bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profile boundary length can be overestimated by as much as 41% when using a digitizer tablet
Authors: Cornelisse J. T. W. A. , van den Berg T. J. T. P. 
Published: August 2011

SUMMARYIn length measurements on digitizer systems a considerable overestimation of the actual value can occur due to improper algorithms by as much as 41%. The effect of cursor speed on this phenomenon is discussed. Possible algorithms are presented to diminish the problem. We used a two‐way filtering algorithm with a practical error of between 0.1% and 0.4%.
A design‐based proof of Wicksell's integral equation
Authors: Jensen E. B. 
Published: August 2011

SUMMARYWicksell's integral equation (1925) describes, for an aggregate of spherical particles, the relation between the distribution of sphere diameters and the distribution of diameters of circular profiles observed on a planar section. Usually, this integral equation is proved under the assumption that the particle aggregate is a realization of a stationary stochastic process while the position of the planar probe is allowed to be arbitrary. In this note, it is shown that, under the alternative assumption that diameters of circular profiles are sampled by means of a planar FUR (fixed orientation uniform random) probe, Wicksell's equation holds for a deterministic aggregate of spherical particles with arbitrary positions and sizes. Since the proof is based on the randomness generated by the sampling (the design), the proof may be characterized as design‐based. It can thus be concluded that Wicksell's equation may be applied to any aggregate of spherical particles if diameters are sampled by means of random (FUR) planar probes.
Immunofluorescence and protein A‐gold techniques in localization of plant pathogen antigens in Lowicryl K4M embedded tissue
Authors: Rey M. E. C. 
Published: August 2011

SUMMARYThis paper investigates the use of Lowicryl K4M in the embedding of apple tissue for immunocytochemistry. The localization of the extracellular protease of the apple pathogen, Nectria galligena Bres., in infected apple tissue by immunofluorescence and protein A‐gold immunoelectron microscopy is also described. Infected apple tissue was fixed in 0.5% glutaraldehyde and 4% paraformaldehyde and embedded in Lowicryl K4M at 313 K. The protease was isolated and purified from rotted apple tissue by gel filtration and ion‐exchange chromatography. Monospecific antibodies against the protease were raised in rabbits and purified by protein A‐affinity chromatography. Incubation of apple tissue sections, infected with N. galligena, with the mono‐specific antibody and tetramethylrhodamine isothiocyanate (TRITC)‐conjugate, resulted in specific fluorescence of fungal hyphae and cytoplasm of apple cells. Similar localization of colloidal gold particles over hyphae and host cell cytoplasm was demonstrated employing protein A‐gold immunochemistry. The low temperature embedding resin Lowicryl K4M appears to provide adequate morphological preservation of apple tissue and excellent retention of antigenicity. TRITC conjugates and protein A‐gold may prove useful in immunocytochemical investigations of plant‐pathogen interactions.
The unbiased estimation of number and sizes of arbitrary particles using the disector
Authors: Sterio D. C. 
Published: August 2011

SUMMARYA three‐dimensional counting rule and its integral test system, the disector, for obtaining unbiased estimates of the number of arbitrary particles in a specimen is presented. Used in combination with ordinary and recently developed stereological methods unbiased estimates of various mean particle sizes and the variance of particle volume are obtainable on sets of two parallel sections with a known separation. The same principle allows the unbiased estimation of the distribution of individual particle volumes in sets of serial sections.
Effects of fixing and staining on images of tropomyosin Mg‐paracrystals
Authors: Lamvik Michael K. , White Linda R. , Eik‐Nes Kristen B. 
Published: August 2011

SUMMARYTropomyosin Mg‐paracrystals have been studied by positive and negative staining with uranyl acetate and sodium phosphotungstate, either unfixed or fixed with glutaraldehyde. Fixation causes changes in some of the paracrystal bands. Some of the bands are more intense when a positively‐charged staining ion is used than when a negatively‐charged ion is used, in both negative and positive‐staining techniques. This result rules out the suggestion that negative staining is not affected by the charge of the stain in tropomyosin, and agrees with findings in other specimens. Therefore it is unlikely that any simple parameter based on residue size can be used to predict the image intensity from the amino acid sequence for tropomyosin. These staining patterns cast doubt on the earlier interpretation of a prominent white band in the paracrystal as an overlap of alpha‐helical molecular ends.
Diffusive motions in living cytoplasm probed by laser Doppler microscopy
Authors: Steer Martin W. , Picton Jill M. , Earnshaw John C. 
Published: August 2011

