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PubMed2006

Sungear: interactive visualization and functional analysis of genomic datasets.

UNLABELLED: Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY: A live online version of Sungear can be found at http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi

Algorithms↗

PubMed2005

A method for 3D reconstruction of tree crown volume from photographs: assessment with 3D-digitized plants.

We developed a method for reconstructing tree crown volume from a set of eight photographs taken from the N, S, E, W, NE, NW, SE and SW. This photographic method of reconstruction includes three steps. First, canopy height and diameter are estimated from each image from the location of the topmost, rightmost and leftmost vegetated pixel; second, a rectangular bounding box around the tree is constructed from canopy dimensions derived in Step 1, and the bounding box is divided into an array of voxels; and third, each tree image is divided into a set of picture zones. The gap fraction of each picture zone is calculated from image processing. A vegetated picture zone corresponds to a gap fraction of less than 1. Each picture zone corresponds to a beam direction from the camera to the target tree, the equation of which is computed from the zone location on the picture and the camera parameters. For each vegetated picture zone, the ray-box intersection algorithm (Glassner 1989) is used to compute the sequence of voxels intersected by the beam. After processing all vegetated zones, voxels that have not been intersected by any beam are presumed to be empty and are removed from the bounding box. The estimation of crown volume can be refined by combining several photographs from different view angles. The method has been implemented in a software package called Tree Analyzer written in C++. The photographic method was tested with three-dimensional (3D) digitized plants of walnut, peach, mango and olive. The 3D-digitized plants were used to estimate crown volume directly and generate virtual perspective photographs with POV-Ray Version 3.5 (Persistence of Vision Development Team). The locations and view angles of the camera were manually controlled by input parameters. Good agreement between measured data and values inferred from the photographic method were found for canopy height, diameter and volume. The effects of voxel size, size of picture zoning, location of camera and number of pictures were also examined.

Imaging, Three-Dimensional↗

PubMedDate not supplied

Right ventricular performance is impaired by full assist of left heart bypass. Analysis of right ventricular performance against change in afterload in heart failure models.

The purpose of this study was to assess right ventricular (RV) performance during left heart bypass (LHB) and to determine the optimum LHB driving conditions to preserve RV performance. LHB was established with a centrifugal pump in eight mongrel dogs weighing 11-19 kg. Failing heart models were induced by normothermic aortic clamping for 20 min. RV volume was measured by a conductance catheter, and RV performance was evaluated by two parameters. One was the slope of the RV end-systolic pressure-volume relationship (ESPVR) as a load independent index, and the other was the peak RV pressure (PRVP)-RV stroke volume (RVSV) relationship as a "force-velocity relationship." These parameters were measured during varying assist ratios of LHB at 0% to 100% of pulmonary artery flow, and varying afterload as induced by bilateral intrapulmonary balloon inflation. In failing hearts, RV ESPVR showed an inverse correlation, with the assist ratio of LHB significantly decreasing from 4.23 +/- 1.35 (mmHg/ml) to 3.52 +/- 1.30 (mmHg/ml; P < 0.05) after 100% LHB assist. The correlation between PRVP and RVSV also was inversely linear, the slope of this correlation becoming significantly steeper after 100% LHB assist compared to that without LHB (-0.131 +/- 0.042 vs. -0.051 +/- 0.038, P < 0.005). These two slopes intersected, and this intersection was considered the critical point of afterload above which RVSV was decreased by LHB compared to that without LHB. In addition, reducing the assist ratio made the slope of the PRVP-RVSV correlation significantly more gentle (70%: -0.072 +/- 0.037 vs. 100%: -0.131 +/- 0.042, P < 0.05), with the intersection of the two slopes shifting rightward (i.e., higher afterload). Consequently, the critical level of afterload at 70% LHB assist was significantly higher than that at 100% LHB assist (70%: 38.1 +/- 6.9 vs. 100%: 29.2 +/- 6.8, P < 0.05). Therefore, RV performance against afterload was improved by reducing the assist ratio of LHB. This study demonstrates that RV performance is impaired by full LHB assist if the RV afterload is above the critical level, and that reducing the assist ratio may improve RV performance against afterload.

Animals↗

PubMed1999

Computerized analysis of gray-value profiles in spongy and cortical bone. Clinical experience.

