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PubMed1999

The RXc graph in evaluating and monitoring fluid balance in patients with liver cirrhosis.

A recent study, using height-standardized resistance (R/H) and reactance (Xc/H) and assuming a bivariate distribution, has proposed the "RXc graph". We applied this new approach for patients with chronic liver disease in differentiating various degrees of fluid unbalance. Our data showed that a 95% confidence ellipse of patients with chronic hepatitis (CH) overlapped that of healthy control subjects (CONTR), while those of patients with liver cirrhosis (CIR), patients with cirrhosis and ascites (ACIR), and patients with cirrhosis, edemas, and ascites (AECIR) were clearly different for both genders. A progressively shorter mean impedance vector proportional to the stage of liver disease and to the degree of fluid unbalance was found. The lower half of the 50% tolerance ellipse for the healthy population proved to be a threshold for cirrhotics, while almost all the subjects with clinically detectable edema fell outside this limit. The RXc graph was shown to be useful in monitoring the treatment of fluid unbalance and for the immediate selection of patients in whom BIA can precisely assess body composition.

Adolescent↗
PubMed2000

Gray-scale skeletonization of small vessels in magnetic resonance angiography.

Interpretation of magnetic resonance angiography (MRA) is problematic due to complexities of vascular shape and to artifacts such as the partial volume effect. We present new methods to assist in the interpretation of MRA. These include methods for detection of vessel paths and for determination of branching patterns of vascular trees. They are based on the ordered region growing (ORG) algorithm that represents the image as an acyclic graph, which can be reduced to a skeleton by specifying vessel endpoints or by a pruning process. Ambiguities in the vessel branching due to vessel overlap are effectively resolved by heuristic methods that incorporate a priori knowledge of bifurcation spacing. Vessel paths are detected at interactive speeds on a 500-MHz processor using vessel endpoints. These methods apply best to smaller vessels where the image intensity peaks at the center of the lumen which, for the abdominal MRA, includes vessels whose diameter is less than 1 cm.

Algorithms↗
PubMed1991

An iterative algorithm for scanning tomographic acoustic microscopy.

Acoustic microscopy is capable of providing high-resolution images of small objects. When such a microscope operates in the transmission mode, it produces simply a shadow-graph of all the structures encountered by the acoustic wave passing through the object. The resultant images are difficult to comprehend because of diffraction and overlapping of complex structures. Scanning tomographic acoustic microscopy (STAM) overcomes these difficulties and produces unambiguous micrographs of objects of substantial thickness and complexity. STAM uses the back-and-forth propagation algorithm to reconstruct tomograms of various layers to be imaged. When these layers are physically close to one another, ambiguities appear in the reconstructed images. Using an iterative algorithm eliminates these ambiguities and resolves layers that are only two wavelengths apart.

Algorithms↗
PubMed2005

Simultaneous determination of dopamine and carvedilol in human serum and urine by first-order derivative fluorometry.

A sensitive and selective method for simultaneous determination of carvedilol and dopamine was described. The emission wavelengths of carvedilol and dopamine were at 354 nm and 314 nm with the excitation at 290 nm, respectively. The determination of carvedilol and dopamine by normal fluorometry was difficult because the emission spectra of carvedilol and dopamine were overlapped seriously. The first derivative peaks of carvedilol and dopamine were at 336 nm and 302 nm, respectively. The linear regression equations of the calibration graphs of carvedilol and dopamine were C = 0.000557H-0.00569 and C = 0.00438H-0.0812, with the correlation coefficients were 0.9953 and 0.9988, respectively. The liner range for the determination of carvedilol was 0.002 microg ml(-1) to 0.02 microg ml(-1), and 0.05 microg ml(-1) to 0.6 microg ml(-1) for dopamine. The detection limits were 1 ng ml(-1) for carvedilol and 0.04 microg ml(-1) for dopamine, respectively. The relative standard derivative (RSD) of 4.38% and 4.35% was observed for carvedilol and dopamine, respectively. The recovery of carvedilol was from 95.00% to 106.7% in human serum and from 97.50% to 105.0% in urine sample. The recovery of dopamine was from 100.0% to 102.5% in human serum and from 97.50% to 105.0% in urine sample. This method is simple and can be used for determination of carvedilol and dopamine in human serum and urine sample with satisfactory results.