SUMMARYWe have examined cytoplasmic motions in growing pollen tube tips using laser Doppler microscopy, a non‐invasive and non‐destructive technique. The observed correlation functions were consistent with the existence of diffusive motions in the tip cytoplasm. Further analysis of the data revealed the existence of at least two major and a third, minor, diffusing species in the cytoplasm. Information from quantitative electron microscopy and from published literature values of cytoplasmic viscosity was used to tentatively identify the organelles contributing to the observed diffusive motions. It is concluded that motions of mitochondria and secretory vesicles dominate the observed correlation functions with a minor component detected from either ribosomes or the microfilament network. Sources of variation in the observed data are discussed, as are the physical limitations that prevent a more positive analysis of the present data.
An automatic pulsed laser microfluorometer with high spatial and temporal resolution
Authors: Docchio F. , Ramponi R. , Sacchi C. A. , Bottiroli G. , Freitas I. 
Published: August 2011

SUMMARYThe paper describes an automatic pulsed laser microfluorometer with high spatial and temporal resolution, developed in our laboratories. The instrument consists of: (i) a nitrogen‐laser‐pumped dye‐laser for the excitation of the fluorescence, (ii) a microscope with additional optics to focus the excitation beam on the sample and to collect the fluorescence, (iii) filters or monochromators to select the output wavelength, (iv) a fast photomultiplier tube to detect the signal, and (v) a dual time‐scale microprocessor‐controlled signal averager for the acquisition and processing of the signal.Examples are given that show the potential of the time‐resolved fluorescence microscopy in studying, quantitatively and qualitatively, the properties of fluorescent molecules.
The appearance in TEM of proteoglycan predentine is fixation dependant
Authors: Goldberg M. , Escaig F. 
Published: August 2011

SUMMARYThe appearance of proteoglycans visualized on thin sections with alcian blue was compared in rat incisor predentine fixed either in aqueous aldehyde solutions or by anhydrous methods (acrolein vapours or rapid freezing‐freeze substitution). The granular or branched chain‐like structures detected after aqueous fixation probably resulted from precipitation or shrinkage of an expanded amorphous gel observed only after anhydrous fixation. In predentine, morphological interactions between proteoglycans and collagen fibres may be also artefactual.
Demonstration of mitochondrial mineral deposits in osteoblasts after anhydrous fixation and processing
Authors: Manston J. , Katchburian E. 
Published: August 2011

SUMMARYThe fine structure of early developing bone was examined using a modification of a new non‐aqueous processing method in which anhydrous glutaraldehyde dissolved in dimethyl‐sulphoxide (GLUT‐DMSO) is used as a fixative.Preliminary results show that the basic morphological features of the cellular and extracellular compartments of developing bone were preserved. The cytoplasm of osteoblasts revealed numerous well‐preserved mitochrondria and other membranous organelles. Inside the mitochrondria there were large and conspicuous electron‐opaque granules of mineral which were more prominent and numerous than in specimens prepared by conventional aqueous procedures. The collagenous matrix also revealed electron‐opaque deposits of mineral. These results support the evidence for the existence of mitochondrial calcium phosphate in osteoblasts in the form of granules.
Pitting and bubbling artefacts in surface replicas made with silicone elastomers
Authors: Gordon Kathleen D. 
Published: August 2011

SUMMARYPitting or bubbling on the surface of epoxy resin replicas is a frequently encountered artefact associated with the use of silicone rubber impression materials. Several variants of this type of artefact are illustrated. It is suggested that bubbles or pits form at the mould: epoxy interface during curing of the epoxy, and that they are caused by gas escaping from the mould material itself. Duration of silicone rubber polymerization, base‐catalyst ratios, and surface porosity of the object may all influence the occurrence of mould degassing.
Modification of the anticontamination device of a Reichert‐Jung freeze fracture apparatus
Authors: Allain Manuel , Ardonceau Jacques 
Published: August 2011

