bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methodology for spectrum evaluation in quantitative electron energy‐loss spectrometry using the Zeiss CEM902
Authors: van Puymbroeck J. , Jacob W. , van Espen P. 
Published: August 2011

SUMMARYThe spectral energy‐loss intensities acquired with the Zeiss CEM902 do not follow a Poisson law. The intensities are normally distributed and their variances are non‐uniform. When fitting the inverse power law after logarithmic transformation, it is expected that the power law coefficients and their uncertainties will be biased. Due to the particular dependence of the variance on the intensity which is observed in our experiments, it appears that no bias is introduced when using unweighted least‐squares fitting after log‐log transformation. Because the sample variances are estimated with low degrees of freedom, the residual variance of the fit is proposed as a criterion rather than the X2 test to evaluate the optimum width of the fitting window. The optimal width for the integration window can be determined as the window where the signal‐to‐noise ratio is at a maximum. Critical limits for qualitative and quantitative analysis are proposed which are based on the variance of the net intensity. They can be used to test the analytical significance of the signals.
Electron spectroscopic imaging of the morphology of in situ polyethylene ‘shish kebabs’
Authors: Huong D. M. , Drechsler M. , Möller M. , Cantow H.‐J. 
Published: August 2011

SUMMARYThe simultaneous imaging of the crystalline and rigid amorphous areas of semi‐crystalline polyethylene is made possible by electron spectroscopic imaging (ESI) in an energy‐filtering transmission electron microscope (EFTEM). Conventional bright‐and dark‐field imaging modes mainly provide information about the non‐crystalline areas which react chemically with classical staining agents such as ruthenium tetroxide. The ability of ESI to image structures which are inaccessible to the staining agent is shown in TEM micrographs of nascent polyethylene ‘shish kebabs’ embedded in a Lowicryl HM20 matrix.
Localization of Ca2+ ‐stores and tissue compartments with a Ca2+ ‐binding capacity in the organ of Corti of the guinea‐pig by electron energy‐loss spectroscopy
Authors: Heinrich U.‐R. , Maurer J. , Mann W. , Kreutz W. 
Published: August 2011

SUMMARYThe addition of 10 mM CaCl2 to glutaraldehyde fixative leads to the formation of small electron‐dense deposits in the organ of Corti of the guinea‐pig. These precipitates are mainly attached to cell membranes in contact with different extracellular lymphatic fluids. A higher number of precipitates is localized in the acellular parts of tectorial and basilar membrane. Electron energy‐loss spectroscopy (EELS) was used to determine the elemental composition of the deposits formed. The spectra showed a prominent signal at the Ca2+ L2,3 ionization edge. Oxygen could also be detected in all the precipitates analysed. EELS analysis of mitochondria of the inner and outer hair cells after conventional fixation (glutaraldehyde followed by post‐fixation in OsO4) revealed a small but significant calcium signal.
Three‐dimensional simulation of flow through a porous medium
Authors: Jernot J. P. , Prasad P. Bhanu , Demaleprade P. 
Published: August 2011

SUMMARYA three‐dimensional simulated random packing of spheres is digitized and progressively densified with dilations of the initial stacking. Flow of fluid through these successive structures is then simulated with geodesic dilations inside the porous phase. The results allow a clear distinction to be made between two factors affecting the flow: the metric properties and the topological properties of the porous network.
Reduction of cross‐talk between fluorescent labels in scanning laser microscopy
Authors: Carlsson Kjell , Mossberg Karin 
Published: August 2011

SUMMARYBy using dual detectors in combination with a dichroic filter, it is possible to record simultaneously the distribution of two fluorescent labels in a specimen. It is often difficult, however, to obtain a good separation, i.e. each detector will generally detect light from more than one fluorophore. In such cases it is desirable to find image‐processing methods to improve the separation. A simple method is to form a linear combination of the recorded images. In this paper we investigate the necessary prerequisites for this method to be successful, and we also investigate to what extent these are fulfilled in some practical cases. In this context the spectral properties of the fluorophores turn out to be of crucial importance. Even when the necessary prerequisites are not strictly fulfilled, a considerable improvement in image quality can, nevertheless, be obtained.
Atomic force microscopy of conventional and unconventional nucleic acid structures
Authors: Henderson Eric 
Published: August 2011

