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Results for “Dimensionality Reduction”

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At least 163 records · Page 9Linked to original sources

PubMed2005

Three-dimensional biplanar reconstruction of scoliotic rib cage using the estimation of a mixture of probabilistic prior models.

In this paper, we present an original method for the three-dimensional (3-D) reconstruction of the scoliotic rib cage from a planar and a conventional pair of calibrated radiographic images (postero-anterior with normal incidence and lateral). To this end, we first present a robust method for estimating the model parameters in a mixture of probabilistic principal component analyzers (PPCA). This method is based on the stochastic expectation maximization (SEM) algorithm. Parameters of this mixture model are used to constrain the 3-D biplanar reconstruction problem of scoliotic rib cage. More precisely, the proposed PPCA mixture model is exploited for dimensionality reduction and to obtain a set of probabilistic prior models associated with each detected class of pathological deformations observed on a representative training scoliotic rib cage population. By using an appropriate likelihood, for each considered class-conditional prior model, the proposed 3-D reconstruction is stated as an energy function minimization problem, which is solved with an exploration/selection algorithm. The optimal 3-D reconstruction then corresponds to the class of deformation and parameters leading to the minimal energy. This 3-D method of reconstruction has been successfully tested and validated on a database of 20 pairs of biplanar radiographic images of scoliotic patients, yielding very promising results. As an alternative to computed tomography-scan 3-D reconstruction this scheme has the advantage of low radiation for the patient, and may also be used for diagnosis and evaluation of deformity of a scoliotic rib cage. The proposed method remains sufficiently general to be applied to other reconstruction problems for which a database of objects to be reconstructed is available (with two or more radiographic views).

Algorithms↗

PubMed1991

Treatment of 813 zygoma-lateral orbital complex fractures. New aspects.

A 10-year experience with surgical treatment of 813 zygomalateral orbital complex fractures is reviewed. Regardless of the type or severity of the fracture pattern, concomitant fractures of the orbital floor and rim were approached exclusively through the transconjunctival approach without a lateral canthotomy. The advantages of this approach compared with the subciliary access are the avoidance of a visible scar and markedly reduced incidence of postoperative lower eyelid complications such as ectropion and edema. Implants of lyophilized dura or cartilage and autogenous bone were used to reconstruct orbital floor defects. Malar asymmetry is a frequent complication of zygoma fractures resulting from inadequate three-dimensional reduction. Methods for accurate reduction and stabilization, indications for closed and open reduction, and management of the fractured infraorbital rim are emphasized. The indications for miniplates vs wire ligatures for the infraorbital rim are discussed. Long-term follow up and evaluation of the results with regard to the fracture pattern, complications, maxillary sinus dysfunction, and facial and orbital symmetry are presented.

Bone Plates↗

PubMed2007

Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia.

Many studies suggest that mitochondrial dysfunction is involved in the pathophysiology of schizophrenia. We performed a case-control study using tag SNPs in the mitochondrial uncoupling protein genes, UCP2, UCP4, and BMCP1/UCP5, to investigate their association with schizophrenia. These neuronal UCPs are expressed in various brain tissues and may exert a neuroprotective effect against increased oxidative stress. We found modest associations between schizophrenia and the four tag SNPs, rs660339 (odds ratio (OR) = 1.330; P = 0.0043) and rs649446 (OR = 0.739; P = 0.0069) in UCP2, and rs10807344 (OR = 0.622; P = 0.0029) and rs2270450 (OR = 0.704; P = 0.0043) in UCP4, all of which were statistically significant even after correcting for multiple comparisons. Moreover, we found a statistically significant synergistic interaction between UCP2 and UCP4 by using the multifactor dimensionality reduction (MDR) method. The synergistic interaction was also confirmed by the logistic regression analysis, where the maximal OR was obtained when the risk alleles at rs660339 and rs10807344 were simultaneously homozygous. Individuals possessing homozygous risk alleles at these two loci have a 7.6-fold risk of developing schizophrenia compared with those of minimal OR. Our findings suggest that UCP2 and UCP4 have a modest but important involvement in the genetic etiology of schizophrenia. This is the first report of the association between schizophrenia and neuronal UCPs.

