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Results for “Dimensionality Reduction”

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At least 19 recordsLinked to original sources

PubMed1992

Two and three dimensional reductions of the Hodgkin-Huxley system: separation of time scales and bifurcation schemes.

We study two different two-dimensional reductions of the Hodgkin-Huxley equations. We show that they display the same qualitative bifurcation scheme as the original equations but overestimate the current range where periodic emission occurs. This is essentially due to the assumption that the evolution of the sodium activation variable m is instantaneous with respect to the dynamics of the variables h and n, an hypothesis that breaks down at high values of the injected current. To prove this point we compare the current-amplitude relation, the current-frequency relation, and the shapes of individual spikes for the two reduced models to the results obtained for the original Hodgkin-Huxley model and for a three-dimensional model with instantaneous sodium activation. We show that a more satisfying agreement with the original Hodgkin-Huxley equations is obtained if we modify the evolution equation for the potential by incorporating the prominent features of the dynamics of m.

Animals↗

PubMed1992

Electrostatics and reduction of dimensionality produce apparent cooperativity when basic peptides bind to acidic lipids in membranes.

The binding of pentalysine to phospholipid vesicles depends in a sigmoidal manner on the mole fraction of acidic lipid in the vesicles. A simple analysis demonstrates that this apparent cooperativity is probably due to both the reduction of dimensionality that occurs when the first basic residue binds to an acidic lipid in the membrane and the Boltzmann accumulation of the peptide in the electrostatic diffuse double layer produced by the charged lipids.

Electrochemistry↗

PubMed1986

Rates of membrane-associated reactions: reduction of dimensionality revisited.

The hypothesis that reactions associated with intracellular membranes enjoy a kinetic advantage from a reduced dimensionality for diffusion is inconsistent with available data on lateral diffusion rates, membrane-substrate affinities, and endogenous concentrations of enzymes and their aqueous substrates.

Animals↗

PubMed1985

Mandibular skeletal dysmorphology in micrognathic mice.

The primary manifestations of micrognathia were microglossia, midline fusion of the right and left sides of the mandible, total absence of incisor and molar toothbuds and, in many cases, absence or perhaps premature resorption of Meckel's cartilage. In addition, there was altered osteogenesis as evidenced by disrupted trabecular patterns, as well as an overall dimensional reduction of the mandible both antero-posteriorly and laterally. Strikingly similar results were reported by Johnson (1926), who studied the progeny of x-irradiated mice. How specifically our results correlate with this much earlier work is a matter for further analysis. It seems clear that the critical factor in the development of micrognathia is not so much an abnormal formation of the bony mandible, but a deficiency of tongue development, specifically its intrinsic musculature. Thus, mandibular micrognathia involves not only a dysmorphology of the first branchial arch, but also the mesenchymal cell migration from the occipital somites. Taken together, the picture is one that suggests an underlying cause that may have its inception at a much earlier developmental stage, when ectomesenchymal migration from the region of the neural tube occurs. In any event, we can report confidently that spontaneous micrognathia in prenatal mice is not a simple dimensional reduction of the lower jaw, but a more complex morphological phenomenon.

Animals↗

PubMed1991

Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin.

A stable, partially structured state of ubiquitin, the A-state, is formed at pH 2.0 in 60% methanol/40% water at 298 K. Detailed characterization of the structure of this state has been carried out by 2D NMR spectroscopy. Assignment of slowly exchanging amide resonances protected from the solvent in the native and A-state shows that gross structural reorganization of the protein has not occurred and that the A-state contains a subset of the interactions present in the native state (N-state). Vicinal coupling constants and NOESY data show the presence of the first two strands of the five-strand beta-sheet that is present in the native protein and part of the third beta-strand. The hydrophobic face of the beta-sheet in the A-state is covered by a partially structured alpha-helix, tentatively assigned to residues 24-34, that is considerably more flexible than the alpha-helix in the N-state. There is evidence for some fixed side-chain--side-chain interactions between these two units of structure. The turn-rich area of the protein, which contains seven reverse turns and a short piece of 3(10) helix, does not appear to be structured in the A-state and is approaching random coil.

Amino Acid Sequence↗

PubMed2025

Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.

