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PubMed2003

A quantitative model for transforming reflectance spectra into the Munsell color space using cone sensitivity functions and opponent process weights.

This article presents a computational model of the process through which the human visual system transforms reflectance spectra into perceptions of color. Using physical reflectance spectra data and standard human cone sensitivity functions we describe the transformations necessary for predicting the location of colors in the Munsell color space. These transformations include quantitative estimates of the opponent process weights needed to transform cone activations into Munsell color space coordinates. Using these opponent process weights, the Munsell position of specific colors can be predicted from their physical spectra with a mean correlation of 0.989.

Color Perception↗
PubMed1995

Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences.

Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity. Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da (N,d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N,d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da (N,d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth. We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da (N,d0) within limitations (d0 = constant (average) coupling probability).

Animals↗
PubMed1994

The solubilities of five cyclic dipeptides in water and in aqueous urea at 298.15 K: a quantitative model for the denaturation of proteins in aqueous urea solutions.

The solubilities of cyclo(L-alanylglycine), cyclo(L-alanyl-L-alanine), cyclo(glycyl-L-leucine), cyclo(L-valyl-L-valine) and cyclo(glycyl-L-phenylalanine) were determined in water and in aqueous urea solutions up to concentrations of 9 molar urea at 298.15 K. The solubilities of all cyclic dipeptides increase with increasing urea concentration. A simple equilibrium model, taking into account the activity of urea and that of water, fits the solubility data yielding apparent equilibrium constants describing the interactions occurring between urea and the peptide groups plus the alkyl groups that are next to these peptide groups. The apparent equilibrium constants were converted to Gibbs energy parameters for each amino acid residue which were then used to make a quantitative estimate of the contribution of urea to the denaturation of proteins.

Chemical Phenomena↗
PubMed2005

A quantitative model of tumor-induced angiogenesis in the nude mouse.

OBJECTIVE: Novel animal models allowing for the quantification of tumor-induced angiogenesis and cell migration may offer significant insight into the characterization and multidisciplinary treatment of brain tumors. In this study, we seek to establish such a model in tumor-bearing brain, allowing for a clear demarcation of primary and satellite tumor tissue in conjunction with precise quantification of cerebral microvasculature. METHODS: We used green fluorescent protein-transfected 9L-gliosarcoma cells stereotactically injected into the brain parenchyma of nude mice perfused with tetramethylrhodamine-dextran immediately before they were killed. New three-dimensional analytical software developed in our laboratory provided a quantitative analysis of laser-scanning confocal microscopy images of dextran-labeled cerebral microvessels. RESULTS: Our data confirm significant angiogenesis in tumor and brain adjacent to tumor. CONCLUSION: Because these highly infiltrative malignant brain tumors interdigitate with normal brain parenchyma through finger-like projections at the periphery of the solid tumor boundary, therapeutic options targeting tumor blood flow--combined with novel three-dimensional imaging to localize and track such interventions--may offer new hope for glioma management. To our knowledge, this system represents the first animal brain tumor model allowing for the precise colocalization and quantification of angiogenesis and tumor cell invasion, which may play an important role in the development of future therapy for brain tumors.

Animals↗
PubMed1992

Murine Kupffer cells and hepatic natural killer cells regulate tumor growth in a quantitative model of colorectal liver metastases.

This investigation aimed to develop a biologically relevant murine model of colorectal liver metastases and determine if Kupffer cells (KC) and hepatic natural killer cells (hNKC) regulate tumor growth. The model involves the injection of murine colon adenocarcinoma 26 (MCA 26) tumor cells into the portal vein of female-specific pathogen-free BALB/c mice. Metastases developed in all animals, and the growth was limited entirely to the liver. To determine if KC and hNKC control the development of liver metastases, the in vivo function of these hepatic effector cells was modulated. Tumor growth was quantitated by the uptake of 125I into tumor DNA. Stimulation of the KC and hNKC produced a significant (P less than 0.01) dose-dependent decrease in 125I uptake in the liver in both treatment groups, which was associated with a significant improvement in survival (P less than 0.05). The in vivo cytotoxic function of the liver was inhibited with an intravenous injection of gadolinium chloride (for KC) or asialo GM1 antiserum (for hNKC). Inhibition of KC and hNKC cytotoxic function led to a significant (P less than 0.01) increase in 125I uptake in the liver and a significant decrease in survival (P less than 0.05).