RATIONALE AND OBJECTIVES: Osteoporosis is characterized by a loss of bone mineral density and deterioration of structure. The authors present a structural parameter for the quantitative assessment of osteoporotic changes in vertebral bone. METHODS: In 40 patients without or with known osteoporotic fractures, spongiosa and cortical bone mineral density was measured in lumbar vertebrae 1 to 3 by quantitative CT. Additional axial high-resolution CT slices were obtained for the structural analysis. In the spongiosa, the gray-value profile along a horizontal line in the CT slice was used, whereas in the cortical shell a profile was obtained from the cortical ridge. Both profiles were intersected with a horizontal line of variable position, and the maximum number of intersections was determined. RESULTS: The maximum number of intersections is significantly higher in cases with fractures (spongiosa 48.6, cortical shell 77.3) than in cases without fractures (spongiosa 42.1, cortical shell 62.4). It also correlates with bone mineral density and age. CONCLUSIONS: The presented method shows significantly different numeric results for patients with and without osteoporotic fractures. The analysis is easy to perform and provides additional information on the bone structure that may be used in combination with bone mineral density measurements.

Adult↗

PubMed2002

Perforator topography of the deep inferior epigastric perforator flap in 100 cases of breast reconstruction.

The anatomic topography of the perforators within the rectus muscle and the anterior fascia largely determines the time needed to harvest the perforator free flap and the difficulty of the procedure. In 100 consecutive cases, the topographic patterns of the perforators were investigated. In 65 percent, a short intramuscular course was seen. In 16 percent, a perforator at the tendinous intersection was encountered. In 9 percent, the largest perforator was found to have a long intramuscular course. In 5 percent, a subfascial course was found, and in another 5 percent, a paramedian course was found. In 74 percent of flaps, just one perforator was used, whereas two perforators were dissected in 20 percent. Only in 6 percent of flaps were three perforators used. A long intramuscular course (>4 cm) lengthens the dissection substantially, especially when the intramuscular course is in a step-wise pattern. The subfascial course requires precarious attention at the early stage of the perforator dissection when splitting the fascia. The perforators at the tendinous intersections are the most accessible and require a short but intense dissection in the fibrotic tissue of intersection. A paramedian perforator, medial to the rectus muscle, is a septocutaneous rather than a musculocutaneous perforator. The straightforward dissection almost extends up to the midline. Therefore, dissection always is performed at one side and, if no good perforators are present, continued at the intact contralateral side. The size of these perforators and their location in the flap determine the choice. One perforator with significant flow can perfuse the whole flap. If in doubt, two perforators can be harvested, especially if they show a linear anatomy so that muscle fibers can be split. The only interference with the muscle exists in splitting the muscle fibers. A perforator that lies in the middle of the flap is preferable. For a large flap, a perforator of the medial row provides better perfusion to zone 4 than one of the lateral row because of the extra choke vessel for the lateral row perforators. The clinical appearance of the perforators is the key element in the dissection of the perforator flap. Perforator topography determines the overall length and difficulty of the procedure.

Adult↗

PubMed1999

Pedicle instrumentation in the thoracic spine. A morphometric and cadaveric study for placement of screws.

STUDY DESIGN: In part 1 of the study, the morphometry of thoracic pedicles and bony landmarks for pedicle screw placement were evaluated. In part 2, pedicle screws were inserted in fresh cadavers, using a different entry point in the left and right pedicles. OBJECTIVES: To identify the safest entry point and screw orientation for pedicle screws in the thoracic spine. SUMMARY OF BACKGROUND DATA: A few morphometric investigations have been performed on thoracic vertebrae, but the safest technique for screw insertion in thoracic pedicles has not been analyzed. METHODS: Mean, range, and standard deviations of pedicle transverse diameter and pedicle orientation were measured in 99 dried thoracic vertebrae. We evaluated the position of the bottom of the superior facet and that of the superior border of the transverse process in relation to the center of the pedicle. The relation between the pedicle axis and the superior facet in the frontal plane was also assessed. In part 2 of the study, pedicle screws were inserted in fresh cadavers at the intersection between the superior border of the transverse process and the middle of the superior facet (entry point A) and between the former and the lateral two thirds of the facet (entry point B). RESULTS: The smallest transverse diameter was found at 16 (mean 4.3 mm) where pedicles measured less than 5 mm in 68% of the specimens. In the frontal plane, the pedicle axis intersected the middle of the superior facet in 15% of specimens, the lateral two-thirds in 62%, and the lateral border of the facet in 23%. Of the 126 screws inserted in fresh human cadavers, 15 (24%) of the screws inserted using entry point A and 10 (16%) of those inserted using entry point B violated the pedicle cortex (P > 0.05). Six (10%) of the screws inserted using entry point A compared with no screw inserted using entry point B penetrated the anterior vertebral cortex (P = 0.03). CONCLUSIONS: Pedicles between T4 and T8 may not be wide enough for screw fixation. An entry point for pedicle screws located at the intersection between the superior border of the transverse process and the lateral two thirds of the superior facet seems more likely to be in line with the pedicle axis than do other entry points. In the lower thoracic vertebrae this entry point, in combination with insertion of the screws more medially oriented than the pedicle axis, significantly reduces the risk of violating the anterior vertebral cortex.

