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PubMed2001

Hickam 2000: the maturation of, and linkages between, medical informatics and bioinformatics.

I have always been infatuated with computers and convinced of their potential for solving problems in biologic research and clinical care. In the 1960s I thought we could use the computer to predict the shape of macromolecules from their chemical formulas and fundamental physical chemical principles. However, with the computers of the 1960s that was a fantasy. So I focused on the use of computers to manage medical record content and to assist with clinical care. The Electronic Medical Record (EMR) we began developing in 1972 with 33 diabetes patients now carries nearly 300 million separate results for more than 3 million patients. The data include lab and other diagnostic studies, dictated notes, orders, encounter records, radiology images, electrocardiograph tracings, and motion cardiac echoes, and the care provider at Indiana University and Wishard Hospital is accessed 10 million times per year. We have also agitated for standards to make the collection of these data easier. This work has become part of a field called medical informatics. In the meantime, the application of computers to biology has rapidly matured into a field called bioinformatics, and researchers in this field now provide annotated databases for many categories of molecules, programs for "matching" newly discovered genomic sequences with previously studied sequences, and systems for storing and processing massive amounts of genomic and molemic data. They have developed sophisticated methods for predicting the shape of biologic macromolecules and other important insights about biology and evolution. Medical informatics and bioinformatics intersect at many points. The most important intersection is between electronic medical records and the human specimen databases that can link genotype to the phenotype, as needed, to unravel polygenetic disease causality. The National Cancer Institute is embarking on an intriguing effort to use EMRs (phenotype) to link to paraffin blocks (genotype) in pathology laboratories where opportunities for cancer genomic discovery are open. We will participate in this effort and look forward to bending the EMR we developed for clinical use to bioinformatics uses as well.

Clinical Medicine↗

PubMed2000

Chiropractic biophysics digitized radiographic mensuration analysis of the anteroposterior cervicothoracic view: a reliability study.

OBJECTIVE: To investigate the reliability of a radiographic measurement procedure that uses a computer and sonic digitizer to determine projected spinal displacements from an ideal, normal position. DESIGN: A blind, repeated-measure design was used. Anteroposterior cervicothoracic spine radiographs were presented in random order to each of 3 examiners. Each film was digitized, and the films were randomized for a second examination. SETTING: Private, primary care chiropractic clinic. MAIN OUTCOME MEASURES: Intraclass correlation coefficients for intraexaminer and interexaminer reliability for measures on radiographs comparing the perpendicular distance (T(x)) from a vertical axis line drawn through the center of T4 and the center of C2, the linear distance (vertebra(apex)) from the center of the vertebra most displaced from a line connecting the centers of C2 and T4, the angle (Rz) formed by the intersection of the vertical axis line and the upper thoracic line, and the angle of intersection (CDA) between the upper thoracic line and the cervical line. RESULTS: Intraexaminer reliability for T(x) distance was 0.99 to 1.00, with confidence intervals from 0.98-1.00; for vertebra(apex) was 0.96 to 0.97, with confidence intervals from 0.92-0.98; for Rz was 0.94 to 0.98, with confidence intervals from 0. 89-0.99; and for CDA was 0.92 to 0.95, with confidence intervals from 0.84-0.97. Interexaminer reliabilities for the 3 examiners ranged from 0.97 to 0.99. CONCLUSIONS: Measures similar to those described in this study are commonly used to quantify and categorize spinal displacements from true vertical alignment (i.e., scoliosis measurements). Intraclass correlation coefficient values >0.70 are considered accurate enough for use in clinical and research applications. The measures tested here would fit within these guidelines of reliability. Establishing reliability is an important first step in evaluating these measures so that future studies of validity may be undertaken.

Biophysics↗

PubMed2001

Cryoablation of ventricular tachycardia guided by return cycle mapping after entrainment.

