M; Cailas, M D; Karuhn, R

    2001-07-01

    The increasing interest in the elimination of amalgam particles from the dental waste (DW) stream, requires efficient devices to remove these particles. The major objective of this project was to perform a comparative evaluation of five basic methods of particle size analysis in terms of the instrument's ability to quantify the size distribution of the various components within the DW stream. The analytical techniques chosen were image analysis via scanning electron microscopy, standard wire mesh sieves, X-ray sedigraphy, laser diffraction, and electrozone analysis. The DW particle stream components were represented by amalgam powders and handpiece/diamond bur generated specimens of enamel; dentin, whole tooth, and condensed amalgam. Each analytical method quantified the examined DW particle stream components. However, X-ray sedigraphy, electrozone, and laser diffraction particle analyses provided similar results for determining particle distributions of DW samples. These three methods were able to more clearly quantify the properties of the examined powder and condensed amalgam samples. Furthermore, these methods indicated that a significant fraction of the DW stream contains particles less than 20 microm. The findings of this study indicated that the electrozone method is likely to be the most effective technique for quantifying the particle size distribution in the DW particle stream. This method required a relative small volume of sample, was not affected by density, shape factors or optical properties, and measured a sufficient number of particles to provide a reliable representation of the particle size distribution curve.

  19. Liquid nitrogen cooling in IR thermography applied to steel specimen

    Science.gov (United States)

    Lei, L.; Ferrarini, G.; Bortolin, A.; Cadelano, G.; Bison, P.; Maldague, X.

    2017-05-01

    Pulsed Thermography (PT) is one of the most common methods in Active Thermography procedures of the Thermography for NDT & E (Nondestructive Testing & Evaluation), due to the rapidity and convenience of this inspection technique. Flashes or lamps are often used to heat the samples in the traditional PT. This paper mainly explores exactly the opposite external stimulation in IR Thermography: cooling instead of heating. A steel sample with flat-bottom holes of different depths and sizes has been tested. Liquid nitrogen (LN2) is sprinkled on the surface of the specimen and the whole process is captured by a thermal camera. To obtain a good comparison, two other classic NDT techniques, Pulsed Thermography and Lock-In Thermography, are also employed. In particular, the Lock-in method is implemented with three different frequencies. In the image processing procedure, the Principal Component Thermography (PCT) method has been performed on all thermal images. For Lock-In results, both Phase and Amplitude images are generated by Fast Fourier Transform (FFT). Results show that all techniques presented part of the defects while the LN2 technique displays the flaws only at the beginning of the test. Moreover, a binary threshold post-processing is applied to the thermal images, and by comparing these images to a binary map of the location of the defects, the corresponding Receiver Operating Characteristic (ROC) curves are established and discussed. A comparison of the results indicates that the better ROC curve is obtained using the Flash technique with PCT processing method.

  20. Enteropathogenic bacteria isolated from specimens of patients with diarrhea

    Directory of Open Access Journals (Sweden)

    Salary M

    1997-09-01

    Full Text Available Acute infectious gastroenteritis is one of the most common infectious diseases of humans in the world. Diarrheal disease still ranks very high as a major cause of illness and death especially in developing nations. This study has been carried out to investigate enteropathogenic bacteria isolated from 2517 specimens of patients with diarrhea. The results obtained are as follow: Salmonella typhimurium: 6 cases 3.1 percent, Salmonella havana: 5 cases 2.6 percent, Shigella dysenteriae: 12 cases 6.2 percent, Shigella flexneri: 26 cases 13.5 percent, Shigella boydii: 8 cases 4.1 percent, Shigella sonnei: 24 cases 12.4 percent, Enteropathogenic E.coli: 11 cases 5.7 percent, Enteroinvasive E.coli: 2 cases 1 percent, Yersinia enterocolitica: - cases - percent, Vibrio cholera: - cases - percent, Aeromonas hydrophila: 6 cases 3.1 percent, Plesiomonas shigelloides: 1 cases 0.5 percent, Toxigenic C.difficile: 36 cases 18.7 percent, Enterotogenic c.perfringens: 6 cases 3.1 percent, Campylobacter jejuni: 50 cases 25.9 percent.

  1. Three-Dimensional scanning transmission electron microscopy of biological specimens

    KAUST Repository

    De Jonge, Niels

    2010-01-18

    A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset. © 2010 Microscopy Society of America.

  2. West Nile Virus lineage-2 in Culex specimens from Iran.

    Science.gov (United States)

    Shahhosseini, Nariman; Chinikar, Sadegh; Moosa-Kazemi, Seyed Hassan; Sedaghat, Mohammad Mehdi; Kayedi, Mohammad Hassan; Lühken, Renke; Schmidt-Chanasit, Jonas

    2017-10-01

    Screening of mosquitoes for viruses is an important forecasting tool for emerging and re-emerging arboviruses. Iran has been known to harbour medically important arboviruses such as West Nile virus (WNV) and dengue virus (DENV) based on seroepidemiological data. However, there are no data about the potential mosquito vectors for arboviruses in Iran. This study was performed to provide mosquito and arbovirus data from Iran. A total of 32 317 mosquitos were collected at 16 sites in five provinces of Iran in 2015 and 2016. RT-PCR for detection of flaviviruses was performed. The PCR amplicons were sequenced, and 109 WNV sequences, including one obtained in this study, were used for phylogenetic analyses. The 32 317 mosquito specimens belonging to 25 species were morphologically distinguished and distributed into 1222 pools. Culex pipiens s.l. comprised 56.429%. One mosquito pool (0.08%), containing 46 unfed Cx. pipiens pipiens form pipiens (Cpp) captured in August 2015, was positive for flavivirus RNA. Subsequent sequencing and phylogenetic analyses revealed that the detected Iranian WNV strain belongs to lineage 2 and clusters with a strain recently detected in humans. No flaviviruses other than WNV were detected in the mosquito pools. Cpp could be a vector for WNV in Iran. Our findings indicate recent circulation of WNV lineage-2 strain in Iran and provide a solid base for more targeted arbovirus surveillance programs. © 2017 John Wiley & Sons Ltd.

  3. Classification of breast cancer cytological specimen using convolutional neural network

    Science.gov (United States)

    Żejmo, Michał; Kowal, Marek; Korbicz, Józef; Monczak, Roman

    2017-01-01

    The paper presents a deep learning approach for automatic classification of breast tumors based on fine needle cytology. The main aim of the system is to distinguish benign from malignant cases based on microscopic images. Experiment was carried out on cytological samples derived from 50 patients (25 benign cases + 25 malignant cases) diagnosed in Regional Hospital in Zielona Góra. To classify microscopic images, we used convolutional neural networks (CNN) of two types: GoogLeNet and AlexNet. Due to the very large size of images of cytological specimen (on average 200000 × 100000 pixels), they were divided into smaller patches of size 256 × 256 pixels. Breast cancer classification usually is based on morphometric features of nuclei. Therefore, training and validation patches were selected using Support Vector Machine (SVM) so that suitable amount of cell material was depicted. Neural classifiers were tuned using GPU accelerated implementation of gradient descent algorithm. Training error was defined as a cross-entropy classification loss. Classification accuracy was defined as the percentage ratio of successfully classified validation patches to the total number of validation patches. The best accuracy rate of 83% was obtained by GoogLeNet model. We observed that more misclassified patches belong to malignant cases.

  4. Microstructural and Mechanical Characterization of Actively Brazed Alumina Specimens

    Energy Technology Data Exchange (ETDEWEB)

    Hosking, F.M.; Cadden, C.H.; Stephens, J.J.; Glass, S.J.; Yang, N.Y.C.; Vianco, P.V.; Walker, C.A.

    1999-08-26

    Alumina (94 and 99.8% grade compositions) was brazed directly to itself with gold-based active brazing alloys (ABA's) containing vanadium additions of 1,2 and 3 weight percent. The effects of brazing conditions on the joint properties were investigated. Wetting behavior, interfacial reactions, microstructure, hermeticity and tensile strength were determined. Wetting was fair to good for the ABA and base material combinations. Microanalysis identified a discontinuous Al-V-O spinel reaction product at the alumina-braze interface. Tensile strength results for 94% alumina were uniformly good and generally not sensitive to the vanadium concentration, with tensile values of 85-105 MPa. There was more variability in the 99.8% alumina strength results, with values ranging from 25-95 MPa. The highest vanadium concentration (3 wt. %) yielded the highest joint strength for the brazed 99.8% alumina. Failures in the 99.8% alumina samples occurred at the braze-alumina interface, while the 94% alumina specimens exhibited fracture of the ceramic substrate.

  5. Can museum egg specimens be used for proteomic analyses?

    Science.gov (United States)

    Portugal, Steven J; Cooper, Helen J; Zampronio, Cleidiane G; Wallace, Laine L; Cassey, Phillip

    2010-07-14

    Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95%) exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry. We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg. These proteins were either entirely absent from the museum eggs or the technique was unable to detect them. There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell. We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

  6. Can museum egg specimens be used for proteomic analyses?

    Directory of Open Access Journals (Sweden)

    Portugal Steven J

    2010-07-01

    Full Text Available Abstract Background Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95% exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry. Results We found that some of the expected key eggshell proteins (3 out of 11 were not present in the samples of museum quail egg. These proteins were either entirely absent from the museum eggs or the technique was unable to detect them. There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell. Conclusion We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

  7. [Protein screening in wheat and broad bean specimens in Gatersleben].

    Science.gov (United States)

    Rudolph, A; Hanelt, P; Lehmann, C; Müntz, K; Scholz, F

    1975-01-01

    Actually and in future times plant proteins will constitute the main and primary source of proteins in animal feeding and human alimentation. Therefore, the main efforts to resolve the world nutrition problems are focused on the increase of the protein production and the improvement of the nutritional quality of plant seed proteins. In this regard plant breeding occupies one of the most important strategic positions. With the aim of selecting forms with elevated grain protein content and improved protein quality the systematic screening of collections of wild forms and cultivated cereals and leguminoses constitutes a pre-requisite of successful breeding work in relation to the above-mentioned task. In 1970 the Central Institute of Genetics and Investigation of Cultivated Plants at Gatersleben, GDR, belonging to the Academy of Sciences, started a systematic protein screening with about 10000 wheat, 6500 barley and 450 broad bean specimens, which are parts of the World Collection of Cultivated Plants at this institute. Protein determination was performed by the traditional KJELDAHL-method. Limiting amino acids, essentially lysin from cereal grains, were estimated by automatic ion exchange technique. The annual analytic capacity amounted to 6000 to 8000 samples. First results and problems of wheat- and broad bean-screening are reported in the present publication.

  8. Human Adenovirus (HAdV) Viremia in Immunocompetent Children with HAdV Infection in Respiratory Specimens: Does Viremia Predict Severity of Illness?

    Science.gov (United States)

    Song, Eunkyung; Wang, Huanyu; Leber, Amy; Jaggi, Preeti

    2017-01-01

    Abstract Background The interpretation of HAdV PCR from upper respiratory tract (RT) specimens can be challenging due to prolonged low grade viral shedding. We hypothesized that HAdV detection in the blood (viremia) is more common in acute HAdV infection with high respiratory viral burden (VB) compared with those with low VB in the RT. We sought to determine the frequency of HAdV viremia in immunocompetent children who have detectable HAdV in the RT. Methods We prospectively identified + HAdV in RT specimens from emergency department or inpatients using semi-quantitative real-time PCR (Ct Leber, BioFIre Diagnostics: Research Contractor and Scientific Advisor, Research support, Speaker honorarium and Travel expenses

  9. Prospects after Major Trauma

    NARCIS (Netherlands)

    Holtslag, H.R.

    2007-01-01

    Introduction. After patients survived major trauma, their prospects, in terms of the consequences for functioning, are uncertain, which may impact severely on patient, family and society. The studies in this thesis describes the long-term outcomes of severe injured patients after major trauma. In

  10. Challenges and Prospects

    African Journals Online (AJOL)

    Erah

    Finally, the prospective areas for biopharmaceutical innovation in Africa include research and development, marketing, workforce development and contract manufacturing. Keywords: Small .... However, in line with the EUs definition, enterprises with less than 250 employees should have turnover of less than €50 million.

  11. Diagnosing breast cancer using Raman spectroscopy: prospective analysis.

    Science.gov (United States)

    Haka, Abigail S; Volynskaya, Zoya; Gardecki, Joseph A; Nazemi, Jon; Shenk, Robert; Wang, Nancy; Dasari, Ramachandra R; Fitzmaurice, Maryann; Feld, Michael S

    2009-01-01

    We present the first prospective test of Raman spectroscopy in diagnosing normal, benign, and malignant human breast tissues. Prospective testing of spectral diagnostic algorithms allows clinicians to accurately assess the diagnostic information contained in, and any bias of, the spectroscopic measurement. In previous work, we developed an accurate, internally validated algorithm for breast cancer diagnosis based on analysis of Raman spectra acquired from fresh-frozen in vitro tissue samples. We currently evaluate the performance of this algorithm prospectively on a large ex vivo clinical data set that closely mimics the in vivo environment. Spectroscopic data were collected from freshly excised surgical specimens, and 129 tissue sites from 21 patients were examined. Prospective application of the algorithm to the clinical data set resulted in a sensitivity of 83%, a specificity of 93%, a positive predictive value of 36%, and a negative predictive value of 99% for distinguishing cancerous from normal and benign tissues. The performance of the algorithm in different patient populations is discussed. Sources of bias in the in vitro calibration and ex vivo prospective data sets, including disease prevalence and disease spectrum, are examined and analytical methods for comparison provided.

  12. Antibiotic Resistance in Staphylococcus aureus Strains Isolated from Clinical Specimens

    Directory of Open Access Journals (Sweden)

    M. Sirin

    2016-04-01

    Full Text Available Aim: The aim of this study was to determine the antibiotic susceptibilities of S.aureus strains isolated from various clinical specimens between the years 2011-2014 and to investigate the changes of these susceptibilities over the years. Material and Method: Identification and antibiotic susceptibility testing of the strains were performed by Vitek 2 compact automated system (bioMérieux, France. The strains found to be intermediate susceptible to vancomycin and teicoplanin were also tested by E-test method. Results: S.aureus strains (n=1442 were most commonly isolated from wound, urine and blood samples. The isolation rates of methicillin-resistant S.aureus (MRSA in hospitalized patients were significantly higher than the isolation rates of MRSA in outpatients. All strains were susceptible to vancomycin, teicoplanin, linezolid and tigecycline. The total of four years resistance rates of MRSA strains to erythromycin, clindamycin, ciprofloxacin, moxifloxacin, gentamicin, co-trimoxazole, fusidic acid were significantly higher than the resistance rates of methicillin-sensitive S.aureus (MSSA. The changes in the rates of antibiotic resistance were not statistically significant in MSSA strains over the years, and statistically significant decrease was found in erythromycin, clindamycin, ciprofloxacin, moxifloxacin and gentamicin resistance in MRSA strains. Discussion: Glycopeptides, linezolid and tigecycline were the most effective antibiotics against S.aureus strains. It was considered as necessary to detect antimicrobial resistance profiles by effective surveillance studies and monitor the changes occurred over the years in order to prevent the development of resistance and control of infections.

  13. Reduction in Blood Culture Contamination Through Use of Initial Specimen Diversion Device.

    Science.gov (United States)

    Rupp, Mark E; Cavalieri, R Jennifer; Marolf, Cole; Lyden, Elizabeth

    2017-07-15

    Blood culture contamination is a clinically significant problem that results in patient harm and excess cost. In a prospective, controlled trial at an academic center Emergency Department, a device that diverts and sequesters the initial 1.5-2 mL portion of blood (which presumably carries contaminating skin cells and microbes) was tested against standard phlebotomy procedures in patients requiring blood cultures due to clinical suspicion of serious infection. In sum, 971 subjects granted informed consent and were enrolled resulting in 904 nonduplicative subjects with 1808 blood cultures. Blood culture contamination was significantly reduced through use of the initial specimen diversion device™ (ISDD) compared to standard procedure: (2/904 [0.22%] ISDD vs 16/904 [1.78%] standard practice, P = .001). Sensitivity was not compromised: true bacteremia was noted in 65/904 (7.2%) ISDD vs 69/904 (7.6%) standard procedure, P = .41. No needlestick injuries or potential bloodborne pathogen exposures were reported. The monthly rate of blood culture contamination for all nurse-drawn and phlebotomist-drawn blood cultures was modeled using Poisson regression to compare the 12-month intervention period to the 6 month before and after periods. Phlebotomists (used the ISDD) experienced a significant decrease in blood culture contamination while the nurses (did not use the ISDD) did not. In sum, 73% of phlebotomists completed a post-study anonymous survey and widespread user satisfaction was noted. Use of the ISDD was associated with a significant decrease in blood culture contamination in patients undergoing blood cultures in an Emergency Department setting. NCT02102087.

  14. Finite element simulations of electrostatic dopant potentials in thin semiconductor specimens for electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Somodi, P.K.; Twitchett-Harrison, A.C.; Midgley, P.A. [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom); Kardynał, B.E. [Peter Grünberg Institute 9, Forschungszentrum Jülich, D-52425 Jülich (Germany); Barnes, C.H.W. [Department of Physics, University of Cambridge, Madingley Road, Cambridge CB3 0HE (United Kingdom); Dunin-Borkowski, R.E., E-mail: rafaldb@gmail.com [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute 5, Forschungszentrum Jülich, D-52425 Jülich (Germany)

    2013-11-15

    Two-dimensional finite element simulations of electrostatic dopant potentials in parallel-sided semiconductor specimens that contain p–n junctions are used to assess the effect of the electrical state of the surface of a thin specimen on projected potentials measured using off-axis electron holography in the transmission electron microscope. For a specimen that is constrained to have an equipotential surface, the simulations show that the step in the projected potential across a p–n junction is always lower than would be predicted from the properties of the bulk device, but is relatively insensitive to the value of the surface state energy, especially for thicker specimens and higher dopant concentrations. The depletion width measured from the projected potential, however, has a complicated dependence on specimen thickness. The results of the simulations are of broader interest for understanding the influence of surfaces and interfaces on electrostatic potentials in nanoscale semiconductor devices. - Highlights: • Finite element simulations are performed to calculate electrostatic dopant potentials in TEM specimens that contain p–n junctions. • The effect of the electrical state of the specimen surface on the projected potential is assessed for equipotential specimen surfaces. • The step in projected potential is always found to be lower than the step in potential in the bulk device. • The step in projected potential is least sensitive to surface state energy for thicker specimens and higher dopant concentrations. • The depletion width measured from the projected potential has a complicated dependence on specimen thickness.

  15. Comparative study of the claws of Pediculus humanus capitis between archaeological and modern specimens.

    Science.gov (United States)

    Núñez, Hipólito; Arriaza, Bernardo; Standen, Vivien; Aravena, Natalia

    2017-04-01

    Metric data of the claws of archaeological specimens of Pediculus humanus capitis (dating between 1500 B.C. and A.D. 1500) and modern lice specimens coming from school children were analyzed and compared. Both sets of samples come from Arica in northern Chile. The overall sample is comprised of 14 archaeological specimens (6 females and 8 males) of Pediculus humanus capitis and 22 modern specimens (13 females and 9 males). All specimens were studied with scanning electron microscopy (SEM), uncoated, using variable pressure mode. The objective of this study was to metrically analyze the first couple of clutches of ancient and modern adult lice specimens (width and length of the tibio-tarsal claw and tarsus length) to test if morphological changes have taken place throughout time in these anatomical elements. We found that archaeological male and female specimens presented significant differences in the tibio-tarsal width (right and left). When comparing data between archaeological and modern male specimens, statistically significant differences were found in almost all the parameters studied, except for the right tarsal length. On the other hand, archaeological and modern female specimens showed no statistically significant change in the variables studied. In brief, our data suggest that modern male specimens have undergone a process of claw reduction, but females have maintained the same dimensions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. The Effect of Specimen Preparation on Post-Excision and Post-Fixation Dimensions, Translation, and Distortion of Canine Cadaver Skin-Muscle-Fascia Specimens.

