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Application of neural computing in pharmaceutical product development.

Neural computing technology is capable of solving problems involving complex pattern recognition. This technology is applied here to pharmaceutical product development. The most commonly used computational algorithm, the delta back-propagation network, was utilized to recognize the complex relationship between the formulation variables and the in vitro drug release parameters for a hydrophilic matrix capsule system. This new computational technique was also compared with the response surface methodology (RSM). Artificial neural network (ANN) analysis was able to predict the response values for a series of validation experiments more precisely than RSM. ANN may offer an alternative to RSM because it allows for the development of a system that can incorporate literature and experimental data to solve common problems in the pharmaceutical industry.

Algorithms↗

Molecular basis of cell integrity and morphogenesis in Saccharomyces cerevisiae.

In fungi and many other organisms, a thick outer cell wall is responsible for determining the shape of the cell and for maintaining its integrity. The budding yeast Saccharomyces cerevisiae has been a useful model organism for the study of cell wall synthesis, and over the past few decades, many aspects of the composition, structure, and enzymology of the cell wall have been elucidated. The cell wall of budding yeasts is a complex and dynamic structure; its arrangement alters as the cell grows, and its composition changes in response to different environmental conditions and at different times during the yeast life cycle. In the past few years, we have witnessed a profilic genetic and molecular characterization of some key aspects of cell wall polymer synthesis and hydrolysis in the budding yeast. Furthermore, this organism has been the target of numerous recent studies on the topic of morphogenesis, which have had an enormous impact on our understanding of the intracellular events that participate in directed cell wall synthesis. A number of components that direct polarized secretion, including those involved in assembly and organization of the actin cytoskeleton, secretory pathways, and a series of novel signal transduction systems and regulatory components have been identified. Analysis of these different components has suggested pathways by which polarized secretion is directed and controlled. Our aim is to offer an overall view of the current understanding of cell wall dynamics and of the complex network that controls polarized growth at particular stages of the budding yeast cell cycle and life cycle.

Cell Wall↗

Comparison of human ictal, interictal and normal non-linear component analyses.

OBJECTIVES: The non-linear properties of EEG and filtered rhythms obtained from healthy subjects and epileptic patients with complex partial seizures were analyzed to investigate whether EEG in different neurological states can be generated by the mechanism that integrates several non-linear dynamic systems. METHODS: The control EEG (from 26 healthy subjects), interictal EEG and ictal EEG (from 25 patients) were digitally filtered into delta (0.5-4 Hz), theta (4-8 Hz), alpha (8-13 Hz), beta (13-30 Hz) and gamma (30-40 Hz) components. The correlation dimension was calculated on each original signal and corresponding surrogate data. A new method was developed to accelerate the calculation of the correlation integral. Function P(m,r) was defined to visualize the meaning of the correlation dimension. The point critical to the estimation was determined by the P(m,r) function. RESULTS: The EEG in the control subjects and patients showed significantly lower correlation dimensions than the surrogate data. The delta, alpha, beta and gamma components from the control EEG exhibited similar complexity to the surrogate data, while only the alpha component from the interictal EEG presented the same dimension as the surrogate data. The correlation dimensions of the theta and alpha components remained the same when the neurological state changed from interictal EEG to ictal EEG. The complexity of the beta component was higher than the complexity of other components in both control subjects and patients. The correlation dimension of EEG was significantly correlated to the complexity of delta, theta, beta and gamma components. CONCLUSIONS: Our results suggest that EEG and filtered components in different neurological states demonstrate varied dynamic properties. The characteristics of neuronal networks can be differentiated by the dynamics of filtered components. Separating EEG into different dynamic systems may facilitate understanding of the mechanisms involved in the human EEG.

Adult↗

Mathematical modeling of differentiation in Dictyostelium discoideum.