BACKGROUND: Although the implantable cardioverter-defibrillator effectively prevents sudden cardiac death, patients are still prone to recurrence of ventricular tachyarrhythmias. Electrophysiologically guided surgery is the most effective modality in abolishing ventricular tachycardia, having a lower recurrence rate than pharmacologic therapy or catheter ablation. Return cycle mapping after entrainment has been shown to localize the central common pathway, which is the target region for ablation, without pacing at the pathway or recording the potentials from the pathway. METHODS: To determine the accuracy and usefulness of return cycle mapping in surgery for ventricular tachycardia, we cryoablated 8 morphologies of ventricular tachycardia induced in postinfarction dogs with the guidance of return cycle mapping. The ventricular tachycardia was entrained from 3 to 5 different epicardial sites at a paced cycle length 10 to 20 ms shorter than the ventricular tachycardia cycle length and the epicardium was mapped with 61 unipolar electrodes during cessation of entrainment to construct return cycle maps. The return cycle was determined by subtracting the first activation time from the second activation time after the last stimulus in each electrode location, and the maps were then displayed on a computer. RESULTS: The total analysis process was completed within 3 minutes by means of a computer with custom-made programs. The activation map during ventricular tachycardia did not localize the central common pathway in any morphology of ventricular tachycardia, because the pattern of activation was concentric and diastolic potentials were not recorded. Cryoablation of the region where the isotemporal lines of the return cycle equal to the ventricular tachycardia cycle length intersected resulted in termination of ventricular tachycardia in all morphologies. The intersection was 26 +/- 9 mm from the earliest activation site. Epicardial mapping with 253 electrodes during cryothermia showed that the region localized by return cycle mapping was the central common pathway sandwiched between the lines of conduction block and that the cryolesion connected the lines of block, blocked the rotating wave front, and resulted in termination of the ventricular tachycardia. CONCLUSION: Return cycle mapping provides an accurate and rapid means of localizing the central common pathway without the need for recording potentials from the pathway or pacing at the pathway in ablation for ventricular tachycardia.

Animals↗

PubMed1978

Iris pigmentation and visual-geometric illusions.

Blur or degrading of the retinal image has been shown to be a factor in the formation of visual-geometric illusions where intersecting line elements are present. Light irises allow more scattered light within the eye, which results in more image degradation than found in dark-eyed subjects. Measurements on 755 observers show that illusion magnitude varies as a function of iris pigmentation for a configuration with intersecting line elements (Müller-Lyer illusion), but not for a configuration devoid of such features (Ebbinghaus illusion).

Eye Color↗

PubMed1981

The many illusions of the Müller-Lyer: comparisons of the wings-in and wings-out illusions and manipulations of standard and dot forms.

The assumed role of peripheral distortion mechanisms in both wings-in and wings-out Müller-Lyer illusions was investigated by requiring subjects to reproduce the central extent of standard Müller-Lyer figures and dot variations. Illusory magnitude of the line and dot variations was also examined with increasing wing length and wing angle. A reduction in the overestimation for the wings-out illusion occurred with the removal of intersecting lines; the dot variations evidenced a significant overestimation effect. In contrast, no reliable decrease in underestimation was found with the removal of intersecting lines in the wings-in illusion, and both standard and dot variations were significantly underestimated. These results support a conclusion that the wings-in and wings-out Müller-Lyer illusions are two distinct illusions, and may be differentially determined at the loci of distortion within the visual system. Parallel changes in illusory magnitude were noted with configural manipulations of standard and dot wings-out illusions. However, standard and dot forms of the wings-in illusion were not equivalently affected by equivalent configural manipulations, which suggests that they are different illusions. Thus, the use of the wings-in dot variation to separate empirically peripheral from non-peripheral distortion mechanisms may be ill-advised.

Discrimination Learning↗

PubMed1981

The Poggendorff illusion: an illusion of linear extent?

In the standard version of the Poggendorff figure a transversal intersects two parallel verticals and the segment of the transversal between the two intersection points, A and B, is not shown. The two portions of the transversal outside the parallels then seem to be misaligned. Besides this illusion of direction, there is also an illusion of size, the distance AB being underestimated in the standard figure. The influence of configural components in determining this spatial distortion of the Poggendorff figure was examined by having subjects reproduce the inner oblique (at 45 degrees) extent AB in variations of the figure. This distance was found to be underestimated in Poggendorff variations which contained parallel (vertical) components that formed an acute angle with AB; and the underestimation increased as the number of these components present in the figure increased. The distance AB was found not be significantly distorted in figures which contained only those parallel (vertical) components that formed an obtuse angle with AB, yet their presence in the figure tended to counteract the underestimation. When the transversals were omitted, the underestimation was found to increase. The findings are interpreted in support of an explanation that reduces the Poggendorff effect to those factors which mediate the Müller-Lyer illusion.