    Science.gov (United States)

    Risselada, Marije; Mathews, Kyle G; Griffith, Emily

    2016-07-01

    To assess the effect of various tissue apposition techniques on specimens after formalin fixation, and to assess canine cadaveric composite skin-muscle-fascia specimen changes after excision without and with addition of a tumor model. Canine cadaveric study; unbalanced paired design. Fresh canine cadavers (n = 30) METHODS: Experiment 1: Paired 7 cm diameter, circular skin-muscle-fascia specimens were harvested bilaterally from three sites (thorax, abdomen, and thigh) on 10 cadavers. For each pair, the skin-to-fascia was sutured with a circumferential continuous pattern in one specimen and left unsutured in the other during excision. Specimen length and width were measured post-excision and post-fixation. Specimen rotation, translation, and distortion was measured post-fixation. Experiment 2: A subcutaneous tumor model was implanted at 2 sites (neck, thorax) on 20 cadavers and specimens were then excised with 2 cm lateral margins and a deep fascial plane. Three suturing techniques of the skin-to-fascia at both sites were performed during excision: unsutured versus circumferential continuous suture (10 pairs) or circumferential versus 4 interrupted quadrant sutures (10 pairs). Lateral margins were compared post-excision and post-fixation. Experiment 1: There was significant reduction in the length and width of the fascia and skin post-excision, but no further reduction after fixation. The circumferential suture decreased rotation and translation of the tissue layers but did not significantly affect specimen shrinkage or distortion compared with the unsutured specimen. Experiment 2: All 4 lateral margins decreased significantly post-excision and post-fixation compared with the planned pre-excision margins. No difference was found between any of the 4 lateral margins for any skin-to-fascia suture technique. Canine skin-muscle-fascia specimens significantly decrease in size from gross pre-excision dimensions after removal. Suturing the specimen during surgery before

  17. Durability of Wood in Ground Contact – Effects of Specimen Size

    Directory of Open Access Journals (Sweden)

    Christian BRISCHKE

    2017-06-01

    Full Text Available The durability of wood in ground contact is affected by its material resistance on the one hand, and the exposure situation in the ground on the other hand. The latter is considered to be one of the most severe not at least due to permanent wetting and direct contact to a well-established microbial flora. In addition to physical, chemical, biological, and ecological soil parameters, the design of a wooden commodity which is in contact with the ground can have an effect on its durability. This study examined the effect of size of specimens used for in-ground durability tests. Standard EN 252 specimens, smaller mini-stake specimens, and larger double-size specimens were made from Scots pine sapwood and heartwood (Pinus sylvestris L., Norway spruce (Picea abies Karst., beech (Fagus sylvatica L., and English oak (Quercus robur L. and exposed in ground in a test field in Hannover-Herrenhausen, Germany. In addition, standard size specimens were exposed on the ground. Decay rates and corresponding durability classes according to European standards were determined. Decay proceeded slightly faster with decreasing specimen size, but for the majority of the tested materials no significant effect became apparent. However, the most durable material tested was English oak, for which durability was clearly affected by the specimen size. It was classified ‚durable’ (durability class DC 2 using double size stakes, ‚moderately durable’ (DC 3 using standard specimens, and ‚less durable’ (DC 4 using mini-stake specimens. Specimens exposed on-ground decayed significantly less rapidly compared to specimens buried in the ground to half of their length. The findings from this study recommend to use also test specimens, which are bigger dimensioned than standard specimens and thus closer in dimension to real size commodities. Otherwise, one might accept to underestimate the durability of particular wood-based materials.

  18. Human Adenovirus (HAdV) Viremia in Immunocompetent Children with HAdV Infection in Respiratory Specimens: Does Viremia Predict Severity of Illness?

    OpenAIRE

    Song, Eunkyung; Wang, Huanyu; Leber, Amy; Jaggi, Preeti

    2017-01-01

    Abstract Background The interpretation of HAdV PCR from upper respiratory tract (RT) specimens can be challenging due to prolonged low grade viral shedding. We hypothesized that HAdV detection in the blood (viremia) is more common in acute HAdV infection with high respiratory viral burden (VB) compared with those with low VB in the RT. We sought to determine the frequency of HAdV viremia in immunocompetent children who have detectable HAdV in the RT. Methods We prospectively identified + HAdV...

  19. Prospective memory: A comparative perspective

    OpenAIRE

    Crystal, Jonathon D.; Wilson, A. George

    2014-01-01

    Prospective memory consists of forming a representation of a future action, temporarily storing that representation in memory, and retrieving it at a future time point. Here we review the recent development of animal models of prospective memory. We review experiments using rats that focus on the development of time-based and event-based prospective memory. Next, we review a number of prospective-memory approaches that have been used with a variety of non-human primates. Finally, we review se...

  20. Quality Assessment of Tissue Specimens for Studies of Diabetic Foot Ulcers

    Science.gov (United States)

    Stojadinovic, Olivera; Landon, Jennifer N.; Gordon, Katherine A.; Pastar, Irena; Escandon, Julia; Vivas, Alejandra; Maderal, Andrea D.; Margolis, David J.; Kirsner, Robert S.; Tomic-Canic, Marjana

    2015-01-01

    Diabetic Foot Ulcers (DFUs) represent an important clinical problem resulting in significant morbidity and mortality. Ongoing translational research studies strive to better understand molecular/cellular basis of DFU pathology that may lead to identification of novel treatment protocols. Tissue at the non-healing wound edge has been identified as one of major contributors to the DFU pathophysiology that provides important tool for translational and clinical investigations. To evaluate quality of tissue specimens and their potential use we obtained 81 DFU specimens from 25 patients and performed histological analyses, immunohistochemistry and RNA quality assessments. We found that depth of the collected specimen is important determinant of research utility, and only specimens containing a full-thickness epidermis could be utilized for immunohistochemistry and RNA isolation. We showed that only two-thirds of collected specimens could be utilized in translational studies. This attrition rate is important for designs of future studies involving tissue specimen collection from DFU. PMID:23489425

  1. Evaluation of HistoGel™-embedded specimens for use in veterinary diagnostic pathology.

    Science.gov (United States)

    Joiner, Kellye S; Spangler, Elizabeth A

    2012-07-01

    HistoGel™ is an aqueous specimen-processing gel that encapsulates and suspends histologic and cytologic specimens in a solidified medium. HistoGel-embedded specimens can then be processed and evaluated by routine histologic and immunohistochemical methods. This methodology has been used in human diagnostic pathology and is especially useful for small, friable, or viscous tissue samples that are difficult to process. In addition, special histochemical stains or immunohistochemistry can be performed on HistoGel-embedded cytologic specimens using standardized methods developed for histopathology. The current report describes several applications for HistoGel, including use with cytologic specimens, bone marrow aspirates, retention of tissue orientation for endoscopic biopsy specimens, and evaluation of friable tissues. Samples were encapsulated in HistoGel, fixed in 10% neutral buffered formalin, routinely processed, paraffin embedded, and sectioned for histochemical and immunohistochemical evaluation. The results of this study support the use of HistoGel in veterinary diagnostic pathology.

  2. Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes.

    Science.gov (United States)

    Hughey, Jeffery R; Gabrielson, Paul W; Rohmer, Laurence; Tortolani, Jacquie; Silva, Mayra; Miller, Kathy Ann; Young, Joel D; Martell, Craig; Ruediger, Erik

    2014-06-04

    Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm(2) of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19(th) and early 20(th) century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

  3. Nocardia arizonensis sp. nov., obtained from human respiratory specimens.

    Science.gov (United States)

    Lasker, Brent A; Bell, Melissa; Klenk, Hans-Peter; Schumann, Peter; Brown, June M

    2015-11-01

    In 2008, three clinical isolates (W9405(T), W9409 and W9575) were obtained from bronchial wash or sputum specimens from patients from the state of Arizona and characterised by polyphasic analysis. All three clinical isolates 16S rRNA gene sequences were found to be 100% identical to each other and showed the strains belong in the genus Nocardia. BLASTn searches in the GenBank database of near full-length 16S rRNA gene sequences showed the highest sequence similarities to the type strains of Nocardia takedensis (98.3%, sequence similarity), Nocardia lijiangensis (97.4%), Nocardia harenae (97.4%), and Nocardia xishanensis (97.1%). The DNA-DNA relatedness between isolate W9405(T) and the type strain of N. takedensis is 26.0 ± 2.4% when measured in silico using genomic DNA sequences. The G+C content of isolate W9405(T) is 68.6 mol%. Chemotaxonomic analyses of the clinical isolates were consistent with their assignment to the genus Nocardia: whole cell hydrolysates contain meso-diaminopimelic acid as the diagnostic diamino acid of peptidoglycan; the whole-cell sugars are arabinose and galactose; the predominant phospholipids include diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol; MK-8-(H4)(ω-cyc) as the major menaquinone; mycolic acids ranging from 38 to 62 carbon atoms; and palmitic acid, tuberculostearic acid, palmitelaidic acid and oleic acid are the major fatty acids. Genus and species specific profiles were obtained following analysis by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectra of the clinical isolates. All isolates were found to be intermediately resistant or resistant to minocycline and resistant to ciprofloxacin but were susceptible to amikacin, imipenem and linezolid. Our polyphasic analysis suggest the three clinical isolates obtained from patients in Arizona represent a novel species of Nocardia for which we propose the name Nocardia arizonensis, with strain W9405(T) (=DSM 45748(T) = CCUG

  4. Growth Prospects in Algeria

    OpenAIRE

    International Monetary Fund

    2007-01-01

    This Selected Issues paper for Algeria analyzes the growth prospects of the Algerian economy. Drawing on the findings of the empirical growth literature, the paper combines growth accounting and cross-country growth regressions to examine the role of macroeconomic and institutional factors in driving economic growth. It reviews the past growth performance in Algeria and explores the reasons underpinning the recent pickup in nonhydrocarbon GDP growth. The paper also analyzes labor market devel...

  5. Exercice de prospective

    OpenAIRE

    Aubert, Francis; Hilal, Mohamed

    2014-01-01

    Après avoir situé la réalité actuelle du quartier de Fontaine-d'Ouche dans l'histoire des transformations urbaines de l'agglomération dijonnaise, les auteurs proposent un exercice de prospective qui prend en compte une batterie d'hypothèses de changement pour construire des images du quartier à l'horizon 2040.

  6. Performance evaluation of the FDA-approved Determine™ HIV-1/2 Ag/Ab Combo assay using plasma and whole blood specimens.

    Science.gov (United States)

    Masciotra, Silvina; Luo, Wei; Westheimer, Emily; Cohen, Stephanie E; Gay, Cynthia L; Hall, Laura; Pan, Yi; Peters, Philip J; Owen, S Michele

    2017-06-01

    The Determine™ HIV-1/2 Ag/Ab Combo (DC) rapid test can identify HIV-1 infection earlier than rapid antibody-only tests in plasma specimens. We compared the performance of DC with a laboratory-based antigen/antibody (Ag/Ab) combo assay in plasma and evaluated antigen reactivity in whole blood specimens. We tested by DC 508 plasma specimens collected in a prospective study and 107 sequential plasma and simulated whole blood specimens from 20 seroconversion panels. Previous results using the ARCHITECT (ARC) Ag/Ab combo assay were compared to DC results. In seroconversion panels, the days from the first HIV1 RNA-positive test to first DC-reactive in plasma and whole blood was compared. McNemar's and Wilcoxon signed rank tests were used for statistical analysis. Of 415 HIV-positive samples, ARC detected 396 (95.4%) and DC 337 (81.2%) (pARC-reactive/MS-negative, 78.6% of ARC-reactive/MS-indeterminate, and 99.6% of ARC-reactive/MS-HIV-1-positive or -undifferentiated specimens. DC antigen reactivity was higher among ARC-reactive/MS-negative than MS-indeterminate samples. In 20 HIV-1 seroconversion panels, there was a significant difference between DC reactivity in plasma (91.1%) and whole blood (56.4%) (pplasma (p=0.008). In plasma, DC was significantly less sensitive than an instrumented laboratory-based Ag/Ab combo assay. DC in plasma was significantly more sensitive compared to whole blood in early HIV-1 infections. With the U.S. laboratory-based diagnostic algorithm, DC as the first step would likely miss a high proportion of HIV-1 infections in early stages of seroconversion. Published by Elsevier B.V.

  7. Searching for DNA in museum specimens: a comparison of sources in a mammal species

    OpenAIRE

    Casas-Marcé, Mireia; Revilla, Eloy; Godoy, José A.

    2010-01-01

    The number of genetic studies that use preserved specimens as sources of DNA has been steadily increasing during the last few years. Therefore, selecting the sources that are more likely to provide a suitable amount of DNA of enough quality to be amplified and at the min- imum cost to the original specimen is an important step for future research. We have com- pared different types of tissue (hides vs. bones) from museum specimens of Iberian lynx and multiple alternative sources...

  8. Tensile-Creep Test Specimen Preparation Practices of Surface Support Liners

    Science.gov (United States)

    Guner, Dogukan; Ozturk, Hasan

    2017-12-01

    Ground support has always been considered as a challenging issue in all underground operations. Many forms of support systems and supporting techniques are available in the mining/tunnelling industry. In the last two decades, a new polymer based material, Thin Spray–on Liner (TSL), has attained a place in the market as an alternative to the current areal ground support systems. Although TSL provides numerous merits and has different application purposes, the knowledge on mechanical properties and performance of this material is still limited. In laboratory studies, since tensile rupture is the most commonly observed failure mechanism in field applications, researchers have generally studied the tensile testing of TSLs with modification of American Society for Testing and Materials (ASTM) D-638 standards. For tensile creep testing, specimen preparation process also follows the ASTM standards. Two different specimen dimension types (Type I, Type IV) are widely preferred in TSL tensile testing that conform to the related standards. Moreover, molding and die cutting are commonly used specimen preparation techniques. In literature, there is a great variability of test results due to the difference in specimen preparation techniques and practices. In this study, a ductile TSL product was tested in order to investigate the effect of both specimen preparation techniques and specimen dimensions under 7-day curing time. As a result, ultimate tensile strength, tensile yield strength, tensile modulus, and elongation at break values were obtained for 4 different test series. It is concluded that Type IV specimens have higher strength values compared to Type I specimens and moulded specimens have lower results than that of prepared by using die cutter. Moreover, specimens prepared by molding techniques have scattered test results. Type IV specimens prepared by die cutter technique are suggested for preparation of tensile test and Type I specimens prepared by die cutter

  9. Stress-deformed state of cylindrical specimens during indirect tensile strength testing

    Directory of Open Access Journals (Sweden)

    Levan Japaridze

    2015-10-01

    Full Text Available In this study, the interaction between cylindrical specimen made of homogeneous, isotropic, and linearly elastic material and loading jaws of any curvature is considered in the Brazilian test. It is assumed that the specimen is diametrically compressed by elliptic normal contact stresses. The frictional contact stresses between the specimen and platens are neglected. The analytical solution starts from the contact problem of the loading jaws of any curvature and cylindrical specimen. The contact width, corresponding loading angle (2θ0, and elliptical stresses obtained through solution of the contact problems are used as boundary conditions for a cylindrical specimen. The problem of the theory of elasticity for a cylinder is solved using Muskhelishvili's method. In this method, the displacements and stresses are represented in terms of two analytical functions of a complex variable. In the main approaches, the nonlinear interaction between the loading bearing blocks and the specimen as well as the curvature of their surfaces and the elastic parameters of their materials are taken into account. Numerical examples are solved using MATLAB to demonstrate the influence of deformability, curvature of the specimen and platens on the distribution of the normal contact stresses as well as on the tensile and compressive stresses acting across the loaded diameter. Derived equations also allow calculating the modulus of elasticity, total deformation modulus and creep parameters of the specimen material based on the experimental data of radial contraction of the specimen.

  10. [A catalog of fish specimens preserved within Kunming Institute of Zoology, Chinese Academy of Sciences].

    Science.gov (United States)

    Du, Li-Na; Chen, Xiao-Yong; Yang, Jun-Xing

    2013-08-01

    As of 2013, some 178 fish type species and 2131 type specimens belonging to 4 orders and 11 families were currently being preserved at the Kunming Natural History Museum of Zoology, located as art of the Kunming Institute of Zoology, Chinese Academy of Sciences. These specimens were collected from across western China, includingYunnan, Sicuan, Guizhou, Guangxi, Hunan, Chongqi, Gansu and Xinjiang. In general, most species are Cyprinidae (71 species and 1103 specimens), followed by Nemacheilidae (52 species and 556 specimens). For the convenience of research and communication, the present paper presents a detailed list of fish type species preserved in the Kunming Natural History Museum of Zoology.

  11. Evaluation of Blast Resistance of Fiber Reinforced Composite Specimens under Contact Blast Load

    Science.gov (United States)

    Janota, O.; Foglar, M.

    2017-09-01

    This paper presents results of experimental programme which took place in 2014, 2015 and 2016. Experiments were focused on the resistance of full scale concrete panels subjected to contact blast loading. Specimens were loaded by contact blast by plastic explosive. All specimens were reinforced concrete slabs made of fiber concrete. Basalt mesh and textile sheets were added to some of the experiments for creating more heterogeneous material to achieve better resistance of the specimens. Evaluation of experiments was mainly focused on the damaged area on the contact side and soffit of the specimens. Dependency of the final damage of concrete panels on the weight of explosive and concrete strength was assessed.

  12. Effect of laminate thickness and specimen configuration on the fracture of laminated composites

    Science.gov (United States)

    Harris, C. E.; Morris, D. H.

    1986-01-01

    Attention is given to the effect of laminate thickness on graphite/epoxy laminates in the present measurements of fracture toughness in center cracked tension specimens, compact tension specimens, and three-point bend specimens. Crack tip damage development prior to fracture is also studied. The results obtained show fracture toughness to be a function of laminate thickness, being in all cases independent of crack size. The fracture surface of all thick laminates was uniform in the interior and self-similar with the starter notch. With only one exception, the fracture toughness of the thicker laminates was relatively independent of specimen configuration.

  13. Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens.

    Directory of Open Access Journals (Sweden)

    Bonnie B Blaimer

    Full Text Available Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs from 51 large carpenter bee specimens (genus Xylocopa, representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE

  14. Small lesion size measured by colposcopy may predict absence of cervical intraepithelial neoplasia in a large loop excision of the transformation zone specimen.

    Science.gov (United States)

    Munmany, M; Marimon, L; Cardona, M; Nonell, R; Juiz, M; Astudillo, R; Ordi, J; Torné, A; Del Pino, M

    2017-02-01

    To evaluate whether colposcopic measurement of the lesion size at diagnosis and/or human papillomavirus (HPV) genotyping can predict the absence of dysplasia in a large loop excision of the transformation zone (LLETZ) specimen in women treated for squamous intraepithelial lesions/cervical intraepithelial neoplasia (SIL/CIN). Prospective observational study. Tertiary university hospital. A cohort of 116 women who underwent LLETZ because of biopsy-proven low-grade SIL/CIN that had persisted for 2 years, or because of a high-grade SIL/CIN diagnosed in the referral visit and squamocolumnar junction completely visible (types 1 or 2, according to the International Federation of Cervical Pathology and Colposcopy, IFCPC). After LLETZ the women were classified by histology into the study group (absence of SIL/CIN in the surgical specimen, 28/116, 24.1%) and the control group (SIL/CIN in the LLETZ specimen, 88/116, 75.9%). The size of the lesion determined in the diagnostic colposcopy and the HPV genotype were evaluated in all women. The lesion size was significantly smaller in the study group (25.7 ± 37.8 versus 84.5 ± 81.7 mm 2 ; P lesion size of ≤12 mm 2 and HPV types other than 16 or 18 were associated with an absence of SIL/CIN in the LLETZ specimen (P lesion size of ≤12 mm 2 predicted the absence of SIL/CIN (odds ratio, OR 10.6; 95% confidence interval, 95% CI 3.6-30.6; P lesion size of ≤12 mm 2 had a specificity of 90.9% (95% CI 83.0-95.3%) and a negative predictive value of 86.0% (95% CI 77.5-91.6%) to predict the absence of SIL/CIN in the surgical specimen. Small lesion size in diagnostic colposcopy could predict the absence of SIL/CIN in the LLETZ specimen. Colposcopy measurement of lesion size prior to LLETZ may avoid unnecessary treatment. Small lesion size in colposcopic evaluation might predict the absence of SIL/CIN in an LLETZ specimen. © 2016 Royal College of Obstetricians and Gynaecologists.

  15. Prospective bonding applications

    Science.gov (United States)

    Ancenay, H.; Benazet, D.

    1981-07-01

    Adhesive bonding in industry and in the laboratory is surveyed and prospects for its wider utilization are assessed. The economic impact of bonding technology on industry is discussed. Research is reviewed, centering on the development of nondestructive testing and inspection techniques. Traditional (wood) as well as new materials susceptible to bonding are considered. Applications in construction and civil engineering, in aeronautics, and in the automobile industry are covered. The use of glues in mechanical constructions, in assembling cylindrical parts, and in metal-metal bonding are examined. Hybrid assembling and bonding of composite materials are included.

  16. Detection of Pathogenic Protozoa in the Diagnostic Laboratory: Result Reproducibility, Specimen Pooling, and Competency Assessment▿

    Science.gov (United States)

    Libman, M. D.; Gyorkos, T. W.; Kokoskin, E.; MacLean, J. D.

