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PubMed2005

Diffuse boundary extraction of breast masses on ultrasound by leak plugging.

We propose a semiautomated seeded boundary extraction algorithm that delineates diffuse region boundaries by finding and plugging their leaks. The algorithm not only extracts boundaries that are partially diffuse, but in the process finds and quantifies those parts of the boundary that are diffuse, computing local sharpness measurements for possible use in computer-aided diagnosis. The method treats a manually drawn seed region as a wellspring of pixel "fluid" that flows from the seed out towards the boundary. At indistinct or porous sections of the boundary, the growing region will leak into surrounding tissue. By changing the size of structuring elements used for growing, the algorithm changes leak properties. Since larger elements cannot leak as far from the seed, they produce compact, less detailed boundary approximations; conversely, growing from smaller elements results in less constrained boundaries with more local detail. This implementation of the leak plugging algorithm decrements the radius of structuring disks and then compares the regions grown from them as they increase in both area and boundary detail. Leaks are identified if the outflows between grown regions are large compared to the areas of the disks. The boundary is plugged by masking out leaked pixels, and the process continues until one-pixel-radius resolution. When tested against manual delineation on scans of 40 benign masses and 40 malignant tumors, the plugged boundaries overlapped and correlated well in area with manual tracings, with mean overlap of 0.69 and area correlation R2 of 0.86, but the algorithm's results were more reproducible.

Algorithms↗
PubMed2000

New CO and Millimeter Continuum Observations of the z = 2.394 Radio Galaxy 53W002.

The z=2.39 radio galaxy 53W002 lies in a cluster of Lyalpha emission-line objects and may itself be undergoing a major burst of star formation. CO (3-2) emission, at 102 GHz, was detected from 53W002 in 1997 by Scoville et al., who also reported a possible 30 kpc extension and velocity gradient suggesting a rotating gaseous disk. In this Letter, we present new interferometric CO (3-2) observations that confirm the previous line detection with improved signal-to-noise ratio, but show no evidence for source extension or velocity gradient. The compact nature of the CO source and the molecular mass found in this object are similar to luminous infrared galaxies and other active galactic nuclei previously studied.

Journal Article↗
PubMed1991

[The qualitative and quantitative diagnostic significance of P-VEP in the evaluation of glaucomatous visual function damage].

The pattern visual evoked potential (P-VEP) and the central visual field in 63 cases (95 eyes) of primary glaucoma were simultaneously measured with the American Compact Four electrophysiology apparatus and the Chinese TBC-IA central field analyzer. The data showed that the mean latency of P1 in the glaucomatous eyes was significantly lengthened, and this occurred before the visual field and disk abnormalities, indicating that VEP is sensitive in the detection of early glaucoma. Furthermore, the VEP changes were consistent with the central visual field defects qualitatively and quantitatively. Therefore, the latency of P1 can be a useful quantitative index in the evaluation of glaucomatous visual function damage. The difference in diagnostic sensitivity to glaucoma between VEP and visual field changes were discussed. The authors suggest that combination of the two may be a more useful index.

Adult↗
PubMed1996

Ultrastructural study of the dorsal lingual epithelium of the soft-shell turtle, Trionyx cartilagineus (Chelonia, Trionychidae).

