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State-dependent weights for neural associative memories.

In this article we study the effect of dynamically modifying the weight matrix on the performance of a neural associative memory. The dynamic modification is implemented by adding, at each step, the outer product of the current state, scaled by a suitable constant eta, to the correlation weight matrix. For single-shot synchronous dynamics, we analytically obtain the optimal value of eta. Although knowledge of the noise percentage is required for calculating the optimal value of eta, a fairly good choice of eta can be made even when the amount of noise is not known. Experimental results are provided in support of the analysis. The efficacy of the proposed modification is also experimentally verified for the case of asynchronous updating with transient length > 1.

Association Learning↗

Comparison of alternative estimation methods in confirmatory factor analyses of the General Health Questionnaire.

This paper examines the implications of violating assumptions concerning the continuity and distributional properties of data in establishing measurement models in social science research. The General Health Questionnaire-12 uses an ordinal response scale. Responses to the GHQ-12 from 201 Hong Kong immigrants on arrival in Australia showed that the data were not normally distributed. A series of confirmatory factor analyses using either a Pearson product-moment or a polychoric correlation input matrix and employing either maximum likelihood, weighted least squares or diagonally weighted least squares estimation methods were conducted on the data. The parameter estimates and goodness-of-fit statistics provided support for using polychoric correlations and diagonally weighted least squares estimation when analyzing ordinal, nonnormal data.

Adolescent↗

Expression of matrix metalloproteinases in the subretinal fluid correlates with the extent of rhegmatogenous retinal detachment.

BACKGROUND: We investigated the activity of matrix metalloproteinase (MMP)-2 and -9 and the protein levels of MMP-1, -3, -8 and the tissue inhibitor of MMPs (TIMP)-1 in the subretinal fluid (SRF) of patients with rhegmatogenous retinal detachment (RRD) and establishment of potential correlations with clinical parameters. METHODS: Thirty-seven SRF from RRD patients and nine vitreous samples from the human eye of organ donors (controls) were collected and assayed for MMP-1,-3,-8 and TIMP-1 levels using ELISA and for MMP-2 and -9 activity employing gelatin zymography. RESULTS: MMP-1, MMP-3, MMP-8, proMMP-2, proMMP-9, MMP-9 and TIMP-1 levels were higher in SRF compared with vitreous fluid. Overall, MMPs and TIMPs were differentially expressed in SRF with respect to duration and extent of RRD, as well as to stage of proliferative vitreoretinopathy. Regression analysis for all data indicated that a model consisting of MMP-3, MMP-8 and proMMP-9 could estimate the extent of RRD. CONCLUSIONS: MMPs and TIMP-1 levels are elevated in SRF during RRD. A regression model consisting of MMP-3, MMP-8 and proMMP-9 may be proved to be of potential use in providing information for evaluation of the extent of RRD.

Adult↗

Quantitative computed tomography analysis of local chemotherapy in liver tissue after radiofrequency ablation.

RATIONALE AND OBJECTIVES: Computed tomography (CT) was used to noninvasively monitor local drug pharmacokinetics from polymer implants in rat livers before and following radiofrequency ablation. MATERIALS AND METHODS: Polymer matrixes containing carboplatin (a platinum-containing chemotherapeutic agent) were implanted into rat livers either immediately after radiofrequency ablation (n = 15) or without prior treatment (n = 15). The animals were divided into five subgroups (n = 3 per group) and subjected to a terminal CT scan at 6, 24, 48, 96, or 144 hours. Carboplatin concentration in tissue and within the implant matrix was correlated with CT intensity, and standard curves were produced for each environment. This correlation was used to evaluate the differences in drug transport properties between normal and ablated rat livers. A quantitative image analysis method was developed and used to evaluate the release rate and tissue distribution of carboplatin in normal and ablated liver tissue. The CT data were validated by previously reported atomic absorption spectroscopy measurement of implant and tissue drug levels. RESULTS: Correlation of carboplatin concentration and Hounsfield units results in a linear relationship with correlation coefficients (slopes) of 15 and 4 Hounsfield units/(mg/mL), for carboplatin in tissue and polymer, respectively. Noninvasive monitoring of local pharmacokinetics in normal and ablated tissues indicates that ablation before local carboplatin delivery increases the retention of carboplatin within the polymer matrix and drastically increases the drug retention in the ablated tissue volume (over 3-fold difference) resulting in a higher average dose to the surrounding tissue. At 1.6 mm from the implant boundary, carboplatin concentration is significantly higher in ablated tissue at 48, 96, and 144 hours (P <.05), and reaches 4.7 mg/mL in ablated tissue at 48 hours. In comparison, the concentration in normal liver at 1.6 mm reaches only 0.7 mg/mL at the same time point. The drug penetrates 3.1 mm in ablated liver compared with 2.3 mm in normal liver also at 48 hours. After 144 hours, the drug is still detected at 3.1 mm in ablated liver but not in normal liver. The differences are significant (P <.05) at both 48 and 144 hours. Correlation with chemical analysis suggests that CT data accurately predicts the drug pharmacokinetics in both ablated and normal livers. CONCLUSION: This work shows that X-ray CT imaging is a useful and promising technique for in vivo monitoring of the release kinetics of locally delivered radiopaque agents.