SUMMARYWe describe a modification in the cooling system of the anticontamination shield of a Reichert‐Jung freeze fracture apparatus. We replaced the flexible pipes by a flexible copper braid in order to increase reliability and keep the high quality of replicas.
The relative efficiency of cryogenic fluids used in the rapid quench cooling of biological samples
Authors: Bald W. B. 
Published: August 2011

SUMMARYThe heat transfer characteristics of various cryogenic fluids used in the rapid quench cooling of biological samples are examined. It is concluded that cryofixation should be achieved during the initial plunge stage of the cooling. Liquid nitrogen maintained near its melting point of 63·1 K at a pressure in excess of the critical value of 33·5 atm will produce the quickest cooling. Nitrogen could also provide the best ultrastructure at atmospheric pressure if the minimum plunge depth and velocity criteria are satisfied. Plunging bare thermocouples into cryogenic fluids will lead to erroneous conclusions about the relative cooling efficiencies of various liquids for cryofixation. A qualitative explanation for the results obtained by Silvester et al. (1982) during the rapid cooling of water drops in various fluids is proposed.
Quantitative analysis of pore patterns on rat prostate nuclei using spatial statistics methods
Authors: Pedro Nuno , Carmo‐Fonseca M. , Fernandes Pedro 
Published: August 2011

SUMMARYSpatial statistics methods have been used to analyse the nuclear pore pattern in rat ventral prostate nuclei isolated from adult animals. The observed results show that: (1) pores on prostate nuclear membranes are not randomly distributed; (2) the data sets obtained from different micrographs are consistent with the same statistical model thus suggesting the existence of a typical pore distribution.
Selective demineralization of hard tissues in organic solvents: retention or extraction of proteoglycan?
Authors: Scott J. E. , Burton Shirley M. 
Published: August 2011

SUMMARYIdeally, demineralization of tissues, fossils, etc., should not result in removal of other chemical species along with the mineral components. Organic solvents containing alkylammonium salts of EDTA are good demineralizing media (Scott & Kyffin, 1978), offering great flexibility and a variety of solvent properties which can be chosen either to extract or to retain tissue polymers in situ. The properties of the alkylammonium cation are crucial in determining whether a given solvent will extract tissue polyanions (i.e. nucleic acids, proteoglycans, acid glycoproteins, etc.) or not. The situation is analysed for the general case, using the fact that a simple ion‐exchange reaction determines the outcome. Some solvent‐alkylammonium combinations, e.g. ethanol‐trimethylammonium, are very poor solvents for proteoglycans, leaving them behind in the tissue, whereas by increasing the size of the organic portion of the alkylammonium salt (e.g. to tri‐n‐butylammonium) or changing the solvents to e.g. dimethyl sulphoxide, the proteoglycan can be extracted from cartilage, etc. The aninic half of the alkylammonium salt plays a relatively minor role. The exception is EDTA itself, which sequestrates inorganic ions (e.g. Na+) in organic solvents, thus driving the ion‐exchange towards completion, with efficient conversion to alkylammonium salts of the polyanion.These results, and the chemical background to them, constitute a general framework within which various strategies for demineralization (with or without extraction of tissue polyanion such as proteoglycans) can be formulated.
A thermoelectric microscope stage for the measurement of the supercooling points of microscopic organisms
Authors: Wharton D. A. , Rowland J. J. 
Published: August 2011

SUMMARYThe design and construction of a thermoelectric cooling stage and its use for the determination of the supercooling points of microscopic organisms is described. Stage cooling is produced by a Peltier unit with a refrigerated circulator as a heat sink. Control is achieved by automatically comparing the temperature input to a reference ramp and varying the power input to the Peltier module accordingly.
A standardized technique for the in toto epoxy resin embedding and precipitate‐free staining of small specimens covered by strong protective outer surfaces
Authors: Mothes‐Wagner U. , Wagner G. , Reitze H. K. , Seitz K. A. 
Published: August 2011