    2008-01-01

    Stool microscopy as performed in clinical parasitology laboratories is a complex procedure with subjective interpretation. Quality assurance (QA) programs often emphasize proficiency testing as an assessment tool. We describe a result reproducibility assessment tool, which can form part of a broader QA program, and which is based on the blinded resubmission of selected clinical samples, using concordance between the reports of the initial and resubmitted specimen as an indicator. Specimens preserved in sodium acetate-acetic acid-formalin can be stored for several months for use in such a program. The presence of multiple protozoa in one specimen does not affect concordance. Some dilution of specimens occurs in this process, and this may explain poor concordance when specimens with low protozoal concentrations are resubmitted. Evaluation of this tool in a large parasitology laboratory revealed concordance rates for pathogenic protozoa (Entamoeba histolytica/Entamoeba dispar, Giardia lamblia, and Dientamoeba fragilis) of about 80%, which may be considered for use as a benchmark value. We also used this tool to demonstrate that when pairs of specimens from one patient are pooled to create a single specimen, concordance between the results of the individual and pooled specimens is high. PMID:18448690

  17. Assessment of Chlamydia trachomatis infection of semen specimens by ligase chain reaction

    NARCIS (Netherlands)

    Pannekoek, Yvonne; Westenberg, Steven M.; Eijk, Paul P.; Repping, Sjoerd; van der Veen, Fulco; van der Ende, Arie; Dankert, Jacob

    2003-01-01

    Diagnostic potential of the Chlamydia trachomatis ligase chain reaction system (LCx) to assess the presence of C. trachomatis in urine and semen specimens was evaluated. Paired urine and semen specimens from 153 asymptomatic male partners of subfertile couples attending our Center for Reproductive

  18. Automation of specimen selection and data acquisition for protein electron crystallography

    NARCIS (Netherlands)

    Oostergetel, G.T.; Keegstra, W.; Brisson, A.D R

    A system is presented for semi-automatic specimen selection and data acquisition for protein electron crystallography, based on a slow-scan CCD camera connected to a transmission electron microscope and control from an external computer. Areas of interest on the specimen are localised at low

  19. Specimen charging on thin films with one conducting layer:Discussion of physical principles

    Energy Technology Data Exchange (ETDEWEB)

    Glaeser, Robert M.; Downing, Kenneth H.

    2003-04-15

    While the most familiar consequences of specimen charging in transmission electron microscopy can be eliminated by evaporating a thin conducting film (such as a carbon film) onto an insulating specimen, or by preparing samples directly on such a conducting film to begin with, a more subtle charging effect still remains. We argue here that specimen charging is in this case likely to produce a dipole sheet rather than a layer of positive charge at the surface of the specimen. A simple model of the factors that control the kinetics of specimen charging, and its neutralization, is discussed as a guide for experiments that attempt to minimize the amount of specimen charging. Believable estimates of the electrostatic forces and the electron optical disturbances that are likely to occur suggest that specimen bending and warping may have the biggest impact on degrading the image quality at high resolution. Electron optical effects are likely to be negligible except in the case of a specimen that is tilted to high angle. A model is proposed to explain how both the mechanical and electron-optical effects of forming a dipole layer would have much greater impact on the image resolution in a direction perpendicular to the tilt axis, a well-known effect in electron microscopy of two-dimensional crystals.

  20. Residual stress state in pipe cut ring specimens for fracture toughness testing

    Energy Technology Data Exchange (ETDEWEB)

    Damjanovic, Darko [J.J. Strossmayer Univ. of Osijek, Slavonski Brod (Croatia). Mechanical Engineering Faculty; Kozak, Drazan [Zagreb Univ. (Croatia). Dept. for Mechanical Design; Marsoner, Stefan [Materials Center, Leoben (Austria).; Gubeljak, Nenad [Maribor Univ. (Slovenia). Chair of Mechanics

    2017-07-01

    Thin-walled pipes are not suitable for measuring fracture toughness parameters of vital importance because longitudinal crack failure is the most common failure mode in pipes. This is due to the impossibility to manufacture standard specimens for measuring fracture toughness, such as SENB or CT specimens, from the thin wall of the pipe. Previous works noticed this problem, but until now, a good and convenient solution has not been found or developed. To overcome this problem, very good alternative solution was proposed, the so-called pipe ring notched bend specimen (PRNB) [1-5]. Until now, only the idealized geometry PRNB specimen is analyzed, i. e., a specimen which is not cut out from an actual pipe but produced from steel plate. Based on that, residual stresses are neglected along with the imperfections in geometry (elliptical and eccentricity). The aim of this research is to estimate the residual stress state(s) in real pipes used in the boiler industry produced by hot rolling technique. These types of pipes are delivered only in normalized condition, but not stress relieved. Therefore, there are residual stresses present due to the manufacturing technique, but also due to uneven cooling after the production process. Within this paper, residual stresses are estimated by three methods: the incremental hole drilling method (IHMD), X-ray diffraction (XRD) and the splitting method (SM). Knowing the residual stress state in the ring specimen, it is possible to assess their impact on fracture toughness measured on the corresponding PRNB specimen(s).

  1. Polycarbonate and co-continuous polycarbonate/ABS blends: influence of specimen thickness

    NARCIS (Netherlands)

    Inberg, J.P.F.; Gaymans, R.J.

    2002-01-01

    The influence of specimen thickness on the fracture behaviour of polycarbonate (PC) and co-continuous PC/ABS (50/50) blends was studied in single edge notch tensile tests at 1 m/s and different temperatures (−80 to 130 °C). Specimen thickness ranged from 0.1 to 8 mm. In the co-continuous PC/ABS

  2. Some modifications of electric circuitry for internal friction measurements of U-shape specimens

    OpenAIRE

    Osamu, Yoshinari; M., KOIWA; H., Sugawara; I., SATO

    1980-01-01

    Some modifications of the electric circuitry are described for the apparatus of the internal friction measurement of thin wire specimens; the apparatus has been developed by Franklin et al. The improved apparatus has been successfully used in the internal friction measurements of cold‐worked vanadium specimens.

  3. Method for quantifying percentage wood failure in block-shear specimens by a laser scanning profilometer

    Science.gov (United States)

    C. T. Scott; R. Hernandez; C. Frihart; R. Gleisner; T. Tice

    2005-01-01

    A new method for quantifying percentage wood failure of an adhesively bonded block-shear specimen has been developed. This method incorporates a laser displacement gage with an automated two-axis positioning system that functions as a highly sensitive profilometer. The failed specimen is continuously scanned across its width to obtain a surface failure profile. The...

  4. 10 CFR 26.129 - Assuring specimen security, chain of custody, and preservation.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Assuring specimen security, chain of custody, and... Testing Facilities § 26.129 Assuring specimen security, chain of custody, and preservation. (a) Each... custody-and-control forms. Licensee testing facility personnel shall attempt to resolve any discrepancies...

  5. Effectiveness of Plastinated Anatomical Specimens Depicting Common Sports Injuries to Enhance Musculoskeletal Injury Evaluation Education

    Science.gov (United States)

    Tamura, Kaori; Stickley, Christopher D.; Labrash, Steven J.; Lozanoff, Scott

    2014-01-01

    Context: Plastination techniques have emerged as effective methods for preserving human tissue and enabling human specimens to be utilized in a fashion similar to anatomical models with much greater accuracy. Opportunities to observe and experience human specimens in classroom settings should be beneficial to undergraduate and graduate students in…

  6. Evaluation of the ARCHITECT urine NGAL assay: Assay performance, specimen handling requirements and biological variability

    NARCIS (Netherlands)

    Grenier, F.C.; Ali, S.; Syed, H.; Workman, R.; Martens, F.; Liao, M.; Wang, Y.; Wong, P.Y.

    2010-01-01

    Objectives: NGAL (Neutrophil Gelatinase-Associated Lipocalin) has emerged as a new biomarker for the identification of acute kidney injury. Reliable clinical evaluations require a simple, robust test method for NGAL, and knowledge of specimen handling and specimen stability characteristics. We

  7. Crack Propagation on ESE(T) Specimens Strengthened with CFRP Sheets

    DEFF Research Database (Denmark)

    Hansen, Christian Skodborg; Jensen, Peter Holmstrøm; Dyrelund, Jens

    2009-01-01

    In this paper fatigue tests on side notched steel test specimens strengthened with adhesive bonded fibre reinforced polymer (FRP) sheets are presented. The specimens are subject to crack growth both in the steel and bond line. Influence of the load ratio and initial crack length on the overall en...

  8. Histopathological Changes in Laparoscopic Sleeve Gastrectomy Specimens: Prevalence, Risk Factors, and Value of Routine Histopathologic Examination

    OpenAIRE

    Safaan, Tamer; Bashah, Moataz; El Ansari, Walid; Karam, Mohsen

    2017-01-01

    Background Laparoscopic sleeve gastrectomy (LSG) is a common surgical therapeutic option for obese patients, with debate about the value of routine histopathologic examination of LSG specimens. We assessed the following: prevalence of different histopathologic changes in LSG specimens, risk factors associated with premalignant and with frequent histopathologic changes, and whether routine histopathologic examination is warranted for LSG patients with nonsignificant clinical history. Methods R...

  9. Type specimens of Maastrichtian fossils in the National Museum of Natural History, Leiden

    NARCIS (Netherlands)

    Leloux, J.

    2002-01-01

    The type specimens of Maastrichtian invertebrate fossils from Limburg, The Netherlands, present in the National Museum of Natural History, Leiden, are listed. The Upper Cretaceous plant type specimens from Limburg of Miquel that were once part of the Staring collection present in the Palaeobotanical

  10. 49 CFR Appendix D to Part 40 - Report Format: Split Specimen Failure To Reconfirm

    Science.gov (United States)

    2010-10-01

    .... The following items are required on each report: 1. MRO name, address, phone number, and fax number. 2. Collection site name, address, and phone number. 3. Date of collection. 4. Specimen I.D. number. 5. Laboratory accession number. 6. Primary specimen laboratory name, address, and phone number. 7. Date result...

  11. 42 CFR 414.510 - Laboratory date of service for clinical laboratory and pathology specimens.

    Science.gov (United States)

    2010-10-01

    ... and pathology specimens. 414.510 Section 414.510 Public Health CENTERS FOR MEDICARE & MEDICAID... date of service for clinical laboratory and pathology specimens. The date of service for either a clinical laboratory test or the technical component of physician pathology service is as follows: (a...

  12. Modelling of the Residual Stress State in a new Type of Residual Stress Specimen

    DEFF Research Database (Denmark)

    Jakobsen, Johnny; Andreasen, Jens Henrik

    2014-01-01

    The paper presents a study on a new type residual stress specimen which is proposed as a simple way to conduct experimental validation for model predictions. A specimen comprising of a steel plate with circular hole embedded into a stack of CSM glass fibre and further infused with an epoxy resin...

  13. Sizing Single Cantilever Beam Specimens for Characterizing Facesheet/Core Peel Debonding in Sandwich Structure

    Science.gov (United States)

    Ratcliffe, James G.

    2010-01-01

    This paper details part of an effort focused on the development of a standardized facesheet/core peel debonding test procedure. The purpose of the test is to characterize facesheet/core peel in sandwich structure, accomplished through the measurement of the critical strain energy release rate associated with the debonding process. The specific test method selected for the standardized test procedure utilizes a single cantilever beam (SCB) specimen configuration. The objective of the current work is to develop a method for establishing SCB specimen dimensions. This is achieved by imposing specific limitations on specimen dimensions, with the objectives of promoting a linear elastic specimen response, and simplifying the data reduction method required for computing the critical strain energy release rate associated with debonding. The sizing method is also designed to be suitable for incorporation into a standardized test protocol. Preliminary application of the resulting sizing method yields practical specimen dimensions.

  14. The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies

    Directory of Open Access Journals (Sweden)

    Pan Zhang

    2017-01-01

    Full Text Available High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.

  15. Additive Manufacturing of PLA and CF/PLA Binding Layer Specimens via Fused Deposition Modeling

    Science.gov (United States)

    Li, Yuhang; Gao, Shiyou; Dong, Rongmei; Ding, Xuebing; Duan, Xiaoxi

    2018-02-01

    As one of the most popular additive manufacturing techniques, fused deposition modeling (FDM) is successfully applied in aerospace, automotive, architecture, and other fields to fabricate thermoplastic parts. Unfortunately, as a result of the limited nature of the mechanical properties and mass in raw materials, there is a pressing need to improve mechanical properties and reduce weight for FDM parts. Therefore, this paper presents an experiment of a special polylactic acid (PLA) and carbon fiber (CF)/PLA-laminated experimental specimen fabricated using the FDM process. The mechanical properties and mass analysis of the new composites for the PLA and CF/PLA binding layer specimen are investigated experimentally. Through the experimental analysis, one can conclude that the mass of laminated specimen is lighter than the CF/PLA specimen, and the tensile and flexural mechanical properties are higher than the pure PLA specimen.

  16. Correction of constraint loss in fracture toughness measurement of PCVN specimens based on fracture toughness diagram

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Shin Beom; Kim, Young Jin [Sungkyunkwan University, Suwon (Korea, Republic of); Chang, Yoon-Suk [Kyung Hee University, Yongin (Korea, Republic of); Kim, Min Chul; Lee, Bong Sang [Korea Atomic Energy Reserch Institute, Daejeon (Korea, Republic of)

    2010-03-15

    The aim of this paper is to suggest an approach to generate master curves by using miniature specimens, especially pre-cracked Charpy V-notched (PCVN) specimen, made of SA508 carbon steel. Firstly, fracture toughness diagram is derived from comparing finite element analyses results with the fixed mesh size at crack tip between standard compact tension and PCVN specimens. To compensate the constraint effects from different geometry, further examination based on the fracture toughness diagram was performed. In this context, a scale factor to deal with specimen size effects is proposed by statistically manipulating the numerical analysis data. Finally, the proposed scale factor is applied to calculate reference temperature which affects on the master curve. We expect that the approach can be applicable to compensate the geometrical constraint effects on fracture toughness of SA508 carbon steel when the PCVN specimen is used

  17. Alfredo Dugès' type specimens of amphibians and reptiles revisited.

    Science.gov (United States)

    Flores-Villela, Oscar; Ríos-Muñoz, César A; Magaña-Cota, Gloria E; Quezadas-Tapia, Néstor L

    2016-03-14

    The type specimens of amphibians and reptiles of the Museo de Historia Natural Alfredo Dugès, at the University of Guanajuato (MADUG) were reviewed following Smith & Necker's (1943) summary. Owing to this collection's eventful history and its historical importance as the oldest herpetological collection in Mexico, a review of its conservation status was needed. After many years, the collection has received proper recognition at the University of Guanajuato with a portion of the herpetological types considered "Precious Assets" of the university. We found 34 type specimens pertaining to 18 taxa; six are additional specimens to those previously reported; six herpetological types are missing, including the body of the type of Adelophis copei. All specimens are in good to reasonable condition except for the type of Rhinocheilus antonii, which has dried out completely. All specimens are illustrated to show their condition.

  18. Additive Manufacturing of PLA and CF/PLA Binding Layer Specimens via Fused Deposition Modeling

    Science.gov (United States)

    Li, Yuhang; Gao, Shiyou; Dong, Rongmei; Ding, Xuebing; Duan, Xiaoxi

    2018-01-01

    As one of the most popular additive manufacturing techniques, fused deposition modeling (FDM) is successfully applied in aerospace, automotive, architecture, and other fields to fabricate thermoplastic parts. Unfortunately, as a result of the limited nature of the mechanical properties and mass in raw materials, there is a pressing need to improve mechanical properties and reduce weight for FDM parts. Therefore, this paper presents an experiment of a special polylactic acid (PLA) and carbon fiber (CF)/PLA-laminated experimental specimen fabricated using the FDM process. The mechanical properties and mass analysis of the new composites for the PLA and CF/PLA binding layer specimen are investigated experimentally. Through the experimental analysis, one can conclude that the mass of laminated specimen is lighter than the CF/PLA specimen, and the tensile and flexural mechanical properties are higher than the pure PLA specimen.

  19. Combatting Global Infectious Diseases: A Network Effect of Specimen Referral Systems.

    Science.gov (United States)

    Fonjungo, Peter N; Alemnji, George A; Kebede, Yenew; Opio, Alex; Mwangi, Christina; Spira, Thomas J; Beard, R Suzanne; Nkengasong, John N

    2017-02-13

    The recent Ebola virus outbreak in West Africa clearly demonstrated the critical role of laboratory systems and networks in responding to epidemics. Because of the huge challenges in establishing functional laboratories at all tiers of health systems in developing countries, strengthening specimen referral networks is critical. In this review article, we propose a platform strategy for developing specimen referral networks based on 2 models: centralized and decentralized laboratory specimen referral networks. These models have been shown to be effective in patient management in programs in resource-limited settings. Both models lead to reduced turnaround time and retain flexibility for integrating different specimen types. In Haiti, decentralized specimen referral systems resulted in a 182% increase in patients enrolling in human immunodeficiency virus treatment programs within 6 months. In Uganda, cost savings of up to 62% were observed with a centralized model. A platform strategy will create a network effect that will benefit multiple disease programs.

  20. Detection of Borrelia miyamotoi and other tick-borne pathogens in human clinical specimens and Ixodes scapularis ticks in New York State, 2012-2015.

    Science.gov (United States)

    Wroblewski, Danielle; Gebhardt, Linda; Prusinski, Melissa A; Meehan, Lisa J; Halse, Tanya A; Musser, Kimberlee A

    2017-03-01

    Borrelia miyamotoi (Bm) is a recently emerging bacterial agent transmitted by several species of ixodid ticks. Diagnosis of Bm infection can be challenging, as the organism is not easily cultivable. We have developed and validated a multiplex real-time PCR to simultaneously identify Bm infection and the agents causing human granulocytic anaplasmosis and human monocytic ehrlichiosis, Anaplasma phagocytophilum and Ehrlichia chaffeensis, respectively. The assay is 100% specific; highly sensitive, detecting 11 gene copies of Bm DNA in both whole blood and cerebral spinal fluid; and provides rapid results in less than two hours. A retrospective study of 796 clinical specimens collected between the years 2012 and 2014 and a prospective study of 366 clinical specimens were performed utilizing this novel assay to evaluate the frequency of Bm infection in New York State (NYS). Eight clinical specimens (1%) were found to be positive for Bm, 216 were positive for A. phagocytophilum, and 10 were positive for E. chaffeensis. Additionally, we tested 411 I. scapularis ticks collected in NYS during 2013 and 2014 in a separate multiplex real-time PCR to determine the prevalence of Bm, A. phagocytophilum, Borrelia burgdorferi s.s., and Borrelia species. Our results indicated rates of 1.5%, 27%, 19.7%, and 8.8% respectively. The ability to monitor both the frequency and geographic distribution of Bm cases and the prevalence and geographic distribution of Bm in ticks will help create a better understanding of this emerging tick-borne pathogen. Published by Elsevier GmbH.

  1. Enhanced radiometric detection of Mycobacterium paratuberculosis by using filter-concentrated bovine fecal specimens

    Energy Technology Data Exchange (ETDEWEB)

    Collins, M.T.; Kenefick, K.B.; Sockett, D.C.; Lambrecht, R.S.; McDonald, J.; Jorgensen, J.B. (Univ. of Wisconsin, Madison (USA))

    1990-11-01

    A commercial radiometric medium, BACTEC 12B, was modified by addition of mycobactin, egg yolk suspension, and antibiotics (vancomycin, amphotericin B, and nalidixic acid). Decontaminated bovine fecal specimens were filter concentrated by using 3-microns-pore-size, 13-mm-diameter polycarbonate filters, and the entire filter was placed into the radiometric broth. Comparison of the radiometric technique with conventional methods on 603 cattle from 9 Mycobacterium paratuberculosis-infected herds found that of 75 positive specimens, the radiometric technique detected 92% while conventional methods detected 60% (P less than 0.0005). Only 3.9% of radiometric cultures were contaminated. To measure the effect of filter concentration of specimens on the detection rate, 5 cattle with minimal and 5 with moderate ileum histopathology were sampled weekly for 3 weeks. M. paratuberculosis was detected in 33.3% of nonfiltered specimens and 76.7% of filtered specimens (P less than 0.005). Detection rates were directly correlated with the severity of disease, and the advantage of specimen concentration was greatest on fecal specimens from cattle with low-grade infections. Detection times were also correlated with infection severity: 13.4 +/- 5.9 days with smear-positive specimens, 27.9 +/- 8.7 days with feces from cows with typical subclinical infections, and 38.7 +/- 3.8 days with fecal specimens from cows with low-grade infections. Use of a cocktail of vancomycin, amphotericin B, and nalidixic acid for selective suppression of nonmycobacterial contaminants was better than the commercial product PANTA (Becton Dickinson Microbiologic Systems, Towson, Md.) only when specimens contained very low numbers of M. paratuberculosis.