Animals↗

Repression of a matrix metalloprotease gene by E1A correlates with its ability to bind to cell type-specific transcription factor AP-2.

Adenovirus E1A 243-amino acid protein can repress a variety of enhancer -linked viral and cellular promoters. This repression is presumed to be mediated by its interaction with and sequestration of p3OO, a transcriptional coactivator. Type IV 72-kDa collagenase is one of the matrix metalloproteases that has been implicated in differentiation, development, angiogenesis, and tumor metastasis. We show here that the cell type-specific transcription factor AP-2 is an important transcription factor for the activation of the type IV 72-kDa collagenase promoter and that adenovirus E1A 243-amino acid protein represses this promoter by targeting AP-2. Glutathione S-transferase-affinity chromatography studies show that the E1A protein interacts with the DNA binding/dimerization region of AP-2 and that the N-terminal amino acids of E1A protein are required for this interaction. Further, E1A deletion mutants which do not bind to p3OO can repress this collagenase promoter as efficiently as the wildtype E1A protein. Because the AP-2 element is present in a variety of viral and cellular enhancers which are repressed by E1A, these studies suggest that E1A protein can repress cellular and viral promoter/enhancers by forming a complex with cellular transcription factors and that this repression mechanism may be independent of its interaction with p3OO.

Adenovirus E1A Proteins↗

Glycoprotein CD44 expression in colorectal neoplasms. An immuno-histochemical study including correlation with cathepsin D, extracellular matrix components, p53, Rb, bcl-2, c-erbB-2, EGFR and proliferation indices.

CD44 has diverse functions in cell-cell and cell-matrix interactions and may be a determinant of metastatic and invasive behaviour in carcinomas. The immunohistochemical expression of CD44 in a series of 110 colorectal carcinomas and 25 adenomas was examined using the monoclonal mouse anti-human phagocytic glycoprotein-1, CD44 (clone DF 1485) in correlation with the expression of basement membrane (BM) antigens (type IV collagen, laminin), fibronectin, cathepsin D, p53, Rb, bcl-2, c-erbB-2, EGFR, proliferation indices (Ki-67, PCNA) and with other conventional clinicopathological variables. In adenomas, low CD44 expression (<10% of neoplastic cells) was present in 16%, moderate (10-50% of neoplastic cells) in 52% and extensive (>50% of neoplastic cells) in 32% of cases. In carcinomas, low CD44 expression was found in 14.5%, moderate in 28.2% and extensive in 57.30%. Although the CD44 expression was higher in carcinomas than in adenomas, we found no statistically significant difference between these two groups. CD44 expression in carcinomas was positively correlated with tumour size (P=0.018), tumour cells cathepsin D (P=0.022), stromal cell cathepsin D (P=0.003) and Rb protein (P=0.021). An inverse correlation was observed between CD44 and the anti-apoptotic protein expression bcl-2 in adenocarcinomas (P=0.039) and in adenomas (P=0.021). These data suggest that CD44 may be involved in the process of invasion and metastasis, probably with the cooperation of cathepsin D. Its expression may be an indicator of poor prognosis in colorectal adenocarcinomas.

Adult↗

[Changes in the osteoinductive activity of the bone matrix in ontogeny].

Correlation between the animal's age, degree of mineralization of its bone tissue and the osteoinductive activity of the bone organic matrix was established in experiments with rats of the same litter at an age of 2, 4, 8, 16 weeks. The osteoinductive activity was estimated by the capacity of matrix to induce ectopic osteogenesis using biochemical methods. Bone mineralization increased and the capacity for osteoinduction decreased roughly 1,5-fold with the age of donor animals. It is suggested that the reduction of osteoinductive potencies is based on the decrease in lability of the bond between the protein osteoinducer and the collagen matrix, as shown by unequal sensitivity of bone matrix of rats of different age to the doubling of the shortest possible time of bone demineralization.