Methods for the dynamic analysis of biochemical differentiation are presented. These are demonstrated in the analysis of biochemical differentiation of the carbohydrate system in D. discoideum. Procedures for simplification which are presented are projection and contraction of the system trajectory in state space and the generation of reduced equivalent dynamic metabolic networks. The importance of the hierarchical structure of differentiating systems is discussed and the concept of a dynamic embedding diagram is introduced. It is shown that complex systems must be analyzed on an epoch by epoch basis, each epoch being a period of time characterized by a constant dynamic embedding diagram, and that widely different time scales and state space scales may be necessary in different epochs. In particular there is no a priori lower limit to the time scale which may be necessary during the analysis. Some problems in mathematically defining differentiation are discussed.

Carbohydrate Metabolism↗

Keratin 14 protein in cultured nonparenchymal rat hepatic epithelial cells: characterization of keratin 14 and keratin 19 as antigens for the commonly used mouse monoclonal antibody OV-6.

We have recently reported that cell lines of nonparenchymal origin isolated from rat liver and pancreas, which have been suggested to be the progeny of a facultative stem cell compartment in vivo, express an unusual combination of keratins (K). These cell lines express K8 and K14 but not K18 and K5, their normal partners in filament formation (Bisgaard HC, Thorgeirsson SS, J Cell Physiol 147:333-343, 1991). However, upon spontaneous transformation and differentiation toward a hepatoblastlike progeny, K14 expression is abrogated and replaced by expression of K18 (Wirth et al., Electrophoresis 13:305-332, 1992). In the study presented here, we confirmed by protein sequence analysis that K14 was a major component of the intermediate filaments in a nonparenchymal cell line of hepatic origin. Immunocytochemical analysis of the cells in monolayer demonstrated that K8 as well as K14 were incorporated in the cellular cytoskeleton. Further analysis by immunoprecipitation showed that filament complexes were formed between K8 and K14 as atypical partners. Thus, we concluded that in some nonparenchymal cell lines isolated from rat liver, K8 and K14 form a major intermediate filament network. Finally, we showed that an antibody widely used in studies of the cell lineages of hepatic and pancreatic tissues and their neoplasms, the mouse monoclonal antibody OV-6, recognizes a common epitope in K14 and K19.

Amino Acid Sequence↗

Superposition of arteriolar vasomotion waves and regulation of blood flow in skeletal muscle microcirculation.

In skin muscle microcirculation of Syrian hamsters, rhythmic diameter changes were studied along the arteriolar network, under normoxic conditions, at rest. A teflon coated-aluminum chamber was implanted in the dorsum skin of animals. The microcirculation was investigated using intravital microscopy technique. Vessel diameters were determined by a computer-assisted method. Power spectrum analysis of vasomotion recordings was carried out with Fast Fourier Transform and Autoregressive modelling. To determine vasomotion waveform spreading, cross-spectral data (amplitude and phase) were computed, using the modified periodogram method (FFT). The arterioles were classified according to Strahler's method. Order 1 vessels (diameter: 7.50 +/- 1.16 microns) showed the highest frequency, 4-15 cycles per min, and percentage amplitude in the range 60-100%. Order 2 and 3 arterioles had intermediate frequencies, and amplitude in the range 50-100%, and 15-50%, respectively. The largest order 4 vessels (diameter: 28.97 +/- 9.55 microns) had the lowest frequency, 0.3-3 cpm, and amplitude in the range 5-20%. In most networks, cross-correlation analysis revealed two groups of frequency components. Low frequency group was propagated from order 4 and 3 vessels downstream. High frequency components were transmitted upstream from order 1 and 2 arterioles. Therefore, a complex superposition of waveforms resulted from the activity of discrete points along the microvasculature. In conclusion, rhythmic diameter changes of arterioles in skeletal muscle microcirculation regulate blood flow distribution in capillary units and control tissue oxygenation.

Animals↗

Resolution of batch variations in pyrolysis mass spectrometry of bacteria by the use of artificial neural network analysis.

