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Non-linear CT windows.

The display of computerized tomographic (CT) data requires data compression because of the limited shades of grey which the eye can differentiate. This may lead to information loss which can be minimized by a more efficient utilization of the available levels of grey than that afforded by conventional linear windows. Automated histogram equalization for grey level assignment has not been satisfactory because of the underlying assumption that the information content at any given CT level is proportional to the number of pixels at that level. For four different anatomic regions; the lumber spine, abdomen, brain and chest, an empiric graph of the clinical information content vs CT levels was integrated to yield the shape of a graph assigning shades of grey vs CT level i.e. a non-linear window. This non-linear window curve was utilized in the same manner as the linear window, namely the window center and width were under the direct control of the observer through the window center and width knobs. Each non-linear window was implemented on images of its anatomic region and interactively optimized on the screen till a maximal display of information was obtained. These optimal non-linear windows compared favorably with linear windows in most cases. This method provides the means to display more information on a CT image with no extra processing time, additional equipment or special training.

Brain↗
PubMed1996

Simultaneous quantitation of buspirone and its major metabolite 1-(2-pyrimidinyl)piperazine in human plasma by high-performance liquid chromatography with coulometric detection.

Buspirone is a member of the azapirone group of anxiolytic drugs and has one major metabolite, 1-(2-pyrimidinyl)piperazine (1-PP). The analyte, its metabolite and the internal standard were extracted from plasma utilizing solid-phase extraction columns. Chromatography was performed using isocratic reversed-phase high-performance liquid chromatography with coulometric end-point detection. The calibration graph was linear over the range 0-50 ng ml-1 of plasma. The lower limits of quantitation for buspirone and 1-PP were 0.5 and 2 ng ml-1, respectively, when 1 ml of plasma was extracted. The intra-assay relative standard deviations (RSD) over the range of the calibration graph varied from 4 to 12.5% for buspirone and 1-PP. The inter-assay RSD was 6.9% for 1-PP and 9.6% for buspirone. The recovery averaged 96% for buspirone and 66% for 1-PP. Plasma profiles of buspirone and 1-PP following oral dosing are presented.

Adult↗
PubMed1992

Frequency analysis of signal-averaged electrocardiogram in patients with right ventricular tachycardia.

OBJECTIVES: The purpose of this study was to analyze the frequency content of signal-averaged electrocardiograms (ECGs) in patients with idiopathic ventricular tachycardia of right ventricular origin and in patients with arrhythmogenic right ventricular dysplasia. BACKGROUND: The late potentials in the time domains are usually found in patients with arrhythmogenic right ventricular dysplasia. They are not usually found in patients with idiopathic ventricular tachycardia of right ventricular origin. METHODS: Fast Fourier transform analysis of signal-averaged ECGs was performed with the use of a Blackman-Harris window in 43 subjects: 20 normal volunteers (group I), 12 patients with idiopathic ventricular tachycardia of right ventricular origin (group II) and 11 patients with arrhythmogenic right ventricular dysplasia (group III), and the frequency spectrum was displayed in a three-dimensional graph. Area ratio (ratio of the area under the spectral plot from 40 to 120 Hz to the area from 0 to 120 Hz) was calculated in all subjects. RESULTS: Area ratio was significantly higher in group II than in group I (243 +/- 45 vs. 196 +/- 15, p < 0.01) and significantly higher in group III (396 +/- 51) than in group I or II (p < 0.001). The high frequency components in group II were confined within the QRS complex in the three-dimensional graph, whereas those in group III extended outside the QRS complex. CONCLUSIONS: Frequency analysis of the signal-averaged ECG with fast Fourier transform analysis can detect the high frequency components in patients with right ventricular tachycardia, including idiopathic ventricular tachycardia and arrhythmogenic right ventricular dysplasia.

Adult↗
PubMed1983

Comparative studies of sheep liver and lung microsomal aniline 4-hydroxylase.