Distance Perception↗

PubMed2006

Effects of surface markings on judgments of motion direction.

The effects of surface markings on perceived motion direction were examined for a rotating sphere in a structure-from-motion display. The markings were dot patterns representing separate line segments or intersecting line segments (crosses) covering the surface of the sphere. The orientation of the surface markings and their intersection angles affected the perceived direction of motion, suggesting that the markings were not interpreted as geodesics or planar cuts on the surface. The perceived direction of motion was biased towards the mean orientation of the markings over the visible area of the surface. A similar bias was observed for translating planar stimuli covered with crosses, suggesting that the bias is not specific to curved surfaces or motion in depth. The deviation between the simulated motion direction and the external horizontal and vertical axes also affected the perceived motion direction. These results suggest that the average orientation of surface contours with respect to an external reference frame influences the perceived direction of motion.

Depth Perception↗

PubMed2006

Background stripes affect apparent speed of rotation.

A gray line that rotated about its own center against a stationary background of vertical stripes appeared to double in perceptual speed as it rotated through the vertical position and thus momentarily aligned with the background. Four factors may contribute to this speed-up: (i) landmarks, in which the tip of the moving vertical line moves horizontally across the maximum number of stationary stripes; (ii) orientation repulsion of the moving line by the vertical stripes, which may distort the line's perceived position and hence its perceived speed; (iii) the orientation of an induced brightness pattern along the line; and (iv) the motion of the induced brightness pattern, which moves physically most rapidly along the line when the line is near vertical. To test these possibilities, an annulus display provided landmarks but no intersections, and this almost abolished the effect. A rotating-slit display provided an oriented, moving pattern that mimicked the induced brightness but had no landmarks, and this increased the effect. We conclude that the motion, but not the orientation, of the intersections [option (iv)] was responsible for the illusion. The fact that this motion along the length of the line affected the perceived speed of the line orthogonal to its own length indicates a failure on the part of the visual system to fully decouple tangential from radial motion.

Contrast Sensitivity↗

PubMed1970

Is the breakdown of the born-oppenheimer approximation responsible for internal conversion in large molecules?

Vibronic radiationless transitions in large polyatomic molecules can be thought of as a process whereby the molecule, initially prepared in a discrete quasistationary state, makes a transition to an adjoining vibronic continuum belonging to a lower electronic state of the same multiplicity. In many instances the transition is analogous to penetration through a barrier between two "nested" potential sheets far away from an actual intersection of the sheets. Simultaneous distortions of vibrational and electronic parts of the wavefunction are required for such a tunneling process. The vibrational distortion manifests itself in the familiar Franck-Condon effect. The electronic distortion can be caused by nontotally symmetric vibrations of the molecule either because of the displaced nuclear configuration, to which the electrons instantly respond (Herzberg-Teller effect), or because of the protracted response of the electrons to the kinetic energy of nuclear motion (nonadiabatic effect or the breakdown of the Born-Oppenheimer approximation). It is found here that Herzberg-Teller coupling is more effective in causing radiationless transitions than the breakdown of the Born-Oppenheimer approximation when the potential surfaces involved are not close to an intersection.

Journal Article↗

PubMed1989

Biregular classification of Fano 3-folds and Fano manifolds of coindex 3.