A simple, but stringent, three group model of bacterial interstrain identity (two cultures of the same strain of Escherichia coli) and difference (a culture of a serologically distinct strain) was used in multiple serial weekly subcultures for five weeks to demonstrate the effect of both growth-related (phenotypic) and machine-related variation on pyrolysis mass spectra. An aliquot of serum from a single sample was included in each pyrolysis batch to distinguish machine drift from culture drift. Conventional principal component (PC) canonical variate (CV) analysis was successful within each pyrolysis batch but the variations between batches precluded the use of data from more than one batch in successful PCCV analysis. In contrast, artificial neural networks (ANNs) trained with data from one batch could be successfully used to identify groups in data from non-contemporaneous pyrolysis batches. Although the ANN method will require validation in more complex settings than this simple model, it is a promising approach to the problem of batch constraint in pyrolysis mass spectrometry.

Bacterial Typing Techniques↗

Beyond one-to-one mappings: Modelling distributed lesion-symptom relationships with multilayer networks.

Lesion-symptom mapping is widely used to identify causal relationships between brain structures and behaviour, and has played a central role in neuropsychologically informed network models of cognition. However, even recent approaches remain constrained by a one-to-one mapping framework, which oversimplifies the complex relationships between network-level damage and cognitive deficits. In addition, the non-orthogonality of cortical and white matter damage makes it difficult to disentangle their distinct contributions. Here, we used graph-based multilayer network analysis to address these limitations and evaluate clinical relevance. Using neuroanatomical and longitudinal neuropsychological data from 252 patients who underwent awake neurosurgery for low-grade glioma, we constructed interactive, three-layer networks for each hemisphere. Layer 1 comprised neuropsychological tasks (NT), layer 2 structural disconnections (SD), and layer 3 cortical damage (CD). Nodes represented tasks, white matter tracts, and cortical parcels, respectively, whereas within-layer edges captured correlations in performance or co-occurring damage patterns. Multilayer community detection identified domain- and hemisphere-specific brain-behaviour motifs linking executive, language, and spatial functions to distinct combinations of cortical and white matter disruption, a pattern confirmed by two spatial embedding approaches. Centrality analyses revealed a continuum of mapping relationships, ranging from one-to-one to one-to-many associations, indicating that tasks such as verbal fluency are better explained by multiple disconnection mechanisms. Additional analyses uncovered many-to-one and many-to-many relationships and highlighted tracts and cortical regions with domain-general relevance. Together, these findings support a neurobiologically grounded, network-oriented account of how structural brain damage gives rise to cognitive deficits, with implications for clinical care.

Humans↗

Synergistic effect of interleukin-1 and CD40L on the activation of human renal tubular epithelial cells.

BACKGROUND: Renal tubular epithelial cells are a central cell type in tubulointerstitial inflammation because they can produce inflammatory mediators such as cytokines and chemokines. Several signals derived from either monocytes or activated T cells have been reported to regulate the activation of tubular epithelial cells. We studied this regulation in more detail by combined treatment with CD40 ligand and the proinflammatory cytokine interleukin-1 (IL-1) in vitro. METHODS: The regulation of cytokine and chemokine production was studied in primary cultures of human proximal tubular epithelial cells (PTECs). PTECs were activated by coculture with CD40L-transfected murine fibroblasts in combination with recombinant human cytokines. The production of IL-6, IL-8, monocyte chemoattractant protein-1 (MCP-1), and RANTES were measured by specific enzyme-linked immunosorbent assay. RESULTS: The combined activation of PTECs with CD40L and IL-1 resulted in strong synergistic effects on the production of IL-6, IL-8, and RANTES, whereas only an additive stimulation of MCP-1 production was observed. The effects were specific for IL-1 and could be neutralized by the addition of the IL-1R antagonist. Both IL-1alpha and IL-1beta showed similar effects on cytokine production by PTECs. The effects of IL-1 were dose dependent, and kinetic experiments showed that synergistic effects were observed after 24 hours of activation and remained present for at least five days. Reverse transcription-polymerase chain reaction analysis showed that human PTECs could express both IL-1alpha and IL-1beta. The activation of PTECs with IL-1 resulted in an up-regulation of CD40 expression on these cells. CONCLUSIONS: A complex network of regulation exists for the production of cytokines and chemokines by PTECs. The combined treatment results in strong synergistic effects on IL-6, IL-8, and RANTES production. This strengthens the potential role of tubular epithelial cells in inflammatory responses within the kidney.