Adenocarcinoma↗
PubMedDate not supplied

A quantitative model of invasive Pseudomonas infection in burn injury.

To evaluate newer therapies for wound infections, it becomes necessary to quantify bacteria that invade from the infected wounds into the adjacent tissues. For example, antibody-targeted photolysis targets the invasive Pseudomonas with antibodies carrying photochemical dyes. A full-thickness burn wound was infected with Pseudomonas aeruginosa with a modification of previous methods. In mice, a skin fold was elevated, and two preheated brass blocks at 92 degrees to 95 degrees C were applied for 5 seconds, producing a 5% total body surface area injury with discrete margins. The eschars were immediately inoculated with Pseudomonas. Survival at 10 days was 100% with burn injury alone and 60% with infected burns. Pseudomonas (10(8)/gm) were recovered from the unburned muscle by 24 hours. The method produced uniform and reproducible quantitative bacteriology within the muscle immediately beneath the burn injury (SL < 0.05). Quantitative comparisons can be used to determine the effectiveness of newer modalities to control Pseudomonas burn wound infections.

Animals↗
PubMed1996

Proliferative response of mouse spermatogonial stem cells after irradiation: a quantitative model analysis of experimental data.

The testes of CDF1 mice were irradiated with single doses of X-rays ranging from 2-16 Gy. The number of haploid cells in the testis at different times after irradiation (42-350 days) was determined by one-parameter flow cytometry both for irradiated animals and for age-matched controls. Based on literature data on the kinetics of the spermatogenesis in mice, a mathematical model of the (hierarchical) germ tissue was developed. Using this model, the processes of radiation-induced cell loss and subsequent recovery were simulated and free parameters of the model were estimated by fitting the model prediction to the experimental data. One of the aims of the study was to investigate the kinetic behaviour of spermatogonial stem cells and the corresponding control mechanisms. In order to fit the data, the model has to include the following features: (i) A preferential self-repopulation of spermatogonial stem cells following tissue injury. The model-estimated probability of a self-renewing division rises from 50% (the steady-state value) to 95% if the stem-cell population is reduced to 10% of its normal size. (ii) A relatively low, almost constant turnover rate of the stem-cell compartment. It is suggested by the analysis that less than 10% of the spermatogonial stem cells present in the testis divide per day, regardless of the degree of cellular depletion. (iii) A mechanism responsible for incomplete recovery. The observed incomplete recovery of spermatogenesis after single doses exceeding 10 Gy can be described quantitatively assuming that the stem cells are organized into discrete proliferative structures, the number of cells per structure being about 60.

Animals↗
PubMed1987

A quantitative model of myosin phosphorylation and the photomechanical response of the isolated sphincter pupillae of the frog iris.

The time courses of isometrically recorded photomechanical responses of isolated sphincter pupillae of Rana pipiens can be accurately predicted by a set of differential equations derived from phosphorylation theory of smooth muscle contraction. We compared actual light-stimulated contractions with calculated ones over a wide range of stimulus intensities (56-fold) and durations (0.4-4.0 s). The hypothetical Ca++-calmodulin-myosin light chain kinase cascade acts as a "valve" to control the flow of ATP through a phosphorylation-dephosphorylation cycle. When the rate of flow of ATP through the phosphorylation-dephosphorylation cycle is increased, the percentage of phosphorylated myosin increases. The time courses of the concentrations of phosphorylated myosin during different responses are seen to be functions of the time courses of the opening and closing of the coupling cascade "valve." The calculations predict experimentally measurable intermediate variables, which can aid the investigation of the application of quantitative phosphorylation theory to amphibian sphincter pupillae and to smooth muscle in general.

Adenosine Triphosphate↗
PubMed2005

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.

BACKGROUND: Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM). This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP) and proteasomal cleavage of protein sequences. RESULTS: Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1) the output generated is easy to interpret, (2) input and output are both quantitative, (3) specific computational strategies to handle experimental noise are built in, (4) the algorithm is designed to effectively handle bounded experimental data, (5) experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6) it is possible to incorporate pair interactions between positions of a sequence. CONCLUSION: Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.

Algorithms↗
PubMed2004

Quantitative models of the rat pulmonary arterial tree morphometry applied to hypoxia-induced arterial remodeling.