Calibration↗
PubMed2005

Geometric morphometric analysis of mandibular ramus flexure.

Many characteristics of the human skeleton can only be assessed morphologically, which may be problematic due to factors such as interobserver error and difficulties with standardization. Flexure of the mandibular ramus is one of these traits, and various researchers found widely differing results using this morphological feature. The aim of this study was to determine whether differences between male and female mandibular rami could be observed using the computerized method of geometric morphometrics, a valuable tool that helps quantify shape differences. Twenty-eight mandibular rami of black females and 43 of black males were photographed in a standard plane and assessed. It was found that the females were more scattered on the graph (more variable in shape), while the males clustered more around the center point where the two axes met (shape more constant). There was, however, considerable overlap between the sexes. Although different tendencies exist between the rami of males (being more flexed) and females (tending to be straight), the extent of these differences is not adequate to predict the sex of a single individual.

Adult↗
PubMed2026

Optimizing sparse and skew hashing: faster k-mer dictionaries.

MOTIVATION: Representing a set of k-mers-strings of length k-in small space under fast lookup queries is a fundamental requirement for several applications in Bioinformatics. A data structure based on sparse and skew hashing (SSHash) was recently proposed for this purpose (Pibiri 2022): it combines good space effectiveness with fast lookup and streaming queries. It is also order-preserving, i.e. consecutive k-mers (sharing a prefix-suffix overlap of length k-1) are assigned consecutive hash codes which helps compressing satellite data typically associated with k-mers, like abundances and color sets in colored De Bruijn graphs. RESULTS: We study the problem of accelerating queries under the sparse and skew hashing indexing paradigm, without compromising its space effectiveness. We propose a refined data structure with less complex lookups and fewer cache misses. We give a simpler and faster algorithm for streaming lookup queries. The refined architecture translates to substantial performance gains, outperforming the original version of SSHash in both index construction speed and query efficiency. Compared to indexes with similar capabilities and based on the Burrows-Wheeler transform, like SBWT and FMSI, SSHash is significantly faster to build and query. SSHash is competitive in space with the fast (and default) modality of SBWT when both k-mer strands are indexed. While larger than FMSI, it is also more than one order of magnitude faster to query. AVAILABILITY AND IMPLEMENTATION: The SSHash software is available at https://github.com/jermp/sshash, and also distributed via Bioconda. A benchmark of data structures for k-mer sets is available at https://github.com/jermp/kmer_sets_benchmark. The datasets used in this article are described and available at https://zenodo.org/records/17582116.

Algorithms↗
PubMed1991

The use of modified constellation graph method for computer-aided classification of congenital heart diseases.

This paper describes a new method of data reduction and classification in a multidimensional symptom space for diagnostic aid of congenital heart diseases. The algorithm developed here is to reduce interactively a multidimensional symptom space to sectorial regions representing each disease in a semicircle using the modified constellation graph method. This method enables us to classify patients using the angle in the semicircle as a single classifying parameter with an accuracy of about 90%, that is, with little overlapping between disease sectors. Comparing this method with conventional factor analysis, we have found the former far more effective than the latter for disease region separation.

Algorithms↗
PubMed1998

Model-guided labeling of coronary structure.

Assigning anatomic labels to coronary arteries in X-ray angiograms is an important task in medical imaging, motivated by the desire to standardize the assessment of coronary artery disease and to facilitate the three-dimensional (3-D) reconstruction and visualization of the coronary vasculature. However, automatic labeling poses a number of significant challenges, including the presence of noise, artifacts, competing structures, misleading visual cues, and other difficulties associated with a dynamic and inherently complex structure. We have developed a model-guided approach that addresses these challenges and automatically labels the vascular structure in coronary angiographic images. The approach consists of two models: 1) a symbolic model, represented through a directed acyclic graph, that captures vascular tree hierarchies and branch interrelationships and 2) a generalized 3-D model that captures spatial and geometric relationships. Importantly, the approach detects ambiguities (such as vessel overlaps) that may be found in a frame of a ciné sequence, and resolves these ambiguities by considering the information derived from other (unambiguous) frames in the temporal sequence, employing dynamic programming methods to match the image features found in the different (ambiguous and unambiguous) frames. This paper presents this model-guided labeling algorithm and discusses the experimental results obtained from implementing and applying the resulting labeling system to a variety of clinical images. The results indicate the feasibility of achieving robust and consistently accurate image labeling through this model-guided, temporal disambiguation method.