Animals↗

Quantitative analysis of the interactions between prenyl Rab9, GDP dissociation inhibitor-alpha, and guanine nucleotides.

Rab9 is a Ras-like GTPase required for the transport of mannose 6-phosphate receptors between late endosomes and the trans Golgi network. Rab9 occurs in the cytosol as a complex with GDP dissociation inhibitor (GDI), which we have shown delivers prenyl Rab9 to late endosomes in a functional form. We report here basal rate constants for guanine nucleotide dissociation and GTP hydrolysis for prenyl Rab9. Both rate constants were influenced in part by the hydrophobic environment of the prenyl group. Guanine nucleotide dissociation and GTP hydrolysis rates were lower in the presence of lipid; detergent stimulated intrinsic nucleotide exchange. GDI-alpha inhibited GDP dissociation from prenyl Rab9 by 2.4-fold. GDI-alpha associated with prenyl Rab9 with a KD of 60 nM in 0.1% Lubrol and 23 nM in 0.02% Lubrol. In 0.1% Lubrol, GDI-alpha inhibited GDP dissociation half maximally at 72 +/- 18 nM, consistent with the KD determinations. These data suggest that GDI-alpha associates with prenyl Rab9 with a KD of < or = 23 nM under physiological conditions. Finally, a previously uncharacterized minor form of GDI-alpha inhibited GDP dissociation from prenyl Rab9 by 1.9-fold and bound prenyl Rab9 with a KD of 67 nM in 0.1% Lubrol.

Animals↗

Instrumental measurement of skin colour and skin type as risk factors for melanoma: a statistical classification procedure.

A statistical procedure to evaluate melanoma risk in Caucasian subjects on the basis of colorimetric measurement of skin colour and Fitzpatrick phototype is described. One hundred and sixty melanoma patients and 546 randomized healthy subjects of similar age, sex and place of origin were examined in the same period for skin colour using a tristimulus colorimeter and for Fitzpatrick phototype. A clinical score for classification purposes was obtained by statistical discriminant analysis with multivariate data transformation and dimension reduction techniques. A Fisher linear classifier was chosen for its simplicity and robustness in correctly predicting melanoma risk in new subjects. The classification rule was designed to avoid classifying subjects at high risk for melanoma as low risk, i.e. to give a negligible number of false negatives at the expense of more false positives. The procedure is objective and readily adapted to different clinical requirements. This is only a preliminary study but it is hoped that by performing more complex statistical analyses, e.g. neural networks, and adding other parameters (proven risk factors such as number of naevi) the performance will be further improved.

Colorimetry↗

Toward a kinetic theory of connective tissue micromechanics.

The aim of this study is to develop unifying concepts at the microstructural level to account for macroscopic connective tissue dynamics. We establish the hypothesis that rate-dependent and rate-independent dissipative stresses arise in the interaction among fibers in the connective tissue matrix. A quantitative theoretical analysis is specified in terms of geometry and material properties of connective tissue fibers and surrounding constituents. The analysis leads to the notion of slip and diffusion boundary layers, which become unifying concepts in understanding mechanisms that underlie connective tissue elasticity and energy dissipation during various types of loading. The complex three-dimensional fiber network is simplified to the interaction of two ideally elastic fibers that dissipate energy on slipping interface surfaces. The effects of such interactions are assumed to be expressed in the aggregate matrix. Special solutions of the field equations are obtained analytically, whereas the general solution of the model field equations is obtained numerically. The solutions lead to predictions of tissue behavior that are qualitatively, if not quantitatively, consistent with reports of a variety of dynamic moduli, their dependencies on the rate and amplitude of load application, and some features associated with preconditioning.