1. The specific activity of the aniline 4-hydroxylase which catalyses hydroxylation of aniline to p-aminophenol was found to be 0.65 (N = 10) and 0.15 (N = 13) nmol p-aminophenol formed/mg protein/min, in sheep liver and lung microsomes, respectively. 2. The effects of aniline concentration, pH, cofactors, amount of enzyme and incubation period, on enzyme activity were studied, and the optimum conditions for maximum activity of liver and lung microsomes were determined. 3. Liver and lung microsomal aniline 4-hydroxylase activity was found to be completely dependent on the presence of cofactor NADPH. 4. The Lineweaver Burk and Eadie Hofstee plots of the liver enzyme were found to be curvilinear, suggesting that the enzyme did not follow the Michaelis Menten kinetics. From these graphs, two different Km values were calculated for the liver enzyme as 3.21 and 0.072 mM aniline. Km of the lung enzyme was calculated to be 1.43 mM aniline from its Lineweaver Burk graph. 5. The effects of magnesium, nickel and cadmium ions on the liver and lung aniline 4-hydroxylase activity were examined. Magnesium ion was found to have stimulatory effect, whereas nickel and cadmium ions inhibited the activity of the both liver and lung enzyme.

Aniline Hydroxylase↗
PubMed1993

A tutorial introduction to stochastic simulation algorithms for belief networks.

Belief networks combine probabilistic knowledge with explicit information about conditional independence assumptions. A belief network consists of a directed acyclic graph in which the nodes represent variables and the edges express relationships of conditional dependence. When information about one variable's state is given to the network in the form of evidence, an update algorithm computes the posterior marginal probability distributions for the remaining variables in the network. Many algorithms for performing this inference task have been proposed. Exact algorithms report precise results for some classes of networks, but take exponential time (in the number of nodes) both in the worst case and for many interesting networks. Stochastic simulation algorithms estimate the posterior marginal probability distribution for many graph topologies that would require exponential time when using an exact algorithm. Nonetheless, for some belief networks, stochastic simulation algorithms are also known to have exponential worst case performance. This article describes at a tutorial level several stochastic simulation algorithms for belief networks, and illustrates them on some simple examples. In addition, the theoretical and empirical performance of the algorithms is briefly surveyed.

Algorithms↗
PubMed1993

Amino acid titration curves--misshapen or mislabeled?

Titration curves are frequently used to illustrate the change in charge of amino acids with pH, and as such are a fundamental part of most biochemistry courses. We have noticed that the graphs of titration curves appearing in many biochemistry textbooks are drawn incorrectly near the origin of the titration. This article demonstrates that this curve is misshapen, or, alternatively, that the axis of the graph is incorrectly labelled.

Amino Acids↗
PubMed2006

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks.

We introduce a mathematical framework that allows to test the compatibility between differential data and knowledge on genetic and metabolic interactions. Within this framework, a behavioral model is represented by a labeled oriented interaction graph; its predictions can be compared to experimental data. The comparison is qualitative and relies on a system of linear qualitative equations derived from the interaction graph. We show how to partially solve the qualitative system, how to identify incompatibilities between the model and the data, and how to detect competitions in the biological processes that are modeled. This approach can be used for the analysis of transcriptomic, metabolic or proteomic data.

Fatty Acids↗
PubMed2026

Disagreement-informed arbitration for gene regulatory network inference: A score-level meta-classifier and a diagnostic typology of inter-method conflict.

Gene regulatory network inference methods routinely disagree about individual edges, and practitioners resolve those conflicts by choosing one method or averaging them all. We ask whether the conflict can instead be arbitrated per edge. A gradient-boosted classifier is trained on the raw scores that ten inference methods-correlation-based, information-theoretic, sparse-regression and tree-ensemble, including GENIE3, GRNBoost2, CLR and ARACNe-assign to each candidate regulator-target pair, so that the weight given to each method varies from edge to edge. Across six single-cell perturbation screens spanning four cell types, arbitration improves on mean ensembling by +0.056 AUROC on Adamson and +0.083 on Shifrut under target-grouped cross-validation. The evaluation protocol turns out to matter more than the model. Edge-level cross-validation, standard in this literature, inflates apparent gains by 0.060 AUROC through target-gene leakage-comparable to the entire honest improvement. The effect is far larger for methods that represent genes implicitly: a supervised graph-attention link predictor trained on identical folds scores AUROC 0.930 under edge-level cross-validation, better than anything else we evaluate, and 0.533 once target genes are held out. Any method that parameterises genes is exposed, which covers most graph- and embedding-based approaches. A five-category typology of inter-method conflict localises where arbitration pays off, with the largest gains on edges where the methods disagree and the smallest where they already agree, while adding nothing as model input; we therefore report it as a diagnostic instrument rather than a modelling contribution. We also characterise what the ground truth measures: most perturbed genes in widely used screens are not transcription factors, and a mediation screen bounds how much of the perturbation response can be direct.

