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At least 199 records · Page 11Linked to original sources
PubMed2005

Investigation of an HMM/ANN hybrid structure in pattern recognition application using cepstral analysis of dysarthric (distorted) speech signals.

Computer speech recognition of individuals with dysarthria, such as cerebral palsy patients requires a robust technique that can handle conditions of very high variability and limited training data. In this study, application of a 10 state ergodic hidden Markov model (HMM)/artificial neural network (ANN) hybrid structure for a dysarthric speech (isolated word) recognition system, intended to act as an assistive tool, was investigated. A small size vocabulary spoken by three cerebral palsy subjects was chosen. The effect of such a structure on the recognition rate of the system was investigated by comparing it with an ergodic hidden Markov model as a control tool. This was done in order to determine if this modified technique contributed to enhanced recognition of dysarthric speech. The speech was sampled at 11 kHz. Mel frequency cepstral coefficients were extracted from them using 15 ms frames and served as training input to the hybrid model setup. The subsequent results demonstrated that the hybrid model structure was quite robust in its ability to handle the large variability and non-conformity of dysarthric speech. The level of variability in input dysarthric speech patterns sometimes limits the reliability of the system. However, its application as a rehabilitation/control tool to assist dysarthric motor impaired individuals holds sufficient promise.

Algorithms↗
PubMed2002

A methodology to explain neural network classification.

Neural networks are still frustrating tools in the data mining arsenal. They exhibit excellent modelling performance, but do not give a clue about the structure of their models. We propose a methodology to explain the classification obtained by a multilayer perceptron. We introduce the concept of 'causal importance' and define a saliency measurement allowing the selection of relevant variables. Once the model is trained with the relevant variables only, we define a clustering of the data built from the hidden layer representation. Combining the saliency and the causal importance on a cluster by cluster basis allows an interpretation of the neural network classifier to be built. We illustrate the performances of this methodology on three benchmark datasets.

Classification↗
PubMedDate not supplied

Structural interpretation of a topological index. 1. External factor variable connectivity index (EFVCI).

The external factor variable connectivity index (EFVCI) is interpreted by mining out the structural features hidden in the space spanned by the EFVCI indices through projection pursuit combining with number-theory net (NT-net) on the unit sphere U(Us). Projection pursuit is concerned with "interesting" projections of high-dimensional data sets to machine-pick "interesting" low-dimensional projections of a high-dimensional point cloud by numerically maximizing a certain objective function or projection index. At first, the optimal EFVCI index reaches to -0.80 in the correlation with a retention index of 207 hydrocarbons produced by insects. The EFVCI indices, with regression results of R = 0.99998, s = 3.49, RMSECV = 3.90, and F = 7.9560e+005, obtain high regression quality. The model is proven valid by leave-one-out cross validation. Second, the EFVCI index is interpreted by the structure information, that is, size, branch number, graph center, and branching position of topological structures, which is searched out on the unit sphere U(Us) by projection pursuit. Finally, the interpretation information is used to discover some chemical knowledge concerning the variation of the retention index with the change in chemical structures.

Journal Article↗
PubMed1997

Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.

The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded by viruses, bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are characterized by the sequence motifs 'LAGLIDADG' and 'HNH', respectively. These endonucleases have been shown to occur in different environments: LAGLIDADG endonucleases are found in inteins, archaeal and group I introns and as free standing open reading frames (ORFs); HNH endonucleases occur in group I and group II introns and as ORFs. Here, statistical models (hidden Markov models, HMMs) that encompass both the conserved motifs and more variable regions of these families have been created and employed to characterize known and potential new family members. A number of new, putative LAGLIDADG and HNH endonucleases have been identified including an intein-encoded HNH sequence. Analysis of an HMM-generated multiple alignment of 130 LAGLIDADG family members and the three-dimensional structure of the I- Cre I endonuclease has enabled definition of the core elements of the repeated domain (approximately 90 residues) that is present in this family of proteins. A conserved negatively charged residue is proposed to be involved in catalysis. Phylogenetic analysis of the two families indicates a lack of exchange of endonucleases between different mobile elements (environments) and between hosts from different phylogenetic kingdoms. However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type. Such events are suggested to be important for the formation of elements of new specficity.

Amino Acid Sequence↗
PubMed1995

Lateral thigh free flap in head and neck reconstruction.