Coronary Angiography↗
PubMed1996

The hippocampus as a cognitive graph.

A theory of cognitive mapping is developed that depends only on accepted properties of hippocampal function, namely, long-term potentiation, the place cell phenomenon, and the associative or recurrent connections made among CA3 pyramidal cells. It is proposed that the distance between the firing fields of connected pairs of CA3 place cells is encoded as synaptic resistance (reciprocal synaptic strength). The encoding occurs because pairs of cells with coincident or overlapping fields will tend to fire together in time, thereby causing a decrease in synaptic resistance via long-term potentiation; in contrast, cells with widely separated fields will tend never to fire together, causing no change or perhaps (via long-term depression) an increase in synaptic resistance. A network whose connection pattern mimics that of CA3 and whose connection weights are proportional to synaptic resistance can be formally treated as a weighted, directed graph. In such a graph, a "node" is assigned to each CA3 cell and two nodes are connected by a "directed edge" if and only if the two corresponding cells are connected by a synapse. Weighted, directed graphs can be searched for an optimal path between any pair of nodes with standard algorithms. Here, we are interested in finding the path along which the sum of the synaptic resistances from one cell to another is minimal. Since each cell is a place cell, such a path also corresponds to a path in two-dimensional space. Our basic finding is that minimizing the sum of the synaptic resistances along a path in neural space yields the shortest (optimal) path in unobstructed two-dimensional space, so long as the connectivity of the network is great enough. In addition to being able to find geodesics in unobstructed space, the same network enables solutions to the "detour" and "shortcut" problems, in which it is necessary to find an optimal path around a newly introduced barrier and to take a shorter path through a hole opened up in a preexisting barrier, respectively. We argue that the ability to solve such problems qualifies the proposed hippocampal object as a cognitive map. Graph theory thus provides a sort of existence proof demonstrating that the hippocampus contains the necessary information to function as a map, in the sense postulated by others (O'Keefe, J., and L. Nadel. 1978. The Hippocampus as a Cognitive Map. Clarendon Press, Oxford, UK). It is also possible that the cognitive mapping functions of the hippocampus are carried out by parallel graph searching algorithms implemented as neural processes. This possibility has the great attraction that the hippocampus could then operate in much the same way to find paths in general problem space; it would only be necessary for pyramidal cells to exhibit a strong nonpositional firing correlate.

Animals↗
PubMed1986

Common functional origin for simple and complex responses of atrioventricular node in dogs.

The possibility that variations in atrioventricular nodal conduction time observed during transient and steady-state nodal responses share common characteristics was examined in six anesthetized dogs. Atrioventricular conduction times (AV intervals) obtained during transient (incremental atrial pacing rates, short frequency steps, and Wenckebach cycles) and steady state (periodic premature stimulation performed at 5 basic rates) responses were plotted together against the corresponding preceding ventriculoatrial (VA) intervals on a graph for each dog. Despite their diversity, nodal responses consistently resulted in AV intervals that fell within a well-defined, relatively narrow, crescent-shaped zone on the graphs. AV interval variations were small in the long VA interval range and increased slightly but predictably as the VA intervals decreased. AV intervals of transient and steady state nodal responses overlapped markedly. These results show that AV intervals of transient and steady-state nodal responses vary within a given common functional domain despite the diversity of their sequential patterns and suggest that the AV node may be obeying the same set of conduction rules during these very distinct responses.

Animals↗
PubMed2004

From paragraph to graph: latent semantic analysis for information visualization.