Ensemble methods↗
PubMed2006

Correlation weighting of valence shells in QSAR analysis of toxicity.

In the rainbow trout (Oncorhynchus mykiss), we studied the acute toxicity LC(50)-96 h of 274 organic pesticides with a wide variety of molecular structures. Optimization of correlation weights of local and global graph invariants (OCWLGI) gave quantitative structure-activity relationships (QSARs) for predicting toxicity. We used a labeled hydrogen-filled graph (LHFG) to elucidate the molecular structure. We also used the extended connectivity of zero ((0)EC(k)), first ((1)EC(k)), and second ((2)EC(k)) order, numbers of path lengths 2 (P2(k)) and 3 (P3(k)) starting from a given vertex in the LHFG, and valence shells of second order (S2(k)). S2(k) is the sum of the degree of vertices at distance 2 from a given vertex k. The presence of three-, five-, and six-member cycles and hydrogen bond indices suggested they might be used as global LHFG invariants. We applied this method to a broad set of pesticides, to predict toxicity for the trout. The best model used weighted S2(k) and global LHFG invariants. Statistical characteristics of this model are as follows: n=233, r(2)=0.7689, r(2)(pred)=0.7688, s=0.75, F=769 (training set); n=41, r(2)=0.6421, r(2)(pred)=0.4241, s=1.14, F=70 (test set).

Animals↗
PubMed2005

QSAR study for mycobacterial promoters with low sequence homology.

The general belief is that quantitative structure-activity relationship (QSAR) techniques work only for small molecules and, protein sequences or, more recently, DNA sequences. However, with non-branched graph for proteins and DNA sequences the QSAR often have to be based on powerful non-linear techniques such as support vector machines. In our opinion, linear QSAR models based on RNA could be useful to assign biological activity when alignment techniques fail due to low sequence homology. The idea bases the high level of branching for the RNA graph. This work introduces the so-called Markov electrostatic potentials (k)xi(M) as a new class of RNA 2D-structure descriptors. Subsequently, we validate these molecular descriptors solving a QSAR classification problem for mycobacterial promoter sequences (mps), which constitute a very low sequence homology problem. The model developed (mps=-4.664.(0)xi(M)+0. 991.(1)xi(M)-2.432) was intended to predict whether a naturally occurring sequence is an mps or not on the basis of the calculated (k)xi(M) value for the corresponding RNA secondary structure. The RNA-QSAR approach recognises 115/135mps (85.2%) and 100% of control sequences. Average predictability and robustness were greater than 95%. A previous non-linear model predicts mps with a slightly higher accuracy (97%) but uses a very large parameter space for DNA sequences. Conversely, the (k)xi(M)-based RNA-QSAR encodes more structural information and needs only two variables.

Bacterial Proteins↗
PubMed2006

Effect of waist circumference on reference intervals of liver-related enzyme tests in apparently healthy adult Mexican Americans, black and white Americans.

BACKGROUND: We used a more comprehensible and more physiologically valid indicator of obesity-related liver disease, waist circumference (WC), rather than BMI to study the effect of obesity on liver enzymes, easily measurable surrogates of liver disease. METHODS: WC, liver enzymes and pertinent demographic data were abstracted from NHANES III. After exclusion criteria were applied, we stratified the populations by sex and ethnicity and graphed the percentage of elevated enzymes per WC interval. RESULTS: There was a significant relationship between enzyme activity and WC (p<0.001 for ALT, p<0.01 for ALP, p<0.01 for AST, p=0.02 for GGT and p<0.05 for LD), and the relationship was stronger in females (p<0.002) and Mexican Americans (p<0.001). The enzyme-WC relationship is much weaker in non-Hispanic black females and males. CONCLUSION: As increases in liver enzyme activity can indicate potentially reversible liver disease, our graphs should be used by physicians to motivate obese, apparently healthy Mexican American and non-Hispanic white patients with elevated liver enzymes to reduce their WC.

Adult↗
PubMed2004

Quantitative arthroscopic ultrasound evaluation of living human cartilage.

