Unknown Specimens Research Articles

Computational Model of DIC Microscopy for Reconstructing 3-D Specimens

Differential Interference Contrast (DIC) microscopy is a powerful visualization tool used to study live biological cells. Its use, however, has been limited to qualitative observations. The inherent non-linear relation between the object properties and the image intensity makes quantitative analysis difficult. As a first step towards measuring optical properties of objects from DIC images, we develop a model for the image formation process using methods consistent with energy conservation laws. We verify our model by comparing real image data of manufactured specimens to simulated images of virtual objects. As the next step, we plan to use this model to reconstruct the three-dimensional properties of unknown specimens.

Risk investigations involving genetic identification.

Risk managers should consider misidentifications as causes of otherwise unexplained diagnostic and process errors. Genetic tests are powerful tools that can resolve problem cases and indicate ways to improve patient-sample identification. Genetic typing, especially for DNA markers, has provided evidence of patient or sample identity in 21 of 22 hospital and laboratory cases of accidental or intentional patient misidentification, specimen mislabeling, and sample contamination. Identity is established with very high probability if infrequent genetic markers are observed in both unknown and reference specimens. The odds of a match of markers express both the infrequency of finding the match by chance (in specified populations) and the adequacy of testing. Genetic tests establish nonidentity with virtual certainty.

MED22/401: Hypertext Atlas For Pathology Education

IntroductionMacro- and microscopic pictures play the key role in the pathology diagnosis and education. Collections of annotated digital histological images are being prepared and an interface offering convenient way of dealing with high resolution images and their descriptions was developed. The atlas will be primary used in pre-graduate course of pathology at the University.MethodsLeica DMLB microscope equipped with the Leica~S1 scanning camera is used to obtain pictures at the resolution of up to5112*5112 pixels, 3*12~bit color. These pictures are digitally manipulated (esp. contrast enhancement and sharpening), downsized to 3000*3000 pixels, 3*8 bit color and archived. Subsequently, these raw images are compressed using JPEG (JFIF lossy format) to 900*900 and 2000*2000 pixel images used in the actual collection. These pictures are logically glued together and described in the atlas source text prepared using the TeX/LaTeX typesetting system. LaTeX2HTML converter is used to produce the actual hypermedia document, while the same source can be used to obtain a more classical printed version of the atlas. The static character of the HTML hypertext document is made dynamic through JavaScript functions, which add the required interactivity.ResultsThe atlas is accessible using standard JavaScript enabled Web browsers. There is always one main window with the text, table of content, index, active section headers and other hypertext links, and links to individual images. All the images are displayed in separate windows. The 900*900 pixels images are used as standard resolution pictures, the higher resolution images (2000*2000) are displayed on demand in a separated ``magnifying glass'' window. This interface can be used to compare several pictures displaying them in the same time and providing also a tool to focus on the most important parts of the large windows. Use of the higher resolution images leads to no information loss through this process. The interface could mimic the fine focusing of the microscope that provided the picture and is a series of images taken in consecutive planes of focus.DiscussionThe atlas was primary produced as a stand-alone package, stored on local disc or CD-ROM. In this form it is suitable for pre-graduate and initial postgraduate education. Currently, it is being converted into very flexible, easily available and expandable diagnostic tool available through Internet. The Internet accessible atlas may be easily updated and expanded with new images and text. Images at different compression levels could be stored, the low resolution one used to fast scan and the highest resolution images used for detailed comparison with unknown specimen. Through the very high speed network (e.g. TEN-155) it will be possible to transfer even the raw data images with resolution above3000*3000 pixels.

Fundamental Constants for Quantitative X-Ray Microanalysis

Abstract The development of quantitative X-ray microanalysis in the 1950s spurred the need for knowledge of the many parameters which describe the electron interaction, such as the ionization cross-sections, fluorescent yields, the electron stopping power, mass absorption coefficients, and others. Although classical microanalysis, which proceeds by measurements of the unknown specimen against a standard, can eliminate the need to know many of these parameters accurately, much current microanalysis is done on highly inhomogeneous samples for which comparison with a standard is much less useful procedure. The increased use of low beam energies also means that data is now required for L-, and M-lines which previously have been little used. Consequently there is an enhanced need for a reliable and agreed set of data on which to base calculations. A common misconception is the belief that all of the quantities that are needed must already have been measured by somebody and so it is simply a matter of accessing this data.