To understand the role of the lateral thigh flap in head and neck reconstruction, we performed injection studies and anatomic dissections in 2 fresh and 61 preserved cadaver extremities followed by 10 clinical cases involving defects after tumor ablation. The flap, based on the third perforator of the profunda femoris artery, is designed on the posterolateral aspect of the distal thigh. The pedicle courses through the biceps short head, allowing optional transfer of this muscle. Defects of the oral cavity, pharynx, cervical esophagus, and external skin were successfully restored. One flap was unsuccessful because of intraoperative injury to the vascular pedicle. Compared with the radial forearm flap, the lateral thigh flap provides more tissue and the donor scar is more easily hidden, but the vascular pedicle is shorter, of smaller caliber, and more variable. The lateral thigh flap provides thin, pliable, and reliable tissue for a variety of needs in properly selected patients.

Adult↗
PubMed2005

Transcription factors GATA-4 and GATA-6, and their potential downstream effectors in ovarian germ cell tumors.

Ovarian germ cell tumors (GCTs) are histologically heterogeneous neoplasms originating from activated germ cells, the oocyte stem cells. These rare tumors often contain many different tissues mixed together, and malignant components are occasionally hidden within benign tissues thus complicating the diagnosis. The reasons for the variable differentiation of germ cells are still largely unknown. As transcription factors GATA-4 and GATA-6 as well as their downstream factors (e.g. HNF-4, BMP-2 and Ihh) are essential for normal yolk sac development, we studied their expression in 19 ovarian GCTs. Endodermal markers were expressed distinctively in different GCT types. The malignant endoderm in yolk sac tumors expressed all factors of endodermal development included in the study. Dysgerminomas, on the contrary, expressed only GATA-4 and, in a minority of cases, Ihh and BMP-2. The results suggest that GATA-4 and GATA-6 detected in the ovarian GCTs have retained their normal function. The fact that GATA-6 and HNF-4 are expressed exclusively in endodermal tissues indicates that these transcription factors play a role in the differentiation of germ cells towards the endodermal phenotype. Analysis of the nuclear transcription factors in tumor tissue could serve as a new informative diagnostic tool for ovarian GCTs.

Adolescent↗
PubMed2003

Generalized synchronization of chaos in identical systems with hidden degrees of freedom.

We demonstrate generalized synchronization of chaos in a two-mode laser system. The total intensity of the laser output (the sum of the individual mode intensities) is used as the drive signal. This lumped variable transmitted to the identical response system does not generate identical synchronization. Generalized synchronization is observed instead of identical synchronization because of the hidden internal degrees of freedom.

Feedback↗
PubMed1984

Antibody responses to lambda 1J558 and lambda 2315 light chains. Specificity and genetic regulation.

Specificity of BALB/c antibody responses to lambda chains of isologous myeloma proteins 315 and J558 was explored by enzyme-linked immunosorbent assay. lambda-chain binding antibodies were not detected when immunizing with assembled (H + L) myeloma proteins. However, relatively high titred IgG antibodies were elicited by free lambda 2(315) immunization. Antibodies were directed to 'hidden' determinants since binding was abrogated upon H + L assembly of chains. At least a portion of antibodies bound antigenic determinants in the variable region and cross-reacted with lambda 1 land lambda 3 chains. Free lambda 1J558 immunization induced low-titred, predominantly IgM antibodies that also only reacted with 'hidden' determinants. These determinants were most probably located in the constant (C) region and no cross-reaction to lambda 2 or lambda 3 was observed. An artefact of technical importance was noted: myeloma proteins exposed 'hidden' determinants on their lambda chains when coated directly to polystyrene walls. This artefactual exposition was lost when anti C-region antibody spacer molecules were inserted between the wall and the myeloma proteins. Antibody and T helper cell (Th) responses to free lambda 2(315) covaried significantly in various strains while antibody and Th responses to free lambda 1J558 did not. In some strains, weak antibody responses were detected without detectable Th.

Animals↗
PubMed1997

The application of image analysis and neural network technology to the study of large-cell liver-cell dysplasia and hepatocellular carcinoma.

Liver cell dysplasia (LCD) is considered a preneoplastic lesion, whose characterization and differentiation from hepatocellular carcinoma (HCC) and from the reactive changes seen in cirrhosis has been controversial. We studied 12 cases of LCD (large cell type) with image analysis techniques (IA) and compared the findings with those of HCC (n = 40), and a spectrum of non-neoplastic hepatic lesions including normal liver and cirrhosis (n = 49). A minimum of 200 Feulgen-stained nuclei were measured from each lesion with the CAS 200 image analysis system. The data were collected with the aid of CellSheet software. Thirty-four variables were measured, including geometric, textural, and photometric nuclear features and DNA ploidy. The data were analyzed with multivariate statistics and a backpropagation neural network (NN). Stepwise statistical analysis selected 22 variables that were statistically significant in the three groups with P values <.05. Various NN architectures were developed using these variables. The best NN architecture included a sigmoidal transfer function, 14 input, 16 hidden, and 3 output neurons. It trained to completion after 8,887 runs using 90% of the lesions. This NN yielded a 100% cross-validation rate for unknown cases. These data support the concept of LCD (large cell type) as a lesion that can be objectively distinguished from HCC and non-neoplastic liver. Our study also demonstrates the potential usefulness of IA for the evaluation of difficult histopathological problems.