Little is known about the constituent hemodynamic consequences of structural changes that occur in the pulmonary arteries during the onset and progression of pulmonary arterial remodeling. Many disease processes are known to be responsible for vascular remodeling that leads to pulmonary arterial hypertension, cor pulmonale, and death. Histology has been the primary tool for evaluating pulmonary remodeling, but it does not provide information on intact vascular structure or the vessel mechanical properties. This study is an extension of our previous work in which we developed an alternative imaging technique to evaluate pulmonary arterial structure. The lungs from Sprague-Dawley rats were removed, perfusion analysis was performed on the isolated lungs, and then an X-ray contrast agent was used to fill the arterial network for imaging. The lungs were scanned over a range of intravascular pressures by volumetric micro-computed tomography, and the arterial morphometry was mapped and measured in the reconstructed isotropic volumes. A quantitative assessment of hemodynamic, structural, and biomechanical differences between rats exposed for 21 days to hypoxia (10% O(2)) or normoxia (21.0% O(2)) was performed. One metric, the normalized distensibility of the arteries, is significantly (P < 0.001) larger [0.025 +/- 0.0011 (SE) mmHg(-1)] (n = 9) in normoxic rats compared with hypoxic [0.015 +/- 0.00077 (SE) mmHg(-1)] (n = 9). The results of the study show that these models can be applied to the Sprague-Dawley rat data and, specifically, can be used to differentiate between the hypoxic and the control groups.

Animals↗
PubMed2023

Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

RNA, Transfer↗
PubMed1994

Quantitative modeling and biology: the multivariate approach.

Even though elegant examples of mathematical modeling of biological problems exist, such approaches still remain outside the domain of most biologists. It is proposed that, for a wider and more systematic use of mathematical models in biology, the soft modeling approaches, which are applicable to phenomena with a limited level of definition, should be investigated and preferred. In particular, multivariate data analysis (MDA) is indicated as an important tool toward fulfilling this goal. This paper reviews the general principles of MDA and examines in detail principal component analysis and cluster analysis, which are two of the most important MDA techniques. A number of applications to real biological problems are presented. These examples show how the construction of classifications corresponds to the generation of new knowledge and new concepts, which are hierarchically on a higher level than the initial information. This new form of knowledge is obtained without superimposing a priori theories on the data. It is demonstrated how the MDA can lead to the identification of biological systems; also shown is their ability to describe multiple scale phenomena, a typical feature of biological systems. Moreover, the multivariate analyses provide new descriptors for a given biological system; these descriptors are quantitative, thus allowing the system to be described in a "metric space," where it then becomes possible to use any other mathematical tool.

Animals↗
PubMed1998

Modelling quantitative structure-activity relationships between animal behaviour and environmental signal molecules.

Quantitative structure-activity relationships (QSARs) between the physicochemical properties of environmental signal molecules and animal behaviour have been determined. Past work has shown that oyster and barnacle larval settlement and mud crab abdominal pumping (for larval dispersal) are stimulated by small peptide cues. In all the peptides examined that were active at ecologically relevant concentrations, arginine or lysine was found at the carboxy terminus, but the amino acids found at preceding positions were highly variable. We used the multivariate partial least squares algorithm to relate composite properties for the hydrophilicity, size and charge of each amino acid and the sequence position to oyster, barnacle and crab behaviour patterns. From the information in these QSAR models, the apparent variability in amino acid sequences eliciting behavioural responses was explained in each case, and more potent peptide analogues are hypothesized on the basis of untested amino acid sequences. Remarkably, these peptide signals are all structurally related to the carboxy-terminal sequence of mammalian C5a anaphylatoxin, a potent white blood cell chemoattractant. Even more striking is the fact that these different animal species should rely on apparently similar environmental signal molecules when residing within a common habitat (southeastern US estuaries). Through the physicochemical properties of amino acids, the current QSAR models clearly differentiate between the optimal sequences for eliciting oyster, barnacle and mud crab behaviour. Thus, QSARs provide a novel and powerful method not only for relating the physicochemical properties of molecules to animal behaviour but also for differentiating responses to chemicals by individuals of different species.

Animals↗
PubMed1985

Study of the carcinogenic mechanism for polycyclic aromatic hydrocarbons--extended bay region theory and its quantitative model.