Alleles↗

PubMed1975

Genetic differentiation among Sardinian villages.

The present study reports an analysis of genetic differentiation among 14 Sardinian villages located mainly in the center of the island. Chi-square tests show significant genetic heterogeneity among villages, and analyses by F- and R- statistics indicate an essentially random pattern of differentiation for all alleles. Using the kinship methods of Morton, a matrix, R, with elements rij describing the correlations between the gene frequencies of villages i and j is obtained. Use of Malécot's formula relating the rij to the geographic distances between villages shows a rapid decline of kinship with increasing distance but reveals essentially no relationship for distances over 40 km. Rotation of a two-dimensional reduction of the kinship matrix to maximum congruence with the geographic distances indicates that about 25% of the genetic distances can be accounted for by the geographic location of the villages. Isolation due in part to cultural factors, genetic drift, and special local or regional patterns of villages associations appear to be involved in the pattern of genetic variation.

Adolescent↗

PubMed1987

On multiparameter data analysis in flow cytometry.

Increasing numbers of parameters that are accessible to simultaneous measurement in flow cytometric instruments, combined with the extremely large sample sizes common in flow cytometry, make it necessary to examine methods of multivariate statistics for their applicability to problems of visualization and quantitative analysis of flow cytometric data. This article describes some approaches to dimensionality reduction that appear well suited for data sets obtained by flow cytometry.

Flow Cytometry↗

PubMed2005

Approaches to detecting gene x gene interaction in Genetic Analysis Workshop 14 pedigrees.

Whether driven by the general lack of success in finding single-gene contributions to complex disease, by increased knowledge about the potential involvement of specific biological interactions in complex disease, or by recent dramatic increases in computational power, a large number of approaches to detect locus x locus interactions were recently proposed and implemented. The six Genetic Analysis Workshop 14 (GAW14) papers summarized here each applied either existing or refined approaches with the goal of detecting gene x gene, or locus x locus, interactions in the GAW14 data. Five of six papers analyzed the simulated data; the other analyzed the Collaborative Study on the Genetics of Alcoholism data. The analytic strategies implemented for detecting interactions included multifactor dimensionality reduction, conditional linkage analysis, nonparametric linkage correlation, two-locus parametric linkage analysis, and a joint test of linkage and association. Overall, most of the groups found limited success in consistently detecting all of the simulated interactions due, in large part, to the nature of the generating model.

Alcoholism↗

PubMed2006

A novel method to identify gene-gene effects in nuclear families: the MDR-PDT.

It is now well recognized that gene-gene and gene-environment interactions are important in complex diseases, and statistical methods to detect interactions are becoming widespread. Traditional parametric approaches are limited in their ability to detect high-order interactions and handle sparse data, and standard stepwise procedures may miss interactions that occur in the absence of detectable main effects. To address these limitations, the multifactor dimensionality reduction (MDR) method [Ritchie et al., 2001: Am J Hum Genet 69:138-147] was developed. The MDR is well-suited for examining high-order interactions and detecting interactions without main effects. The MDR was originally designed to analyze balanced case-control data. The analysis can use family data, but requires a single matched pair be selected from each family. This may be a discordant sib pair, or may be constructed from triad data when parents are available. To take advantage of additional affected and unaffected siblings requires a test statistic that measures the association of genotype with disease in general nuclear families. We have developed a novel test, the MDR-PDT, by merging the MDR method with the genotype-Pedigree Disequilibrium Test (geno-PDT)[Martin et al., 2003: Genet Epidemiol 25:203-213]. MDR-PDT allows identification of single-locus effects or joint effects of multiple loci in families of diverse structure. We present simulations to demonstrate the validity of the test and evaluate its power. To examine its applicability to real data, we applied the MDR-PDT to data from candidate genes for Alzheimer disease (AD) in a large family dataset. These results show the utility of the MDR-PDT for understanding the genetics of complex diseases.