BACKGROUND: The soft-shell turtle, Trionyx cartilagineus, is classified phylogenetically to the family Trionychidae, whose members live in small rivers or ponds. The purpose of the present study was to examine the ultrastructure of the dorsal epithelium of the tongue of the soft-shell turtle and to compare the results of the observations with those reported for the tongue of other freshwater turtles. METHODS: Light microscopy, transmission electron microscopy, and scanning electron microscopy were used to examine the dorsal epithelium of the tongue of the soft-shell turtle. RESULTS: The tongue is triangular with a slightly round apex when viewed dorsally but it appears flattened when viewed laterally. Lingual papillae were visible on the dorsal surface of the tongue with some localized variations. Irregular, dome-shaped or ridge-like papillae were observed on the anterior part of the dorsal lingual surface. Large, cylindrical papillae were located along the midline of the posterior part of the tongue. Low, disk-like papillae were located on both sides of the dorsal surface of the posterior part of the tongue. Taste pores were recognizable in the center of the disk-like papillae. At higher magnification, scanning electron microscopy revealed microridges on the surface of cells located on the outermost side of the anterior part of the tongue, and the thickenings of cell margins were clearly seen. Microvilli were distributed compactly over the entire posterior part of the tongue. Light microscopy revealed that the mucosal epithelium of the anterior part of the tongue was of the keratinized, stratified squamous type, while the mucosal epithelium of the posterior part of the tongue was of the nonkeratinized, stratified cuboidal type. In the latero-posterior part of the tongue, taste buds were recognized. Transmission electron microscopy revealed that the epithelium of the anterior part of the tongue was of a typical keratinized type. Small numbers of keratohyalin granules and membrane-coating granules appeared in the cytoplasm of the shallow intermediate layer. On the apical side of the lingual papillae located on the posterior side of the tongue, cells from the intermediate layer to the surface layer of the non-keratinized epithelium contained many fine, discoidal granules. A large part of the epithelium consisted of mucous cells in the concave area on the posterior side. CONCLUSIONS: The dorsal surface and epithelium of the tongue of the soft-shell turtle differed significantly from those of other freshwater turtles, in spite of the similarity in terms of gross morphology among the tongues of such turtles.

Animals↗
PubMed1976

Synchronous bilateral fluorescein angiography. A new technique.

Simultaneous angiography of both eyes allows the synchronous measurement of the arm-retina-time and the retinal circulation time in each eye. The dye-filling pattern of retinal arteries, choroid, disc, and cilioretinal vessels can be compared. A new method of simultaneous fluorescein angiography of both eyes, using two fundus cameras, is demonstrated. Each camera is operated by a separate power unit, thereby providing sufficient light energy for one picture every 0.6 second. The fluorescein is injected by means of an automatic injector in order to create a compact dye bolus. Simultaneous angiograms of a healthy patient and of a patient with unilateral carotid occlusion are shown.

Choroid↗
PubMed1995

[Photo Compact Disc: proposal for the electronic storage of images].

We applied the Photo-CD technology to create an electronic image file easy and quick to use to optimize the retrieval of medical images for teaching purposes. We digitized 1,500 slides of diagnostic examinations from the archive of our Institution: the corresponding electronic files were stored on Photo-CD disks. The data relevant to every image were collected and recorded with the help of a relational data-base program. Thus, each user could retrieve the suitable images from the optical disks by a multiple and flexible key-word search. We compared the use of the electronic archive with a traditional hand-based file with the help of 3 teachers committed to prepare a lesson containing 5 slides on different subjects. The use of the electronic image archive corresponded to markedly shorter searching and file updating times. We tried also to assess the capabilites of this filing procedure for image post-processing and for the build-up of self-assessment programs.

CD-ROM↗
PubMed1998

Global spiral patterns in galaxies: complexity and simplicity.