Viral Load Determination in Plasma and CSF From HTLV-I-Infected Patients. Real-Time Quantitation Using the Prism 7700.

SP-19 A quantitative RT PCR assay for determining HTLV-I virus RNA load using the ABI Prism 7700 Sequence Detection System has been developed. The assay uses two enzymes in a single tube for ease of use and to limit cross contamination. MuLV (Superscript™) RT is used to generate a cDNA template which is then amplified by taq polymerase. The HTLV-I primer specific cDNA's are used to generate, in real-time, a threshold cycle (Ct) value using Taqman chemistry. The copy number of a preparation of an HTLV-I tax RNA transcript of uniform length and molecular weight (1173 bp) was determined. A standard curve using this RNA was constructed and validated. Quantitation of the unknown specimen is determined by interpolating the Ct value of the co-amplified unknown specimen against the standard curve Ct's generated from the HTLV-I tax RNA dilutions. The assay can detect as few as 30 HTLV RNA copy equivalents per reaction and provides 5 logs of linear dynamic range. This assay is rapid, reproducible, and allows quantification of virus RNA load in patient plasma specimens as will be shown.

Simple polarimetric method for electro-optic coefficients

A simple technique to measure electro-optic coefficients has been developed. It is based on rotating analyzer polarimetry. With a coaxial configuration of the optically active polarizing devices, the synchronously digitized signals are Fourier analyzed to quantitatively determine the elliptical polarization of light and, hence, the electric field induced birefringence. This technique has the advantage that it does not require waveguiding, and since it is improved from the crossed polarizer method it measures the phase retardation directly. It has been applied for the precise determination of electro-optic coefficients of uniaxial LiNbO3 single crystals. The excellent agreeement with reported values confirms its usefulness toward accurate characterization of electro-optic coefficients of unknown specimens.

X-Ray diffraction: a practical approach

Basics: X-Rays and Diffraction. Lattices and Crystal Structures. Practical Aspects of X-Ray Diffraction. Experimental Modules: Crystal Structure Determination, I: Cubic Structures. Crystal Structure Determination, II: Hexagonal Structures. Precise Lattice Parameter Measurements. Phase Diagram Determination. Detection of Long-Range Ordering. Determination of Crystallite Size and Lattice Strain. Quantitative Analysis of Powder Mixtures. Identification of an Unknown Specimen: Appendices: Plane-Spacing Equations and Unit Cell Volumes. Quadratic Forms of Miller Indices for the Cubic System. Atomic and Ionic Scattering Factors of Some Selected Elements. Summary of Structure Factor Calculations. Mass Absorption Coefficients mu/rho (cm2/g) and Densities rho (g/cm3) of Some Selected Elements. Multiplicity Factors. Lorentz-Polarization Factor. Physical Constants and Conversion Factors. JCPDS-ICDD Card Numbers for Some Common Materials. Index.

Land mammals of Oregon

This is the first comprehensive, up-to-date treatment of mammals in the state of since 1936, when Vernon Bailey's Mammals and Life Zones of Oregon was published. It provides a basic reference for mammalogists, wildlife biologists, students, and anyone interested in mammalian life in the northwestern United States. Indeed, researchers in states adjacent to will find much useful information regarding the mammals their regions share with Oregon. Descriptions of all 136 extant or recently extirpated mammal species in are in the book, with information on geographical variation, diet, reproduction, ontogeny, mortality, and behavior. The authors provide range maps and lists of collection localities based on their examination of 55,265 museum specimens and brief accounts of morphology, species diversity, distribution, and fossil records. Keys to orders, families, and species are provided for identification of unknown specimens. Also helpful is the introductory section with its discussion of skull morphology, evolutionary history, basic taxonomy, zoogeography, zoonotic diseases, and the history of mammalogy in Oregon. A bibliography of 2,925 references makes the volume especially useful for anyone wishing to do further research.