OBJECTIVE: To investigate whether living human articular cartilage can be evaluated quantitatively by means of a new diagnostic technique that introduces an ultrasonic probe into the knee joint under arthroscopy and then analyzes the A-mode echogram by means of wavelet transformation. DESIGN: Intact and injured sites of living human articular cartilage were evaluated under arthroscopy. The maximum magnitude and the echo duration (defined as the length of time that included 95% of echo signal) were selected as the quantitative indices on the wavelet map. BACKGROUND: Quantitative evaluation of articular cartilage in situ has the potential to contribute to our understanding of cartilage breakdown and to the effectiveness of cartilage regeneration. However, a reliable method of quantitative cartilage evaluation has yet to be developed for clinical use. METHODS: Living human articular cartilage was analyzed using an ultrasonic probe under arthroscopy and the cartilage characteristics on the echo duration-maximum magnitude graph were examined. RESULTS: Unlike the L-shape distribution of human cadaver cartilage data, the distribution of the living human articular cartilage data showed a smooth curve with a steep initial gradient that flattens gradually at the highest value of echo duration on the echo duration-maximum magnitude graph. CONCLUSIONS: The present study suggests a new quantitative evaluation system for articular cartilage with clinical potential.

Arthroscopy↗
PubMed2006

Visualizing the dual space of biological molecules.

An important part of protein structure characterization is the determination of excluded space such as fissures in contact interfaces, pores, inaccessible cavities, and catalytic pockets. We introduce a general tessellation method for visualizing the dual space around, within, and between biological molecules. Using Delaunay triangulation, a three-dimensional graph is constructed to provide a displayable discretization of the continuous volume. This graph structure is also used to compare the dual space of a system in two different states. Tessellator, a cross-platform implementation of the algorithm, is used to analyze the cavities within myoglobin, the protein-RNA docking interface between aspartyl-tRNA synthetase and tRNA(Asp), and the ammonia channel in the hisH-hisF complex of imidazole glycerol phosphate synthase.

Algorithms↗
PubMed2006

Comparison of fast Fourier transformation and autoregressive modelling as a diagnostic tool in analysis of lower extremity venous signals.

In this study, we have compared the efficacy of autoregressive modelling (ARM) and fast Fourier transformation (FFT) of Doppler signals from lower extremity veins of healthy volunteers in various physiologic situations. Compared to FFT, ARM produced smooth spectra and less spectral broadening both in sonograms and power spectra. However, faulty positioning of the peaks along the time axis in FFT-derived power spectral density curves show that FFT is not a suitable method if these graphs are to be used as a diagnostic tool. Analysis of ARM-based venous sonograms and power spectral density graphs revealed that FFT should not be used in signals with high power spectral density levels and low-frequency bandwidth within limited segments of time.

Adult↗
PubMed2005

Geometric diffusions for the analysis of data from sensor networks.

Harmonic analysis on manifolds and graphs has recently led to mathematical developments in the field of data analysis. The resulting new tools can be used to compress and analyze large and complex data sets, such as those derived from sensor networks or neuronal activity datasets, obtained in the laboratory or through computer modeling. The nature of the algorithms (based on diffusion maps and connectivity strengths on graphs) possesses a certain analogy with neural information processing, and has the potential to provide inspiration for modeling and understanding biological organization in perception and memory formation.

Algorithms↗
PubMed2004

Minimal preparation computed tomography instead of barium enema/colonoscopy for suspected colon cancer in frail elderly patients: an outcome analysis study.