With the help of results on the metabolism and the carcinogenic activities of polycyclic aromatic hydrocarbons (PAH), the comprehensive metabolic process in vivo is discussed. It is thought that the carcinogenic activity exhibited by a PAH is determined by the competition between the carcinogenesis and detoxification in which it participates. It is suggested that the essential agent of carcinogenesis should be, as a rule, the highest delocalization energy (beta unit) of the carbonium ion at the aromatic angular ring (A region), which is obtained by the pertubational molecular orbit (PMO) method. Since there are no essential distinctions in the molecular geometry and delocalization energy states between two carbonium ions of the aromatic angular ring and of the bay region, the A region can be looked upon as the extended bay region. On the basis of discussion of the overall metabolism, evaluation of the detoxification efficacy of each kind of the competing carcinogenic factors, including the biological factor B and three structural factors of the PAH molecule: K, A and L, was made. After making necessary approximation, K = 0.228, A = 0.5, L = 1.22 and B = 0.7 are obtained. It can be seen from these values that the L region plays the most important role in detoxification processes, and the K region plays the least important role. The effect of biological factor B is approximately the sum of the K region and the A region. This paper suggests the concept of a carcinogenic constant. For the PAHs with the same number of aromatic rings (N), C is a constant. The curve of function C = f(N), including the extensional line, is an isosceles triangle. The author suggests that it should be called the 'Pyramid Rule'. The final form of the quantitative equation is log R = C[delta E3deloc/(0.7 + 0.228nk + 0.5na + 1.22n1)]. The values for 50 PAHs which had been tested by animal experiments were calculated. Of these, 92% of the PAHs are in agreement with experiments on carcinogenic activities.

Animals↗
PubMedDate not supplied

Quantitative model of cellulite: three-dimensional skin surface topography, biophysical characterization, and relationship to human perception.

Gynoid lipodystrophy (cellulite) is the irregular, dimpled skin surface of the thighs, abdomen, and buttocks in 85% of post-adolescent women. The distinctive surface morphology is believed to result when subcutaneous adipose tissue protrudes into the lower reticular dermis, thereby creating irregularities at the surface. The biomechanical properties of epidermal and dermal tissue may also influence severity. Cellulite-affected thigh sites were measured in 51 females with varying degrees of cellulite, in 11 non-cellulite controls, and in 10 male controls. A non-contact high-resolution three-dimensional laser surface scanner was used to quantify the skin surface morphology and determine specific roughness values. The scans were evaluated by experts and naive judges (n=62). Body composition was evaluated via dual-energy x-ray absorptiometry; dermal thickness and the dermal-subcutaneous junction were evaluated via high-resolution 3D ultrasound and surface photography under compression. Biomechanical properties were also measured. The roughness parameters Svm (mean depth of the lowest valleys) and Sdr (ratio between the roughness surface area and the area of the xy plane) were highly correlated to the expert image grades and, therefore, designated as the quantitative measures of cellulite severity. The strength of the correlations among naive grades, expert grades, and roughness values confirmed that the data quantitatively evaluate the human perception of cellulite. Cellulite severity was correlated to BMI, thigh circumference, percent thigh fat, architecture of the dermal-subcutaneous border (ultrasound surface area, red-band SD from compressed images), compliance, and stiffness (negative correlation). Cellulite severity was predicted by the percent fat and the area of the dermal-subcutaneous border. The biomechanical properties did not significantly contribute to the prediction. Comparison of the parameters for females and males further suggest that percent thigh fat and surface area roughness deviation are the distinguishing features of cellulite.

Absorptiometry, Photon↗
PubMed1996

Cellular sociology applied to neuroendocrine tumors of the lung: quantitative model of neoplastic architecture.

This paper reports on cellular sociology, which consists of modeling tissular architecture based on graph theory. Voronoi's diagram was chosen to build the models. This diagram derives from a cell neighborhood concept and generates parameters which objectively represent tissue architecture. Minimal spanning tree (MST) is probably the more frequently used among graphs and successfully discriminates different grades of pathological process. However, Voronoi's diagram is more comprehensive and a more complete representation of architecture with the advantage of stability. The lung neuroendocrine tumor classification is far from being consensual, especially for lesions which don't fall in with typical carcinoid and small cell carcinoma groups. By comparing architectural models of 20 neuroendocrine tumors of the lung, this work supports the morphologic spectrum concept of these tumors and also supports the recently proposed concept of large-cell neuroendocrine tumors of the lung. Finally, architectural parameters separate small-cell-lung carcinomas from neuroendocrine non-small-cell lung carcinomas.

Carcinoid Tumor↗