Discovery of the lost type species of Caberea (Bryozoa) and the identity of Caberea pinnata Lamouroux, 1816 (Hydroida)

The bryozoan genus Caberea was established in 1816 by J.V.F. Lamouroux, with two included species, C. dichotoma and C. pinnata, both collected in Australian waters by the 1800–1804 French exploring expedition of Captain Nicolas Baudin. Only C. dichotoma was illustrated, though very poorly, and subsequently chosen as type species of the genus. Notwithstanding, both species have remained unknown and Lamouroux's specimens were assumed lost or destroyed. The recent rediscovery of some original material of many Lamouroux taxa allows a positive identification of both Caberea species in relation to subsequent synonymy. Pluriserial Caberea dichotoma Lamouroux, 1816 is a senior synonym of Caberea grandis Hincks, 1881. Caberea pinnata Lamouroux, 1816 is a senior synonym of the thecate hydroid Thuiaria lata Bale, 1882, and should be named Sertularella pinnata n. comb. The provenance of Lamouroux's species was almost certainly southeastern Australia, possibly Bass Strait.

Cranial morphometrics of the southern fur seals Arctocephalus forsteri and A. pusillus (Carnivora : Otariidae)

The identification and classification of unknown specimens of Arctocephalus from regions of Australasia has proven difficult. Skulls from the New Zealand fur seal (Arctocephalus forsteri) and the Australian fur seal (A. pusillus doriferus), and data from specimens of the South African fur seal (A. p. pusillus), were examined. A visual method was devised to identify and separate A. p. doriferus from A. forsteri for both sexes and for most physiological age-groups. A statistical method for morphometric separation of these species was applied to adult specimens. Characteristics of males and females for both species fell into two broad categories: sexually dimorphic – mainly those characters that increase the ability of males to hold and defend territories; and non-dimorphic – those of functional importance. Studies of geographical variation showed that adult male A. forsteri from Australia were generally larger than those from Macquarie Island and New Zealand. Characteristics of A. p. doriferus were generally larger than those of A. p. pusillus. Nine specimens of New Zealand fur seals were morphologically different from the typical A. forsteri, which indicates the presence of extreme outliers or hybrids in the sample.

The Ocruranus–Eohalobia group of small shelly fossils from the Lower Cambrian of Yunnan

Lower Cambrian phosphorite samples from Maotianshan, Yunnan Province, South China, yielded a variety of small shelly fossils. Sclerites of the second pre-trilobite faunal assemblage of Meishucun, the Paragbborilus-Siphogonuchites–Lapworthella association of Nemakit–Daldynian to Tommotían age, were dominant. They comprise previously unknown spine-bearing specimens of Ocruranus finial Liu, 1979, and new morphotypes of Eohalobia diandongensis Jiang, 1982. Well-preserved sclerites reveal a laminated, composite fine structure with marginal, incremental growth. Each lamella consists of radial series of minute growth elements. The shells are phosphatically preserved, but micropetrographic evidence from drill-core samples indicates calcium carbonate as primary shell material. In the light of this new evidence, Ocruranus–Eohalobia group fossils are interpreted as parts of coeloscleritophoran scleritomes.

Direct total-reflection X-ray fluorescence trace element analysis of organic matrix materials with a semiempirical standard

In this work we describe a method for trace element analysis in organic matrix materials using direct irradiation of the sample in a total-reflection X-ray fluorescence spectrometer. The method avoids: (i) the need to digest the organic material, (ii) the need to add an internal standard to the unknown specimens, and (iii) the need to weigh the test specimen. Quantification of unknowns is achieved with the scattered peak as the internal standard and a semiempirical computational model of a standard, instead of a real reference material, for spectrometer sensitivity calibration. Spectra of certified standard reference materials with an organic matrix, obtained with a monochromatized beam from an X-ray tube, were quantified, showing good agreement with nominal, certified or previously reported values for solid and liquid samples. © 1997 Elsevier Science B.V.