The Fano 3-folds and their higher dimensional analogues are classified over an arbitrary field k [unk] C by applying the theory of vector bundles (in the case B(2) = 1) and the theory of extremal rays (in the case B(2) >/= 2). An n-dimensional smooth projective variety X over k is a Fano manifold if its first Chern class c(1)(X) epsilon H(2)(X, Z) is positive in the sense of Kodaira [Kodaira, K. (1954) Ann. Math. 60, 28-48] (or ample). If n = 3 and c(1)(X) generates H(2)(X, Z), then either (i) X is a complete intersection in a Grassmann variety G with respect to a homogeneous vector bundle E on G: the rank of E is equal to codim(G)X and X is isomorphic to the zero locus of a global section of E, (ii) X is a linear section of a 10-dimensional spinor variety X(12) (10) [unk] P(k) (15), or (iii) X is isomorphic to a double cover of P(k) (3), a 3-dimensional quadric Q(k) (3), or a quintic del Pezzo 3-fold V(5) [unk] P(k) (6). If n = 4 and c(1)(X) is divisible by 2, then X [unk] C is isomorphic to (a) a complete intersection in a homogeneous space or its double cover, (b) a product of P(1) and a Fano 3-fold, (c) the blow-up of Q(4) [unk] P(5) along a line or along a conic, or (d) a P(1)-bundle compactifying a line bundle on P(3) or on Q(3) [unk] P(4).

Journal Article↗

PubMed2004

Antifreeze protein-induced morphological modification mechanisms linked to ice binding surface.

The mechanisms by which the antifreeze protein (AFP) modifies the ice morphology are identified precisely as surface poisoning by the ice binding surface (IBS) of insect AFPs and as bridge-induced surface reconstruction by the IBS of fish AFPs and antifreeze glycoproteins. The primary surfaces of hexagonal ice have predetermined face indices. The "two-dimensional" insect type IBS has regularly spaced binding intervals in two directions. It causes surface poisoning by matching and reinforcing simultaneously intersecting strong bonding directions on the primary ice surfaces. The secondary ice surfaces have variable face indices. The "one-dimensional" and "irregular" IBS variants of fish AFPs and antifreeze glycoproteins are either linearly extended with regular ice binding intervals or have ice binding sites lacking spacing regularity. These variants can bridge transversely lattice periods or shorter oxygen-oxygen distances between parallel adjacent strong bonding directions that do not intersect. Thus, one-dimensional and irregular IBS variants induce supplementary bridges cross-wise on selected secondary surfaces by mimicking strong bonding directions that are not present in the ice structure. These proteins cause surfaces with variable face indices, which in the absence of the AFPs would not grow flat, to appear in the morphology. Whereas for the primary ice surfaces it is only the morphological importance that is determined by the experimental conditions, for the secondary ice surfaces it is the face indices themselves that become adjusted in the process of maximizing the AFP-substrate interaction through attainment of the best structural match. The growth morphology of the AFP-ice system is derived from various factors, including the face indices, surface molecular compositions, relative growth rates, and the mechanisms responsible for that morphology. The theoretical formulation agrees with experiments over a wide range and resolves these, to date, unexplained phenomena.

Animals↗

PubMed2002

Correction of the glosso-larynx and resultant positional changes of the hyoid bone and cranium.

In ankyloglossia with deviation of the epiglottis and larynx (ADEL) the tongue is located forward and as a result the epiglottis is elevated and leans towards the mouth. The larynx is also raised and curves ventrally. Various symptoms have been observed as a result of this condition. Correction of the glosso-larynx (CGL) is the operation performed to treat ADEL. The CGL procedure and the results obtained with it are reported in this paper. In addition, we studied the following six parameters using head and neck X-rays before and after CGL (the changes in these parameters as a result of CGL are shown in parentheses): (i) the shortest vertical length between the hyoid bone and mandible (+ 10.3 mm); (ii) the vertical length between the hyoid bone and the tangent line of C2-4 (+ 4.6 mm); (iii) the shortest length between the hyoid bone and the chin (+ 2.9 mm); (iv) the angle between the hyoid bone and the tangent line of C2-4 (+ 3.3 degrees); (v) the length of H-M, where H is the intersection of a tangent line of C2-4 and a vertical line from the hyoid bone and M is the intersection of a tangent line of C2-4 and the mandible (+ 7.4 mm); and (vi) the width of the narrowest part of the hypopharynx (+ 3.0 mm). The changes in all the measured parameters after CGL were significantly different (p <0.05).

Adolescent↗

PubMed1978

Fiber counting: a source of error corrected.

Optical counting of fibers (from a filter sample of industrial air, for example) involves determining how many fibers are within counting fields which are squares of side lengths. It is correct to count all those fibers which are completely within the field and half of those which intersect only one side. It is shown here to be incorrect to count half those fibers which intersect two sides; the magnitude of this error is calculated, the calculations being verified through a Monte Carlo simulation. The fractional overcount for fibers of length L less than or equal to s is (L/s)2/2pi.