Carcinoma, Hepatocellular↗
PubMedDate not supplied

Follow-up of 146 children with epilepsy after withdrawal of antiepileptic therapy.

The relapse rate after discontinuation of antiepileptic drug treatment was investigated in 146 children with epilepsy, in whom medication was withdrawn according to a predesigned protocol, after a seizure-free period of at least 2 years and normalization of the EEG. The cumulative probability of remaining seizure-free in this series was 74.5%. Three-quarters of the relapses occurred during the withdrawal period and in the 2 years thereafter. From multivariate analysis, the factors indicating a significantly higher relapse risk were seizures with a known cause and female sex. In primary generalized epilepsy, no factor significantly increased the likelihood of a recurrence. In partial epilepsy, significant factors predictive of recurrence were the presence of a neurological deficit (focal neurological signs and/or mental retardation), female sex, a positive family history for epilepsy, and the number of drugs necessary for control of the seizures. The present results are compared with the available literature data. It is argued that using multivariate analysis after elimination of EEG variables uncovers significant clinical predictive factors that in other studies may have remained hidden. Finally, it is argued that statistical analysis may be used to enable the clinician to predict the likelihood of recurrence in individual children with a given set of relevant predictive factors.

Adolescent↗
PubMed1995

Mechanisms of the origin of a G-positive band within the secondary constriction region of human chromosome 9.

We report on a so-called rare variant where a G-positive band was sandwiched within the secondary constriction (qh) region of chromosome 9 and is apparently different from previous cases when characterized by the fluorescence in situ hybridization technique. The major differences included duplication of beta-satellite and satellite III DNA sequences and bands 9q13-->q21.1, without duplication or inversion of the alphoid sequences. Based on the reported cases, at least four types of variations can be accounted for. A variety of mechanisms have been proposed to describe the origin of a G-positive band within the 9qh region, which appears to be similar when studied by routine cytogenetic techniques but differs by molecular methods. It is hypothesized that the clinical consequences depend upon the size of the G-positive band(s) duplicated, and a genetic inactivation mechanism might have some sort of influence during the so-called heterochromatinization process. It appears that heterochromatin, once thought to be composed of junk DNA, may have some role after all in suppression of gene(s) and/or spreading of inactivation, if genes are embedded within the heterochromatic region. Apparently, the mixture of different types of DNA creating patches of genetic debris have become a fundamental hidden treasure, where genetically active chromatin could be inactivated without dire consequences. The variable nature of heterochromatin has resulted in cytogenetic heteromorphisms of a number of human chromosomes. Their characterization by molecular techniques is becoming imperative, because fetal wastage have occurred in many situations where variant chromosomes were wrongly identified as chromosomal abnormalities.

Chromosome Banding↗
PubMed2000

Heart rate variability and autonomic diabetic neuropathy.

Aim of this paper is to briefly summarize available evidence about potential usefulness of heart rate variability (HRV) analysis for the clinical evaluation of autonomic diabetic neuropathy. HRV contains hidden information that can be extracted from tachogram sections of several hundred beats with spectral analysis. Subsequent normalization and the use of a paradigm including standardized stimuli (such as tilt) are commonly employed to assess autonomic cardiac regulation. In the resulting spectra, two major components of similar amplitude are usually observed (at low--LF--and high frequency--HF), their relative power is best appreciated using normalized units that provide an estimate of the balance between sympathetic and vagal modulatory activity. In states of sympathetic predominance, such as during orthostatic positions, LF increases and HF decreases. In diabetics, consistent alterations in spectral properties are a frequent early finding: initially a reduction of HRV (ie spectral power) is followed by progressive functional denervation, which is associated to severe autonomic dysfunction. The spectral methodology provides some useful potential advantages in respect to the more traditional approach employing several simple bedside tests. In conclusion, spectral analysis of HRV appears a convenient method to assess various degrees of diabetic autonomic dysfunction: it appears easy to perform, while giving results similar to traditional methods, with greater sensibility.