SUMMARYImages of conventional (Watson–Crick base paired) and unconventional (G4 RNA) nucleic acid structures have been obtained by atomic force microscopy. The images are reproducibly generated from samples deposited on freshly cleaved mica. Periodic substructural features are evident in fibres observed in both cases. In the case of G4 RNA, tip‐induced formation of large fibres is observed.
Colour thresholding and objective quantification in bioimaging
Authors: Fermin C. D. , Gerber M. A. , Torre‐Bueno J. R. 
Published: August 2011

SUMMARYComputer imaging is rapidly becoming an indispensable tool for the quantification of variables in research and medicine. Whilst its use in medicine has largely been limited to qualitative observations, imaging in applied basic sciences, medical research and biotechnology demands objective quantification of the variables in question. In black and white densitometry (0–256 levels of intensity) the separation of subtle differences between closely related hues from stains is sometimes very difficult. True‐colour and real‐time video microscopy analysis offer choices not previously available with monochrome systems. In this paper we demonstrate the usefulness of colour thresholding, which has so far proven indispensable for proper objective quantification of the products of histochemical reactions and/or subtle differences in tissue and cells. In addition, we provide interested, but untrained readers with basic information that may assist decisions regarding the most suitable set‐up for a project under consideration. Data from projects in progress at Tulane are shown to illustrate the advantage of colour thresholding over monochrome densitometry and for objective quantification of subtle colour differences between experimental and control samples.
The application of cryo‐SEM techniques to the study of the symbiotic association in the Azolla leaf cavity
Authors: Klein Eugenia , Bari Etan , Forni Cinzia , Malkin Shmuel , Tel‐Or Elisha 
Published: August 2011

SUMMARYThe preparation of frozen‐hydrated samples for scanning electron microscopy to observe symbionts in Azolla is described and compared to the conventional method of chemical fixation followed by critical‐point drying. The frozen‐hydrated specimens preserve the structure of the associating symbionts and the liquid phase in the Azollaleaf cavity. The leaf cavity structure and the endosymbionts in the frozen‐hydrated specimens were intact and unharmed throughout the fixation. The cyanobiont cells were distributed along the envelope of the leaf cavity, and did not aggregate around the hair cells, as reported for chemical fixation specimens. The mucilage layer removed by the chemical fixation could be observed in the cryo‐fixation specimens, especially at the lower part of the cavity.
An acoustic depth alarm device to monitor vertical translation of the microscope stage: A practical optical disector, selector and unbiased brick for routine light microscopy
Authors: Laroye Guy J. , Taylor William B. 
Published: August 2011

SUMMARYA description is given of a simple device, which, when attached to the fine adjustment vernier of a regular light microscope, alerts the operator by sound to the vertical distances travelled by the microscope stage without losing visual contact with the specimen. Depending on whether the depth calibration is deemed to be accurate or not, this device can be used as a practical stereological disector or a selector in routine light microscopy, or as an unbiased brick in confocal microscopy.
Experimental determination of light‐element k‐factors using the extrapolation technique: Oxygen segregation in aluminium nitride
Authors: Westwood A. D. , Michael J. R. , Notis M. R. 
Published: August 2011

SUMMARYIt is shown that quantitative light‐element (Z < 10) analysis and κ‐factor determination of light elements can be routinely conducted, analogous to quantification of elements with Z >, using X‐ray energy‐dispersive spectroscopy. The extrapolation technique was used to determine the κ‐factors, κOAI = 0.88 ± 0.10 and κNAI = 1.61 ±0.22 at zero thickness. These values are found to be in good agreement with theoretically calculated κ‐factors. The limitations and applicability of the extrapolation technique for light‐element analyses are discussed. An example of light‐element quantification is provided in the analysis of oxygen segregation to inversion domain boundaries in aluminium nitride.
Beam heating in an asymmetrically illuminated thin circular film
Authors: Curzon A. E. 
Published: August 2011