  2. Methane Clathrate Hydrate Prospecting

    Science.gov (United States)

    Duxbury, N.; Romanovsky, V.

    2003-01-01

    A method of prospecting for methane has been devised. The impetus for this method lies in the abundance of CH4 and the growing shortages of other fuels. The method is intended especially to enable identification of subpermafrost locations where significant amounts of methane are trapped in the form of methane gas hydrate (CH4(raised dot)6H2O). It has been estimated by the U.S. Geological Survey that the total CH4 resource in CH4(raised dot) 6H2O exceeds the energy content of all other fossil fuels (oil, coal, and natural gas from non-hydrate sources). Also, CH4(raised dot)6H2O is among the cleanest-burning fuels, and CH4 is the most efficient fuel because the carbon in CH4 is in its most reduced state. The method involves looking for a proxy for methane gas hydrate, by means of the combination of a thermal-analysis submethod and a field submethod that does not involve drilling. The absence of drilling makes this method easier and less expensive, in comparison with prior methods of prospecting for oil and natural gas. The proposed method would include thermoprospecting in combination with one more of the other non-drilling measurement techniques, which could include magneto-telluric sounding and/or a subsurface-electrical-resistivity technique. The method would exploit the fact that the electrical conductivity in the underlying thawed region is greater than that in the overlying permafrost.

  3. Astronautics summary and prospects

    CERN Document Server

    Kiselev, Anatoly Ivanovich; Menshikov, Valery Alexandrovich

    2003-01-01

    The monograph by A.I.Kiselev, A.A. Medvedev and Y.A.Menshikov, Astronautics: Summary and Prospects, aroused enthusiasm both among experts and the public at large. This is due to the felicitous choice of presentation that combines a simple description of complex space matters with scientificsubstantiation of the sub­ jectmatter described. The wealth of color photos makes the book still more attractive, and it was nominated for an award at the 14th International Moscow Book Fair, being singled out as the "best publication of the book fair". The book's popularity led to a second edition, substantially revised and enlarged. Since the first edition did not sufficiently cover the issues of space impact on ecology and the prospective development of space systems, the authors revised the entire volume, including in it the chapter "Space activity and ecology" and the section "Multi-function space systems". Using the federal monitoring system, now in the phase of system engi­ neering, as an example, the authors consi...

  4. Evaluation of three rapid assays for detection of Clostridium difficile toxin A and toxin B in stool specimens.

    Science.gov (United States)

    Rüssmann, H; Panthel, K; Bader, R-C; Schmitt, C; Schaumann, R

    2007-02-01

    Diagnosis of Clostridium difficile-associated disease continues to be difficult for clinical microbiology laboratories. The aim of this study was to evaluate the performance of three enzyme immunoassays for detection of C. difficile toxins A and B: the recently marketed rapid enzyme immunoassay Ridascreen Clostridium difficile Toxin A/B (R-Biopharm, Darmstadt, Germany) and two established enzyme immunoassays, the C. difficile Tox A/B II Assay (TechLab, Blacksburg, VA, USA) and the ProSpecT C. difficile Toxin A/B Microplate Assay (Remel, Lenexa, KS, USA). Stool specimens (n = 383) from patients with a clinical diagnosis of antibiotic-associated diarrhea were examined by these three enzyme immunoassays and were additionally cultured for C. difficile on selective agar. Samples giving discordant enzyme immunoassay results underwent confirmatory testing by tissue culture cytotoxin B assay and by PCR for toxin A (tcdA) and toxin B (tcdB) genes from C. difficile. Using the criteria adopted for this study, 60 (15.7%) samples tested positive for toxins A and/or B. Sensitivity and specificity of the enzyme immunoassays were, respectively, 88.3 and 100% for the TechLab enzyme immunoassay, 91.7 and 100% for the R-Biopharm enzyme immunoassay, and 93.3 and 100% for the Remel enzyme immunoassay. The differences between these results are statistically not significant (p > 0.05). The results show that all three enzyme immunoassays are acceptable tests for the detection of C. difficile toxins A and B directly in fecal specimens or in toxigenic cultures.

  5. Estimation of absolute renal uptake with technetium-99m dimercaptosuccinic acid: direct comparison with the radioactivity of nephrectomy specimens

    Directory of Open Access Journals (Sweden)

    Mariana da Cunha Lopes de Lima

    Full Text Available CONTEXT AND OBJECTIVE: Studies using radionuclides are the most appropriate method for estimating renal function. Dimercaptosuccinic acid chelate labeled with technetium-99m (99mTc-DMSA is the radiopharmaceutical of choice for high-resolution imaging of the renal cortex and estimation of the functional renal mass. The aim of this study was to evaluate a simplified method for determining the absolute renal uptake (ARU of 99mTc-DMSA prior to nephrectomy, using the radioactivity counts of nephrectomy specimens as the gold standard. DESIGN AND SETTING: Prospective study at the Division of Nuclear Medicine, Department of Radiology, Universidade Estadual de Campinas. METHODS: Seventeen patients (12 females; range 22-82 years old; mean age 50.8 years old underwent nephrectomy for various reasons. Renal scintigraphy was performed three to four hours after intravenous administration of a mean dose of 188.7 MBq (5.1 mCi of 99mTc-DMSA, which was done six to 24 hours before surgery. The in vivo renal uptake of 99mTc-DMSA was determined using the radioactivity of the syringe before the injection (measured using a dose calibrator and the images of the syringe and kidneys, obtained from a scintillation camera. After surgery, the reference value for renal uptake of 99mTc-DMSA was determined by measuring the radioactivity of the nephrectomy specimen using the same dose calibrator. RESULTS: The ARU measurements were very similar to those obtained using the reference method, as determined by linear regression (r-squared = 0.96. CONCLUSION: ARU estimation using the proposed method before nephrectomy seems to be accurate and feasible for routine use.

  6. The Effects of Specimen Geometry on the Plastic Deformation of AA 2219-T8 Aluminum Alloy Under Dynamic Impact Loading

    Science.gov (United States)

    Owolabi, G. M.; Bolling, D. T.; Odeshi, A. G.; Whitworth, H. A.; Yilmaz, N.; Zeytinci, A.

    2017-12-01

    The effects of specimen geometry on shear strain localization in AA 2219-T8 aluminum alloy under dynamic impact loading were investigated. The alloy was machined into cylindrical, cuboidal and conical (frustum) test specimens. Both deformed and transformed adiabatic shear bands developed in the alloy during the impact loading. The critical strain rate for formation of the deformed band was determined to be 2500 s-1 irrespective of the specimen geometry. The critical strain rate required for formation of transformed band is higher than 3000 s-1 depending on the specimen geometry. The critical strain rate for formation of transformed bands is lowest (3000 s-1) in the Ø5 mm × 5 mm cylindrical specimens and highest (> 6000 s-1) in the conical specimens. The cylindrical specimens showed the greatest tendency to form transformed bands, whereas the conical specimen showed the least tendency. The shape of the shear bands on the impacted plane was also observed to be dependent on the specimen geometry. Whereas the shear bands on the compression plane of the conical specimens formed elongated cycles, two elliptical shaped shear bands facing each other were observed on the cylindrical specimens. Two parallel shear bands were observed on the compression planes of the cuboidal specimens. The dynamic stress-strain curves vary slightly with the specimen geometry. The cuboidal specimens exhibit higher tendency for strain hardening and higher maximum flow stress than the other specimens. The microstructure evolution leading to the formation of transformed bands is also discussed in this paper.

  7. Effect of out-of-plane specimen movement on the accuracy of the smallest specimen strain measurable using the digital image correlation technique

    Science.gov (United States)

    Poling, Joel; Desai, Niranjan

    2017-04-01

    This investigation determined the smallest strain accurately measurable by a state-of-the-art digital image correlation (DIC) - based tool used in structural health monitoring, in a specimen subjected to out-of-plane movement, building upon a study that concluded that out-of-plane specimen movement results in noise in DIC-based strain measurements. This study was motivated by initially undetected damage at low strains in connections of a real-world bridge, whose detection would have prevented its propagation, resulting in lower repair costs. The smallest strains accurately measurable using the state-of-the-art DIC tool, over a range of specimen out-of-plane displacement amplitudes, were determined.

  8. Test methodology and technology of fracture toughness for small size specimens

    Energy Technology Data Exchange (ETDEWEB)

    Wakai, E.; Takada, F.; Ishii, T.; Ando, M. [Japan Atomic Energy Agency, Naga-gun, Ibaraki-ken (Japan); Matsukawa, S. [JNE Techno-Research Co., Kanagawa-ken (Japan)

    2007-07-01

    Full text of publication follows: Small specimen test technology (SSTT) is required to investigate mechanical properties in the limited availability of effective irradiation volumes in test reactors and accelerator-based neutron and charged particle sources. The test methodology guideline and the manufacture processes for very small size specimens have not been established, and we would have to formulate it. The technology to control exactly the load and displacement is also required in the test technology under the environment of high dose radiation produced from the specimens. The objective of this study is to examine the test technology and methodology of fracture toughness for very small size specimens. A new bend test machine installed in hot cell has been manufactured to obtain fracture toughness and DBTT (ductile - brittle transition temperature) of reduced-activation ferritic/martensitic steels for small bend specimens of t/2-1/3PCCVN (pre-cracked 1/3 size Charpy V-notch) with 20 mm length and DFMB (deformation and fracture mini bend specimen) with 9 mm length. The new machine can be performed at temperatures from -196 deg. C to 400 deg. C under unloading compliance method. Neutron irradiation was also performed at about 250 deg. C to about 2 dpa in JMTR. After the irradiation, fracture toughness and DBTT were examined by using the machine. Checking of displacement measurement between linear gauge of cross head's displacement and DVRT of the specimen displacement was performed exactly. Conditions of pre-crack due to fatigue in the specimen preparation were also examined and it depended on the shape and size of the specimens. Fracture toughness and DBTT of F82H steel for t/2-1/3PCCVN, DFMB and 0.18DCT specimens before irradiation were examined as a function of temperature. DBTT of smaller size specimens of DFMB was lower than that of larger size specimen of t/2-1/3PCCVN and 0.18DCT. The changes of fracture toughness and DBTT due to irradiation were also

  9. Urine specimen collection following consensual intercourse - A forensic evidence collection method for Y-DNA and spermatozoa.

    Science.gov (United States)

    Joki-Erkkilä, Minna; Tuomisto, Sari; Seppänen, Mervi; Huhtala, Heini; Ahola, Arja; Karhunen, Pekka J

    2016-01-01

    The purpose of the prospective research was to evaluate the benefit of urine specimen as a collection technique for biological forensic evidence in adult volunteers following consensual intercourse. For detecting Y-chromosomal material Buccal Swab Spin Protocol(®) was used in DNA extraction and purification and samples were analysed with Quantifiler Y Human Male DNA Quantification Kit(®). The time frame for positive Y-DNA was evaluated. Immediate microscopy for detection of spermatozoa was performed. Y-DNA was detected in 173/205 (84.4%) urine samples. Of the 86 first post-coital void urine samples available, Y-DNA was detected in 83 (96.5%) specimens. Of the 119 urine samples from volunteers with post-coital activities Y-DNA was still measurable in 70 (58.8%) urine specimens. The male DNA amount was below 0.023 ng/μl in 28/153 (18.3%) urine samples. Of the 22 urine samples obtained after 24 post-coital hours, 9 (40.9%) were still Y-DNA positive. No associations were found between coital durance, coital frequency during the past two weeks prior to the study intercourse, post-coital activities, and the urine sample Y-DNA positivity. Of the 111 urine samples where the immediate microscopy was performed, in 66 (59.5%) samples spermatozoa were verified and one sample even contained motile spermatozoa. Microscopy detected 66 (67.3%) and failed to detect spermatozoa in 32 (32.7%) of Y-DNA positive samples. In addition to conventional invasive swab techniques, urine samples seem to be an effective biological trace collection method for Y-DNA and spermatozoa within 24 h following penile-vaginal penetration. Furthermore, it may be considered as a non-invasive collection method in suspected acute child sexual abuse cases to diminish time delay in forensic evidence collection and to improve patients' positive attitudes towards evidence collection. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  10. Failure Behaviors Depending on the Notch Location of the Impact Test Specimens on the HAZ

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Yun Chan; Kim, Dong Wook; Lee, Young Suk [Chungang Univ., Seoul (Korea, Republic of); Hong, Jae Keun; Park, Ji Hong [Korea Institute of Machinery and Materials, Daejeon (Korea, Republic of)

    2007-07-01

    Numerical studies were performed to examine the effects of notch location of impact specimens on the failure behavior of HAZ (Heat Affected Zone) when Charpy V-notch impact test were made at a low temperature (1 .deg. C). Carbon steel plate (SA-516 Gr. 70) with thickness of 25mm for pressure vessel was welded by SMAW (Shielded Metal-Arc Welding) and specimens were fabricated from the welded plate. Charpy tests were then performed with specimens having different notch positions of specimens varying from the fusion line through HAZ to base metal. A series of finite element analysis which simulates the Charpy test and crack propagation initiating at the tip of V-notch was carried out as well. The finite element analysis takes into account the irregular fusion line and non-homogenous material properties due to the notch location of the specimen in HAZ. Results reveals that the energies absorbed during impact test depend significantly on the notch location and direction of specimen. Finite element analysis also demonstrates that the notch location of specimens, to a great extent, influences the reliability and consistency of the test.

  11. DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis

    Science.gov (United States)

    Erlich, Yaniv; Chang, Kenneth; Gordon, Assaf; Ronen, Roy; Navon, Oron; Rooks, Michelle; Hannon, Gregory J.

    2009-01-01

    Next-generation sequencers have sufficient power to analyze simultaneously DNAs from many different specimens, a practice known as multiplexing. Such schemes rely on the ability to associate each sequence read with the specimen from which it was derived. The current practice of appending molecular barcodes prior to pooling is practical for parallel analysis of up to many dozen samples. Here, we report a strategy that permits simultaneous analysis of tens of thousands of specimens. Our approach relies on the use of combinatorial pooling strategies in which pools rather than individual specimens are assigned barcodes. Thus, the identity of each specimen is encoded within the pooling pattern rather than by its association with a particular sequence tag. Decoding the pattern allows the sequence of an original specimen to be inferred with high confidence. We verified the ability of our encoding and decoding strategies to accurately report the sequence of individual samples within a large number of mixed specimens in two ways. First, we simulated data both from a clone library and from a human population in which a sequence variant associated with cystic fibrosis was present. Second, we actually pooled, sequenced, and decoded identities within two sets of 40,000 bacterial clones comprising approximately 20,000 different artificial microRNAs targeting Arabidopsis or human genes. We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals. PMID:19447965

  12. Use of a compact sandwich specimen to evaluate fracture toughness and interfacial bonding of bone.

    Science.gov (United States)

    Wang, X; Lankford, J; Agrawal, C M

    1994-01-01

    The objective of the present study was to develop a reliable and statistically valid test to measure the fracture toughness of small specimens of bone, and by extension, prosthetic materials, using a compact sandwich specimen. Samples of bone were sandwiched between holders of a different material and using this specimen configuration a new technique was developed to test the fracture toughness of the bone interlayer. The effects of different specimens sizes and holder materials were investigated empirically. Using finite element analysis a correction factor was determined to account for the finite thickness of the interlayer and the analytical solutions governing the test specimen were accordingly modified. Bulk compact tension specimens of bone were tested for comparison. Both wet and dry bone were evaluated and the fracture surface morphology characterized using scanning electron microscopy. The results indicate no statistically significant differences between the fracture toughness values obtained from the compact tension and sandwich specimens. The application of this technique to the testing of interfacial bonding between bone and biomaterials is discussed.

  13. Wide range stress intensity factor expressions for ASTM E 399 standard fracture toughness specimens

    Science.gov (United States)

    Srawley, J. E.

    1976-01-01

    For each of the two types of specimens, bend and compact, described previously for plane strain fracture toughness of materials, E 399, a polynominal expression is given for calculation of the stress intensity factor, K, from the applied force, P, and the specimen dimensions. It is explicitly stated, however, that these expressions should not be used outside the range of relative crack length, a/W, from 0.45 to 0.55. While this range is sufficient for the purpose of E 399, the same specimen types are often used for other purposes over a much wider range of a/W; for example, in the study of fatigue crack growth. Expressions are presented which are at least as accurate as those in E 399-74, and which cover much wider ranges of a/W: for the three-point bend specimen from 0 to 1; and for the compact specimen from 0.2 to 1. The range has to be restricted for the compact specimen because of the proximity of the loading pin holes to the crackline, which causes the stress intensity factor to be sensitive to small variations in dimensions when a/W is small. This is a penalty inherently associated with the compactness of the specimen.

  14. Micropapillary urothelial carcinoma: Cytologic features in a retrospective series of urine specimens

    Directory of Open Access Journals (Sweden)

    Jonas John Heymann

    2013-01-01

    Full Text Available Background : The micropapillary variant of urothelial carcinoma (uPC is a rare variant of urothelial carcinoma that carries a poor prognosis. Definitive surgery may represent optimal management of low stage tumors. Urine cytology is indispensable in the screening and follow-up of urinary tract cancer. However, cytopathological criteria for diagnosis of uPC and its differentiation from conventional urothelial carcinoma (CUC are not well-defined. Materials and Methods : Twenty-five cases of histologically confirmed micropapillary uPC from 21 patients were compared to 25 cases of histologically confirmed high-grade CUC. Results : In uPC cases, cell clusters were identified in 13 of 25 specimens from 10 patients. Six of the 13 specimens containing cell clusters corresponded to surgical pathology specimens in which micropapillary carcinoma accounted for at least 50% of total carcinoma. In contrast, only 1 of the 12 urine specimens devoid of cell clusters corresponded to surgical specimens in which micropapillary carcinoma accounted for at least 50% of total carcinoma. Cytomorphologic features of urinary specimens from patients with histologically confirmed micropapillary carcinoma were generally similar to those from patients with high-grade CUC, making it difficult to distinguish these entities in exfoliative urine specimens. Conclusions and Summary : Further investigation of the core cytopathological characteristics of uPC is warranted to refine its diagnostic criteria by exfoliative urine cytology.

  15. Progress in the preparation of cross-sectional TEM specimens by ion-beam thinning

    CERN Document Server

    Strecker, A; Kelsch, M; Salzberger, U; Sycha, M; Gao, M; Richter, G; Benthem, K V

    2003-01-01

    In transmission electron microscopy (TEM), often the preparation of samples is the most critical part. Specimens have to have disk geometries of 3 mm diameter laterally, and they have to be transparent for the electron beam vertically. Therefore, a specimen thickness in the range of some 1-10 nm has to be achieved by the preparation process. While shrinking the specimen dimensions, care has to be taken to recover the materials properties in the nm-regime. We report and shortly discuss some TEM specimen preparation techniques mainly used in the Stuttgart TEM specimen preparation laboratory. Furthermore, we demonstrate how more advanced techniques lead to a more reliable preparation of weakly-bonded metal/SrTiO sub 3 interfaces. In addition, the advantage of low-voltage ion-milling is demonstrated by a case study for bulk SrTiO sub 3. As a result, low-voltage ion polishing as a final step in the TEM specimen preparation by conventional ion-thinning turns out to significantly increase the specimen quality. In tu...

  16. Yield of two consecutive sputum specimens for the effective diagnosis of pulmonary tuberculosis.

    Directory of Open Access Journals (Sweden)

    Mohammad R Islam

    Full Text Available BACKGROUND: From long instances, it is debatable whether three sputum specimens are required for the diagnosis of pulmonary tuberculosis (TB or TB can be diagnosed effectively using two consecutive sputum specimens. This study was set out to evaluate the significance of examining multiple sputum specimens in diagnosis of TB. METHODS: We retrospectively reviewed the acid-fast bacillus (AFB smear and culture results of three consecutive days' sputum specimens from 413 confirmed TB patients which were detected as part of a larger active case finding study in Dhaka Central Jail, the largest correctional facility in Bangladesh. RESULTS: AFB was detected from 81% (n = 334 patients, of which 89% (n = 297 were diagnosed from the first and additional 9% (n = 30 were from the second sputum specimen. M. tuberculosis growth was observed for 406 patients and 85% (n = 343 were obtained from the first sputum and additional 10% (n = 42 were from the second one. The third specimen didn't show significant additional diagnostic value for the detection of AFB by microscopy or growth of the M. tuberculosis. CONCLUSIONS: We concluded from our study results that examining two consecutive sputum specimens is sufficient enough for the effective diagnosis of TB. It can also decrease the laboratory workload and hence improve the quality of work in settings with high TB burden like Bangladesh.