Adult↗

PubMed2005

Mixing and transport in urban areas.

Concern over terrorist releases of harmful material has generated interest in short-range air-borne dispersion in urban areas. Here, we review the important fluid dynamical processes that control dispersion in the first kilometre, the neighbourhood scale, when much of the material remains within the urban canopy. Dispersion is then controlled by turbulent mixing and mean flow transport through the network of streets. We consider mixing and transport in a long straight street, street intersections and then a network of streets connected by intersections. The mixing and transport in these systems are illustrated with results from recent fine-resolution numerical simulations and laboratory models, which then inform simpler scaling estimates and modelling schemes. Finally, we make some tentative steps to pull the process studies together to begin to understand results from full-scale observations. In particular, it is shown that the positions of 'shear layers' and 'dividing streamlines' largely control the patterns of mixing and transport. It is also shown that neighbourhood-scale dispersion follows one scaling in the near field and another in the far field after passage through many intersections. The challenge for the future is to bring these threads together into a coherent mathematical model.

Air Movements↗

PubMed2005

Site-bond percolation of polyatomic species.

A generalization of the classical monomer site-bond percolation problem is studied in which linear k-uples of nearest neighbor sites (site k-mers) and linear k-uples of nearest neighbor bonds (bond k-mers) are independently occupied at random on a square lattice. We called this model the site-bond percolation of polyatomic species or k-mer site-bond percolation. Motivated by considerations of cluster connectivity, we have used two distinct schemes (denoted as S intersection of B and S union of B) for k-mer site-bond percolation. In S intersection of B(S union of B), two points are said to be connected if a sequence of occupied sites and (or) bonds joins them. By using Monte Carlo simulations and finite-size scaling theory, data from S intersection of B and S union of B are analyzed in order to determine the critical curves separating the percolating and nonpercolating regions.

Journal Article↗

PubMed2000

Infinitely large new dimensions

We construct intersecting brane configurations in anit-de Sitter (AdS) space which localize gravity to the intersection region, generalizing the trapping of gravity to any number n of infinite extra dimensions. Since the 4D Planck scale M(Pl) is determined by the fundamental Planck scale M(*) and the AdS radius L via the familiar relation M(2)(Pl) approximately M(2+n)(*)L(n), we get two kinds of theories with TeV scale quantum gravity and submillimeter deviations from Newton's law. With M(*) approximately TeV and L approximately submillimeter, we recover the phenomenology of theories with large extra dimensions. Alternatively, if M(*) approximately L-1 approximately M(Pl), and our 3-brane is at a distance of approximately 100M(-1)(Pl) from the intersection, we obtain a theory with an exponential determination of the weak/Planck hierarchy.

Journal Article↗

PubMed2001

Tag surface reconstruction and tracking of myocardial beads from SPAMM-MRI with parametric B-spline surfaces.

Magnetic resonance imaging (MRI) is unique in its ability to noninvasively and selectively alter tissue magnetization, and create tag planes intersecting image slices. The resulting grid of signal voids allows for tracking deformations of tissues in otherwise homogeneous-signal myocardial regions. In this paper, we propose a specific spatial modulation of magnetization (SPAMM) imaging protocol together with efficient techniques for measurement of three-dimensional (3-D) motion of material points of the human heart (referred to as myocardial beads) from images collected with the SPAMM method. The techniques make use of tagged images in orthogonal views by explicitly reconstructing 3-D B-spline surface representation of tag planes (tag planes in two orthogonal orientations intersecting the short-axis (SA) image slices and tag planes in an orientation orthogonal to the short-axis tag planes intersecting long-axis (LA) image slices). The developed methods allow for viewing deformations of 3-D tag surfaces, spatial correspondence of long-axis and short-axis image slice and tag positions, as well as nonrigid movement of myocardial beads as a function of time.

Humans↗

PubMed1984

Geometric model of the rat intestinal mucosa for stereological evaluation of villus amplification factors.

This 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/pi (to obtain an estimate of surface amplification due to villi).

Animals↗

PubMed2004

Golgi inheritance under a block of anterograde and retrograde traffic.