Multivariate analysis to discriminate species of phlebotomine sand flies (Diptera:Psychodidae): Lutzomyia townsendi, L. spinicrassa, and L. youngi.

Multivariate discriminant analysis was employed to discriminate on a morphological basis females of 3 closely related sand fly species, Lutzomyia townsendi (Ortiz), L. spinicrassa Morales, Osorno-Mesa, Osorno & Hoyos, and L. youngi Feliciangeli & Murillo. Principal component and canonical discriminant analysis compared a set of 31 morphological characters measured from known specimens to detect differences among the 3 species. A subset of 6 characters separated the 3 species with a high level of confidence. A simple method is presented to identify an unknown specimen as L. townsendi, L. spinicrassa, or L. youngi using these 6 morphological characters.

Problems Identifying Japanese Cedar Cultivated in the United States

Japanese cedar [Cryptomeria japonica (Thun. ex L.f.) D. Don. (Taxodiaceae)] cultivars have become quite popular in the U.S. landscape and nursery industries. Their popularity is expected to increase as more attractive and adaptable horticultural selections gain recognition. Taxonomic problems include an inadequate inventory of selected variants cultivated in the United States, instability of names at the infraspecific taxonomic level, poor descriptions of the cultivars, and a lack of representative specimens and identification aids to help horticulturists identify unknown specimens. A study of Cryptomeria japonica cultivated in the United States is needed to address these problems.

A key for freshwater invertebrates using fuzzy logic.

This paper summarizes a biological key using a fuzzy logic expert system. This approach allows the user to make some errors, be uncertain about some answers and not answer questions if unsure, but have an opportunity to identify unknown specimens correctly. This approach was adopted in order to develop a 'forgiving' key for users with little or no prior knowledge of identification. The system was implemented using a multi-media expert system builder, 'Matcher', operating in a Microsoft Windows environment. The paper reports the design issues for a key to identify freshwater invertebrates to family level and describes the types of questions used within the key, the fuzzy inference engine, the structure of the system and the methodology adopted for testing it. Following this, an empirical test is reported of the hypothesis that a fuzzy logic expert system can improve identification accuracy for a sample of intended users. Finally, the discussion considers the practicalities of using such a system as an aid to organism identification.

A plea to curators: remember substrata

Fungal curatorial practices are quite similar all over the world. Desperately we try to file every specimen under the correct name or at least the most likely name. As long as we work with groups familiar to us, this filing system works well. Specimens are filed under names or aliases, likely to facilitate their rediscovery by a materialhungry taxonomist, and the fungal collection looks neat. The only bothersome lapse is a small number of folders lurking under Fungi indet. What does this neatness cost us? Field researchers knowing the fate awaiting totally unknown material seldom actively collect fungal groups where a long laborious process is required merely to append a generic name to a specimen. Consequently we explore nature, but we leave part of it unstudied because of curatorial filing problems! If somehow an unknown specimen has penetrated our prejudiced defences, it is frequently consigned to oblivion when a wild guess as to the possible genus is made. This is particularly true in ascomycetous (sexual and asexual) fungi where no one can hope to master the vast number of orders, families or genera. To put it crudely: snakes are filed as giraffes and the material remains essentially useless. No scientist, writing for material on loan, is able to fancy all the names under which the material crucial to his research might possibly be hidden. Thus, mycologists respond, illogically, by either leaving the unknown in nature or misfiling it. The costs in vain research time, when fungal material is consigned to oblivion, can be high. Filing inaccuracies may deprive a monographer of material on a global scale. As a rule, a request for material from some ascomycetous genus yields the predictable result: no material from the exotical herbaria strategically situated but plenty of specimens from areas around large, well-known herbaria. Success in receiving peripheral collections on loan hinges on whether an expedition by experts has ever visited a given remote area. Local herbaria all over the world could, of course, collect excellent material, had they only a mycologist. But with no mycologist on the staff, no fungi are collected because they cannot be accurately filed. Yet many local herbaria could serve the mycological community even without a mycologist on their staff. Usually curatorial expertise at these herbaria is focused on local vascular plants. From a mycological point of view that can be already most significant. A professional botanist recognizes when dead plant parts or wood bear fungi; in fact, senescent or dead plants almost always contain fungi. Nonetheless the practice is to wait for a mycologist to visit an area before any fungi are collected there. This means that we have become dependent on material collected during short expeditions. Furthermore, the expert collects just one or a few groups. Tunnel vision results: discomycetologists leave all anamorphs in the field while pyrenomycetologists discard all that is not black, because the experts save their precious time for their own particular group. Yet the local herbarium staffbeing there throughout the year could make a substrate-based collection at relatively low cost. Such a collec-