  17. Non tuberculous mycobacteria isolated from clinical specimens at a tertiary care hospital in South India

    Directory of Open Access Journals (Sweden)

    Jesudason M

    2005-01-01

    Full Text Available Purpose: This is a retrospective analysis of the isolation rates of nontuberculous mycobacteria (NTM from various clinical specimens and their antimicrobial susceptibility patterns. Methods: All NTM isolated between 1999 and 2004 at Christian Medical College, Vellore, South India, were identified with various biochemical tests. Antimicrobial susceptibility test for all NTM was performed by standard methods. Results : A total of 32,084 specimens were received for culture, of which 4473 (13.9% grew acid fast bacilli (AFB. Four thousand three hundred (96.1% of the AFB were M. tuberculosis while 173 (3.9% were NTM. Of the 173 NTM, 115 (66.5% were identified to the species level. Pus, biopsy specimens and sputum specimens yielded most of the NTM of which M. chelonae (46% and M. fortuitum (41% accounted for majority of them. M. chelonae and M. fortuitum , showed highest susceptibility to amikacin (99.2%. NTM were repeatedly isolated from seven sputum specimens, 15 biopsy and pus specimens, two CSF and two blood cultures. Six were isolated from patients with AIDS and five from post transplant patients. Conclusions: The isolation of NTM from various clinical specimens is reported in this study to highlight the associated diseases and therapeutic options in these infections.

  18. Replicate PCR Testing and Probit Analysis for Detection and Quantitation of Chlamydia pneumoniae in Clinical Specimens

    Science.gov (United States)

    Smieja, M.; Mahony, J. B.; Goldsmith, C. H.; Chong, S.; Petrich, A.; Chernesky, M.

    2001-01-01

    Nucleic acid amplification of clinical specimens with low target concentration has variable sensitivity. We examined whether testing multiple aliquots of extracted DNA increased the sensitivity and reproducibility of Chlamydia pneumoniae detection by PCR. Nested and non-nested C. pneumoniae PCR assays were compared using 10 replicates of 16 serial dilutions of C. pneumoniae ATCC VR-1310. The proportion positive versus the C. pneumoniae concentration was modeled by probit regression analysis. To validate the model, 10 replicates of 26 previously positive patient specimens of peripheral blood mononuclear cells (PBMC), sputum, or nasopharyngeal swabs (NPS) were tested. The proportion of replicates that were positive varied with the concentration of C. pneumoniae in the sample. At concentrations above 5 infection-forming units (IFU)/ml, both nested and non-nested PCR assay sensitivities were 90% or greater. The nested PCR was more sensitive (median detection, 0.35 versus 0.61 IFU/ml; relative median detection, 0.58; 95% confidence interval, 0.31 to 0.99; P = 0.04). In clinical specimens, replicate PCR detected 15 of 26 (nested) versus 1 of 26 (non-nested, P < 0.001). For PBMC specimens, testing 1, 3, or 5 replicates detected 3, 5, or 9 of 10 positive specimens, respectively. Median C. pneumoniae concentrations were estimated at 0.07 IFU/ml for PBMC and at <0.03 IFU/ml for NPS specimens. We conclude that performing 5 or 10 replicates considerably increased the sensitivity and reproducibility of C. pneumoniae PCR and enabled quantitation for clinical specimens. Due to sampling variability, PCR tests done without replication may miss a large proportion of positive specimens, particularly for specimens with small amounts of target C. pneumoniae DNA present. PMID:11325993

  19. Characterization of Cement Particles Found in Peri-implantitis-Affected Human Biopsy Specimens.

    Science.gov (United States)

    Burbano, Maria; Wilson, Thomas G; Valderrama, Pilar; Blansett, Jonathan; Wadhwani, Chandur P K; Choudhary, Pankaj K; Rodriguez, Lucas C; Rodrigues, Danieli C

    2015-01-01

    Peri-implantitis is a disease characterized by soft tissue inflammation and continued loss of supporting bone, which can result in implant failure. Peri-implantitis is a multifactorial disease, and one of its triggering factors may be the presence of excess cement in the soft tissues surrounding an implant. This descriptive study evaluated the composition of foreign particles from 36 human biopsy specimens with 19 specimens selected for analysis. The biopsy specimens were obtained from soft tissues affected by peri-implantitis around cement-retained implant crowns and compared with the elemental composition of commercial luting cement. Nineteen biopsy specimens were chosen for the comparison, and five test cements (TempBond, Telio, Premier Implant Cement, Intermediate Restorative Material, and Relyx) were analyzed using scanning electron microscopy equipped with energy dispersive x-ray spectroscopy. This enabled the identification of the chemical composition of foreign particles embedded in the tissue specimens and the composition of the five cements. Statistical analysis was conducted using classification trees to pair the particles present in each specimen with the known cements. The particles in each biopsy specimen could be associated with one of the commercial cements with a level of probability ranging between .79 and 1. TempBond particles were found in one biopsy specimen, Telio particles in seven, Premier Implant Cement particles in four, Relyx particles in four, and Intermediate Restorative Material particles in three. Particles found in human soft tissue biopsy specimens around implants affected by peri-implant disease were associated with five commercially available dental cements.

  20. Causes and impact of specimen rejection in a clinical chemistry laboratory.

    Science.gov (United States)

    Cao, Liyun; Chen, Meng; Phipps, Ron A; Del Guidice, Robert E; Handy, Beverly C; Wagar, Elizabeth A; Meng, Qing H

    2016-07-01

    Pre-analytical errors necessitate specimen rejection and negatively affect patient safety. Our purpose was to investigate the factors leading to specimen rejection and its impact. Specimen rejections in a clinical chemistry laboratory during a 1-year period were reviewed retrospectively and analyzed for frequency, cause, circumstances, and impact. Of the 837,862 specimens received, 2178 (0.26%) were rejected. The most common reasons for specimen rejection were contamination (n=764, 35.1%), inappropriate collection container/tube (n=330, 15.2%), quantity not sufficient (QNS) (n=329, 15.1%), labeling errors (n=321, 14.7%), hemolyzed specimen (n=205, 9.4%), and clotted specimen (n=203, 9.3%). The analytes most often affected were glucose (n=192, 8.8%); calcium (n=152, 7.0%), magnesium (n=148, 6.8%), potassium (n=137, 6.3%), creatinine (n=100, 4.6%), and blood urea nitrogen (n=97, 4.4%). Outpatient service and blood draw by phlebotomists were associated with low rejection rates (536/493,501 or 0.11% and 368/586,503 or 0.06%, respectively). Recollection due to specimen rejection increased the turnaround time by an average of 108min. The total cost for the recollection was around $43,210 USD with an average cost around $21.9 USD. The factors associated with rejection are remediable by improved training and quality assurance measures. Policies and procedures specific to specimen collection, transportation, and preparation should be strictly followed. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Residual Stress State in Single-Edge Notched Tension Specimen Caused by the Local Compression Technique

    Directory of Open Access Journals (Sweden)

    Huang Yifan

    2016-12-01

    Full Text Available Three-dimensional (3D finite element analyses (FEA are performed to simulate the local compression (LC technique on the clamped single-edge notched tension (SE(T specimens. The analysis includes three types of indenters, which are single pair of cylinder indenters (SPCI, double pairs of cylinder indenters (DPCI and single pair of ring indenters (SPRI. The distribution of the residual stress in the crack opening direction in the uncracked ligament of the specimen is evaluated. The outcome of this study can facilitate the use of LC technique on SE(T specimens.

  2. Fungal Deterioration of Tsunami-Affected Plant Specimens in the Great East Japan Earthquake

    OpenAIRE

    久米田, 裕子; 坂田, 淳子; 高鳥, 浩介; 木川, りか; 佐藤, 嘉則; 佐久間, 大輔

    2015-01-01

    A large number of important cultural objects in museums were seriously damaged by the tsunami that accompanied the Great East Japan Earthquake on March 11,2011.Many plant specimens were also affected by the tsunami and were left wet for several months. When they were salvaged, different degrees of fungal damage were observed in the specimens though they remained under the same conditions.In this study,34 mount papers were examined after plant specimens had bee removed.As a result of identific...

  3. The first specimen of Camarasaurus (Dinosauria: Sauropoda from Montana: The northernmost occurrence of the genus.

    Directory of Open Access Journals (Sweden)

    D Cary Woodruff

    Full Text Available A partial skeleton from the Little Snowy Mountains of central Montana is the first referable specimen of the Morrison Formation macronarian sauropod Camarasaurus. This specimen also represents the northernmost occurrence of a sauropod in the Morrison. Histological study indicates that, although the specimen is relatively small statured, it is skeletally mature; this further emphasizes that size is not a undeviating proxy to maturity in dinosaurs, and that morphologies associated with an individual's age and stature may be more nebulous in sauropods.

  4. Experimental studies the evolution of stress-strain state in structured rock specimens under uniaxial loading

    Science.gov (United States)

    Oparin, Viktor; Tsoy, Pavel; Usoltseva, Olga; Semenov, Vladimir

    2014-05-01

    The aim of this study was to analyze distribution and development of stress-stress state in structured rock specimens subject to uniaxial loading to failure. Specific attention was paid to possible oscillating motion of structural elements of the rock specimens under constraints (pre-set stresses at the boundaries of the specimens) and the kinetic energy fractals. The detailed studies into the micro-level stress-strain state distribution and propagation over acting faces of rock specimens subject to uniaxial loading until failure, using automated digital speckle photography analyzer ALMEC-tv, have shown that: • under uniaxial stiff loading of prismatic sandstone, marble and sylvinite specimens on the Instron-8802 servohydraulic testing machine at the mobile grip displacement rate 0.02-0.2 mm/min, at a certain level of stressing, low-frequency micro-deformation processes originate in the specimens due to slow (quasi-static) force; • the amplitude of that deformation-wave processes greatly depends on the micro-loading stage: — at the elastic deformation stage, under the specimen stress lower than half ultimate strength of the specimen, there are no oscillations of microstrains; —at the nonlinearly elastic deformation stage, under stress varied from 0.5 to 1 ultimate strength of the specimens, the amplitudes of microstrains grow, including the descending stage 3; the oscillation frequency f=0.5-4 Hz; —at the residual strength stage, the amplitudes of the microstrains drop abruptly (3-5 times) as against stages 2 and 3; • in the elements of the scanned specimen surface in the region with the incipient crack, the microstrain rate amplitudes are a few times higher than in the undamged surface region of the same specimen. Sometimes, deformation rate greatly grows with increase in the load. The authors have used the energy scanning function of the deformation-wave processes in processing experimental speckle-photography data on the surface of the test specimen

  5. An investigation on the fatigue behavior of DCB specimen bonded with aluminum foam at Mode III

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H.; Cho, J. U. [Kongju University, Cheonan (Korea, Republic of); Zhao, G [School of Aerospace, Xian Jiaotong University, Xian (China); Cho, C. [Dept. of Mechanical Engineering, Inha University, Incheon (Korea, Republic of)

    2016-10-15

    Aluminum foam with its excellent physical and mechanical characteristics is a lightweight metallic material used with good quality in vehicle bumpers, internal shock absorbers on planes, as materials for vessel joints etc. On the contrary, when aluminum foam is used without sufficient investigation, there is the likelihood of damage or destruction of the machine or mechanical structure, and in extreme case it may cause to human casualties. This study aims to analyze the characteristics of adhesive structures with aluminum foam for the closed-type aluminum foam used primarily as shock absorbers. The fatigue analyses of the DCB test specimens at mode III with aluminum foam are verified through a fatigue experiment. As the analysis results, test specimen models with the thicknesses (t) of 35 mm, 45 mm and 55 mm showed the peak load occurrence approximately after the progress from 0 to 50 cycles. And afterwards the load gradually decreased as the cycles increased. The peak loads for each DCB test specimens were ±0.80 kN for the specimen thickness(t) of 35 mm, ±0.98 kN for the specimen thickness(t) of 45 mm and ±1.18 kN for the specimen thickness(t) of 55 mm. It is also shown that the peak load occurring on the specimen increased as specimen thickness increased. These study results are compared with the specimen thickness of 35 mm model as the basis. When the specimen thickness is increased as much as 10 mm, the peak load is increased approximately 1.25 times. When the specimen thickness is also increased as much as 20 mm, the peak load is increased 1.5 times. The analysis data and the real experiment data showed similar results each other. Therefore, it can be thought that the analysis data is applicable in real field. And it is estimated that the mechanical characteristics of the DCB test specimen at mode III during the fatigue load conditions can be systematically and efficiently analyzed.

  6. Two Records of large specimens of Fire Salamander Salamandra salamandra (Linnaeus, 1758 (Amphibia: Caudata in Bulgaria

    Directory of Open Access Journals (Sweden)

    ALEXANDER PULEV

    2016-03-01

    Full Text Available Two particularly large specimens of Fire Salamander have been registered in southwestern Bulgaria in late winter/early spring. Both of them are adult females with total body length 231 mm, and 219 mm. The two specimens recorded are the largest ones found in Bulgaria so far. Their dimensions are impressive for the entire range of the species. Both specimens have been found during the day in a sunny and dry weather, which has not been registered by other researchers in the cold half of the year in Bulgaria. The winter activity of the species has been confirmed.

  7. A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite.

    Science.gov (United States)

    Hone, David; Henderson, Donald M; Therrien, François; Habib, Michael B

    2015-01-01

    Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.

  8. A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite

    Directory of Open Access Journals (Sweden)

    David Hone

    2015-08-01

    Full Text Available Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.

  9. The isector: a simple and direct method for generating isotropic, uniform random sections from small specimens

    DEFF Research Database (Denmark)

    Nyengaard, Jens Randel; Gundersen, Hans Jørgen Gottlieb

    1992-01-01

    The very simple and strong principle of vertical sections devised by Baddeley et al. has been a major advance in stereology when any kind of anisotropy is present in the specimen under study. On the other hand, some important stereological estimators still require isotropic, uniform random sectio....... This paper deals with a simple technique for embedding specimens in rubber moulds with spherical cavities. After the embedding, any handling or the resulting sphere independent of the specimen will induce isotropy of the final histological sections....

  10. prospective mathematics and physics teachers

    African Journals Online (AJOL)

    prospective mathematics and physics teachers. Claudio Fazio and Filippo Spagnolo spagnolo@math.unipa.it. We present a study on the conceptions of Italian prospective mathematics and physics teachers with respect to modelling activities. Common ground for both the mathematician and the physicist, these activities are ...

  11. Agreement between self- and clinician-collected specimen results for detection and typing of high-risk human papillomavirus in specimens from women in Gugulethu, South Africa

    NARCIS (Netherlands)

    Jones, Heidi E.; Allan, Bruce R.; van de Wijgert, Janneke H. H. M.; Altini, Lydia; Taylor, Sylvia M.; de Kock, Alana; Coetzee, Nicol; Williamson, Anna-Lise

    2007-01-01

    We assessed the agreement in detection of high-risk human papillomavirus (HPV), as well as specific HPV types, between self- and clinician-obtained specimens for 450 women over 18 years of age attending a community health center in Gugulethu, South Africa. Both self-collected swabs and tampons had

  12. Routine calcium measurement is not necessary after most thyroid surgeries: a prospective clinical study.

    LENUS (Irish Health Repository)

    Quinn, E M

    2010-12-01

    Calcium levels are often measured to diagnose postoperative hypocalcaemia following thyroidectomy. The aims of this study were to (i) prospectively determine the incidence of symptomatic and biochemical hypocalcaemia following thyroidectomy, (ii) to identify if any associations exist between hypocalcaemia, type of surgery, histological diagnosis, specimen size\\/weight and the presence of histological parathyroid tissue and (iii) to evaluate the necessity of routine measurement of calcium levels following all thyroidectomies.

  13. Multi-Specimen Variable-G Facility for Life and Microgravity Sciences Research Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Techshot, Inc. proposes to develop a Multi-specimen Variable-G Facility (MVF) for life and microgravity sciences research. The MVF incorporates a generic...

  14. Protocols for the collection of fortuitous specimens : [Rocky Mountain Arsenal National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This protocol describes in detail every aspect of how fortuitous specimens from the Rocky Mountain Arsenal National Wildlife Refuge (Refuge) will be handled by the...

  15. Specimen and Genetic Information for Phylogeny of Blue-winged Ducks (Anas spp.), 2001-2011

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Data set containing specimen information and GenBank accession numbers for five nuclear DNA introns and mitochondrial DNA control region sequence information for the...

  16. INVESTIGATIONS TO IMPROVE THE TRANSFERABILITY OF SPECIMEN RESULTS BY REAL COMPONENT

    Directory of Open Access Journals (Sweden)

    Martin Riedler

    2010-12-01

    Full Text Available For the improvement of the lifetime calculation of components made of the titanium alloy Ti-6-4, a closed loop methodology from specimen to the component is presented. Based on forged pre-material specimens fatigue tests are done as a basic research, which are presented as S/N-curves. With the determined material data a lifetime calculation with the program FEMFAT is done on a typically fitting element. Finally the results of the lifetime calculation are compared to real component tests, which are done to evaluate the results of the lifetime calculation. The component tests are performed with constant and variable load. Therewith the transferability of specimen results to real components is shown. Additional fracture analysis by light microscope and scanning electron microscope is carried out to give further information of the influence factor of the lifetime and a further description between fracture behaviour of specimen and components.

  17. Generation of R-Curve from 4ENF Specimens: An Experimental Study

    Directory of Open Access Journals (Sweden)

    V. Alfred Franklin

    2014-01-01

    Full Text Available The experimental determination of the resistance to delamination is very important in aerospace applications as composite materials have superior properties only in the fiber direction. To measure the interlaminar fracture toughness of composite materials, different kinds of specimens and experimental methods are available. This article examines the fracture energy of four-point end-notched flexure (4ENF composite specimens made of carbon/epoxy and glass/epoxy. Experiments were conducted on these laminates and the mode II fracture energy, GIIC, was evaluated using compliance method and was compared with beam theory solution. The crack growth resistance curve (R-curve for these specimens was generated and the found glass/epoxy shows higher toughness values than carbon/epoxy composite. From this study, it was observed that R-curve effect in 4ENF specimens is quite mild, which means that the measured delamination toughness, GIIC, is more accurate.

  18. HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

    Science.gov (United States)

    Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

    2015-12-01

    The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Application of Iosipescu specimen geometry to determination of shear strength in unidirectional composites

    Science.gov (United States)

    Hurwitz, F. I.; Behrendt, D. R.

    1984-01-01

    The Iosipescu (1967) test method, in conjunction with a finite element analysis of anisotropic, unidirectionally reinforced composite specimens, can be used to derive composite shear strength values despite the small size of the samples used. When such a specimen is loaded parallel to the fiber direction, fracture occurs by shear within a narrow region near the center of the specimen; this is consistent with the maximum shear area determined by finite element analysis. The resulting fracture surface, as observed, is characteristic of shear failure, occurring either within the matrix or at the fiber-matrix interface. Problems of compressive and mixed mode failure which accrue to short beam shear specimens are by the present method precluded.

  20. Growth behavior of fatigue cracks in ultrafine grained Cu smooth specimens with a small hole

    National Research Council Canada - National Science Library

    Masahiro Goto; Kakeru Morita; Junichi Kitamura; Takaei Yamamoto; Masataka Baba; Seung-zeon Han; Sangshik Kim

    2015-01-01

      In order to study the growth mechanism of fatigue cracks in ultrafine grained copper, stresscontrolled fatigue tests of round-bar specimens with a small blind hole as a crack starter were conducted...

  1. Biomarker Testing in Lung Carcinoma Cytology Specimens: A Perspective From Members of the Pulmonary Pathology Society.

    Science.gov (United States)

    Roy-Chowdhuri, Sinchita; Aisner, Dara L; Allen, Timothy Craig; Beasley, Mary Beth; Borczuk, Alain; Cagle, Philip T; Capelozzi, Vera; Dacic, Sanja; da Cunha Santos, Gilda; Hariri, Lida P; Kerr, Keith M; Lantuejoul, Sylvie; Mino-Kenudson, Mari; Moreira, Andre; Raparia, Kirtee; Rekhtman, Natasha; Sholl, Lynette; Thunnissen, Eric; Tsao, Ming Sound; Vivero, Marina; Yatabe, Yasushi

    2016-04-15

    The advent of targeted therapy in lung cancer has heralded a paradigm shift in the practice of cytopathology with the need for accurately subtyping lung carcinoma, as well as providing adequate material for molecular studies, to help guide clinical and therapeutic decisions. The variety and versatility of cytologic-specimen preparations offer significant advantages to molecular testing; however, they frequently remain underused. Therefore, evaluating the utility and adequacy of cytologic specimens is critical, not only from a lung cancer diagnosis standpoint but also for the myriad ancillary studies that are necessary to provide appropriate clinical management. A large fraction of lung cancers are diagnosed by aspiration or exfoliative cytology specimens, and thus, optimizing strategies to triage and best use the tissue for diagnosis and biomarker studies forms a critical component of lung cancer management. This review focuses on the opportunities and challenges of using cytologic specimens for molecular diagnosis of lung cancer and the role of cytopathology in the molecular era.