Connective Tissue↗

Genetic dissection of the Leishmania paraflagellar rod, a unique flagellar cytoskeleton structure.

The paraflagellar rod (PFR) is a unique network of cytoskeletal filaments that lies alongside the axoneme in the flagella of most trypanosomatids. While little is known about how two major Leishmania mexicana PFR protein components, PFR1 and PFR2, assemble into this complex structure, previous analysis of PFR2 null mutants demonstrated that the PFR is essential for proper cell motility. The structural roles of PFR1 and PFR2 are now examined through comparison of PFR2 null mutants with new PFR1 null mutant and PFR1/PFR2 double null mutant parasites. Both PFR1 and PFR2 were essential for PFR formation and cell motility. When elimination of one PFR gene prevented assembly of a native PFR structure, the other PFR protein accumulated at the distal flagellar tip. Comparison of PFR substructures remaining in each mutant revealed that: (1) fibers that attach the PFR to the axoneme did not contain PFR1 or PFR2, and assemble in the absence of a PFR. (2) PFR1 was synthesized and transported to the flagella in the absence of PFR2, where it formed a stable association with the axoneme attachment fibers. (3) PFR2 was synthesized and transported to the flagella in the absence of PFR1, though it was not found associated with the axoneme attachment fibers. (4) PFR1 and PFR2 were located throughout the subdomains of the PFR. These data suggest that while PFR filaments contain both PFR1 and PFR2, the PFR is attached to the axoneme by interaction of PFR1 with the axoneme attachment fibers.

Animals↗

Structure of the reticular lamina and repair after noise injury.

Laser Scanning Confocal Microscopy (LSCM) and specific labeling techniques were employed to examine the distributing of F-actin and microtubules in the reticular lamina of the guinea pig and monkey organ of Corti. Actin specific label was found in the circumferential belt of adherens junction at the borders between cells in the reticular lamina, and in the cuticular plate of hair cells. The distribution of actin in the adherens junction belt was asymmetric. Actin label was not found in the fonticulus, where the microtubule organizing center resides. Actin free areas were also found between the junctional actin and the cuticular plate. Microtubule specific label was very intense in supporting cells. In normal hair cells, the spatial distribution of tubulin at the reticular lamina is mutually exclusive with that of actin. After noise exposure, a belt of actin was found in the central portion of degenerating outer hair cells, possibly representing a constricted circumferential junction. Expanded supporting cells replaced degenerating hair cells and maintained the confluence of the reticular lamina during the dynamic process of scar formation. A complex network of actin-rich cables appeared at sites of degenerating inner hair cells, suggesting that more than two supporting cells are involved in scar formation for inner hair cells. LSCM proved an attractive method for analysis of the organ of Corti since preparation of the tissue is relatively rapid, preparation artefacts are minimized, different markers in the same specimen may be co-localized and out-of focus fluorescence blurring is eliminated.

Actins↗

Three-dimensional reconstruction of perineural invasion in carcinoma of the extrahepatic bile ducts.

Three-dimensional (3D) reconstruction can be used to study the structural relationships between various tissue components and can help in the understanding of disease processes. Examples of perineural invasion have been reconstructed in two cases of adenocarcinoma of the extrahepatic bile duct. Ninety-six serial 5 microns sections were taken from both cases stored on file and 3D images were constructed using a Kontron VIDAS image analysis system. Both cases showed continuity of tumour cells within the perineural space. The isolated islands of malignant glands seen by conventional microscopy were shown to be in continuity with larger tumour cell masses via a complex branching network. In addition, direct continuity was demonstrated between malignant glands within the perineural space and those within the surrounding stromal tissue. During growth, the tumour appeared to have followed the plane of least resistance, although the availability of the perineural space may itself have been shaped by pressure effects and/or proteolytic enzyme secretion. Three-dimensional reconstruction of perineural invasion in adenocarcinoma of the extrahepatic bile ducts shows the value of this technique in demonstrating the structural relationships between the tumour and the host nerve bundle.