Quantification of rat pre-pro-thyrotropin releasing hormone (TRH) mRNA by reverse transcription-polymerase chain reaction using external and internal standardisation

We have developed a quantitative reverse transcription polymerase chain reaction (RT-PCR) method, using both internal and external standardisation, to quantitate fg amounts of pre-pro-thyrotropin releasing hormone (pre-pro-TRH) mRNA in the paraventricular nucleus (PVN) of individual laboratory rats. A constant amount of internal standard is coamplified with both the cDNA of each unknown specimen and a dilution series of an identical RT-PCR generated external standard, allowing quantitation of the samples by interpolation from the external standard curve. Pre-pro-TRH mRNA levels in the PVN were reduced by thyroxine (T 4) treatment to 48% of those in control animals, and were increased by thyroidectomy to 155% of the control levels. By combining external and internal standardisation, our method allows multiple samples and treatment groups to be assayed concurrently, thereby eliminating inter-assay variability, whilst retaining the advantages of internal standardisation. It will facilitate further studies of the control of TRH gene expression in pathophysiological conditions.

Fourier transform-Raman spectroscopy of amber

The FT-Raman spectra of specimens of genuine amber and of those of unknown origin are reported. Vibrational assignments are made for the genuine species and characteristic bands are identified. Comparison with the Raman spectra of samples of modern pine resin has facilitated the vibrational description of the bands; the unknown specimens were identified as being false ambers of acrylate and polyurethane origin. The presence of small amounts of sulphur and succinic acid in the genuine amber samples have provided a guide to the geographical origin of these samples.

The separation of Liriomyza huidobrensis (Diptera: Agromyzidae) from related indigenous and non‐indigenous species encountered in the United Kingdom using cellulose acetate electrophoresis

SummaryThe non‐indigenous pest leaf miner Liriomyza huidobrensis and its close relatives L. bryoniae and L. strigata belong to a natural group. These species can be separated from one another by means of protein electrophoresis on a cellulose acetate membrane. The protocol for this diagnostic assay involves staining for two enzymes, glucose‐6‐phosphate dehydrogenase (G6PDH) and leucine‐glycine peptidase (PEP). Other leaf miner species that might also be found under glass, Chromatomyia syngenesiae, C. horticola and the non‐indigenous L. trifolii and L. sativae, are clearly distinguishable from the L. huidobrensis group of species by this assay. The effect of parasitism on L. huidobrensis by Dacnusa sibirica was investigated and shown unlikely to cause misidentification of the leaf miner host. Results obtained from practical use of the assay to identify unknown specimens from ports and nurseries are compared with those obtained from flies kept in laboratory culture and used during development of the assay. No new variation was found for G6PDH. New PEP variation was found for both L. huidobrensis and L. bryoniae but this did not affect the integrity of the assay. A biochemical key to these agromyzid leaf miners is presented.

The morphological distinction between bones and teeth of fallow deer (Dama dama) and red deer (Cervus elaphus)

Morphological characters for the separation of red and fallow deer remains are described. These encompass antlers, permanent dentition, and postcranial bones. The characters were tested on samples of known red and fallow deer from an array of contexts, thus helping to ensure their validity across different populations. An attempt is made to quantify the reliability of each character, using a simple arithmetic method of scoring and analysing the test data. This forms the basis for a more objective assessment of the identity of an unknown specimen.