  2. Elastic compliance of single-edge-notched tension SE(T (or SENT specimens

    Directory of Open Access Journals (Sweden)

    B. Tyson

    2014-10-01

    Full Text Available There has been a trend recently to use specimen geometries for toughness measurement that are more representative of actual flaw geometries in service. A prominent example is the use of single-edge-notched tension specimens for assessment of surface flaws in pipelines. To obtain a resistance (R curve, i.e. J-integral or CTOD as a function of crack growth, it is necessary to monitor the crack size as a function of J or CTOD. To facilitate obtaining these data from a single specimen, the elastic CMOD unloading compliance C has been used in several testing programs to estimate crack size. C is a function of several variables in addition to crack size – notably, specimen constraint (plane stress or plane strain. In this paper, the dependence of C on these variables will be discussed.

  3. Multifunctional TEM-specimen holder equipped with a piezodriving probe and an electron irradiation port.

    Science.gov (United States)

    Shindo, Daisuke; Suzuki, Satoshi; Sato, Kuniaki; Akase, Zentaro; Murakami, Yasukazu; Yamazaki, Kazuya; Ikeda, Yuuta; Fukuda, Tomohisa

    2013-08-01

    The charging effect due to electron irradiation in an electron microscope has been studied so far with incident electrons. Here we report on a new specimen holder to control the charging effect by using electrons emitted from an irradiation port in the holder while maintaining a constant intensity of the incident electron beam. Details of the charging effect, such as electric field variation, are expected to be investigated by electron holography. The new specimen holder was developed by modifying a double-probe piezodriving specimen holder to introduce an electron irradiation port in one of its two arms. As a result, the new modified specimen holder consists of a piezodriving probe and an electron irradiation port, both of which can be controlled in three dimensions, using piezoelectric elements and micrometers. We demonstrate that variations in the charging effect for epoxy resin and surface contamination can be observed by electron holography.

  4. Reports of envenomation by brown recluse spiders exceed verified specimens of Loxosceles spiders in South Carolina.

    Science.gov (United States)

    Frithsen, Ivar L; Vetter, Richard S; Stocks, Ian C

    2007-01-01

    To determine whether the number of brown recluse spider bites diagnosed by South Carolina physicians coincides with evidence of brown recluse spiders found in the state. Brown recluse spider bite diagnosis data were extracted from 1990 and 2004 surveys of South Carolina physicians. This was compared with the known historical evidence of brown recluse spiders collected in South Carolina and derived from various sources, including state agencies, arachnologists, and museum specimens. South Carolina physicians diagnosed 478 brown recluse spider bites in 1990 and 738 in 2004. Dating to 1953, 44 brown recluse spider specimens have been verified from 6 locations in South Carolina. The number of brown recluse bites reportedly diagnosed in South Carolina greatly outnumbers the verified brown recluse specimens that have been collected in the state. The pattern of bite diagnoses outnumbering verified brown recluse specimens has been reported in other areas outside of this spider's known endemic range.

  5. Radiofrequency identification specimen tracking in anatomical pathology: pilot study of 1067 consecutive prostate biopsies.

    Science.gov (United States)

    Bostwick, David G

    2013-10-01

    Improved methods such as radiofrequency identification (RFID) are needed to optimize specimen tracking in anatomical pathology. We undertook a study of RFID in an effort to optimize specimen tracking and patient identification, including the following: (1) creation of workflow process maps, (2) evaluation of existing RFID hardware technologies, (3) creation of Web-based software to support the RFID-enabled workflow, and (4) assessment of the impact with a series of prostate biopsies. We identified multiple steps in the workflow process in which RFID enhanced specimen tracking. Multiple product choices were found that could withstand the harsh heat and chemical environments encountered in pathology processing, and software that was compatible with our laboratory information system was designed in-house. A total of 1067 prostate biopsies were received, and 78.3% were successfully processed with the RFID system. Radiofrequency identification allowed dynamic specimen tracking throughout the workflow process in anatomical pathology. Copyright © 2013. Published by Elsevier Inc.

  6. A Technique for Measurement of Insulating Powder Specimens by Secondary Ion Mass Spectrometry

    National Research Council Canada - National Science Library

    MORIKAWA, Hisashi; UWAMINO, Yoshinori; ISHIZUKA, Toshio

    1991-01-01

    ...). An insulating specimen buried in a circular hole on a conducting disk was measured by using a standard Cameca IMS-3F ion microscope under the normal working conditions with a negatively charged oxygen primary beam...

  7. A new approach to standardize multicenter studies: mobile lab technology for the German Environmental Specimen Bank

    National Research Council Canada - National Science Library

    Lermen, Dominik; Schmitt, Daniel; Bartel-Steinbach, Martina; Schröter-Kermani, Christa; Kolossa-Gehring, Marike; von Briesen, Hagen; Zimmermann, Heiko

    2014-01-01

    .... Annually the German Environmental Specimen Bank (ESB) collects, characterizes, and stores blood, plasma, and urine samples of 120-150 volunteers each on four different sampling sites in Germany...

  8. Effects of loading sequence for notched specimens under high-low two-step fatigue loading

    Science.gov (United States)

    Crews, J. H., Jr.

    1971-01-01

    The effects of loading sequence on crack-initiation period were investigated for notched aluminum-alloy specimens under high-low two-step loading with special emphasis on local cyclic stresses and strains at the notch root. Local stress and strain were determined by a procedure based on an equation proposed by Neuber which relates elastoplastic stress and strain at a notch. Local stress and strain were also measured experimentally to verify the Neuber equation. The effects of initial high load on the crack-initiation periods were demonstrated with notched specimens and were simulated in unnotched specimens fatigue tested with local stress sequences. An analysis of the results indicated that sequence effects were not caused solely by local residual stresses, as is usually assumed; the existence of a damaging effect, resulting from the high local strain cycles, was demonstrated. The sequence effects observed with notched specimens were interpreted as the combined result of residual stresses and high local strain cycles.

  9. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species

    Science.gov (United States)

    Min Yu; Lichao Jiao; Juan Guo; Alex C. Wiedenhoeft; Tuo He; Xiaomei Jiang; Yafang Yin

    2017-01-01

    ITS2+trnH-psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens.

  10. Standard practice for preparation and use of direct tension stress-corrosion test specimens

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    1985-01-01

    1.1 This practice covers procedures for designing, preparing, and using ASTM standard tension test specimens for investigating susceptibility to stress-corrosion cracking. Axially loaded specimens may be stressed quantitatively with equipment for application of either a constant load, constant strain, or with a continuously increasing strain. 1.2 Tension test specimens are adaptable for testing a wide variety of product forms as well as parts joined by welding, riveting, or various other methods. 1.3 The exposure of specimens in a corrosive environment is treated only briefly because other standards are being prepared to deal with this aspect. Meanwhile, the investigator is referred to Practices G35, G36, G37, and G44, and to ASTM Special Technical Publication 425 (1).

  11. Stress analysis of the cracked lap shear specimens: An ASTM round robin

    Science.gov (United States)

    Johnson, W. S.

    1986-01-01

    This ASTM Round Robin was conducted to evaluate the state of the art in stress analysis of adhesively bonded joint specimens. Specifically, the participants were asked to calculate the strain-energy-release rate for two different geometry cracked lap shear (CLS) specimens at four different debond lengths. The various analytical techniques consisted of 2- and 3-dimensional finite element analysis, beam theory, plate theory, and a combination of beam theory and finite element analysis. The results were examined in terms of the total strain-energy-release rate and the mode I to mode II ratio as a function of debond length for each specimen geometry. These results basically clustered into two groups: geometric linear or geometric nonlinear analysis. The geometric nonlinear analysis is required to properly analyze the CLS specimens. The 3-D finite element analysis gave indications of edge closure plus some mode III loading. Each participant described his analytical technique and results. Nine laboratories participated.

  12. Stress analysis of the cracked-lap-shear specimen - An ASTM round-robin

    Science.gov (United States)

    Johnson, W. S.

    1987-01-01

    This ASTM Round Robin was conducted to evaluate the state of the art in stress analysis of adhesively bonded joint specimens. Specifically, the participants were asked to calculate the strain-energy-release rate for two different geometry cracked lap shear (CLS) specimens at four different debond lengths. The various analytical techniques consisted of 2- and 3-dimensional finite element analysis, beam theory, plate theory, and a combination of beam theory and finite element analysis. The results were examined in terms of the total strain-energy-release rate and the mode I to mode II ratio as a function of debond length for each specimen geometry. These results basically clustered into two groups: geometric linear or geometric nonlinear analysis. The geometric nonlinear analysis is required to properly analyze the CLS specimens. The 3-D finite element analysis gave indications of edge closure plus some mode III loading. Each participant described his analytical technique and results. Nine laboratories participated.

  13. Investigation of Entamoeba histolytica in stool specimens by ELISA during a year

    Directory of Open Access Journals (Sweden)

    Mehmet Sinan Dal

    2011-03-01

    Full Text Available The aim of this study was to investigate Entamoebahistolytica in the stool samples that have beensent to microbiology laboratory by ELISA method.Materials and methods: This study was performed on800 stool specimens belonging to different age groupsand different patients sent to Microbiology Laboratory ofa State Hospital between January 2009 and December2009.Results: In this study Entamoeba histolytica/dispar cystsand/or trophozoites were observed in 31 (3.9% out of atotal of 800 stool specimens which were examined bynative-lugol. Entamoeba histolytica specific antigen wasinvestigated by ELISA in all stool specimens. Entamoebahistolytica specific antigen was detected in 12 (1.5% ofthese stool specimens. The diagnosis of amoebiasis forthe patients whose ELISA tests were “positive” and appropriatetherapy was begun.Conclusion: Entamoeba histolytica in the stool samplesshould be investigated and unnecessary treatmentsshould not given to patients. J Clin Exp Invest 2011; 2(1:50-54

  14. Multi-Specimen Variable-G Facility for Life and Microgravity Sciences Research Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Multi-specimen Variable-G Facility (MVF) is a single locker sized centrifuge facility for life and microgravity sciences research on the International Space...

  15. Sources of Bias in Specimens for Research About Molecular Markers for Cancer

    National Research Council Canada - National Science Library

    David F. Ransohoff; Margaret L. Gourlay

    2010-01-01

    .... This article describes a framework to help simplify and organize current problems in marker research by focusing on the role of specimens as a source of bias in observational research and using...

  16. Evaluation of three types of cell culture for recovery of adenovirus from clinical specimens.

    Science.gov (United States)

    Krisher, K K; Menegus, M A

    1987-07-01

    The performance characteristics of HEK, HDF, and MK cells for adenovirus isolation were examined for eye and respiratory tract specimens. HEK cells were superior to HDF and MK cells in terms of both speed of virus detection and sensitivity.

  17. Minimally invasive surgical technique integrating multiple procedures with large specimen extraction via inguinal hernia orifice.

    Science.gov (United States)

    Mani, Vishnu R; Ahmed, Leaque

    2015-12-24

    While laparoscopic surgery can be performed using small skin incisions, any resected specimen must still be able to fit through these opening. For procedures, such as cholecystectomies and appendectomies, this is not usually a problem; however, for large specimens such as bowel or large tumors, this becomes problematic. Currently, the standard technique is to attempt piecemeal removal of the specimen or enlarge one of the laparoscopic incisions, effectively creating a mini laparotomy. Creating a larger incision adds many of the drawbacks of open laparotomy and should be avoided whenever possible. In this article, we present a new technique of combining the repair of an inguinal hernia, umbilical hernia with a duodenal tumor resection in order to extract the specimen through the inguinal hernia orifice. Published by Oxford University Press and JSCR Publishing Ltd. All rights reserved. © The Author 2015.

  18. A Specimen Size Effect on the Fatigue Crack Growth Rate Threshold of IN 718

    Science.gov (United States)

    Garr, K. R.; Hresko, G. C., III

    1998-01-01

    Fatigue crack growth rate (FCGR) tests were conducted on IN 718 in the solution annealed and aged condition at room temperature in accordance with E647-87. As part of each test, the FCGR threshold was measured using the decreasing Delta K method. A new heat of material was being tested and some of this material was sent to a different laboratory which wanted to use a specimen with a 127 mm width. Threshold data previously had been established on specimens with a width of 50.8 mm. As a check of the laboratory, tests were conducted at room temperature and R equal to 0.1 for comparison with the earlier data. The results were a threshold significantly higher than previously observed. Interchanging of specimen sizes and laboratories showed that the results were not due to a heat-to-heat or lab-to-lab variation. The results to be presented here are those obtained at the original laboratory. Growth rates were measured using the electric potential drop technique at R values of 0.1, 0.7, and 0.9. Compact tension specimen sizes with planer dimensions of 25.4 mm, 50.8 mm, and 127 mm were used. Crack growth rates at threshold were generally below 2.5 X 10(exp -8) mm / cycle. Closure measurements were made on some of the specimens by a manual procedure using a clip gage. When the crack growth rate data for the specimens tested at R equal to 0.1 were plotted as a function of applied Delta K, the thresholds varied with specimen width. The larger the width, the higher the threshold. The thresholds varied from 6.5 MPa-m(exp 1/2) for the 25.4 mm specimen to 15.4 MPa-m(exp 1/2) for the 127 mm specimen. At R equal to 0.7, the 25.4 mm and 50.8 mm specimens had essentially the same threshold, about 2.9 MPa-m(exp 1/2)while the 127 mm specimen had a threshold of 4.5 MPa-m(exp 1/2). When plotted as a function of effective Delta K, the R equal to 0.1 data are essentially normalized. Various aspects of the test procedure will be discussed as well as the results of analysis of the data using

  19. An Experimental Study of Shear-Dominated Failure in the 2013 Sandia Fracture Challenge Specimen

    Energy Technology Data Exchange (ETDEWEB)

    Corona, Edmundo [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Deibler, Lisa Anne [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Reedlunn, Benjamin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ingraham, Mathew Duffy [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Williams, Shelley [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-04-01

    This report presents an experimental study motivated by results obtained during the 2013 Sandia Fracture Challenge. The challenge involved A286 steel, shear-dominated compression specimens whose load-deflection response contained a load maximum fol- lowed by significant displacement under decreasing load, ending with a catastrophic fracture. Blind numerical simulations deviated from the experiments well before the maximum load and did not predict the failure displacement. A series of new tests were conducted on specimens machined from the original A286 steel stock to learn more about the deformation and failure processes in the specimen and potentially improve future numerical simulations. The study consisted of several uniaxial tension tests to explore anisotropy in the material, and a set of new tests on the compression speci- men. In some compression specimen tests, stereo digital image correlation (DIC) was used to measure the surface strain fields local to the region of interest. In others, the compression specimen was loaded to a given displacement prior to failure, unloaded, sectioned, and imaged under the microscope to determine when material damage first appeared and how it spread. The experiments brought the following observations to light. The tensile tests revealed that the plastic response of the material is anisotropic. DIC during the shear- dominated compression tests showed that all three in-plane surface strain components had maxima in the order of 50% at the maximum load. Sectioning of the specimens revealed no signs of material damage at the point where simulations deviated from the experiments. Cracks and other damage did start to form approximately when the max- imum load was reached, and they grew as the load decreased, eventually culminating in catastrophic failure of the specimens. In addition to the steel specimens, a similar study was carried out for aluminum 7075-T651 specimens. These specimens achieved much lower loads and displacements

  20. Anterolateral Ligament of the Knee Shows Variable Anatomy in Pediatric Specimens.

    Science.gov (United States)

    Shea, Kevin G; Milewski, Matthew D; Cannamela, Peter C; Ganley, Theodore J; Fabricant, Peter D; Terhune, Elizabeth B; Styhl, Alexandra C; Anderson, Allen F; Polousky, John D

    2017-06-01

    Anterior cruciate ligament (ACL) reconstruction failure rates are highest in youth athletes. The role of the anterolateral ligament in rotational knee stability is of increasing interest, and several centers are exploring combined ACL and anterolateral ligament reconstruction for these young patients. Literature on the anterolateral ligament of the knee is sparse in regard to the pediatric population. A single study on specimens younger than age 5 years demonstrated the presence of the anterolateral ligament in only one of eight specimens; therefore, much about the prevalence and anatomy of the anterolateral ligament in pediatric specimens remains unknown. We sought to (1) investigate the presence or absence of the anterolateral ligament in prepubescent anatomic specimens; (2) describe the anatomic relationship of the anterolateral ligament to the lateral collateral ligament; and (3) describe the anatomic relationship between the anterolateral ligament and the physis. Fourteen skeletally immature knee specimens (median age, 8 years; range, 7-11 years) were dissected (12 male, two female specimens). The posterolateral structures were identified in all specimens, including the lateral collateral ligament and popliteus tendon. The presence or absence of the anterolateral ligament was documented in each specimen, along with origin, insertion, and dimensions, when applicable. The relationship of the anterolateral ligament origin to the lateral collateral ligament origin was recorded. The anterolateral ligament was identified in nine of 14 specimens. The tibial attachment point was consistently located in the same region on the proximal tibia, between the fibular head and Gerdy's tubercle; however, the femoral origin of the anterolateral ligament showed considerable variation with respect to the lateral collateral ligament origin. The median femoral origin of the anterolateral ligament was 10 mm (first interquartile 6 mm, third interquartile 13) distal to the distal

  1. Ideal number of biopsy tumor fragments for predicting HER2 status in gastric carcinoma resection specimens

    Science.gov (United States)

    Lee, Minju; Ha, Sang Yun; Lee, Hyuk; Min, Byung-Hoon; Lee, Jun Haeng; Kim, Jae J.; Choi, Sunkyu; Jung, Sin-Ho; Choi, Min Gew; Lee, Jun-Ho; Sohn, Tae Sung; Bae, Jae Moon; Kim, Sung; Kim, Kyoung-Mee

    2015-01-01

    Intratumoral heterogeneity of HER2 expression is common in gastric cancers and pose a challenge for identifying patients who would benefit from anti-HER2 therapy. The aim of this study is to compare HER2 expression in biopsy and resection specimens of gastric carcinoma by immunohistochemistry (IHC) and to find the ideal number of biopsy tumor fragments that can accurately predict HER2 overexpression in the corresponding surgically resected specimen. The HER2 IHC results of 702 paired biopsy and resection specimens of gastric cancer were compared. The mean number of biopsy fragments among all cases was 4.3 (range 1–11). HER2 was positive in 130 (18.5%) endoscopic biopsies and in 102 (14.5%) gastrectomy specimens. Intratumoral heterogeneity of HER2 was found in 80 (61.5%) biopsies and 70 (68.6%) resection specimens. Out of the 70 surgical specimens with intratumoral heterogeneity, 24 (34.3%) of the corresponding biopsies were categorized as negative (positive conversion). In the 86 (12.3%) discrepant cases, negative conversion was observed in 57 (66.3%) cases and positive conversion in 29 (33.7%). The fragment numbers were significantly correlated with the discrepancy of results and positive predictability (P = 0.0315 and P = 0.0052). ROC curve analysis and positive predictability showed that 4 fragments should be obtained to minimize the differences in HER2 scores between biopsy and resection specimen. In gastric carcinomas with discrepant HER2 results between biopsy and surgical resection specimens, intratumoral heterogeneity is common with most of them showing positive conversion. To predict HER2 status precisely, at least 4 biopsy fragments containing tumor cells are required. PMID:26460823

  2. An inset CT specimen for evaluating fracture in small samples of material.

    Science.gov (United States)

    Yahyazadehfar, M; Nazari, A; Kruzic, J J; Quinn, G D; Arola, D

    2014-02-01

    In evaluations on the fracture behavior of hard tissues and many biomaterials, the volume of material available to study is not always sufficient to apply a standard method of practice. In the present study an inset Compact Tension (inset CT) specimen is described, which uses a small cube of material (approximately 2×2×2mm(3)) that is molded within a secondary material to form the compact tension geometry. A generalized equation describing the Mode I stress intensity was developed for the specimen using the solutions from a finite element model that was defined over permissible crack lengths, variations in specimen geometry, and a range in elastic properties of the inset and mold materials. A validation of the generalized equation was performed using estimates for the fracture toughness of a commercial dental composite via the "inset CT" specimen and the standard geometry defined by ASTM E399 (2006). Results showed that the average fracture toughness obtained from the new specimen (1.23±0.02MPam(0.5)) was within 2% of that from the standard. Applications of the inset CT specimen are presented for experimental evaluations on the crack growth resistance of dental enamel and root dentin, including their fracture resistance curves. Potential errors in adopting this specimen are then discussed, including the effects of debonding between the inset and molding material on the estimated stress intensity distribution. Results of the investigation show that the inset CT specimen offers a viable approach for studying the fracture behavior of small volumes of structural materials. © 2013 Elsevier Ltd. All rights reserved.