Aging↗

Building phenotypic character matrices for phylogenetic inference: exploration of 35&#x2009;years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35&#x2009;years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗

Expression of transforming growth factor-beta isoforms in human glomerular diseases.

Protein and mRNA expression of TGF-beta isoforms, TGF-beta 1, -beta 2 and -beta 3, and deposition of fibronectin containing extra domain A (fibronectin EDA+) and plasminogen activator inhibitor-1 (PAI-1) were studied in human chronic glomerulonephritis and diabetic nephropathy. Normal kidneys showed similar, weak immunostaining for all three TGF-beta isoforms. TGF-beta mRNA expression was weak for all isoforms with TGF-beta 1 > TGF-beta 3 >> TGF-beta 2. In thin basement membrane disease and minimal change disease, disorders where extracellular matrix accumulation is not a feature, immunoreactivity and mRNA expression did not differ from normal. In contrast, diseases characterized by extracellular matrix accumulation (IgA nephropathy, focal and segmental glomerulosclerosis, crescentic glomerulonephritis, lupus nephritis and diabetic nephropathy) all showed significantly increased expression of the three TGF-beta isoforms in glomeruli and the tubulointerstitium. While glomerular and tubulointerstitial deposition of two matrix components induced by TGF-beta, fibronectin EDA+ and PAI-1, was significantly elevated in all diseases with matrix accumulation, correlation analysis revealed a close relationship primarily with TGF-beta 1. We conclude that, for a spectrum of human glomerular disorders, increased protein expression of all three TGF-beta isoforms and proteins induced by TGF-beta is associated with pathological accumulation of extracellular matrix.

Antibody Specificity↗

The bovine tyrosine hydroxylase gene associates in vitro with the nuclear matrix by its first intron sequence.

Recently we have shown that in vitro binding of the proximal part of the human tyrosine hydroxylase gene to the nuclear matrix is correlated with its transcriptional activity. The strongest binding potential was predicted by computing for the first intron sequence (Lenartowski & Goc, 2002, Neurosci Lett.; 330: 151-154). In this study a 16 kb fragment of the bovine genomic DNA containing the tyrosine hydroxylase gene was investigated for its affinity to the nuclear matrix. Only a 950 bp fragment encoding the distal part of the first intron, second exon and a few nucleotides of the second intron bound to the nuclear matrix. The binding was independent of the tissue-specific tyrosine hydroxylase gene activation. The fragment was subcloned and sequenced. Computer search pointed to one potential intronic matrix attachment region with two AP1-like sites embedded in the sequence. We conclude that even if the position of the matrix binding region is conserved among the tyrosine hydroxylase genes in mammals, its tissue specificity and/or function is not preserved or is achieved by different mechanisms.

Adrenal Glands↗

Construction of the nuclear matrix at the transition from maternal to zygotic control of development in the mouse: an immunocytochemical study.

The nuclear matrix is thought to be responsible for DNA organization, DNA replication, RNA synthesis, and RNA processing. We have looked for the presence of nuclear matrix antigens during early mouse embryogenesis. Antibodies to peripheral and interior antigens (P1, Pl1, Pl2, and lamin B) were used to immunolocalize nuclear matrix antigens in germinal vesicle oocytes, metaphase II oocytes, zygotes, two-cell-stage embryos, and eight-cell stage embryos. All antibodies reacted with the nuclei of germinal vesicle oocytes, and two- and eight-cell-stage embryos; however, only P1 and lamin B were present at the pronuclear stage. In eggs collected at the pronuclear stage and cultured to the late two-cell stage in the presence of alpha-amanitin, the matrix morphology was altered for Pl1 and Pl2. alpha-Amanitin had no affect on the distribution of P1 or lamin B antigens. If alpha-amanitin was added 2 hr after cleavage to the two-cell stage, the normal staining pattern of Pl2 was retained. These results suggest that the presence of specific components of an internal matrix is correlated with normal genomic activity.

Animals↗

The interrelation between DNA synthesis rates and DNA polymerases bound to the nuclear matrix in synchronized HeLa cells.