SUMMARYA method is described for the in toto embedding and precipitate‐free staining of small invertebrates covered by strong protective outer surfaces.The difficulties of tissue infiltration in undissected animals with cuticles were overcome by the use of ethanol and 1,4‐dioxane as dehydrating agents, and Spurr's medium as the embedding resin. (1) Fixation as appropriate, followed by embedment in aqueous agar; (2) dehydration: 50% ethanol, 70% ethanol, 2 times 100% 1,4‐dioxane, 15–20 min for each step; (3) infiltration: dioxane:resin 1:1 90 min, dioxane:resin 1:3 90 min, pure resin overnight, changed once for an additional 10 h, all steps with constant shaking; (4) polymerization 16 h at 343 K; (5) sectioning; (6) staining: 0·9% cacodylate buffered KMnO4 (pH 6·5) 30–60 s, washing, Reynolds' lead citrate 5 min, washing by grid floating.The advantage of the method is discussed in relation to serial sectioning of entire invertebrates which could not be dissected prior to embedding.
The use of touch‐sensitive screen in interactive morphometry
Authors: Silage Dennis A. , Gil Joan 
Published: August 2011

SUMMARYWe propose the use of a touch‐sensitive screen as a tool to facilitate acquisition of data both in point counting and morphometric planimetry. It obviates the use of a ‘correspondence image’ required with many planimetric devices in which the means for data acquisition and display are separate. The touch‐sensitive screen offers operational advantages over the light pen. The characteristics of this new graphical input device, its assembly and basic operational considerations are introduced and discussed.
Review of the principal contrast effects observed at interphase boundaries using transmission electron microscopy
Authors: Pond R. C. 
Published: August 2011

SUMMARYThis review is concerned with the interpretation of contrast features observed at interphase interfaces using conventional transmission electron microscopy. The principal features which arise are interfacial dislocations and steps, four types of fringes, namely thickness, Δw, displacement and moiré fringes, and lattice images. The contrast mechanisms leading to these features are discussed in the framework of the dynamical theory of electron diffraction. In particular, the influence on image contrast of the cyrstal composition and structure, the interfacial configuration and the crystallographic relationship of the two phases in the specimen is considered. In general, electron diffraction in bi‐crystalline specimens is complicated, and reliable interpretation can only be carried out when the diffraction conditions have been carefully established. The diffraction conditions most widely used are discussed, and their relative merits compared.
Optimized acquisition parameters and statistical detection limit in quantitative EELS
Authors: Pun Thierry , Ellis James R. , Eden Murray 
Published: August 2011

SUMMARYOptimizing the acquisition parameters for EELS recording has to be accomplished simultaneously from the physical and the statistical points of view; the statistical aspect of the question is covered here. Approximate probability density functions of the variables of interest are derived, which provide a global measure of signal‐to‐noise ratio taking into account every step of the EELS edge area estimation process. Qualitative and quantitative advice is given regarding the critical choice of the estimation and integration energy regions. The notion of visual contrast is presented; it permits the introduction of the concept of statistical detection limit. It is found that for typical experimental conditions, when other factors are equal, the required analysis time for the sample varies approximately as the inverse square of the concentration.
Geometric model of the rat intestinal mucosa for stereological evaluation of villus amplification factors
Authors: Mayhew T. M. 
Published: August 2011

SUMMARYThis study was prompted by a desire to compare villus amplification factors at various sites along the small intestine of the laboratory rat. The paper describes a precise and efficient stereological method for achieving this objective. The method relies on conventional intersection counts performed exclusively on transverse sections.Analyses are based on six adult rats. Pieces of small bowel fixed by in situ perfusion were taken from proximal, middle and distal regions. Intersection counts on villus and primary mucosal surfaces were performed on transverse and longitudinal sections through the same regions. These counts revealed that intestinal architecture can be reasonably approximated by the simple geometric model of an isotropic villus surface on an anisotropic (cylindrical) primary mucosal surface. As a result, intersection counts may be confined to transverse sections (to reduce sampling variance) and the appropriate ratio estimator multiplied by the numerical coefficient 4/¶ (to obtain an estimate of surface amplification due to villi).
Flash X‐ray microscopy with a gas jet plasma source
Authors: Feder R. , Pearlman J. S. , Riordan J. C. , Costa J. L. 
Published: August 2011