SUMMARYThe method of images is used to calculate the temperature increase produced in a circular film when the film is illuminated at any point by an electron beam of circular cross‐section and constant current density over its cross‐section. Formulae are given in dimensionless form for (i) the temperature increase anywhere along the line joining the centres of the beam and of the film, (ii) the temperature increase at the centre of the beam (vc), and (iii) the position and value of the maximum temperature increase in the film vm. The relative sizes of vc and vm are discussed and it is shown that (vm – vc)/vm ≤ 0.079. The theory applies best to metallic films where power loss by means of thermal conductivity is dominant. A brief discussion is given of the cases where thermal radiation is important, sample calculations are given for carbon and copper films, and the effect of focusing the electron beam at constant current is considered.
Study of the liquid‐phase sintering process by probabilistic models: Application to the coarsening of WC‐Co cermets
Authors: Quenec‘H Jean‐Louis , Coster Michel , Chermant Jean‐Louis , Jeulini Dominique 
Published: August 2011

SUMMARYA new method using probabilistic models is used to study the growth of WC grains in WC‐Co cermets. Two different models are tested: a Boolean model and a two‐colour mosaic model. The Boolean Poisson model is the simplest for describing and predicting material evolution, and depends only on two independent parameters. They allow the estimation of the connectivity numbers and, moreover, are used to determine the type of reaction which controls the WC‐Co coarsening kinetics.
A tilting device for three‐dimensional microscopy: Application to in situ imaging of interphase cell nuclei
Authors: Bradl Joachim , Hausmann Michael , Ehemann Volker , Komitowski Dymitr , Cremer Christoph 
Published: August 2011

SUMMARYThe resolution of an optical microscope is considerably less in the direction of the optical axis (z) than in the focal plane (x‐y plane). This is true of conventional as well as confocal microscopes. For quantitative microscopy, for instance studies of the three‐dimensional (3‐D) organization of chromosomes in human interphase cell nuclei, the 3‐D image must be reconstructed by a point spread function or an optical transfer function with careful consideration of the properties of the imaging system. To alleviate the reconstruction problem, a tilting device was developed so that several data sets of the same cell nucleus under different views could be registered. The 3‐D information was obtained from a series of optical sections with a Zeiss transmission light microscope Axiomat using a stage with a computer‐controlled stepping motor for movement in the z‐axis. The tilting device on the Axiomat stage could turn a cell nucleus through any desired angle and also provide movement in the x‐y direction.The technique was applied to 3‐D imaging of human lymphocyte cell nuclei, which were labelled by in situ hybridization with the DNA probe pUC 1.77 (mainly specific for chromosome 1). For each nucleus, 3‐D data sets were registered at viewing angles of 0°, 90° and 180°; the volumes and positions of the labelled regions (spots) were calculated. The results also confirm that, in principle, any angle of a 2p geometry can be fixed for data acquisition with a high reproducibility. This indicates the feasibility of axiotomographical microscopy of cell nuclei.
An appraisal of low‐temperature embedding by progressive lowering of temperature into Lowicryl HM20 for immunocytochemical studies
Authors: Robertson David , Monaghan Paul , Clarke Catherine , Atherton Amanda J. 
Published: August 2011

SUMMARYThe progressive lowering of temperature (PLT) method of embedding for electron microscope immunolabelling has been examined with the objective of formulating a standardized protocol which can be applied to a wide variety of samples. The methods described cover fixation, processing of samples by the PLT method, embedding in Lowicryl HM20 and subsequent immunolabelling. Each of the steps in the fixation and embedding protocol has been assessed for its potential to retain both morphology and antigenicity. Comparison of samples embedded in Lowicryl K4M and HM20 at −25°C indicate an increased membrane contrast in HM20 sections, and a further improvement in morphology when samples were embedded in HM20 at −50°C rather than at −25°C. The results of applying the methods described are demonstrated in a range of samples of both mammalian and botanical origin, which includes solid tissues, cells in suspension, and cells grown in vitro as a monolayer culture and embedded in situ. Samples processed by this method have been immunolabelled using a wide range of antibodies recognizing nuclear, cytoplasmic, cell membrane and extracellular matrix antigens.
Artefacts and morphological changes during chemical fixation
Authors: Kellenberger Eduard , Johansen Renata , Maeder Marlies , Bohrmann Bernd , Stauffer Esther , Villiger Werner 
Published: August 2011