Air Pollutants↗

PubMed2000

Random breakage and reunion chromosome aberration formation model; an interaction-distance version based on chromatin geometry.

PURPOSE: Using published FISH data for chromosome aberration production in human fibroblasts by hard X-rays to test a breakage-and-reunion model. METHODS: The model assumed pairwise misrejoining, random apart from proximity effects, of DNA double-strand break (DSB) free ends. CAS (chromosome aberration simulator) Monte Carlo computer software implementing the model was modified to use a distance algorithm for misrejoining instead of using DSB interaction sites. The modification (called CAS2) allowed a somewhat more realistic approach to large-scale chromatin geometry, chromosome territories and proximity effects. It required adding a third adjustable parameter, the chromosome territory intersection factor, quantifying the amount of intertwining among different chromosomes. RESULTS: CAS2 gave somewhat better results than CAS. A reasonable fit with a few discrepancies was obtained for the frequencies at three different radiation doses of many different aberration types and of aberrations involving various specific chromosomes in a large data set using one-paint FISH scoring. The optimal average chromosome territory intersection factor was approximately 1.1, indicating that, for an arbitrarily chosen location in the nucleus, on average slightly more than two chromosomes have very nearby loci. Without changing the three parameter values, a fit was also obtained for a corresponding, smaller, two-paint data set. CONCLUSIONS: A random breakage-and-reunion model incorporating proximity effects by using a distance algorithm gave acceptable approximations for many details of hard X-ray aberration patterns. However, enough discrepancies were found that the possibility of an additional or alternate formation mechanism remains.

Algorithms↗

PubMed1997

Evaluation of virtual source beam configurations for rapid tomographic reconstruction of gas and vapor concentrations in workplaces.

Beam path average data from an Open Path Fourier Transform Infrared (OP-FTIR) spectrometer can be used to reconstruct two-dimensional concentration maps of the gas and vapor contaminants in workplaces and the environment using computed tomographic (CT) techniques. However, a practical limitation arises because in the past, multiple-source and detector units were required to produce a sufficient number of intersecting beam paths in order to reconstruct concentration maps. Such a system can be applied to actual field monitoring situations only with great expense and difficulty. A single monostatic OP-FTIR system capable of rapid beam movement can eliminate this deficiency. Instead of many source and detector units, a virtual source arrangement has been proposed using a number of flat mirrors and retroreflectors to obtain intersecting folded beam paths. Three virtual source beam configurations generated for a single-beam steerable FTIR system were tested using 54 flat mirrors and four retroreflectors or 54 flat mirrors and 56 retroreflectors mounted along the perimeter walls of a typical 24- x 21-ft test room. The virtual source CT configurations were numerically evaluated using concentration maps created from tracer gas concentration distributions measured experimentally in a test chamber. Synthetic beam path integral data were calculated from the test maps and beam configurations. Computer simulations of different beam configurations were used to determine the effects of beam geometry. The effects of noise and peak reducing artifacts were evaluated. The performance of the tomographic reconstruction strategy was tested as a function of concentration and concentration gradients.

Air Pollution, Indoor↗

PubMed2002

Roadside particulate air pollution in Bangkok.