Algorithms↗

PubMed2002

Conformational analysis: a new approach by means of chemometrics.

In conformational analysis, the systematic search method completely maps the space but suffers from the combinatorial explosion problem because the number of conformations increases exponentially with the number of free rotation angles. This study introduces a new methodology of conformational analysis that controls the combinatorial explosion. It is based on a dimensional reduction of the system through the use of principal component analysis. The results are exactly the same as those obtained for the complete search but, in this case, the number of conformations increases only quadratically with the number of free rotation angles. The method is applied to a series of three drugs: omeprazole, pantoprazole, lansoprazole-benzimidazoles that suppress gastric-acid secretion by means of H+, K+-ATPase enzyme inhibition.

2-Pyridinylmethylsulfinylbenzimidazoles↗

PubMedDate not supplied

Processing and classification of protein mass spectra.

Among the many applications of mass spectrometry, biomarker pattern discovery from protein mass spectra has aroused considerable interest in the past few years. While research efforts have raised hopes of early and less invasive diagnosis, they have also brought to light the many issues to be tackled before mass-spectra-based proteomic patterns become routine clinical tools. Known issues cover the entire pipeline leading from sample collection through mass spectrometry analytics to biomarker pattern extraction, validation, and interpretation. This study focuses on the data-analytical phase, which takes as input mass spectra of biological specimens and discovers patterns of peak masses and intensities that discriminate between different pathological states. We survey current work and investigate computational issues concerning the different stages of the knowledge discovery process: exploratory analysis, quality control, and diverse transforms of mass spectra, followed by further dimensionality reduction, classification, and model evaluation. We conclude after a brief discussion of the critical biomedical task of analyzing discovered discriminatory patterns to identify their component proteins as well as interpret and validate their biological implications.

Algorithms↗

PubMed2003

Machine learning approaches to lung cancer prediction from mass spectra.

We addressed the problem of discriminating between 24 diseased and 17 healthy specimens on the basis of protein mass spectra. To prepare the data, we performed mass to charge ratio (m/z) normalization, baseline elimination, and conversion of absolute peak height measures to height ratios. After preprocessing, the major difficulty encountered was the extremely large number of variables (1676 m/z values) versus the number of examples (41). Dimensionality reduction was treated as an integral part of the classification process; variable selection was coupled with model construction in a single ten-fold cross-validation loop. We explored different experimental setups involving two peak height representations, two variable selection methods, and six induction algorithms, all on both the original 1676-mass data set and on a prescreened 124-mass data set. Highest predictive accuracies (1-2 off-sample misclassifications) were achieved by a multilayer perceptron and Naïve Bayes, with the latter displaying more consistent performance (hence greater reliability) over varying experimental conditions. We attempted to identify the most discriminant peaks (proteins) on the basis of scores assigned by the two variable selection methods and by neural network based sensitivity analysis. These three scoring schemes consistently ranked four peaks as the most relevant discriminators: 11683, 1403, 17350 and 66107.

Algorithms↗

PubMed2006

Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping.

Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T-->R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion.

Amino Acid Substitution↗

PubMed1996

Tobacco smoke upper respiratory response relationships in healthy nonsmokers.

This study determined exposure-response relationships to side-stream tobacco smoke (2 hrs; 0, 1, 5, and 15 ppm CO) in 29 healthy nonsmoking young adults. Sixteen subjects had no history of environmental tobacco smoke rhinitis (ETS-NS) while 13 subjects had a history of ETS rhinitis (ETS-S). Eye irritation and odor perception showed a statistically significant exposure response in both groups; headache was significant in ETS-S and nose irritation was significant in ETS-NS subjects. Significant postexposure (P1) symptoms were first reported at 1 ppm CO among both groups, but in 3/9 symptoms were significantly greater at this exposure level in ETS-S subjects. Nasal congestion, rhinorrhea, and cough increased significantly at 15 ppm CO only. In ETS-S subjects, nasal volume decreased and nasal resistance increased in an exposure-response fashion. ETS-NS subjects had a qualitatively different shape to the exposure-response curve; significant dimensional reductions in mid- and posterior nasal volume occurred with exposure at 1 ppm CO but not at 5 ppm CO and reductions in posterior nasal volume occurred at 15 ppm CO exposure. These studies indicate subjective and objective response relationships with exposure to sidestream tobacco smoke at concentrations from 1 to 15 ppm CO. Some differences are noted among the two subject groups in the magnitude of some symptoms at the lowest exposure level and in the qualitative shape of the acoustic rhinometry and nasal resistance exposure-response curves.