A coherent exposition of the density wave theory of galactic spirals is presented in a recent monograph. It is centered on the working hypothesis of quasi-stationary spiral structure, a possibility first proposed by Bertil Lindblad. This hypothesis has since been found to be widely applicable in a number of physical contexts, including the explanation of the Hubble classification system and other categorical classes. Direct empirical support of this hypothesis has been provided especially by the regularity of the infrared images frequently observed in a number of galaxies (e.g., NGC 309), and by the observed amplitude modulation along the spiral arms (e.g., M51, M81, and NGC 1300). The present paper is a brief review of this theory with further clarification of the fundamentals and of certain specific issues raised in the literature. On the theoretical side, the likelihood for the validity of this hypothesis has been supported by modal studies. Emphasis is placed on the widely observed coexistence of a single regular structure in the Pop II objects and the more complex irregular structures in the Pop I objects, a contrast first discovered by Zwicky many years ago in the main disk of M51. It is pointed out that, in both barred and nonbarred spirals, this basic phenomenon may be understood by noting the fact that the microscale of the collisionless system of Pop II stars--i.e., the diameter of the epicycle--is typically on the same order of magnitude as the observed spacing between the spiral arms. The spiral pattern is thus a very compact structure which is unlikely to respond readily to internal and external disturbances of moderate magnitudes. This apparent robustness in structure is suggested by its observed regularity despite the impact from the coexisting Pop I objects with their strong irregular turbulent motions. This physical picture supports Oort's conjecture of a limited role for tidal interaction in most of the spiral structure of galaxies. It also enables us to place in proper perspective a controversy between two schools of thought, with different emphasis placed on intrinsic mechanisms and on tidal interaction. It is primarily a matter of applicability, or frequency of occurrence of the different scenarios proposed. There is, as yet, little observational evidence presented in the literature that would support the need of an interpretation of the global spiral structure in the galactic disk in terms of a fast evolving structure recently generated from a featureless initial state through tidal interaction. Dynamically, the likelihood for realizing such a scenario is also estimated to be quite low. The above discussions are placed in the context of a general point of view much advocated in current scientific literature; namely, the need to analyze alternative mathematical models for diverse physical contexts in the study of "complex" systems and to judge separately the merits of each model on the basis of its empirical confirmation in an appropriate physical context.

Journal Article↗
PubMed2002

ZTR: a new format for DNA sequence trace data.

MOTIVATION: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth. RESULTS: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive. lmb.cam.ac.uk/pub/staden/io_lib/test_data.

Algorithms↗
PubMed1995

Myocardial gap junction organization in ischemia and infarction.

Ischemia causes an increase in myocardial resistivity and a decrease in conduction velocity, thereby enhancing cardiac contractile dysfunction and arrhythmic tendency. Myocardial gap junctions, as principal determinants of conduction velocity, may, therefore, be expected to be deranged in ischemia. Despite a lack of consensus, attempts at correlating gap junction ultrastructural morphology with functional state have revealed the component connexons of gap junctions in freeze-fractured myocardium to be in multiple small hexagonal arrays, tending to become randomly distributed and compacted under uncoupling conditions. Further hypoxic uncoupling causes ultrastructural damage and a reduction in gap-junctional surface area. Immunohistochemical detection of connexin43 gap junctions in chronically ischemic non-infarcted human myocardium demonstrates a reduction in junctional surface area within a normal number of intercalated disks per myocyte, and with a normal distribution of junction sizes. In healed canine infarction there are smaller and fewer gap junctions in the fibrotic myocardium adjacent to infarcts, with reductions in overall gap-junctional content and the proportion of side-to-side vs. end-to-end intercellular connections. Immunohistochemical examination of intact human ventricular myocardium shows the myocytes immediately abutting healed infarcts to have connexin43 gap junctions spread longitudinally over the cell surfaces, and not in discrete transversely orientated intercalated disks as in normal myocardium. Early after canine infarction, and before fibrotic healing, the connexin43 gap junctions in myocytes abutting the infarct show disorganization similar to that described in healed human infarcts, suggesting that this disturbance is an early pathophysiological cellular response, and not simply due to later fibrotic distortion. Such changes in gap-junctional organization in myocardial ischemia and infarction may be implicated in the elusive link between subcellular structure, contractile dysfunction and arrhythmogenesis.

Animals↗
PubMed1992

Microtubule organization during maturation of Xenopus oocytes: assembly and rotation of the meiotic spindles.