SUMMARYThe normally ‘condensed’ (darkly stained) chromosomes of dinofiagellates decondense by swelling. This occurs in an increasing number of cells when the concentration of added OsO4 is decreased. With different fixatives other types of disintegration can be observed, which vary with the concentration. With cryofixation and freeze‐substitution the chromosomes are most ‘condensed’. Escherichia colt infected with bacteriophage T4, with or without active lysozyme production, were studied by optical densitometry for partial lysis and by light and electron microscopy for observing swelling. When active lysozyme is present some of the acrolein (2.5%) ‐ glutaraldehyde (2%)‐fixed cells swell at 0°C, but do not in the absence of lysozyme nor when fixed at room temperature. If OsO4 is added at concentrations ≤0.5%, partial lysis occurs when lysozyme is present. The optical density decreases, the cells lose some matter and swell slightly. The corresponding electron micrographs show gap formation by curdling and/or a decreased concentration of the cytoplasm which reveals certain phage‐related particles.
The use of Lucifer yellow, bodipy, FITC, TRITC, RITC and Texas red for dual immunofluorescence visualized with a confocal scanning laser microscope
Authors: Entwistle A. , Noble M. 
Published: August 2011

SUMMARYA new method of comparing the relative merits of different fluorophores that undergo relatively rapid irreversible photo‐inactivation is described. This method showed that the levels of fluorescent emission seen with both fluorescein isothiocyanate (FITC) and bodipy fl conjugated to streptavidin were similar when examined under conditions where they exhibited equal rates of irreversible photo‐inactivation. Bodipy fl and FITC give lower levels of cross‐talk into images of cells immunofluorescently stained with either rhodamine isothiocyanate (RITC) or tetramethyl rhodamine isothiocyanate (TRITC) than into images of cells stained with Texas red, under conditions where the three red fluorophores exhibited an equal level of sensitivity. Furthermore, bodipy fl gave much lower levels of cross‐talk into images of RITC‐stained cells than either FITC or Lucifer yellow. TRITC, but not RITC or Texas red, gave significant levels of cross‐talk into the green band‐pass filters used to visualize FITC and bodipy fl. From these results it seems that a combination of bodipy fl and RITC provides the best contrast when visualizing dual immunofluorescence with a confocal scanning laser microscope if the 488‐nm line of an argon ion laser is used as the excitation source.
Low‐energy electron microscopy (LEEM) and mirror electron microscopy (MEM) of biological specimens: Preliminary results with a novel beam separating system
Authors: Griffith O. Hayes , Hedberg Karen K. , Desloge Denis , Rempfer Gertrude F. 
Published: August 2011

SUMMARYLow‐energy electron microscopy (LEEM) and mirror electron microscopy (MEM) utilize a parallel beam of slow‐moving electrons backscattered from the specimen surface to form an image. If the electrons strike the surface an LEEM image is produced and if they are turned back just before reaching the surface an MEM image results. The applications thus far have been in surface physics. In the present study, applications of LEEM and MEM in the biological sciences are discussed. The preliminary results demonstrate the feasibility of forming images of uncoated cultured cells and cellular components using electrons in the threshold region (i.e. 0–10 V). The results also constitute a successful test of a novel beam‐separating system for LEEM and MEM.
Digital image acquisition in in vivo confocal microscopy
Authors: Petroll W. M. , Cavanagh H. D. , Lemp M. A. , Andrews P. M. , Jester J. V. 
Published: August 2011

SUMMARYA flexible system for the real‐time acquisition of in vivo images has been developed. Images are generated using a tandem scanning confocal microscope interfaced to a low‐light‐level camera. The video signal from the camera is digitized and stored using a Gould image processing system with a real‐time digital disk (RTDD). The RTDD can store up to 3200 512 times 512 pixel images at video rates (30 images s−1). Images can be input directly from the camera during the study, or off‐line from a Super VHS video recorder. Once a segment of experimental interest is digitized onto the RTDD, the user can interactively step through the images, average stable sequences, and identify candidates for further processing and analysis. Examples of how this system can be used to study the physiology of various organ systems in vivo are presented.
Confocal differential interference contrast (DIC) microscopy: including a theoretical analysis of conventional and confocal DIC imaging
Authors: Cogswell C. J. , Sheppard C. J. R. 
Published: August 2011