In mitosis, the Golgi complex is inherited following its dispersion, equal partitioning and reformation in each daughter cell. The state of Golgi membranes during mitosis is controversial, and the role of Golgi-intersecting traffic in Golgi inheritance is unclear. We have used brefeldin A (BFA) to perturb Golgi-intersecting membrane traffic at different stages of the cell cycle and followed by live cell imaging the fate of Golgi membranes in those conditions. We observed that addition of the drug on cells in prometaphase prevents mitotic Golgi dispersion. Under continuous treatment, Golgi fragments persist throughout mitosis and accumulate in a Golgi-like structure at the end of mitosis. This structure localizes at microtubule minus ends and contains all classes of Golgi markers, but is not accessible to cargo from the endoplasmic reticulum or the plasma membrane because of the continuous BFA traffic block. However, it contains preaccumulated cargo, and intermixes with the reforming Golgi upon BFA washout. This structure also forms when BFA is added during metaphase, when the Golgi is not discernible by light microscopy. Together the data indicate that independent Golgi fragments that contain all classes of Golgi markers (and that can be isolated from other organelles by blocking anterograde and retrograde Golgi-intersecting traffic) persist throughout mitosis.

Brefeldin A↗

PubMed1992

Dependence of stereomotion on the orientation of spatial-frequency components.

It is known that sensitivity to stereoscopic motion in depth is not based upon the fine analysis of static disparities but instead is based on the binocular combination of motion-sensitive mechanisms. We show in this paper that an 'aperture problem' arises for the analysis of motion in depth, just as it does for monocular motion sensitivity. We extend Adelson and Movshon's solution to the aperture problem by intersection of perpendicular constraints to the three-dimensional case, and show that it predicts velocity matches for oblique gratings moving in depth, for orientations close to vertical. We show that binocular plaids give rise to motion in depth when the component orientations match in each eye, and the monocular motions are horizontal. The match velocities are consistent with intersection of perpendicular constraints. In three dimensions intersection of perpendicular constraints may be necessary, but is not a sufficient condition for the perception of coherent stereoscopic motion in depth.

Contrast Sensitivity↗

PubMed2000

Sidetracks in the diagnosis of gastrointestinal disease.

Patients usually visit a physician for a particular reason, which medicine has termed the "chief complaint." As patients often have more than a single complaint, it is common for physicians to lose focus, get distracted, and venture down a path other than the one toward resolution of the chief complaint--in other words, to get sidetracked. The aim of the present review is to describe the nature of diagnostic sidetracking, why it occurs, mechanisms in action, and means to prevent it. During a regular diagnostic process, the physician's suspicions about a diagnosis advance from broad and general to narrow and specific concepts. Each step in the diagnostic process is potentially driven by its own hypothesis, and each individual hypothesis becomes verified or falsified by pointed questions during the history or by medical tests. If a diagnostic process were to focus on the correct diagnosis that eventually explained the chief complaint, the intersections among the consecutively refined diagnostic concepts would converge toward one specific set, with the final diagnosis located inside the nonzero intersection of all consecutive diagnostic concepts. In a faulty diagnostic process, consecutive diagnostic concepts fail to converge, and the final diagnosis and chief complaint do not intersect. In this regard, the physician has pursued a false path and has become sidetracked. The effects of sidetracking range from minimal to disastrous. Sidetracking can delay diagnosis, delay treatment, and waste resources investigating or treating irrelevant medical problems. To avoid sidetracking, physicians should focus on the main problem, avoid getting involved with complementary solutions to secondary medical problems, and verify repetitively during the diagnostic process the relationship between each current working hypothesis and the patient's major medical problem.

Decision Making↗

PubMed1984

Chromatic mechanisms in lateral geniculate nucleus of macaque.