Adult↗

PubMed1988

Auto-association by multilayer perceptrons and singular value decomposition.

The multilayer perceptron, when working in auto-association mode, is sometimes considered as an interesting candidate to perform data compression or dimensionality reduction of the feature space in information processing applications. The present paper shows that, for auto-association, the nonlinearities of the hidden units are useless and that the optimal parameter values can be derived directly by purely linear techniques relying on singular value decomposition and low rank matrix approximation, similar in spirit to the well-known Karhunen-Loève transform. This approach appears thus as an efficient alternative to the general error back-propagation algorithm commonly used for training multilayer perceptrons. Moreover, it also gives a clear interpretation of the rôle of the different parameters.

Mathematics↗

PubMed1993

Time-course of recovery of atrial contraction after cardioversion of chronic atrial fibrillation.

We aimed to study the time-course of recovery of atrial contraction after cardioversion of chronic atrial fibrillation (duration of more than 3 months) to sinus rhythm. Using M-mode, two-dimensional and pulsed Doppler echocardiography, we determined left atrial (LA) and ventricular (LV) dimensions, peak velocities, and velocity-time integrals of early and atrial filling velocity-time profiles in both LV and right ventricular (RV) inflows (peak E and peak A, Ea and Aa). Results of the LA and LV functions in seven elderly patients (an initial study group) were as follows. The extent of the LA dimensional reduction resulting from atrial contraction was significantly increased up to 5-8 weeks compared with values 0-1 day after cardioversion [from 1.3 +/- 0.8 (mean +/- SD) mm to 3.9 +/- 1.1, P < 0.01]. In conjunction with the progressive increase in peak A, the ratio of peak E to peak A (peak E/A) was significantly decreased and reached a plateau at 5-8 weeks (from 1.93 +/- 0.59 to 0.67 +/- 0.11, P < 0.01). LV fractional shortening was increased significantly 5-8 weeks after cardioversion (from 0.20 +/- 0.06 to 0.29 +/- 0.05, P < 0.01). Since a large part of the improvement in LA contraction was expected to occur in an early stage after cardioversion, we studied eight additional patients more frequently in the early stage (an additional study group). Furthermore, we studied the time course of LA and right atrial (RA) contractions.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗

PubMed2000

Characterisation of three-dimensional anatomic shapes using principal components: application to the proximal tibia.

The objective of the research is to determine if principal component analysis (PCA) provides an efficient method to characterise the normative shape of the proximal tibia. Bone surface data, converted to analytical surface descriptions, are aligned, and an auto-associative memory matrix is generated. A limited subset of the matrix principal components is used to reconstruct the bone surfaces, and the reconstruction error is assessed. Surface reconstructions based on just six (of 1452) principal components have a mean root-mean-square (RMS) reconstruction error of 1.05% of the mean maximum radial distance at the tibial plateau. Surface reconstruction of bones not included in the auto-associative memory matrix have a mean RMS error of 2.90%. The first principal component represents the average shape of the sample population. Addition of subsequent principal components represents the shape variations most prevalent in the sample and can be visualised in a geometrically meaningful manner. PCA offers an efficient method to characterise the normative shape of the proximal tibia with a high degree of dimensionality reduction.

Adult↗

PubMed2004

[Therapy of unstable sacrum fractures in pelvic ring fractures with dorsal sacrum distraction osteosynthesis].