Quantitative rates of DNA synthesis can be determined by DNA:propidium fluorescence measurements of synchronized cells progressing through S-phase. We have previously reported that HeLa cells have discontinuous rates with values of about 2.9, 1.6, and 4.4 pg of DNA/h for early, middle, and late S-phase, respectively. In attempts to understand why two peaks of DNA synthesis rates are observed, we have examined the nuclear DNA polymerases alpha and beta over the S-phase. Nuclear matrices isolated from HeLa cells contained 2% of the alpha polymerase and 12% of the beta polymerase that was present in cell lysates, and about 2% of the original DNA. The amounts of endogenous DNA synthesis in isolated nuclear matrices were comparable to the amounts observed when exogenous DNA was added. DNase treatment abolished the endogenous DNA synthesis but not the exogenous DNA synthesis, suggesting that polymerase alpha binding does not depend on matrix-bound DNA. As synchronized cells progressed through the S-phase, there appeared two peaks of enzymatic activity of alpha polymerase bound to the nuclear matrix which correlated with in vitro DNA synthesis in these nuclear matrices and with the two peaks of quantitative DNA synthesis rates. Two peaks of alpha polymerase activity were also observed with isolated nuclei, but not with cell lysates or cytosol. Our results suggest that, over the S-phase, the differential binding of polymerase alpha to the nuclear matrix determines the differential rates of DNA synthesis.

Cell Nucleus↗

Efficient and reliable numerical integration of exchange-correlation energies and potentials.

An adaptive numerical integrator for the exchange-correlation energy and potential is presented. It uses the diagonal elements of the exchange-correlation potential matrix as a grid generating function. The only input parameter is the requested grid tolerance. In combination with a defined cell function the adaptive grid generation scales almost linear with the number of basis functions in a system. With the adaptive numerical integrator the self-consistent field energy error, which is due to the numerical integration of the exchange-correlation energy, converges with increasing adaptive grid size to a reference value. The performance of the adaptive numerical integration is analyzed using molecules with first, second, and third row elements. Especially for transition metal systems the adaptive numerical integrator shows considerably improved performance and reliability.

Journal Article↗

Irreducible correlation functions of the S matrix in the coordinate representation: application in calculating Lorentzian half-widths and shifts.

By introducing the coordinate representation, the derivation of the perturbation expansion of the Liouville S matrix is formulated in terms of classically behaved autocorrelation functions. Because these functions are characterized by a pair of irreducible tensors, their number is limited to a few. They represent how the overlaps of the potential components change with a time displacement, and under normal conditions, their magnitudes decrease by several orders of magnitude when the displacement reaches several picoseconds. The correlation functions contain all dynamical information of the collision processes necessary in calculating half-widths and shifts and can be easily derived with high accuracy. Their well-behaved profiles, especially the rapid decrease of the magnitude, enables one to transform easily the dynamical information contained in them from the time domain to the frequency domain. More specifically, because these correlation functions are well time limited, their continuous Fourier transforms should be band limited. Then, the latter can be accurately replaced by discrete Fourier transforms and calculated with a standard fast Fourier transform method. Besides, one can easily calculate their Cauchy principal integrations and derive all functions necessary in calculating half-widths and shifts. A great advantage resulting from introducing the coordinate representation and choosing the correlation functions as the starting point is that one is able to calculate the half-widths and shifts with high accuracy, no matter how complicated the potential models are and no matter what kind of trajectories are chosen. In any case, the convergence of the calculated results is always guaranteed. As a result, with this new method, one can remove some uncertainties incorporated in the current width and shift studies. As a test, we present calculated Raman Q linewidths for the N2-N2 pair based on several trajectories, including the more accurate "exact" ones. Finally, by using this new method as a benchmark, we have carried out convergence checks for calculated values based on usual methods and have found that some results in the literature are not converged.

Journal Article↗

Regional trabecular bone matrix degeneration and osteocyte death in femora of glucocorticoid- treated rabbits.