Autonomic Nervous System Diseases↗
PubMed1994

Changing root system architecture through inhibition of putrescine and feruloyl putrescine accumulation.

Plant roots provide anchorage and absorb the water and minerals necessary for photosynthesis in the aerial parts of the plant. Since plants are sessile organisms, their root systems must forage for resources in heterogeneous soils through differential branching and elongation [(1988) Funct. Ecol. 2, 345-351; (1991) Plant Roots: The Hidden Half, pp. 3-25, Marcel Dekker, NY]. Adaptation to drought, for instance, can be facilitated by increased root growth and penetration. Root systems thus develop as a function of environmental variables and the needs of the plant [(1988) Funct. Ecol. 2, 345-351; (1986) Bot. Gaz. 147, 137-147; (1991) Plant Roots: The Hidden Half, pp. 309-330, Marcel Dekker, NY]. We show, in a model system consisting of excised tobacco roots, that both alpha-DL-difluoromethylornithine (an inhibitor of putrescine biosynthesis) and the rolA gene (from the root-inducing transferred DNA of Agrobacterium rhizogenes) stimulate overall root growth and cause a conversion in the pattern of root system formation, producing a dominant or 'tap' root. These morphological changes are correlated with a depression in the accumulation of polyamines and their conjugates.

Coumaric Acids↗
PubMed2006

Prediction of the concentration of chlorophyll-a for Liuhai urban lakes in Beijing City.

The weekly water quality monitor data of Liuhai lakes between April 2003 and November 2004 in Beijing City were used as an example to build an artificial neural networks (ANN) model and a multi-varieties regression model respectively for predicting the fresh water algae bloom. The different predicted abilities of the two methods in Liuhai lakes were compared. A principle analysis method was first used to select the input variables of the models to avoid the phenomenon of collinearity in the data. The results showed that the input variables for the artificial neural networks were T, TP, transparency(SD), DO, chlorophyll-a (Chl-a), pH and the output variable was Chl-a. A three layer Levenberg-Marguardt feed forward learning algorithm in ANN was used to model the eutrophication process of Liuhai lakes. 20 nodes in hidden layer and 1 node of output for the ANN model had been optimized by trial and error method. A sensitivity analysis of the input variables was performed to evaluate their relative significance in determining the predicted values. The correlation coefficient between predicted value and observed value in all data and in test data were 0.717 and 0.816 respectively in the artificial neural networks. The stepwise regression method was used to simulate the linear relation between Chl-a and temperature, of which the correlation coefficient was 0.213. By comparing the results of the two models, it was found that neural network models were able to simulate non-linear behavior in the water eutrophication process of Liuhai lakes reasonably and could successfully estimate some extreme values from calibration and test data sets.

China↗
PubMed2004

Autonomic and emotional responses to open and hidden stimulations of the human subthalamic region.

We performed a microstimulation study of the subthalamic region of Parkinsonian patients who underwent bilateral electrode implantation in the subthalamic nuclei and whose heart rate and heart rate variability were recorded. The stimulation of the dorsalmost region, which includes the zona incerta and the dorsal pole of the subthalamic nucleus, produced autonomic responses that were constant over time. In fact, hidden stimulations (the patient is not aware of being stimulated) and open stimulations (the patient is aware of being stimulated) always induced the same responses. By contrast, the stimulation of the ventralmost region, which includes the ventral pole of the subthalamic nucleus and the substantia nigra pars reticulata, produced autonomic and emotional responses that were inconstant over time and varied according to the condition. In fact, different responses were elicited with hidden and open stimulations. These data suggest that the dorsal subthalamic nucleus and/or the zona incerta are involved in autonomic control, whereas the ventral subthalamic nucleus and/or the substantia nigra reticulata are involved in associative/limbic-related autonomic activity. The difference between the open and hidden stimulations in the ventral subthalamic region can explain previous studies in which open and hidden stimulations produced different therapeutic outcomes.

Aged↗
PubMed1996

Pharmaceutical fingerprinting: evaluation of neural networks and chemometric techniques for distinguishing among same-product manufacturers.