  3. Evaluation of DNA Extraction and PCR Methods for Detection of Enterocytozoon bienuesi in Stool Specimens

    OpenAIRE

    Subrungruang, Ittisak; Mungthin, Mathirut; Chavalitshewinkoon-Petmitr, Porntip; Rangsin, Ram; Naaglor, Tawee; Leelayoova, Saovanee

    2004-01-01

    An evaluation of the sensitivities of three DNA extraction methods, i.e., FTA filter paper, a QIAamp stool mini kit, and a conventional phenol-chloroform method, by using specimens with known concentrations of Enterocytozoon bieneusi spores was performed. FTA filter paper and the QIAamp stool mini kit were the most sensitive methods, which could detect E. bieneusi in specimens with a concentration of 800 spores/ml. We also compared five previously described PCR methods that use five different...

  4. Face compression yield strength of the copper-Inconel composite specimen

    Energy Technology Data Exchange (ETDEWEB)

    Horie, T.

    1987-05-01

    A new equation for the face compression yield strength of copper-Inconel composite material has been derived. Elastic-plastic finite element analyses were also made for composite specimens with various aspect ratios to examine the edge effect of the specimen. According to the results of both the new equation and the analyses, the face compression yield strength of the composite should be decreased by about 25% from the value obtained with Becker's equation.

  5. Cell Block Preparation from Cytology Specimen with Predominance of Individually Scattered Cells

    OpenAIRE

    Varsegi, George M.; Shidham, Vinod

    2009-01-01

    This video demonstrates Shidham's method for preparation of cell blocks from liquid based cervicovaginal cytology specimens containing individually scattered cells and small cell groups. This technique uses HistoGel (Thermo Scientific) with conventional laboratory equipment. The use of cell block sections is a valuable ancillary tool for evaluation of non-gynecologic cytology. They enable the cytopathologist to study additional morphologic specimen detail including the architecture of the les...

  6. Mongolian Rotifers on Micr oscope Slides: Instructions to Permanent Specimen Mounts from Expedition Material

    Directory of Open Access Journals (Sweden)

    Christian D. Jersabek

    2010-06-01

    Full Text Available We here describe a method for permanently mounting specimens on microscope slides, as we applied it in the newly established rotifer collection in Ulaanbaatar, Mongolia. The liquid photopolymer NOA 61 was used as a primary sealant for pure glycerine mounts. We furthermore outline simple methods of rotifer narcotization and fi xation in the fi eld that yield, for the majority of species, adequately preserved specimen material for further preparation and identifi cation purposes.

  7. Observation of fracture behavior of 3-D printed specimens under rolling contact fatigue in water

    Directory of Open Access Journals (Sweden)

    Mizobe Koshiro

    2017-01-01

    Full Text Available Polymer bearing was widely used in the corrosive conditions because of its high corrosion durability. The polymer bearing had been formed using molding and machining until the new 3-D printing method was developed. In this study, we performed the rolling contact fatigue tests of the 3-D printed specimens in water and observed the fracture behaviour of the specimens. We found that the surface cracks are related to both the rolling direction and the lamination directions.

  8. A new slurry-based method of preparation of specimens of sand containing fines

    OpenAIRE

    Carraro, JAH; Prezzi, M

    2007-01-01

    A new method of specimen reconstitution is presented that is appropriate for element testing of sands containing either plastic or nonplastic fines. The method allows reconstitution of homogeneous, saturated specimens of sands containing fines whose stress-strain response closely resembles the stress-strain response of natural soil deposits formed underwater (e.g., alluvial and offshore submarine deposits, hydraulic fills, and tailings dams). A procedure is described to evaluate the maximum v...

  9. A NOVEL METHOD FOR COLORING AND LABELING SPECIMENS IN THE ANATOMY MUSEUM

    OpenAIRE

    Prabhu,Latha V.; Mangala M Pai; Divya Premchandran; Rajanigandha Vadgaonkar; Murlimanju B.V

    2015-01-01

    Introduction: In today’s medical educational programs in various institutes anatomy is an essential part of the curriculum in the first year of the medical course. An attractive and innovative anatomical museum forms a vital role in furthering the interest and educating a medical student. Once a specimen has undergone fixation it is essential to color and label the specimens in order to ensure better visualization of required structures and for its proper placement in the museum. Material...

  10. Influence at Work Distance between the Sonotrode and Specimen to Cavitational Erosion

    Directory of Open Access Journals (Sweden)

    Relu-Costel Ciubotariu

    2015-07-01

    Full Text Available The paper presents the results of cavitation erosion tests performed on five samples from pure aluminum using the vibratory method with stationary specimen. The main purpose of this research is for determine which is the distance between the sonotrode and specimen favorable for an aggressive cavitational attack. For this, has been calculated the Mean Depth of Erosion (MDE and the cavitation erosion rate (Vec. After that the specific curve for Vec has been analytically processed.

  11. Mixed mode fracture toughness characterization of sandwich interfaces using the modified TSD specimen

    DEFF Research Database (Denmark)

    Berggreen, Christian; Andreasen, J.H.; Carlsson, L.A.

    2009-01-01

    An extensive parametric analysis shows that the modified Tilted Sandwich Debond (TSD) specimen provides a methodology for characterization of the face/core fracture resistance over a range of mode-mixities. A pilot experimental mixed mode characterization of the fracture toughness of sandwich spe...... specimens, with composite faces and various PVC foam cores spanning a range of phase angles, has been achieved by specific steel bar reinforcements and testing over a range of tilt angles....

  12. Alkaline decontamination of sputum specimens adversely affects stability of mycobacterial mRNA.

    OpenAIRE

    Desjardin, L E; Perkins, M D; Teixeira, L; Cave, M D; Eisenach, K D

    1996-01-01

    Reverse transcriptase PCR (RT-PCR) is an important tool for Mycobacterium tuberculosis research and diagnostics. A standard procedure using N-acetyl-L-cysteine (NALC) and NaOH has been widely adopted for digestion and decontamination of sputum specimens for mycobacterial culture. The objective of this study was to determine the compatibility of this method with the recovery of RNA for RT-PCR assays. Nineteen sputum specimens were collected from smear-positive, pretreatment tuberculosis patien...

  13. Quantitative urine confirmatory testing for synthetic cannabinoids in randomly collected urine specimens.

    Science.gov (United States)

    Castaneto, Marisol S; Scheidweiler, Karl B; Gandhi, Adarsh; Wohlfarth, Ariane; Klette, Kevin L; Martin, Thomas M; Huestis, Marilyn A

    2015-06-01

    Synthetic cannabinoid intake is an ongoing health issue worldwide, with new compounds continually emerging, making drug testing complex. Parent synthetic cannabinoids are rarely detected in urine, the most common matrix employed in workplace drug testing. Optimal identification of synthetic cannabinoid markers in authentic urine specimens and correlation of metabolite concentrations and toxicities would improve synthetic cannabinoid result interpretation. We screened 20 017 randomly collected US military urine specimens between July 2011 and June 2012 with a synthetic cannabinoid immunoassay yielding 1432 presumptive positive specimens. We analyzed all presumptive positive and 1069 negative specimens with our qualitative synthetic cannabinoid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, which confirmed 290 positive specimens. All 290 positive and 487 randomly selected negative specimens were quantified with the most comprehensive urine quantitative LC-MS/MS method published to date; 290 specimens confirmed positive for 22 metabolites from 11 parent synthetic cannabinoids. The five most predominant metabolites were JWH-018 pentanoic acid (93%), JWH-N-hydroxypentyl (84%), AM2201 N-hydroxypentyl (69%), JWH-073 butanoic acid (69%), and JWH-122 N-hydroxypentyl (45%) with 11.1 (0.1-2,434), 5.1 (0.1-1,239), 2.0 (0.1-321), 1.1 (0.1-48.6), and 1.1 (0.1-250) µg/L median (range) concentrations, respectively. Alkyl hydroxy and carboxy metabolites provided suitable biomarkers for 11 parent synthetic cannabinoids; although hydroxyindoles were also observed. This is by far the largest data set of synthetic cannabinoid metabolites urine concentrations from randomly collected workplace drug testing specimens rather than acute intoxications or driving under the influence of drugs. These data improve the interpretation of synthetic cannabinoid urine test results and suggest suitable urine markers of synthetic cannabinoid intake. This article is a U

  14. Analytical performance of cervista HPV 16/18 in SurePath pap specimens.

    Science.gov (United States)

    Guo, Ming; Khanna, Abha; Feng, Jie; Patel, Shobha; Zhang, Wei; Gong, Yun; Huo, Lei; Staerkel, Gregg

    2015-04-01

    To evaluate the performance of Cervista HPV 16/18 in SurePath specimens, we compared the analytical sensitivity of Cervista HPV 16/18 with that of a previously validated PCR-based, commercially available HPV genotyping assay, EasyChip HPV Blot, in residual specimens collected after routine Pap tests at our cancer center. We retrospectively selected 79 consecutive Cervista HPV HR (high risk)-positive SurePath residual Pap specimens. The cytology results for these specimens comprised 42 negative, 22 ASC-US/ASC-H, 10 low-grade squamous intraepithelial lesions, and 5 high-grade squamous intraepithelial lesions. HPV 16/18 genotypes of the 79 specimens were analyzed by Cervista HPV 16/18 assay and EasyChip genotyping assay and compared with the patient's follow-up results. Of the 79 cases, 33 (42%) were positive for HPV16/18 by Cervista HPV 16/18 and 37 (47%) were positive by EasyChip. The overall agreement between the 2 assays, at 85% (67/79), was good (kappa = 0.698, 95% CI: 0.541-0.855). In the 65 patients with follow-up results, the sensitivity for predicting cervical intraepithelial neoplasia grade 2 or higher (CIN2+) was 77% for Cervista HPV 16/18 assay and 69% for EasyChip. The predictive values for CIN2+ in cases stratified by Pap results were highly consistent between the Cervista HPV16/18 and EasyChip assays; there was one false negative HPV16 result, in a specimen identified as NILM by EasyChip. Our findings support use of the Cervista HPV 16/18 assay for HPV16/18 genotyping in SurePath Pap specimens. However, further studies of larger cohorts with clinical follow-up data are required to verify the efficacy of Cervista HPV16/18 assay in SurePath Pap specimens. © 2014 Wiley Periodicals, Inc.

  15. Correlation between strength properties in standard test specimens and molded phenolic parts

    Science.gov (United States)

    Turner, P S; Thomason, R H

    1946-01-01

    This report describes an investigation of the tensile, flexural, and impact properties of 10 selected types of phenolic molding materials. The materials were studied to see in what ways and to what extent their properties satisfy some assumptions on which the theory of strength of materials is based: namely, (a) isotropy, (b) linear stress-strain relationship for small strains, and (c) homogeneity. The effect of changing the dimensions of tensile and flexural specimens and the span-depth ratio in flexural tests were studied. The strengths of molded boxes and flexural specimens cut from the boxes were compared with results of tests on standard test specimens molded from the respective materials. The nonuniformity of a material, which is indicated by the coefficient of variation, affects the results of tests made with specimens of different sizes and tests with different methods of loading. The strength values were found to depend on the relationship between size and shape of the molded specimen and size and shape of the fillers. The most significant variations observed within a diversified group of materials were found to depend on the orientation of fibrous fillers. Of secondary importance was the dependence of the variability of test results on the pieces of filler incorporated into the molding powder as well as on the size of the piece. Static breaking strength tests on boxes molded from six representative phenolic materials correlated well with falling-ball impact tests on specimens cut from molded flat sheets. Good correlation was obtained with Izod impact tests on standard test specimens prepared from the molding materials. The static breaking strengths of the boxes do not correlate with the results of tensile or flexural tests on standard specimens.

  16. Status of lithium-filled specimen subcapsules for the HFIR-MFE-RB10J experiment

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, J.P.; Howell, M.; Lenox, K.E. [Oak Ridge National Lab., TN (United States)

    1998-09-01

    The HFIR-MFE-RB-10J experiment will be irradiated in a Removable Beryllium position in the HFIR for 10 reactor cycles, accumulating approximately 5 dpa in steel. The upper region of the capsule contains two lithium-filled subcapsules containing vanadium specimens. This report describes the techniques developed to achieve a satisfactory lithium fill with a specimen occupancy of 26% in each subcapsule.

  17. STS-40 crewmembers remove specimens from SLS-1 Rack 9 Refrigerator / Freezer

    Science.gov (United States)

    1991-01-01

    STS-40 crewmembers remove specimens from the Spacelab Life Sciences 1 (SLS-1) module Rack 9 Refrigerator / Freezer after problems with the refrigerator were discovered. Mission Specialist (MS) Tamara E. Jernigan (right) balances two trays of specimens as MS James P. Bagian investigates the source of the problem in the SLS-1 Refrigerator / Freezer unit. The SLS-1 module is located in Columbia's, Orbiter Vehicle (OV) 102's, payload bay (PLB) and is connected to the crew compartment via a spacelab (SL) tunnel.

  18. The clinical and economic implications of specimen provenance complications in diagnostic prostate biopsies.

    Science.gov (United States)

    Wojno, Kirk; Hornberger, John; Schellhammer, Paul; Dai, Minghan; Morgan, Travis

    2015-04-01

    Inaccurate diagnoses of prostate cancer can result from transposition or contamination of patient biopsy specimens, which are known as specimen provenance complications. We assessed the clinical and economic burden of specimen provenance complications in prostate biopsies in the United States. We performed a comprehensive, systematic review of the literature to approximate the effect of specimen provenance complications on direct medical costs, patient QALYs and medicolegal costs. Data were extracted from published studies on specimen provenance complications rates, prostate cancer treatment efficacy, treatment cost, litigation/settlement costs after false diagnoses of prostate biopsies and patient quality of life. Sensitivity analysis was done to identify factors that most influenced the outcomes and assess the robustness of the findings. Of the estimated 806,251 primary and secondary prostate biopsies performed annually in the United States 20,322 specimen provenance complications were projected to result in 4,570 clinically meaningful false diagnoses and an expected loss of 634 QALYs. The total burden of specimen provenance complications was projected to exceed $879.9 million or $3,776 per positive cancer diagnosis. This estimate was most sensitive to the indemnity cost per false-positive case and the rate of transpositions at independent reference laboratories. The societal burden of specimen provenance complications in patients who undergo prostate biopsy exceeds $880 million annually in the United States. This analysis framework may be useful as policy makers, health organizations and researchers seek to decrease false diagnoses of prostate cancer and the consequent effects of delayed or unnecessary treatment. Further study is warranted to quantify the economic burden among additional diseases. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  19. Room temperature fatigue behavior of OFHC copper and CuAl25 specimens of two sizes

    DEFF Research Database (Denmark)

    Singhal, A.; Stubbins, J.F.; Singh, B.N.

    1994-01-01

    requiring an understanding of their fatigue behavior.This paper describes the room temperature fatigue behavior of unirradiated OFHC (oxygen-free high-conductivity) copper and CuAl25 (copper strengthened with a 0.25% atom fraction dispersion of alumina). The response of two fatigue specimen sizes to strain...... controlled fatigue loading is examined, and differences in behavior are discussed. Specimens with the smaller size are now being irradiated in several reactors...

  20. The Impact of Storage Times of Museum Insect Specimens on PCR Success: Case Study on Moth Collections in Indonesia

    Directory of Open Access Journals (Sweden)

    HARI SUTRISNO

    2012-06-01

    Full Text Available Museum specimens are vast repositories of genetic information of interests to biological researchers. Since a new method in DNA extraction, a non destructive method, has been reported to be successful in extracting DNA of museum specimens even fossils without any morphological damages, using museum specimens as resources of genetic information for molecular studies is becoming popular recently. However, the PCR success depends on the quality of the specimens. To evaluate the impact of the storage times of museum specimens on PCR success,we conducted DNA extraction of 14 dry museum specimens of the moths collected from 1992 to 2010 by using a non destructive method. The results showed that the DNA specimens museum were fragmented into various sizes (100-1000 bp depend on the storage times. On the other hand, fresh specimens which were preserved withinabsolute ethanol were almost not fragmented. The specimens of < 6 years old (2005-2010 succeed to amplify in 650 bp amplicon but for some specimens of 7 years old (2 of 3 specimens resulted in a very weak amplification. These specimens, however, were able to amplify strongly in 300 bp amplicon. The results also showed that specimens of 1-19 years old were success to amplify in 100 bp amplicon.

  1. Automated detection of breast cancer in resected specimens with fluorescence lifetime imaging

    Science.gov (United States)

    Phipps, Jennifer E.; Gorpas, Dimitris; Unger, Jakob; Darrow, Morgan; Bold, Richard J.; Marcu, Laura

    2018-01-01

    Re-excision rates for breast cancer lumpectomy procedures are currently nearly 25% due to surgeons relying on inaccurate or incomplete methods of evaluating specimen margins. The objective of this study was to determine if cancer could be automatically detected in breast specimens from mastectomy and lumpectomy procedures by a classification algorithm that incorporated parameters derived from fluorescence lifetime imaging (FLIm). This study generated a database of co-registered histologic sections and FLIm data from breast cancer specimens (N  =  20) and a support vector machine (SVM) classification algorithm able to automatically detect cancerous, fibrous, and adipose breast tissue. Classification accuracies were greater than 97% for automated detection of cancerous, fibrous, and adipose tissue from breast cancer specimens. The classification worked equally well for specimens scanned by hand or with a mechanical stage, demonstrating that the system could be used during surgery or on excised specimens. The ability of this technique to simply discriminate between cancerous and normal breast tissue, in particular to distinguish fibrous breast tissue from tumor, which is notoriously challenging for optical techniques, leads to the conclusion that FLIm has great potential to assess breast cancer margins. Identification of positive margins before waiting for complete histologic analysis could significantly reduce breast cancer re-excision rates.

  2. Deginerative changes of femoral articular cartilage in the knee : comparative study of specimen sonography and pathology

    Energy Technology Data Exchange (ETDEWEB)

    Park, Ju Youn; Hong, Sung Hwan; Sohn, Jin Hee; Wee, Young Hoon; Chang, Jun Dong; Park, Hong Seok; Lee, Eil Seoung; Kang Ik Won [Hallym Univ. College of Medicine, Seoul (Korea, Republic of)

    2001-04-01

    To determine the sonographic findings of degenerative change in femoral articular cartilage of the knee by comparative study of specimen sonography and pathology. We obtained 40 specimens of cartilage of the femur (20 medial and 20 lateral condylar) from 20 patients with osteoarthritis of the knee who had undergone total knee replacement. The specimens were placed in a saline-filled container and sonography was performed using a 10-MHz linear transducer. Sonographic abnormalities were evaluated at the cartilage surface, within the cartilage, and at the bone-cartilage interface, and were compared with the corresponding pathologic findings. In addition, cartilage thickness was measured at a representative portion of each femoral cartilage specimen and was compared with the thickness determined by sonography. 'Dot' lesions, irregularity or loss of the hyperechoic line, were demonstrated by sonography at the saline-cartilage interface of 14 cartilages. Pathologic examination showed that these findings corresponded to cleft, detachment, erosion, and degeneration. Irregularities in the hyperechoic line at the bone-cartilage interface were revealed by sonography in eight cartilages and were related to irregularity or loss of tidemark, downward displacement of the cartilage, and subchondral callus formation. Dot lesions, corresponding to cleft and degeneration, were noted within one cartilage. Cartilage thickness measured on specimen and by sonography showed no significant difference (p=0.446). Specimen sonography suggested that articular cartilage underwent degenerative histopathological change. Cartilage thickness measured by sonography exactly reflected real thickness.