Adenocarcinoma↗

Genetics of gliding motility and development in Myxococcus xanthus.

Successful development in multicellular eukaryotes requires cell-cell communication and the coordinated spatial and temporal movements of cells. The complex array of networks required to bring eukaryotic development to fruition can be modeled by the development of the simpler prokaryote Myxococcus xanthus. As part of its life cycle, M. xanthus forms multicellular fruiting bodies containing differentiated cells. Analysis of the genes essential for M. xanthus development is possible because strains with mutations that block development can be maintained in the vegetative state. Development in M. xanthus is induced by starvation, and early events in development suggest that signaling stages have evolved to monitor the metabolic state of the developing cell. In the absence of these signals, which include amino acids, alpha-keto acids, and other intermediary metabolites, the ability of cells to differentiate into myxospores is impaired. Mutations that block genes controlling gliding motility disrupt the morphogenesis of fruiting bodies and sporogenesis in surprising ways. In this review, we present data that encourage future genetic and biochemical studies of the relationships between motility, cell-cell signaling, and development in M. xanthus.

Genes, Bacterial↗

Subplasmalemmal microfilaments and microtubules in resting and phagocytizing cultivated macrophages.

The subplasmalemmal organization of the free and glass-attached surfaces of resting and phagocytizing cultivated macrophages were examined in an attempt to define specific membrane-associated structures related to phagocytosis. From analysis of serial thin sections of oriented cells it was found that the subplasmalemmal region of the attached cell surface has a complex microfilament and microtubule organization relative to the subplasmalemmal area of the free surface. A filamentous network composed of 40-50-A microfilaments extended for a depth of 400-600 A from the attached plasma membrane. Immediately subjacent to the filamentous network was a zone of oriented bundles of 40-50-A microfilaments and a zone of microtubules. Additional microtubules were found to extend from the plasma membrane to the interior of the cell in close association with electron-dense, channellike structures. In contrast, the free aspect of the cultivated macrophage contained only the subplasmalemmal filamentous network. However, after a phagocytic pulse with polystyrene particles (14 microm diam) microtubules and oriented filaments similar to those found on the attached surface were observed surrounding the ingested particles. The observations reported in this paper provide support for the hypothesis that microfilaments and/or microtubules play a role in the translocation of plasma membrane required for the functionally similar processes of phagocytosis and cell attachment to glass.

Animals↗

Wall formation by Candida albicans yeast cells: synthesis, secretion and incorporation of two types of mannoproteins.

The mannoprotein components solubilized from the walls of Candida albicans blastoconidia following degradation of the glucan network with beta-glucanase (Zymolyase) have higher molecular masses than their probable precursors present in the supernatant of regenerating protoplasts. It therefore appears that the mannoproteins are released from the walls as part of supramolecular complexes. Immunological analysis using both polyclonal and monoclonal antibodies has demonstrated the probable relationship between molecules found in a mixed membrane preparation, those secreted by regenerating protoplasts, and those present in yeast cell walls. Some mannoproteins secreted by protoplasts incubated in the presence of tunicamycin had significantly increased mobility on SDS-PAGE, whereas others were not affected by the treatment. It is therefore possible that two types of mannoproteins are secreted by protoplasts: one carrying N-glycosylated chains (mannan) and one lacking them. All the proteins secreted in the presence of tunicamycin stained with Concanavalin A-peroxidase, demonstrating that they all, including the N-glycosylated ones, carried O-glycosylated sugar residues. Both classes of mannoproteins, secreted independently of each other, were found in the molecular complexes rendered soluble from the wall by Zymolyase digestion. Data obtained with a monoclonal antibody demonstrated the presence of a repeated epitope within one wall protein(s) detectable in a mixed membrane preparation and in the wall complexes released by Zymolyase.

Animals↗