Assembly of the meiotic spindles during progesterone-induced maturation of Xenopus oocytes was examined by confocal fluorescence microscopy using anti-tubulin antibodies and by time-lapse confocal microscopy of living oocytes microinjected with fluorescent tubulin. Assembly of a transient microtubule array from a disk-shaped MTOC was observed soon after germinal vesicle breakdown. This MTOC-TMA complex rapidly migrated toward the animal pole, in association with the condensing meiotic chromosomes. Four common stages were observed during the assembly of both M1 and M2 spindles: (1) formation of a compact aggregate of microtubules and chromosomes; (2) reorganization of this aggregate resulting in formation of a short bipolar spindle; (3) an anaphase-B-like elongation of the prometaphase spindle, transversely oriented with respect to the oocyte A-V axis; and (4) rotation of the spindle into alignment with the oocyte axis. The rate of spindle elongation observed in M1 (0.7 microns min-1) was slower than that observed in M2 (1.8 microns min-1). Examination of spindles by immunofluorescence with antitubulin revealed numerous interdigitating microtubules, suggesting that prometaphase elongation of meiotic spindles in Xenopus oocytes results from active sliding of antiparallel microtubules. A substantial number of maturing oocytes formed monopolar microtubule asters during M1, nucleated by hollow spherical MTOCs. These monasters were subsequently observed to develop into bipolar M1 spindles and proceed through meiosis. The results presented define a complex pathway for assembly and rotation of the meiotic spindles during maturation of Xenopus oocytes.

Animals↗
PubMed1991

Access to information about AIDS.

Medical information related to human immunodeficiency virus (HIV) infection is highly diverse, and the practicing physician or researcher may find specific information difficult to locate. To provide timely access to medical information on topics related to the acquired immunodeficiency syndrome (AIDS), several computer-based products have recently been developed. Some are available from vendors of online information systems, whereas others are available only on CD-ROM or floppy disk. We review several computer-based products. AIDSLINE is the most comprehensive bibliographic index, AIDSTRIALS contains specific information about ongoing unpublished investigational studies, and AIDS Knowledge Base from San Francisco General Hospital is an up-to-date electronic textbook covering all aspects of AIDS. COMPACT LIBRARY: AIDS operates on a microcomputer and combines several databases, including full-text AIDS-related articles from nine major medical journals. AIDS References from the Bureau of Hygiene and Tropical Diseases provides critical analysis of publications worldwide. Although smaller in size than AIDSLINE, about one third of the publications covered by this resource are not covered by AIDSLINE.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Scheimpflug attachment for ophthalmological slitlamps.

Scheimpflug imaging is a technique suited for the quantification of minor opacities of the human eye lens. In the past, several Scheimpflug systems have been developed but being fairly complex and expensive, they have not been widely used. At present, only one instrument is on the market. For these reasons, a new Scheimpflug attachment-to be operated in connection with a slitlamp-was developed. The system is of compact, light-weight and modular design and consists of commercially available components. The Scheimpflug image, recorded by a CCD camera, is digitized in real time by a PC. It is displayed on a video monitor for on-line alignment. The data obtained are permanently stored on optical disk and are available for further analysis. The design of a prototype instrument is described. The practical applicability of the instrument and the high quality of the images is demonstrated.

Adult↗
PubMed2006

Structure of plastically compacting granular packings.

In this paper we present results of structural studies of compacting experimental systems of ductile grains in two and three dimensions. The high precision of our two-dimensional experiments enables a detailed study of the evolution of coordination numbers and local crystalline arrangements as a function of the packing fraction. The structure in both dimensions deviates considerably from that of hard disks and spheres, although geometrically, crystalline arrangements dominate on a local scale (in two dimensions). In three dimensions, the evolution of the coordination number is compared to experimental packings of hard and ductile grains from the literature. This comparison shows that the evolution of coordination number with packing fraction is not unique for ductile systems in general, but must depend on rheology and grain size.

Journal Article↗
PubMed2001

Computational modeling predicts the structure and dynamics of chromatin fiber.

BACKGROUND: The compact form of the chromatin fiber is a critical regulator of fundamental processes such as transcription and replication. These reactions can occur only when the fiber is unraveled and the DNA strands contained within are exposed to interact with nuclear proteins. While progress on identifying the biochemical mechanisms that control localized folding and hence govern access to genetic information continues, the internal structure of the chromatin fiber, let alone the structural pathways for folding and unfolding, remain unknown. RESULTS: To offer structural insights into how this nucleoprotein complex might be organized, we present a macroscopic computer model describing the mechanics of the chromatin fiber on the polymer level. We treat the core particles as electrostatically charged disks linked via charged elastic DNA segments and surrounded by a microionic hydrodynamic solution. Each nucleosome unit is represented by several hundred charges optimized so that the effective Debye-Hückel electrostatic field matches the field predicted by the nonlinear Poisson-Boltzmann equation. On the basis of Brownian dynamics simulations, we show that oligonucleosomes condense and unfold in a salt-dependent manner analogous to the chromatin fiber. CONCLUSIONS: Our predicted chromatin model shows good agreement with experimental diffusion coefficients and small-angle X-ray scattering data. A fiber of width 30 nm, organized in a compact helical zigzag pattern with about 4 nucleosomes per 10 nm, naturally emerges from a repeating nucleosome folding motif. This fiber has a cross-sectional radius of gyration of R(c) = 8.66 nm, in close agreement with corresponding values for rat thymus and chicken erythrocyte chromatin (8.82 and 8.5 nm, respectively).