Glucocorticoids at pharmacological concentrations cause osteoporosis and aseptic necrosis, particularly in the proximal femur. Several mechanisms have been proposed, but the primary events are not clear. We studied changes in the bone structure and cellular activity in femora of glucocorticoid-treated rabbits before the occurrence of fracture or collapse. In rabbits treated 28 days with 4 micromol/kg.day of methylprednisolone acetate, changes in the cortical bone were minor. However, metabolic labeling showed that bone formation was virtually absent in the subarticular trabecular bone, and scanning electron microscopy showed resorption of 50-80% of the trabecular surface. Thus, reduction in bone synthesis and increased resorption were involved in bone loss. Vascular changes, which have been hypothesized to mediate glucocorticoid damage, were not seen, but histological changes suggested that trabecular bone was damaged. Matrix integrity was examined using laser scanning confocal microscopy to detect passive tetracycline adsorption. In treated animals, but not controls, tetracycline was adsorbed, in a novel lamellar pattern, in 50--200 microm regions extending deep into trabeculae. This showed that the matrix, which is normally impervious, was exposed at these sites. TUNEL assays showed that matrix damage correlated with cell death in the subarticular trabecular bone of treated animals. The pattern of cell death involving cohorts of osteoblasts and osteocytes comprised up to half of the bone volume in affected regions and is consistent with an apoptotic mechanism. Small numbers of TUNEL-labeled osteoblasts, but no osteocytes, were detected in control bone. We conclude that exposure of bone matrix permeability and that regional cell death consistent with apoptosis is an early event in glucocorticoid-induced bone damage.

Adsorption↗

Bone matrix proteins in osteogenesis and remodelling in the neonatal rat mandible as studied by immunolocalization of osteopontin, bone sialoprotein, alpha 2HS-glycoprotein and alkaline phosphatase.

The neonatal rat mandible was used as a model to study bone formation, mineralization, quiescence, and resorption, using immunolocalization and a variety of tissue-processing techniques. Monospecific antibodies for osteopontin (OPN), bone sialoprotein (BSP), alkaline phosphatase (AP) and alpha 2HS-glycoprotein (alpha 2HS-GP) were used on fixed paraffin-embedded tissue, fixed frozen tissue and unfixed frozen tissue. Immunostaining was correlated with mineral content by two procedures, the von Kossa and the morin techniques. Morin fluorescence was used with secondary immunostaining to provide a way of closely correlating bone matrix proteins and matrix mineralization. Co-immunolocalization procedures were used to compare the sites of bone proteins in the matrix. AP was found earliest during osteogenic cell differentiation, appearing in the preosteoblasts, followed by OPN and BSP, which first appeared in osteoblasts. alpha 2HS-GP expression was not observed in cells. The results provide clear evidence for the presence of OPN in osteoid, while BSP and alpha 2HS-GP were confined to the mineralized matrix. Immunostaining of bone proteins is highly technique-dependent: immunolocalization investigations required several methods of approach to ensure adequate demonstration of these proteins in cells and matrix. The results support the contention that osteopontin is multifunctional in bone metabolism, and that alpha 2HS-GP, though produced in the liver, is abundant in bone matrix and may also have a function in bone metabolism.

Alkaline Phosphatase↗

Magnetic resonance determination of tumor thickness as predictive factor of cervical metastasis in oral tongue carcinoma.

OBJECTIVES: To establish an accurate and reproducible means of measuring tumor thickness as a preoperative prognostic factor for cervical metastasis in oral tongue carcinoma. STUDY DESIGN: Retrospective review. METHODS: Charts from 30 patients were reviewed, and the correlation between histopathological and magnetic resonance imaging (MRI) findings of actual tumor thickness or reconstructed tumor thickness measured between a reconstructed mucosal line and the deepest extent of the tumor was investigated. Magnetic resonance images were acquired on a 1.5 T-scanner with a T2-weighted sequence in the axial plane using 3-mm-thick sections and a 256 x 256 matrix. The correlation between N stage and tumor thickness acquired by histopathological scrutiny or MRI was also assessed. RESULTS: The correlation between histopathological and MRI examinations was more significant in terms of reconstructed than actual tumor thickness. No cervical metastasis was detected in patients with tumors of less than 6 mm of reconstructed thickness in the MRI examination. The difference in cervical metastasis between the two groups, namely, less than 6 or more than 6 mm, was statistically significant (P = .0051). CONCLUSIONS: Magnetic resonance imaging examination provides useful data for prognostic assessment and planning strategies with which to treat oral tongue carcinoma. The preoperative decision as to whether to attempt neck dissection could be based on a tumor thickness of 6 mm for patients with oral tongue carcinoma.

Adult↗

[Heritability index for diagnosing talent and aptitude in children and teenagers].

Longitudinal correlation und heritability in the broad sense are equivalent expressions for the reliability in the long run. Since long-range prediction is the aim of personnel selection in athletics, education and other applied fields, we recommend to use heritability as a weighting factor for phenotypic scores of adolescents in order to calculate true scores and to eliminate error variance. On the basis of the matrix of correlations of 7 tests of physical fitness, body height and weight, and their heritabilities the calculation of the heritability index is demonstrated.

Adolescent↗