AIM: To evaluate the efficacy of minimal preparation computed tomography (MPCT) in diagnosing clinically significant colonic tumours in frail, elderly patients. MATERIALS AND METHODS: A prospective study was performed in a group of consecutively referred, frail, elderly patients with symptoms or signs of anaemia, pain, rectal bleeding or weight loss. The MPCT protocol consisted of 1.5 l Gastrografin 1% diluted with sterile water administered during the 48 h before the procedure with no bowel preparation or administration of intravenous contrast medium. Eight millimetre contiguous scans through the abdomen and pelvis were performed. The scans were double-reported by two gastrointestinal radiologists as showing definite (>90% certain), probable (50-90% certain), possible (<50% certain) neoplasm or normal. Where observers disagreed the more pessimistic of the two reports was accepted. The gold standard was clinical outcome at 1 year with positive end-points defined as (1) histological confirmation of CRC, (2) clinical presentation consistent with CRC without histological confirmation if the patient was too unwell for biopsy/surgery, and (3) death directly attributable to colorectal carcinoma (CRC) with/without post-mortem confirmation. Negative end-points were defined as patients with no clinical, radiological or post-mortem findings of CRC. Patients were followed for 1 year or until one of the above end-points were met. RESULTS: Seventy-two patients were included (mean age 81; range 62-93). One-year follow-up was completed in 94.4% (n=68). Mortality from all causes was 33% (n=24). Five histologically proven tumours were diagnosed with CT and there were two probable false-negatives. Results were analysed twice: assuming all CT lesions test positive and considering "possible" lesions test negative [brackets] (95% confidence intervals): sensitivity 0.88 (0.47-1.0) [0.75 (0.35-0.97)], specificity 0.47 (0.34-0.6) [0.87 (0.75-0.94)], positive predictive value 0.18 [0.43], negative predictive value 0.97 [0.96], positive likelihood ratio result 1.6 [5.63], negative likelihood ratio result 0.27 [0.29], kappa 0.31 [0.43]. Tumour prevalence was 12%. A graph of conditional probabilities was generated and analysed. A variety of unsuspected pathology was also found in this series of patients. CONCLUSIONS: MPCT should be double-reported, at least initially. "Possible" lesions should be ignored. Analysis of the graph of conditional probability applied to a group of frail, elderly patients with a high mortality from all causes (33% in our study) suggests: (1) if MPCT suggests definite or probable carcinoma, regardless of the pre-test probability, the post-test probability is high enough to warrant further action, (2) frail, elderly patients with a low pre-test probability for CRC and a negative MPCT should not have further investigation, (3) frail, elderly patients with a higher pre-test probability of CRC (such as those presenting with rectal bleeding) and a negative MPCT should have either double contrast barium enema (DCBE) or colonoscopy as further investigations or be followed clinically for 3-6 months. MPCT was acceptable to patients and clinicians and may reveal significant extra-colonic pathology.

Aged↗
PubMed2005

GIS analysis for the marine environmental data off Karnataka coast.

Geographic Information System (GIS) is used to develop the Oceanographic Information System (OIS) for marine environmental data off Karnataka coast. Its goal is to provide a set of tools for oceanographic and bathymetry data assessment and products like graphs, query system for the users. The most significant interfaces are the GIS based Map-query and Contour visualization. The interfaces are user-friendly and oriented towards bridging the gap between user's knowledge and the technical knowledge required to operate the software system. The OIS also provides users with other analysis tools like query based reports and graphs. OIS can be used as a powerful tool to synthesize not only all the data off Karnataka coast but for comprehensive interpretation and forecasting of marine environmental ecosystems for any region. This system has been applied to the Karnataka Coastal Environment, India and it is very useful for the clients and policy makers.

Chlorophyll↗
PubMed2006

Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L.

The development of 2D graph-theoretic representations for DNA sequences was very important for qualitative and quantitative comparison of sequences. Calculation of numeric features for these representations is useful for DNA-QSAR studies. Most of all graph-theoretic representations identify each one of the four bases with a unitary walk in one axe direction in the 2D space. In the case of proteins, twenty amino acids instead of four bases have to be considered. This fact has limited the introduction of useful 2D Cartesian representations and the corresponding sequences descriptors to encode protein sequence information. In this study, we overcome this problem grouping amino acids into four groups: acid, basic, polar and non-polar amino acids. The identification of each group with one of the four axis directions determines a novel 2D representation and numeric descriptors for proteins sequences. Afterwards, a Markov model has been used to calculate new numeric descriptors of the protein sequence. These descriptors are called herein the sequence 2D coupling numbers (zeta(k)). In this work, we calculated the zeta(k) values for 108 sequences of different polygalacturonases (PGs) and for 100 sequences of other proteins. A Linear Discriminant Analysis model derived here (PG=5.36.zeta1-3.98.zeta3-42.21) successfully discriminates between PGs and other proteins. The model correctly classified 100% of a subset of 81 PGs and 75 non-PG proteins sequences used to train the model. The model also correctly classified 51 out of 52 (98.07%) of proteins sequences used as external validation series. The uses of different group of amino acids and/or axes orientation give different results, so it is suggested to be explored for other databases. Finally, to illustrates the use of the model we report the isolation and prediction of the PG action for a novel sequence (AY908988) isolated by our group from Psidium guajava L. This prediction coincides very well with sequence alignment results found by the BLAST methodology. These findings illustrate the possibilities of the sequence descriptors derived for this novel 2D sequence representation in proteins sequence QSAR studies.

Algorithms↗