Most techniques for relating textual information rely on intellectually created links such as author-chosen keywords and titles, authority indexing terms, or bibliographic citations. Similarity of the semantic content of whole documents, rather than just titles, abstracts, or overlap of keywords, offers an attractive alternative. Latent semantic analysis provides an effective dimension reduction method for the purpose that reflects synonymy and the sense of arbitrary word combinations. However, latent semantic analysis correlations with human text-to-text similarity judgments are often empirically highest at approximately 300 dimensions. Thus, two- or three-dimensional visualizations are severely limited in what they can show, and the first and/or second automatically discovered principal component, or any three such for that matter, rarely capture all of the relations that might be of interest. It is our conjecture that linguistic meaning is intrinsically and irreducibly very high dimensional. Thus, some method to explore a high dimensional similarity space is needed. But the 2.7 x 10(7) projections and infinite rotations of, for example, a 300-dimensional pattern are impossible to examine. We suggest, however, that the use of a high dimensional dynamic viewer with an effective projection pursuit routine and user control, coupled with the exquisite abilities of the human visual system to extract information about objects and from moving patterns, can often succeed in discovering multiple revealing views that are missed by current computational algorithms. We show some examples of the use of latent semantic analysis to support such visualizations and offer views on future needs.

Animals↗
PubMed1994

Determination of guaiphenesin in anti-tussive pharmaceutical preparations containing dextromethorphan by first- and second-derivative ultraviolet spectrophotometry.

Rapid, simple and direct assay procedures based on selective first (D1)- and second (D2)-derivative spectrophotometry, using a zero-crossing technique of measurement at 279.2 and 280.0 nm, respectively, have been developed for the specific determination of guaiphenesin in the presence of dextromethorphan, drugs with closely overlapping absorption spectra, in synthetic admixtures and in pharmaceutical dosage forms (tablets and syrups). The methods do not require extraction with organic solvents and are easier to perform than their conventional counterparts. Calibration graphs were linear (r = 0.99999 for D1 and 0.99969 for D2, respectively). Good selectivity, accuracy and precision were found. However, the performance of the analysis of guaiphenesin by the second-derivative mode deteriorated when the ratio of dextromethorphan to guaiphenesin was greater than one. Thus, the first-derivative spectrophotometry is the method of choice for the assay of tablets and syrups containing the two drugs.

Antitussive Agents↗
PubMedDate not supplied

Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory.

The novel methodology for protein 2D NMR assignment presented in this paper is based upon protein spin coupling graph theory analysis, fuzzy graph pattern recognition, and tree searching. The method required to formalize the whole assignment procedure into a logical system which can be properly processed by computer software is also discussed. Solutions for peak overlaps, spin coupling network overlaps, and details related to the automated assignment of BPTI are reported as well.

Algorithms↗
PubMedDate not supplied

A standardized technique for efficient platelet and leukocyte collection using the Model 30 Blood Processor.

The Model 30 Blood Processor is a safe and simple means of harvesting blood cell components. Presently cell collection depends on a visual assessment by the operator of the indistinct boundaries of cell fractions. To determine when each cell component could best be harvested, serial samples were taken from the output port at fixed intervals anf the results of counts and differentials were graphed and tabulated. Studies in normal donors were done using acid-citrate-dextrose (ACD), 2 per cent sodium citrate in 6 per cent hydroxyethyl starch (HES), or heparin as anticoagulants. There was considerable overlap between the latter part of the platelet band, the leukocyte band and the rising hematocrit with all three anticoagulants. Normally functional lymphocytes could be harvested efficiently (approximately 80%) using ACD or heparin. Platelets could be harvested from ACD very efficiently (approximately 90%). Granulocytes could not be harvested from ACD (less than 10%) since they were dispersed in the red blood cell (RBC) layer. Using HES, granulocytes could be harvested efficiently (approximately 70%) by extending collection into the RBC layer. Based on these data, a standard technique for cell collection has been devised. The flow rate is slowed to 20 ml/min and collection is carried 30 ml (90 seconds at a rate of 20 ml/min) for platelets. The RBC loss is approximately 6 to 8 and 2 to 3 ml/pass respectively. These studies indicate that the Model 30 is a highly efficient apparatus for blood cell separation, but the volume of blood processed is limited by the intermittent blood flow.

Blood Cell Count↗
PubMed2001

[The effect of the hyper-erupted third molar on chewing movement].