SUMMARYA novel flash X‐ray source, the gas jet plasma source, has been used for contact X‐ray microscopy. Using a wavelength range of 2–7 nm a resolution of the order of 30 nm can be obtained. The gas jet plasma source provides a new and unique tool which should allow future imaging of wet live cells.
Quantitative assessment of radiation damage in a thin protein crystal
Authors: Jeng Tzyy‐Wen , Chiu Wah 
Published: August 2011

SUMMARYRadiation damage is a limiting factor for high resolution structural determination of protein crystals. We have used the median and quartile values of Ne exposures and the structural disordering factor (ΔB) to describe the crystalline disordering due to radiation damage in thin crystals of crotoxin complex embedded in glucose at room and low temperatures and in ice embedded crystals. By approximating the radiation damage to follow first order kinetics, we applied a correction to the diffraction intensities from patterns with high accumulated exposures. We used the structural similarity factor (R) to show that, for some data, the effectiveness of the correction can be as good as those in protein X‐ray crystallography.
A cryoembedding method for cutting ultrathin cryosections from small frozen specimens
Authors: Steinbrecht R. A. , Zierold K. 
Published: August 2011

SUMMARYA technique is described which allows one to embed small frozen specimens for easy sectioning in a cryoultramicrotome. n‐Heptane is recommended as a cryoembedding medium due to its suitable melting point (182.4 K), high vapour pressure, chemical inertia, and good sectioning properties when solid. Freeze dried cryosections of cultured muscle cells, slime moulds, insect antennae and unicellular algae are presented as examples. There is no evidence that the preparation disturbs the distribution of soluble elements in the specimen, since X‐ray spectra of muscle cells exposed to heptane do not differ from those of samples not exposed.
Representation of three‐dimensionally reconstructed objects in electron microscopy by surfaces of equal density
Authors: Radermacher M. , Frank J. 
Published: August 2011

SUMMARYA surface representation algorithm has been developed to visualize the results of three‐dimensional reconstructions from projections in electron microscopy. It produces an easily recognizable image of the reconstructed particle and facilitates comprehension of the three‐dimensional structure. Thus building of physical models can be avoided in many cases. If such a model is needed the algorithm can be used to establish the correct particle boundary in advance. Some further effort has been made to represent long fibres and visualize inner structures of objects, which are obscured by outer high‐density regions. Shading may be used to enhance the depth perception from single views.
Formaldehyde and glutaraldehyde in the fixation of chromatin for electron microscopy
Authors: Sewell B. Trevor , Bouloukos Catherina , von Holt Claus 
Published: August 2011

SUMMARYGlutaraldehyde and formaldehyde have been used to fix chromatin core particles for electron microscopy. Glutaraldehyde crosslinks protein only, whereas formaldehyde crosslinks protein and DNA. This is confirmed by the observation that the detergents sodium dodecyl sulphate, Sarkosyl NL 35 and benzylalkyldimethyl ammonium chloride separate the DNA from the protein in the case of glutaraldehyde fixed core particles but not in the case of formaldehyde fixed core particles. The fixative used in the preparation must therefore be considered as a further variable when evaluating electron microscopic images of chromatin.
Double‐axis rotary replication for deep‐etching
Authors: Shibata Y. , Arima T. , Yamamoto T. 
Published: August 2011

SUMMARYWe have developed a simple new method of rotary shadowing, double‐axis rotary replication, for observing three‐dimensional structures in deep‐etched, rapid‐frozen tissues. The technical details of this method are described and compared with the conventional fixed‐angle rotary shadowing procedure.
Quantitative morphological analysis in a SEM‐microcomputer system—I. Quantitative shape analysis of single objects
Authors: Sergeev Y. M. , Spivak G. V. , Sasov A. Y. , Osipov V. I. , Sokolov V. N. , Rau E. I. 
Published: August 2011

SUMMARYThe combination of a scanning electron microscope and a microcomputer can be used to carry out automatic, quantitative, morphological analysis of a wide range of samples. A system implemented around a commercially available 8‐bit computer and interface hardware is described. Computerized analysis of shape is most accurately carried out by the use of numerically determined Fourier transforms of the high contrast bright field transmitted electron image; however, Walsh functions offer very significantly faster processing times on smaller computer systems.