The present study was undertaken to evaluate several computer-based classifiers as potential tools for pharmaceutical fingerprinting by utilizing normalized data obtained from HPLC trace organic impurity patterns. To assess the utility of this approach, samples of L-tryptophan (LT) drug substance were analyzed from commercial production lots of six different manufacturers. The performance of several artificial neural network (ANN) architectures was compared with that of two standard chemometric methods, K-nearest neighbors (KNN) and soft independent modeling of class analogy (SIMCA), as well as with a panel of human experts. The architecture of all three computer-based classifiers was varied with respect to the number of input variables. The ANNs were also optimized with respect to the number of nodes per hidden layer and to the number of hidden layers. A novel preprocessing scheme known as the Window method was devised for converting the output of 899 data entries extracted from each chromatogram into an appropriate input file for the classifiers. Analysis of the test set data revealed that an ANN with 46 inputs (i.e., ANN-46) was superior to all other classifiers evaluated, with 93% of the chromatograms correctly classified. Among the classifiers studied in detail, the order of performance was ANN-46 (93%) > SIMCA-46 (87%) > KNN-46 (85%) = ANN-899 (85%) > "human experts" (83%) > SIMCA-899 (78%) > or = ANN-22 (77%) = KNN-22 (77%) > or = KNN-899 (76%) > SIMCA-22 (73%). These results confirm that ANNs, particularly when used in conjunction with the Window preprocessing scheme, can provide a fast, accurate, and consistent methodology applicable to pharmaceutical fingerprinting. Particular attention was paid to variations in the HPLC patterns of same-manufacturer samples due to differences in LT production lots, HPLC columns, and even run-days to quantify how these factors might hinder correct classifications. The results from these classification studies indicate that the chromatograms evidenced variations across LT manufacturers, across the three HPLC columns and, for one manufacturer, across lots. The extent of column-to-column variations is particularly noteworthy in that all three columns had identical specifications with respect to their stationary-phase characteristics and two of the three columns were from the same vendor.

Chemistry, Pharmaceutical↗
PubMed2000

[Patient expectations regarding methods and outcomes of their rehabilitation--a controlled study of back pain- and cancer patients].

Although patient expectations are important factors of the success of rehabilitation, they have not yet received much attention in research. In the present cross-sectional study, n = 248 rehabilitation patients, n = 160 suffering from chronic back pain and n = 88 suffering from oncological diseases (breast cancer, cervical cancer, ovarian cancer, colorectal cancer), were assessed at the time of admission to a rehabilitation clinic, using a newly developed self-report questionnaire to evaluate their expectations regarding the process and outcome of their rehabilitation. Results show on an item level that non-specific process expectations such as balneophysical treatments or features of the surroundings of the clinic were most prevailing. Across both diagnostic groups, common goals of rehabilitation such as reduction of complaints, physical fitness and recreation scored highest. On the basis of factor analysis, 10 scales of process expectations were constructed: medical attention, physical training, vocational counselling, balneophysical treatment, health information, stress management training, support groups, relief from the strains of everyday life, alternative medicine, and pleasant surroundings. Nine dimensions of outcome expectations were detected: ability for work, physical fitness, reduction of complaints, behaviour change, reduction of body weight, positive body feeling, vitality, enjoyment of life, and social contact. In the univariate analysis, orthopaedical patients scored higher on balneophysical treatments and vocational counselling (process expectations) as well as reduction of complaints and ability for work (outcome expectations). However, there were effects of age, gender and working status, too. Thus these differences between diagnostic groups turned out to be nonsignificant after controlling for the effects of age, gender, and working status. On the other hand, some effects of the medical condition had been hidden in the univariate comparison and were only revealed when adjusting for the moderator variables. Those differences show that oncological patients had higher expectations than back pain patients. Patients' expectations were correlated with functional status and, to a lesser degree, emotional distress and locus of control. To conclude, our study demonstrated that medical condition, sociodemographic factors, working status and functional capacity are important determinants of patient expectations regarding the process and outcome of rehabilitation.

Adaptation, Psychological↗
PubMed2004

Prediction of nuclear hormone receptor response elements.

The nuclear receptor (NR) class of transcription factors controls critical regulatory events in key developmental processes, homeostasis maintenance, and medically important diseases and conditions. Identification of the members of a regulon controlled by a NR could provide an accelerated understanding of development and disease. New bioinformatics methods for the analysis of regulatory sequences are required to address the complex properties associated with known regulatory elements targeted by the receptors because the standard methods for binding site prediction fail to reflect the diverse target site configurations. We have constructed a flexible Hidden Markov Model framework capable of predicting NHR binding sites. The model allows for variable spacing and orientation of half-sites. In a genome-scale analysis enabled by the model, we show that NRs in Fugu rubripes have a significant cross-regulatory potential. The model is implemented in a web interface, freely available for academic researchers, available at http://mordor.cgb.ki.se/NHR-scan.

Algorithms↗