OBJECTIVE: To investigate the effect of the hyper-erupted third molar contacting closely to the distal surface of the opposing second molar on the chewing movement. METHODS: Twenty-three university student volunteers, 11 with hyper-erupted third molar teeth and 12 with normal occlusion, were enrolled in present study. There were totally 6 unilateral hyper-erupted third molars (3 upper and 3 lower) and 5 bilateral hyper-erupted third molars (1 bilateral upper and 4 bilateral lower). No other significantly abnormal occlusal phenomenon was observed. Five gum-chewing cycles masticated with an each side were separately recorded by means of K6-I mandibular kinesiograph (MKG) and the chewing cycles were analyzed. Both three-dimensional amplitudes and the related velocities were automatically documented with the instrument. RESULTS: (1) The chewing graphs recorded on both frontal and horizontal planes in controls were typically smooth cycles with clearly occlusal phase tracings. On the sagital plane the opening and closing traces around intercuspal position (ICP) were usually overlapped with each other. (2) 63.6% frontal cycles of the subjects with hyper-erupted third molar had an obvious table (0.2 mm to 1.0 mm in width) around ICP, 50% horizontal cycles of the subjects had a 0.2 mm to 0.5 mm step near to ICP, 72.7% opening and closing traces on the sagital plane separated into anterior and posterior branches. The abnormal traces on the three different planes of the hyper-erupted third molar tooth group appeared to be related each other, implying that they might be caused by the same characteristics of occlusion, namely, the hyper-erupted third molar. (3) Subjects with hyper-erupted third molar masticated in more posterior direction, together with a higher chewing terminal velocity. CONCLUSIONS: The hyper-erupted third molar had a significant effect on the chewing cycles around ICP, as well as on the amplitude and velocity of chewing movement.

Adolescent↗
PubMed2005

Identifying optimal incomplete phylogenetic data sets from sequence databases.

We introduce a new method for identifying optimal incomplete data sets from large sequence databases based on the graph theoretic concept of alpha-quasi-bicliques. The quasi-biclique method searches large sequence databases to identify useful phylogenetic data sets with a specified amount of missing data while maintaining the necessary amount of overlap among genes and taxa. The utility of the quasi-biclique method is demonstrated on large simulated sequence databases and on a data set of green plant sequences from GenBank. The quasi-biclique method greatly increases the taxon and gene sampling in the data sets while adding only a limited amount of missing data. Furthermore, under the conditions of the simulation, data sets with a limited amount of missing data often produce topologies nearly as accurate as those built from complete data sets. The quasi-biclique method will be an effective tool for exploiting sequence databases for phylogenetic information and also may help identify critical sequences needed to build large phylogenetic data sets.

Base Sequence↗
PubMed1994

Integration of graph theory and quantum chemistry for structure-activity relationships.

The objective of this article is to outline both graph-theoretically based and quantum chemically based structural indices of potential use in quantitative structure activity correlations. We consider graph-theoretical indices such as the connectivity index, topological index, Wiener index and molecular ID indices. Several structural and geometry-dependent indices can be derived from semiempirical and ab initio quantum calculations based on the charge densities, overlap matrices, frontier orbitals, molecular hardness, free valence, density matrices, quantum spectral difference indices, quantum spectral indices and bond matrices. Finally, the use of electrostatic potentials and charge densities for the prediction of reactive sites will be discussed.

Butadienes↗
PubMed1990

Laboratory diagnosis of inherited protein S deficiency.

The authors investigated assays for free protein S (ProS) antigen, total ProS antigen, and ProS crossed immunoelectrophoresis (CIEP) in the diagnosis of type 1 inherited ProS deficiency. Accurate measurement of the hemostatically important free ProS required showing that, on each specimen, precipitation of the C4b-binding protein (C4b-BP)/protein S complex (C4b-BP/ProS) by polyethylene glycol-8,000 (PEG) was complete. The authors showed this by doing a ProS CIEP on the same PEG supernate that was used for quantitative measurement of free ProS. The +/- 2 standard deviation (+/- 2 SD) ranges for free ProS were 81-133% for males and 50-130% for females. This striking male-female difference has been reported only twice before. With the use of a graph of values for free ProS versus prothrombin time (PT), patients with inherited ProS deficiency segregated cleanly from normals and from patients on warfarin therapy without ProS deficiency until the PT was greater than 20 seconds. There is overlap of total ProS antigen values between normals and patients with inherited ProS deficiency.

Antigens↗