Unstable pelvic ring injuries AO type C ("vertical shear") with a fractured sacrum are treated operatively in less than 50% of the cases (DGU pelvis study group). Furthermore, only 12% of these ORIF involve the sacrum bone itself. No specific technique has gained wide acceptance in treating transsacral instability. In accordance with earlier publications (Käch, Josten) suggesting an internal fixator, we developed the dorsal sacrum fracture distantly anchored ORIF (DSDO). This procedure closes the dorsal pelvic ring by joining the two dorsal iliac crests (fixed-angle screws inserted in the posterior superior iliac spine) and additionally anchors in a lumbar pedicle. Thus, a three-dimensional reduction and stable fixation device with optional local nerve decompression and even plating possibility is achieved. Between January 1996 and July 2001, 35 unstable sacrum disruptions were treated with DSDO in 180 patients operated for pelvic trauma. This allowed immediate mobilization in all cases. The radiologic follow-up examination ( n=20) revealed a solid union in all patients. Complications focused on management of the soft tissue degloving injury (Morel-Lavalleé lesion), which needs special attention.

Adolescent↗

PubMed2007

Evidence for epistasis between SLC6A4 and ITGB3 in autism etiology and in the determination of platelet serotonin levels.

Autism is a neurodevelopmental disorder of unclear etiology. The consistent finding of platelet hyperserotonemia in a proportion of patients and its heritability within affected families suggest that genes involved in the serotonin system play a role in this disorder. The role in autism etiology of seven candidate genes in the serotonin metabolic and neurotransmission pathways and mapping to autism linkage regions (SLC6A4, HTR1A, HTR1D, HTR2A, HTR5A, TPH1 and ITGB3) was analyzed in a sample of 186 nuclear families. The impact of interactions among these genes in autism was assessed using the multifactor-dimensionality reduction (MDR) method in 186 patients and 181 controls. We further evaluated whether the effect of specific gene variants or gene interactions associated with autism etiology might be mediated by their influence on serotonin levels, using the quantitative transmission disequilibrium test (QTDT) and the restricted partition method (RPM), in a sample of 109 autistic children. We report a significant main effect of the HTR5A gene in autism (P = 0.0088), and a significant three-locus model comprising a synergistic interaction between the ITGB3 and SLC6A4 genes with an additive effect of HTR5A (P < 0.0010). In addition to the previously reported contribution of SLC6A4, we found significant associations of ITGB3 haplotypes with serotonin level distribution (P = 0.0163). The most significant models contributing to serotonin distribution were found for interactions between TPH1 rs4537731 and SLC6A4 haplotypes (P = 0.002) and between HTR1D rs6300 and SLC6A4 haplotypes (P = 0.013). In addition to the significant independent effects, evidence for interaction between SLC6A4 and ITGB3 markers was also found. The overall results implicate SLC6A4 and ITGB3 gene interactions in autism etiology and in serotonin level determination, providing evidence for a common underlying genetic mechanism and a molecular explanation for the association of platelet hyperserotonemia with autism.

Adolescent↗

PubMed2002

Multidimensional analysis of the concentrations of 17 substances in the CSF of schizophrenics and controls.

The concentrations of 17 substances were determined in the cerebrospinal fluid (CSF) of 28 paranoid schizophrenic patients and 16 controls. Results were standardized and simultaneously evaluated through Multidimensional Scaling (MDS). The full data set can be considered as a cloud of points consisting of the 44 subjects in the 17-dimensional parameter space. MDS seeks a two-dimensional representation of this 17-dimensional cloud of points, while retaining as much as possible the distances between the subjects. The two-dimensional reduction of the 17 CSF parameters correctly separated 15 of 16 controls from the schizophrenic subjects. This indicates that a biological heterogeneity between schizophrenic and nonschizophrenic subjects can be detected by the simultaneous analysis of the CSF concentrations of substances related directly or indirectly to the neuronal activity in the brain.

Adult↗