This paper introduces a new technique for the analysis of the chromatic properties of neurones, and applies it to cells in the lateral geniculate nucleus (l.g.n.) of macaque. The method exploits the fact that for any cell that combines linearly the signals from cones there is a restricted set of lights to which it is equally sensitive, and whose members can be exchanged for one another without evoking a response. Stimuli are represented in a three-dimensional space defined by an axis along which only luminance varies, without change in chromaticity, a 'constant B' axis along which chromaticity varies without changing the excitation of blue-sensitive (B) cones, a 'constant R & G' axis along which chromaticity varies without change in the excitation of red-sensitive (R) or green-sensitive (G) cones. The orthogonal axes intersect at a white point. The isoluminant plane defined by the intersection of the 'constant B' and 'constant R & G' axes contains lights that vary only in chromaticity. In polar coordinates the constant B axis is assigned the azimuth 0-180 deg, and the constant R & G axis the azimuth 90-270 deg. Luminance is expressed as elevation above or below the isoluminant plane (-90 to +90 deg). For any cell that combines cone signals linearly, there is one plane in this space, passing through the white point, that contains all lights that can be exchanged silently. The position of this 'null plane' provides the 'signature' of the cell, and is specified by its azimuth (the direction in which it intersects the isoluminant plane of the stimulus space) and its elevation (its angle of inclination to the isoluminant plane). A colour television receiver was used to produce sinusoidal gratings whose chromaticity and luminance could be modulated along any vector passing through the white point in the space described. The spatial and temporal frequencies of modulation could be varied over a large range. When stimulated by patterns of low spatial and low temporal frequency, two groups of cells in the parvocellular laminae of the l.g.n. were distinguished by the locations of their null planes. The null planes of the larger group were narrowly distributed about an azimuth of 92.6 deg and more broadly about an elevation of 51.5 deg, which suggests that they receive opposed, but not equally balanced, inputs from only R and G cones. These we call R-G cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗

PubMed1999

Chemical "Double Slits": dynamical interference of photodissociation pathways in water

Photodissociation of water at a wavelength of 121.6 nanometers has been investigated by using the H-atom Rydberg tagging technique. A striking even-odd intensity oscillation was observed in the OH(X) product rotational distribution. Model calculations attribute this oscillation to an unusual dynamical interference brought about by two dissociation pathways that pass through dissimilar conical intersections of potential energy surfaces, but result in the same products. The interference pattern and the OH product rotational distribution are sensitive to the positions and energies of the conical intersections, one with the atoms collinear as H-OH and the other as H-HO. An accurate simulation of the observations would provide a detailed test of global H(2)O potential energy surfaces for the three (&Xtilde;/A/&Btilde;) contributing states. The interference observed from the two conical intersection pathways provides a chemical analog of Young's well-known double-slit experiment.

Journal Article↗

PubMed1971

Distribution and correlation of events during thermal inactivation of Bacillus megaterium spores.

Aqueous suspensions of Bacillus megaterium QM B1551 spores were heated at temperatures from 75 to 85 C. The rapid initial viability loss, followed by a more gradual, almost exponential decline, was not due to mixed populations with discrete heat resistances. The slight "tailing" below 0.01% survival was not the result of heat adaptation. Loss of viability was more rapid than loss of dipicolinic acid (DPA) and germinability and, although these events could not be correlated by use of simple kinetic plots, they had similar activation energies (80 to 90 kcal/mole). Probability (probit) plots of per cent survival as a function of logarithmic time yielded not the single line expected, if the heat resistances of individuals in the population were log-normally distributed, but two straight lines intersecting at a survival level of 1 to 6%. Probit-intersects occurred at times ranging from 8 min for spores heated at 85 C, to 310 min at 75 C. Probit-intersects for DPA release and loss in germinability occurred at the same time as for survival, but at much higher levels of retention. There appeared to be two subpopulations, both log-normally distributed but with different mechanisms of kill. Ninety-four to 99% of the spores died via injury to the cell-division process but retained germinability; the remaining smaller subpopulation (1 to 6%) was nonviable because of loss of the ability to germinate.

Bacillus megaterium↗

PubMedDate not supplied

Representing the UMLS as an object-oriented database: modeling issues and advantages.

OBJECTIVE: The Unified Medical Language System (UMLS) combines many well-established authoritative medical informatics terminologies in one knowledge representation system. Such a resource is very valuable to the health care community and industry. However, the UMLS is very large and complex and poses serious comprehension problems for users and maintenance personnel. The authors present a representation to support the user's comprehension and navigation of the UMLS. DESIGN: An object-oriented database (OODB) representation is used to represent the two major components of the UMLS-the Metathesaurus and the Semantic Network-as a unified system. The semantic types of the Semantic Network are modeled as semantic type classes. Intersection classes are defined to model concepts of multiple semantic types, which are removed from the semantic type classes. RESULTS: The authors provide examples of how the intersection classes help expose omissions of concepts, highlight errors of semantic type classification, and uncover ambiguities of concepts in the UMLS. The resulting UMLS OODB schema is deeper and more refined than the Semantic Network, since intersection classes are introduced. The Metathesaurus is classified into more mutually exclusive, uniform sets of concepts. The schema improves the user's comprehension and navigation of the Metathesaurus. CONCLUSIONS: The UMLS OODB schema supports the user's comprehension and navigation of the Metathesaurus. It also helps expose and resolve modeling problems in the UMLS.

Databases as Topic↗