Airborne fine particles of PM(2.5-10) and PM2.5 in Bangkok, Nonthaburi, and Ayutthaya were measured from December 22, 1998, to March 26, 1999, and from November 30, 1999, to December 2, 1999. Almost all the PM10 values in the high-polluted (H) area exceeded the Thailand National Ambient Air Quality Standards (NAAQS) of 120 microg/m3. The low-polluted (L) area showed low PM10 (34-74 microg/m3 in the daytime and 54-89 microg/m3 at night). PM2.5 in the H area varied between 82 and 143 microg/m3 in the daytime and between 45 and 146 microg/m3 at night. In the L area, PM2.5 was quite low both day and night and varied between 24 and 54 microg/m3, lower than the U.S. Environmental Protection Agency (EPA) standard (65 microg/m3). The personal exposure results showed a significantly higher proportion of PM2.5 to PM10 in the H area than in the L area (H = 0.80 +/- 0.08 and L = 0.65 +/- 0.04). Roadside PM10 was measured simultaneously with the Thailand Pollution Control Department (PCD) monitoring station at the same site and at the intersections where police work. The result from dual simultaneous measurements of PM10 showed a good correlation (correlation coefficient: r = 0.93); however, PM levels near the roadside at the intersections were higher than the concentrations at the monitoring station. The relationship between ambient PM level and actual personal exposures was examined. Correlation coefficients between the general ambient outdoors and personal exposure levels were 0.92 for both PM2.5 and PM10. Bangkok air quality data for 1997-2000, including 24-hr average PM10, NO2, SO2, and O3 from eight PCD monitoring stations, were analyzed and validated. The annual arithmetic mean PM10 of the PCD data at the roadside monitoring stations for the last 3 years decreased from 130 to 73 microg/m3, whereas the corresponding levels at the general monitoring stations decreased from 90 to 49 microg/m3. The proportion of days when the level of the 24-hr average PM10 exceeded the NAAQS was between 13 and 26% at roadside stations. PCD data showed PM10 was well correlated with NO2 but not with SO2, suggesting that automobile exhaust is the main source of the particulate air pollution. The results obtained from the simultaneous measurement of PM2.5 and PM10 indicate the potential environmental health hazard of fine particles. In conclusion, Bangkok traffic police were exposed to high levels of automobile-derived particulate air pollution.

Air Pollutants↗

PubMed2003

Impact of polycyclic aromatic hydrocarbon emissions from medical waste incinerators on the urban atmosphere.

In this study, polycyclic aromatic hydrocarbon (PAH) emissions from two batch-type medical waste incinerators (MWIs), one with a mechanical grate and the other with a fixed grate, both operated by a medical center, were assessed. Both MWIs shared the same air-pollution control devices (APCDs), with an electrostatic precipitator and a wet scrubber installed in series. Results show that when APCDs were used, total PAHs and total benzo[a]pyrene equivalent (total BaP(eq)) emission concentrations of both MWIs were reduced from 2220 to 1870 microg/m3 and 50 to 12.4 microg/m3, respectively. We used the Industrial Source Complex Short Term model (ISCST) to estimate the ground-level concentrations of the residential area and the traffic intersection located at the downwind side of the two MWIs. For the traffic intersection, we found both total PAHs and total BaP(eq) transported from MWIs to both studied areas were not significant. For the residential area, similar results were found when APCDs were used in MWIs. When APCDs were not included, we found that total PAHs transported from MWIs accounted for < 12%, but total BaP(eq) accounted for > 90%, of the on-site measured concentrations. These results suggest that the use of proper APCDs during incineration would significantly reduce the carcinogenic potencies associated with PAH emissions from MWIs to the residential area.

Air Pollutants↗

PubMedDate not supplied

Accounts from the field: a public relations perspective on global AIDS/HIV.

This study is a theoretical as well as empirical exploration of the power and cultural differentials that mark and construct various intersecting discourses, specifically media discourse, on global AIDS/HIV. It applies the language and concepts of public relations to understand how the press coverage of the pandemic is associated with the variables that impact the newsmaking process as well as the public and policy implications of macro news frames generated over time. Theoretical work in the areas of agenda setting and news framing also instruct the conceptual framework of this analysis. Narrative analysis is used as a methodology to qualitatively analyze three pools of accounts-from people either living with AIDS/HIV, involved in AIDS/HIV work, or discursively engaged in the media construction of the pandemic; from transnational wire service journalists who cover the issue at global and regional levels; and policy shapers and communicators who are active at the global level. These three communities of respondents represent important stakeholders in the AIDS/HIV issue. The findings are analyzed from a public relations standpoint. Perhaps the most important finding of this study is that the public relations approaches used to address AIDS/HIV related issues need to be grounded in context-specific research and communicative practices that bring out the lived realities of AIDS/HIV at grassroots levels. The findings also posit that those situated at critical junctions between various stakeholders need to cultivate a finely balanced understanding of the etic and emic intersections and subjectivities of global/local AIDS/HIV.

Anecdotes as Topic↗