SUMMARYA technique for obtaining differential interference contrast (DIC) imaging using a confocal microscope system is examined and its features compared to those of existing confocal differential phase contrast (DPC) techniques as well as to conventional Nomarski DIC. A theoretical treatment of DIC imaging is presented, which takes into account the vignetting effect caused by the finite size of the lens pupils. This facilitates the making of quantitative measurements in DIC and allows the user to identify and select the most appropriate system parameters, such as the bias retardation and lateral shear of the Wollaston prism.
Confocal imaging with bilateral scanning and array detectors
Authors: Brakenhoff G. J. , Visscher K. 
Published: August 2011

SUMMARYA novel arrangement for confocal microscopy is presented, in which the key elements are the use of an array detector such as a CCD for confocal image collection and the use of one double‐sided scanning mirror element for bilaterally scanning the object and collecting the data on the CCD. The resulting arrangement is shown to be capable of confocal imaging with high photon efficiency under adjustable conditions of confocality and varying image acquisition rates, i.e. from slow speed up to real‐time imaging. Either laser or conventional light sources may be utilized. In addition to CCD registration, direct observation by eye of the confocal image in fluorescence is also possible.
In‐vivo confocal scanning laser microscopy of the cerebral microcirculation
Authors: Dirnagl Ulrich , Villringer Arno , Einhäupl Karl Max 
Published: August 2011

SUMMARYConfocal scanning laser microscopy (CSLM) was used to study the microcirculation of the brain neocortex in anaesthetized rats. After removal of the dura mater, implantation of a closed cranial window, and intravenous injection of fluorescein, three‐dimensional reconstructions of cortical capillaries were performed down to a depth of 250 μm below the pial surface. Using a one‐dimensional approach (single line scanning), erythrocyte (negative contrast in fluorescently labelled plasma) and leucocyte (labelled with rhodamine 6 G) velocity and supply rate in cortical capillaries were measured. The effect of CO2‐inhalation on capillary blood flow dynamics was studied. Capillaries were imaged continuously for up to 1 h without changes in flow or fluorescence pattern. However, by increasing the laser power 10–100‐fold, aggregate formation was induced and capillaries were occluded, possibly due to damage to vascular endothelium. We conclude that CSLM can be used to study morphological and dynamic aspects of fluorescently labelled subsurface structures in organs of experimental animals.
Confocal microscopy of the in‐situ crystalline lens
Authors: Masters Barry R. 
Published: August 2011

SUMMARYThe fine structure of the in‐situ rabbit crystalline ocular lens from the ex‐vivo rabbit eye was observed with a confocal scanning laser microscope in the scattered light mode. The images were observed through the full thickness of the cornea and aqueous humour to a depth of 50 μm in the anterior ocular lens. The following structures were observed from optical sections of the ocular lens: two concentric regions of the lens capsule, epithelial cells, lens sutures, and surface and interior regions of individual lenticular fibres. The observed lateral resolution of the microscope objective was degraded by imaging across thick (millimetre) structures. This study shows the feasibility of obtaining high‐contrast images of transparent objects across 1.7 mm of ocular tissue (cornea and aqueous humour) using confocal light microscopy.
Effect of processing dwell‐time on the microstructure of a fibre‐reinforced composite
Authors: SUMMERSCALES J. , GREEN D. , GUILD F. J. 
Published: August 2011

SUMMARYCarbon‐fibre/epoxy‐resin unidirectional laminates were prepared in the laboratory by vacuum‐bag processing. Three plates were produced using different ‘dwell‐times’, before pressure was applied to consolidate the laminate.Sections from the three plates were cut perpendicular to the fibre direction and were examined with a Quantimet 570 Image Analyser. The fibre positions were recorded. The method of microstructural description is based on the size of the Voronoi cell around each fibre; the Voronoi cell around a fibre is defined as the area nearer to that fibre than any other. Thus the dimensions of the cell are a measurement of half the interfibre distance.The measured distributions of Voronoi distances were compared with distributions calculated using the null hypothesis that the fibres are randomly distributed. Comparison showed that fibres from all three sections were clustered, but that the sample from the medium dwell time was most homogeneous. Examination of long Voronoi distances, not predicted by the null hypothesis, showed anisotropy in orthogonal directions arising from the manufacturing process. This method of microstructural analysis revealed a dependence on the plate processing method, and may now be used to evaluate more general processing problems.