  3. Crashworthiness Analysis and Evaluation of Fuselage Section with Sub-floor Composite Sinusoidal Specimens

    Directory of Open Access Journals (Sweden)

    H.L. Mou

    Full Text Available Abstract Crashworthiness is one of the main concerns in civil aviation safety particularly with regard to the increasing ratio of carbon fiber reinforced plastic (CFRP in aircraft primary structures. In order to generate dates for model validations, the mechanical properties of T700/3234 were obtained by material performance tests, and energy-absorbing results were gained by quasi-static crushing tests of composite sinusoidal specimens. The correctness of composite material model and single-layer finite element model of composite sinusoidal specimens were verified based on the simulation results and test results that were in good agreement. A typical civil aircraft fuselage section with composite sinusoidal specimens under cargo floor was suggested. The crashworthiness of finite element model of fuselage section was assessed by simulating the vertical drop test subjected to 7 m/s impact velocity, and the influences of different thickness of sub-floor composite sinusoidal specimens on crashworthiness of fuselage section were also analyzed. The simulation results show that the established finite element model can accurately simulate the crushing process of composite sinusoidal specimens; the failure process of fuselage section is more stable, and the safety of occupants can be effectively improved because of the smaller peak accelerations that was limited to human tolerance, a critical thickness of sub-floor composite sinusoidal specimens can restrict the magnitude of acceleration peaks, which has certain reference values for enhancing crashworthiness capabilities of fuselage section and improving the survivability of passengers.

  4. Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction.

    Science.gov (United States)

    Loeffelholz, M J; Lewinski, C A; Silver, S R; Purohit, A P; Herman, S A; Buonagurio, D A; Dragon, E A

    1992-11-01

    A rapid and sensitive polymerase chain reaction (PCR)-based assay for detection of Chlamydia trachomatis in cervical specimens is described. This assay consists of (i) sample preparation which avoids the use of heat, centrifugation, or organic extractions; (ii) rapid, two-temperature PCR amplification of C. trachomatis cryptic plasmid sequences; and (iii) capture and colorimetric detection of amplified DNA in microwell plates. PCR was compared with culture by using 503 cervical specimens. After resolution of discrepant specimens with a confirmatory PCR assay directed against the chlamydial major outer membrane protein gene, PCR had a sensitivity of 97% and a specificity of 99.7% while culture had a sensitivity of 85.7% and a specificity of 100%. In a separate study, PCR was compared with a direct specimen enzyme immunoassay (Chlamydiazyme; Abbott Diagnostics) by using 375 cervical specimens. After resolution of discrepant specimens, PCR had a sensitivity and specificity of 100%, while the enzyme immunoassay had a sensitivity of 58.8% and a specificity of 100%.

  5. An unusual MR signal reduction artefact in an incompletely thawed cadaver spine specimen

    Energy Technology Data Exchange (ETDEWEB)

    Kurmis, Andrew P. [Bone and Joint Research Laboratory, Division of Tissue Pathology, Institute of Medical and Veterinary Science and Hanson Institute, South Australia (Australia); School of Medicine, Flinders University, South Australia (Australia)], E-mail: andrew.kurmis@flinders.edu.au; Slavotinek, John P. [Department of Medical Imaging, Flinders Medical Centre, South Australia (Australia); Barber, Christine; Smith, Lachlan [Bone and Joint Research Laboratory, Division of Tissue Pathology, Institute of Medical and Veterinary Science and Hanson Institute, South Australia (Australia); Fazzalari, Nicola L. [Bone and Joint Research Laboratory, Division of Tissue Pathology, Institute of Medical and Veterinary Science and Hanson Institute, South Australia (Australia); Department of Pathology, University of Adelaide, South Australia (Australia)

    2009-02-15

    Objective: Within the contemporary constraints associated with in vivo use for research purposes, preservation of macroscopic human tissue specimens is of critical importance. Simple sub-zero freezing remains the method-of-choice for medium-term storage of such material. Despite widespread use, few papers have described the effects of this preservation method on resultant images, or the impact of inadequate tissue thawing. Materials and methods: A series of post-mortem-harvested human lumbar spine specimens were undergoing conventional MR imaging as part of a larger project exploring non-invasive hydration status assessment of the intervertebral disc. Results: A complex central signal reduction artefact was noted during scanning of one specimen, resembling an isotherm distribution. Subtle inadequacies in core specimen thawing lead to an initially confusing pattern of central signal dampening. Conclusions: These findings demonstrate the impact of sub-optimal specimen preparation on image signal characteristics and highlight the importance of appropriate thawing methods of frozen tissue specimens prior to imaging.

  6. The Design of Cruciform Test Specimens for Planar Biaxial Testing of Fabrics for Inflatable Aerodynamic Decelerators

    Science.gov (United States)

    Corbin, Cole K.

    2012-01-01

    A preliminary analytical study was conducted to investigate the effects of cruciform test specimen geometries on strain distribution uniformity in the central gage section under biaxial loads. Three distinct specimen geometries were considered while varying the applied displacements in the two orthogonal directions. Two sets of woven fabric material properties found in literature were used to quantify the influence of specimen geometries on the resulting strain distributions. The uniformity of the strain distribution is quantified by taking the ratio between the two orthogonal strain components and characterizing its gradient across the central area of the gage section. The analysis results show that increasing the specimen s length relative to its width promotes a more uniform strain distribution in the central section of the cruciform test specimen under equibiaxial enforced tensile displacements. However, for the two sets of material properties used in this study, this trend did not necessary hold, when the enforced tensile displacements in the two orthogonal directions were not equal. Therefore, based on the current study, a tail length that is 1.5 times that of the tail width is recommended to be the baseline/initial specimen design.

  7. Fatigue life estimation for different notched specimens based on the volumetric approach

    Science.gov (United States)

    Zehsaz, M.; Hassanifard, S.; Esmaeili, F.

    2010-06-01

    In this paper, the effects of notch radius for different notched specimens has been studied on the values of stress concentration factor, notch strength reduction factor, and fatigue life duration of the specimens. The material which has been selected for this investigation is Al 2024T3 . Volumetric approach has been applied to obtain the values of notch strength reduction factor and results have been compared with those obtained from the Neuber and Peterson methods. Load controlled fatigue tests of mentioned specimens have been conducted on the 250kN servo-hydraulic Zwick/Amsler fatigue testing machine with the frequency of 10Hz. The fatigue lives of the specimens have also been predicted based on the available smooth S-N curve of Al2024-T3 and also the amounts of notch strength reduction factor which have been obtained from volumetric, Neuber and Peterson methods. The values of stress and strain around the notch roots are required to predict the fatigue life of notched specimens, so Ansys finite element code has been used and non-linear analyses have been performed to obtain the stress and strain distributions around the notches. The plastic deformations of the material have been simulated using multi-linear kinematic hardening and cyclic stress-strain relation. The work here shows that the volumetric approach does a very good job for predicting the fatigue life of the notched specimens.

  8. Fatigue life estimation for different notched specimens based on the volumetric approach

    Directory of Open Access Journals (Sweden)

    Esmaeili F.

    2010-06-01

    Full Text Available In this paper, the effects of notch radius for different notched specimens has been studied on the values of stress concentration factor, notch strength reduction factor, and fatigue life duration of the specimens. The material which has been selected for this investigation is Al 2024T3 . Volumetric approach has been applied to obtain the values of notch strength reduction factor and results have been compared with those obtained from the Neuber and Peterson methods. Load controlled fatigue tests of mentioned specimens have been conducted on the 250kN servo-hydraulic Zwick/Amsler fatigue testing machine with the frequency of 10Hz. The fatigue lives of the specimens have also been predicted based on the available smooth S-N curve of Al2024-T3 and also the amounts of notch strength reduction factor which have been obtained from volumetric, Neuber and Peterson methods. The values of stress and strain around the notch roots are required to predict the fatigue life of notched specimens, so Ansys finite element code has been used and non-linear analyses have been performed to obtain the stress and strain distributions around the notches. The plastic deformations of the material have been simulated using multi-linear kinematic hardening and cyclic stress-strain relation. The work here shows that the volumetric approach does a very good job for predicting the fatigue life of the notched specimens.

  9. Plastination of dissected brain specimens and Mulligan-stained sections of the human brain.

    Science.gov (United States)

    Baeres, F M; Møller, M

    2001-12-01

    The difficulties in obtaining human brain material for teaching neuroanatomy have increased the demand for more durable brain specimens. In this paper, we describe results obtained by preparing large, plastinated, dissected human brain specimens and Mulligan-stained sections of the human brain. The brains were fixed in formalin, washed and dissected in order to visualize the fibre tracts and larger nuclei in the central nervous system. This was followed by dehydration at -20 degrees C in acetone. The specimens were then impregnated with silicone, Biodur S10, in vacuo and hardened in Biodur S6 vapour. The grey and white substance in the central nervous system as well as the larger fibre tracts and nuclei were clearly visible in the dissected, plastinated specimens. Coronal and sagittal sections of the human brain were stained according to Tompsett's modification of the Mulligan method. The sections were then dehydrated in cold acetone followed by forced impregnation with Biodur S10 and hardening. The plastinated sections stained distinctly and strongly and the nuclei in the forebrain, cerebellum and brain stem could be identified easily. The sections did not fade when exposed to light and could be easily handled in the classroom without damage. Therefore, the distinct visualization of neuroanatomical structures, the improved durability of the specimens, as well as the lack of odour make plastinated specimens and stained sections of the central nervous system a valuable tool for teaching neuroanatomy that compliments the use of wet preparations.

  10. Offshore oil prospects improve

    Science.gov (United States)

    The issues, prospects, and environmental concerns about drilling for offshore oil and gas are being seen in a different light than at any other time during the past decade. Exploration drilling on offshore locations is proceeding at a high rate, and environmental concerns, while recognized as real, appear to be a lot less worrisome than might have been predicted a decade ago. Part of the reason for the changes in levels of concern results from the close monitoring programs that have been in effect for the past few years. Paul R. Ryan of the Woods Hole Oceanographic Institution recently described exploration activities on Georges Bank: “We now have the results of the first year of monitoring, and, although eight wells are considered a minimal observational test, there were no biological changes in the benthic community that could be attributed to drilling activity.” (Oceanus, 26, 2, 1983). The U.S. Geological Survey studied the Georges Bank drilling activities as well. Barium from drilling muds was detected at the sites, but in decreasing concentrations at distances away from drilling rigs. There was no evidence that the discharges caused biological changes. According to Ryan: “Postdrilling concentrates of barium were found to be within the range of predilling concentrations measured at other locations on the Bank. Concentrations of other metals measured were low and characteristic of unpolluted, coarse-grained sediment in other Continental Shelf areas.”

  11. A 100-year-old anatomical specimen presenting with boomerang-like skeletal dysplasia: diagnostic strategies and outcome

    NARCIS (Netherlands)

    Oostra, R. J.; Dijkstra, P. F.; Baljet, B.; Verbeeten, B. W.; Hennekam, R. C.

    1999-01-01

    The Museum Vrolik collection of human anatomy comprises 360 recently redescribed specimens with congenital anomalies. The specimen described here dated from 1881 and presented with a general embryonic appearance, disproportionate short stature, brachycephaly, widened cranial sutures, hypertelorism,

  12. Revealing Invisible Beauty, Ultra Detailed: The Influence of Low Cost UV Exposure on Natural History Specimens in 2D+ Digitization

    OpenAIRE

    Brecko, Jonathan; Mathys, Aurore; Dekoninck, Wouter; De Ceukelaire, Marleen; VandenSpiegel, Didier; Semal, Patrick

    2016-01-01

    Digitization of the natural history specimens usually occurs by taking detailed pictures from different sides or producing 3D models. Additionally this is normally limited to imaging the specimen while exposed by light of the visual spectrum. However many specimens can see in or react to other spectra as well. Fluorescence is a well known reaction to the ultraviolet (UV) spectrum by animals, plants, minerals etc. but rarely taken into account while examining natural history specimens. Our tes...

  13. Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified

    OpenAIRE

    Shaun Turney; Elyssa R. Cameron; Cloutier, Christopher A.; Buddle, Christopher M.

    2015-01-01

    Scientific findings need to be verifiable and grounded in repeatability. With specimen-level research this is in part achieved with the deposition of voucher specimens. These are labeled, curated, data-based specimens that have been deposited in a collection or museum, available for verification of the work and to ensure researchers are calling the same taxa by the same names. Voucher specimens themselves are the subject of research, from the discovery of new species by taxonomists to ecologi...

  14. Uranium prospecting; La prospection de l'uranium

    Energy Technology Data Exchange (ETDEWEB)

    Roubault, M. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1955-07-01

    This report is an instruction book for uranium prospecting. It appeals to private prospecting. As prospecting is now a scientific and technical research, it cannot be done without preliminary studies. First of all, general prospecting methods are given with a recall of fundamental geologic data and some general principles which are common with all type of prospecting. The peculiarities of uranium prospecting are also presented and in particular the radioactivity property of uranium as well as the special aspect of uranium ores and the aspect of neighbouring ores. In a third part, a description of the different uranium ores is given and separated in two different categories: primary and secondary ores, according to the place of transformation, deep or near the crust surface respectively. In the first category, the primary ores include pitchblende, thorianite and rare uranium oxides as euxenite and fergusonite for example. In the second category, the secondary ores contain autunite and chalcolite for example. An exhaustive presentation of the geiger-Mueller counter is given with the presentation of its different components, its functioning and utilization and its maintenance. The radioactivity interpretation method is showed as well as the elaboration of a topographic map of the measured radioactivity. A brief presentation of other detection methods than geiger-Mueller counters is given: the measurement of fluorescence and a chemical test using the fluorescence properties of uranium salts. Finally, the main characteristics of uranium deposits are discussed. (M.P.)

  15. Metastatic colorectal adenocarcinoma in cervicovaginal cytology specimens confirmed by immunocytochemical stains on liquid base specimens: Two study cases with review of the literature

    Directory of Open Access Journals (Sweden)

    Muhammad Zulfiqar

    2013-01-01

    Full Text Available Only a few cases of adenocarcinoma (ACA metastatic to the female lower genital tract diagnosed on cervicovaginal Pap smear have been reported during the past several decades. Both conventional and liquid based cytology (LBC have limited sensitivity and specificity in diagnosing metastatic disease and immunocytochemical (ICC staining may be needed for confirming the diagnosis. We present two cases of metastatic colorectal ACA diagnosed on cervicovaginal ThinPrep (TP Pap smears, with one confirmed by ICC staining method. Recognition of extra-uterine malignancy in the cervicovaginal cytology specimen is critical for the disease diagnosis, prognosis, and the treatment. ICC staining performed on the residual LBC specimen is an important methodology to confirm the diagnosis.

  16. Effectiveness of saliva and fingerprints as alternative specimens to urine and blood in forensic drug testing.

    Science.gov (United States)

    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.

  17. Comparison of edge chipping resistance of PFM and veneered zirconia specimens.

    Science.gov (United States)

    Quinn, Janet B; Sundar, Veeraraghavan; Parry, Edward E; Quinn, George D

    2010-01-01

    To investigate the chipping resistance of veneered zirconia specimens and compare it to the chipping resistance of porcelain fused to metal (PFM) specimens. Veneered zirconia and PFM bar specimens were prepared in clinically relevant thicknesses. The specimen edges were chipped with different magnitude forces, producing chips of various sizes. The range of sizes included small chips that did not penetrate all the way through the veneers to the substrates, and also chips that were very large and reached the zirconia or metal substrates. The relationship between force magnitude and chip size (edge distance) was graphed. The resulting curves were compared for the veneered zirconia and PFM specimens. Knoop hardness vs. force graphs for the veneers and substrates were also obtained. The zirconia and PFM veneer chipping data followed a power law (coefficient of determination, R(2)>0.93) as expected from the literature. The curves overlapped within the combined data scatter, indicating similar resistance to chipping. The chips made in both types of specimens detached and did not penetrate into the substrate when they reached the veneer/substrate intersections. The hardness-load curves for the veneers and substrates all exhibited an indentation size effect (ISE) at low loads. The Knoop hardness values with uncertainties of +/-one standard deviation at 4N loads for the metal, zirconia, and the metal and zirconia veneers are: (2.02+/-0.08, 12.01+/-0.39, 4.24+/-0.16 and 4.36+/-0.02GPa), respectively, with no statistically significant difference between the veneers (Tukey pairwise comparison at 0.95 family confidence). This work indicates that a similar resistance to chipping might be expected for veneered zirconia and PFM restorations, in spite of the large difference in substrate hardness. Differences in susceptibility to chip spalling were not detected, but the chips in both specimen types detached off the sides in a similar manner instead of extending into the substrates.

  18. Crystal Plasticity Finite Element Method Simulations for a Polycrystalline Ni Micro-Specimen Deformed in Tension

    Science.gov (United States)

    Choi, Yoon Suk; Groeber, Michael A.; Shade, Paul A.; Turner, Todd J.; Schuren, Jay C.; Dimiduk, Dennis M.; Uchic, Michael D.; Rollett, Anthony D.

    2014-12-01

    A micro-tensile test system equipped with in situ monitoring of the in-plane displacements of a surface and an electron backscattered diffraction-based serial-sectioning technique were used to study the deformation (up to 2.4 pct axial plastic strain in tension) of a polycrystalline nickel micro-specimen. The experimental data include the global engineering stress-engineering strain curve, the local mesoscopic in-plane displacement and strain fields, the three-dimensional microstructure of the micro-specimen reconstructed after the tensile test, and the kernel-average misorientation distribution. The crystal plasticity finite element method using elasto-viscoplastic constitutive formulations was used to simulate the global and local deformation responses of the micro-specimen. Three different boundary conditions (BCs) were applied in simulation in order to study the effects of the lateral displacement (perpendicular to the loading direction) of the top and bottom faces of the specimen gage section. The simulation results were compared to the experimental results. The comparison between experiment and simulation results is discussed, based upon their implications for understanding the deformation of micro-specimens and the causes associated with uncertainties embedded in both experimental and numerical approaches. Also, the sensitivity of BCs to near-field and far-field responses of the micro-specimen was systematically studied. Results show that the experimental methodology used in the present study allows for limited but meaningful comparisons to crystal plasticity finite element simulations of the micro-specimen under the small plastic deformation.

  19. Use of flow cytometry in the diagnosis of lymphoproliferative disorders in fluid specimens.

    Science.gov (United States)

    Yu, Gordon H; Vergara, Norge; Moore, Erika M; King, Rebecca L

    2014-08-01

    The diagnostic evaluation of fluid specimens, including serous effusions and cerebrospinal fluids (CSFs), can be challenging for a number of reasons. The evaluation of lymphoid proliferations in these specimens can be particularly problematic, given the frequent presence of coexisting inflammatory conditions and the manner in which these specimens are processed. As a result, immunophenotypic analysis of hematopoietic cell populations by flow cytometry has emerged as a useful ancillary study in the diagnosis of these specimens, both in patients with and without a previous history of a lymphoproliferative disorder. In this study, we review our experience with flow cytometry in fluid specimens over a four-year period. Flow cytometry was performed in 184 of 6,925 total cases (2.7% of all fluids). Flow cytometry was performed in 4.8% of pleural fluids (positive findings in 38%, negative in 40%, and atypical in 18%), 1.1% of peritoneal fluids (positive in 40%, negative in 50%, and atypical in 10%), 1.9% of pericardial fluids (positive in 67%, negative in 33%), and 1.9% of CSFs (positive in 23%, negative in 55%, atypical in 3%). The specimen submitted was inadequate for analysis in 9.2% of cases, most commonly with CSF specimens, but was not related to the volume of fluid submitted. Atypical flow cytometry findings and atypical morphologic findings in the context of negative flow cytometry results led to the definitive diagnosis of a lymphoproliferative disorder in a significant number of cases when repeat procedures and ancillary studies were performed. Copyright © 2014 Wiley Periodicals, Inc.

  20. A combination of four cell types for rapid detection of enteroviruses in clinical specimens.

    Science.gov (United States)

    Dagan, R; Menegus, M A

    1986-07-01

    Isolation in cell culture is currently the most sensitive and reliable way to demonstrate enterovirus (EV) in clinical specimens. During July-October 1982 and 1983, we studied the impact of adding two new cell lines, Buffalo green monkey kidney (BGM) and human rhabdomyosarcoma (RD), to the more traditional cell combination used for EV isolation, human embryonic lung (HEL) and primary cynomolgus monkey kidney (CMK) cells; 2,558 specimens were studied: 632 fecal, 677 respiratory, 537 CSF, and 712 blood. An EV was isolated from 417 (16%); of these, 77 (18%) were positive only in BGM or RD; 35% (146/417) of the specimens were positive in BGM, RD, or both, at least one day earlier than in the traditional cells. BGM cells were helpful in isolation of group B coxsackieviruses (CB): 99% of 121 positive specimens were detected in BGM vs 73% in CMK and 23% in HEL; 72% of the CB isolates were detected by day 2 in BGM vs 48% in CMK and 0% in HEL. RD cells were helpful in the isolation of echoviruses: 59% of the 189 positive specimens were detected in RD vs 67% in HEL and 58% in CMK. RD was the only positive cell type in 28/189 (15%) positive specimens; 31% of the echovirus isolates were detected by day 2 in RD, vs 20% in HEL and 19% in CMK. Using the cell types described, we provided the clinician with results in 42% of the EV-positive specimens by day 2 after inoculation and in 61% by day 4.