Algorithms↗
PubMed1989

The Erlangen micro-lightguide spectrophotometer EMPHO I.

The Erlangen micro-lightguide spectrophotometer EMPHO 1 was designed for fast diffuse reflection (remission) spectrophotometry in small tissue volumes. The aim was to construct a compact, modular instrument with a high repetition rate which can be adapted to moving organs, e.g. the beating heart in situ, by the use of highly flexible micro-lightguides. Focusing problems, which cannot be solved when conventional optical devices such as microscopes are used in moving tissues, become negligible. A bandpass interference filter disk, which is rotated by a motor serves as a monochromating unit. One diffuse reflection spectrum in a selected wavelength domain is recorded during each revolution of the motor. Special filter disks, with spectral ranges of 400-520, 500-630, 600-1200 nm can be used for different tasks. The monochromated light is transmitted by means of a flexible fluid-lightguide to a photomultiplier tube. The electrical signal, which is proportional to the light intensity is recorded by an IBM-compatible AT. An analogue to digital converter has been developed for the AD conversion. Sampling of the spectra occurs in steps of 2 nm triggered by a decoding unit, containing an EPROM where the function between the wavelength-angular position characteristic of the filter disk is stored. A decoder wheel mounted on the same axle as the driving motor is used to program the decoder unit and to recall the wavelength position function. The decoding procedure enables a high wavelength reproducibility to be attained. The monochromating device allows a sampling velocity of 100 spectra per second. The EMPHO I has been successfully applied to experiments in the beating heart, the brain, the eye, the liver, the small intestine and the skeletal muscle of mammals. First investigations have also been performed in the heart during open heart surgery and in human skin. The apparatus has a high sampling rate and the small catchment volume allows measurements of remission spectra in tissue volumes supplied by only a few capillaries. The absolute oxygenation and the relative haemoglobin concentration can be determined by on-line computer evaluation of the recorded spectra and displayed on a screen.

Animals↗
PubMed2004

A multichannel electronic monitor of acoustic behaviors, and software to parse individual channels.

We designed an electronic device to monitor calling behavior in male crickets. The device and its associated software can record to disk the activity of as many as 16 individuals simultaneously. The data recorded contain detailed information about the temporal structure of each individual's calls. The temporal resolution achieved with an ordinary PC is good enough to detect and record the occurrence of every pulse of sound from each cricket. The resulting data files are efficient and compact, and so the system is appropriate for experiments lasting many days.

Acoustics↗
PubMedDate not supplied

Using difference intervals for time-varying isosurface visualization.

We present a novel approach to out-of-core time-varying isosurface visualization. We attempt to interactively visualize time-varying datasets which are too large to fit into main memory using a technique which is dramatically different from existing algorithms. Inspired by video encoding techniques, we examine the data differences between time steps to extract isosurface information. We exploit span space extraction techniques to retrieve operations necessary to update isosurface geometry from neighboring time steps. Because only the changes between time steps need to be retrieved from disk, I/O bandwidth requirements are minimized. We apply temporal compression to further reduce disk access and employ a point-based previewing technique that is refined in idle interaction cycles. Our experiments on computational simulation data indicate that this method is an extremely viable solution to large time-varying isosurface visualization. Our work advances the state-of-the-art by enabling all isosurfaces to be represented by a compact set of operations.

Journal Article↗