Successful DNA transcription demands coordination between proteins that bind DNA while simultaneously binding to one another to form dimers or higher-order complexes. For proteins with numerous DNA targets throughout the genome, measurements that report on their dwell time or occupancy thus represent a convolution over a population interacting with specific DNA, nonspecific DNA, or protein partners on DNA. Dimerization is known to add contacts that can help a single protein to stably bind DNA. However, we show here that dimerization can also impair measured dwell times and occupancy on target sequences because the population redistributes across DNA. We combine mass-action kinetic models of pairwise reversible reactions between proteins and DNA with theory and spatial stochastic simulations to isolate the role of dimerization on observed DNA dwell times, occupancy, and spatial distribution of proteins on DNA. Three key themes emerge: (i) Protein-protein interactions, in addition to protein-DNA interactions, can localize a protein to DNA, and relative binding rates can thus widely tune dwell times. (ii) Dimensional reduction achieved through nonspecific binding and subsequent 1D diffusion controls the order-of-magnitude of enhancements despite nucleosome barriers. (iii) Dimerization enhances selectivity for locally clustered targets and often impairs binding to widely-spaced targets by sequestration. Compared with ChIP-seq data, our model explains how the distribution of the essential GAF protein throughout the genome is highly selective for clustered targets due to protein interactions. This model framework predicts when even weak dimerization can redistribute and stabilize proteins on DNA as a necessary part of transcription.

DNA binding↗

PubMed1992

[Treatment of unstable fractures of thoracolumbar spine with neurologic injury using a reduction fixation spinal pedicle screws system].

Twenty-six patients with unstable burst fractures, chance fractures and fractures dislocations of the lower thoracic and lumbar spine were treated with a spinal pedical screw reduction fixation system (RF system). This system is a new device designed by Chinese scientists. In biomechanical testing, it provided three-dimensional reduction forces. The special design of angle pedicle screw provided accurate angle to restore the normal thoracic lumbar lordosis and to maintain it. The three-column spine in a lordotic position maximized the reduction and indirectly achieved a neurologic decompression in the spinal canal. All patients had an anatomical reduction by RF system except one case operated two weeks after injury, the spinal canal area increased over 30% by CT (P < 0.01). Except four cases with Frankle A out of twenty patients with neurologic deficits, all other patients had at least one grade progress. Of them one improved from A to D, ten from C and D to normal. These twenty patients were followed-up over six months. All of them maintained anatomical reduction by RF system. Bone grafting had successful fusion by follow-up X-ray examinations. There were no important complications after surgery. The system is of simple structure facilitation implantation and enable the patients beginning ambulatory movements early, therefore it gives more satisfactory results over conventional Harrington and other segmental spinal instrumentation systems.

Adolescent↗

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↗

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↗

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↗

PubMed1985

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↗

PubMed2026

An Integrated Machine Learning and Genomic Framework for Precise Detection of Gastric Cancer.

This study presents a novel integrative approach for the analysis of high-dimensional gene expression data, leveraging the complementary strengths of unsupervised clustering and supervised classification. Using K-means clustering, the data set is stratified into three distinct clusters, revealing intrinsic biological patterns and relationships. The resulting cluster assignments are subsequently used as pseudolabels to train machine learning models, including support vector machines, random forest, and a stacking ensemble classifier. To validate and enhance the robustness of clustering, complementary methods, such as hierarchical clustering and density-based spatial clustering of applications with noise (DBSCAN), are used, with results visualized through principal component analysis-driven dimensionality reduction. The high predictive accuracy achieved by the classifiers underlines the separability and reliability of the identified clusters. Furthermore, feature importance analysis highlighted key genetic determinants within each cluster, offering actionable insights into potential biomarkers and critical genomic features. This framework bridges the gap between exploratory unsupervised learning and predictive supervised modeling, providing a scalable and interpretable method for analyzing complex genomic data sets. Its applicability extends to biomarker discovery, patient stratification, and other precision medicine applications, emphasizing its utility in advancing genomic research and clinical practice.

Humans↗

PubMed2026

Methylome Profiling of Cartilage Tumors: A Promising New Diagnostic Tool?

DNA methylation and copy number variation (CNV) profiling has emerged as a promising tool for the classification of bone and soft tissue tumors. We evaluated its utility in cartilage tumors, where distinguishing low-grade from high-grade conventional central chondrosarcomas (CSs) and atypical cartilaginous tumors (ACTs) from enchondromas (ECs) is a frequent diagnostic challenge, particularly on biopsy material. We analyzed 214 chondrogenic tumors, including ECs, ACTs, conventional CSs, dedifferentiated chondrosarcomas (DDCSs), and clear cell CSs, and determined their IDH1/2 mutation status. Unsupervised dimensionality reduction of genome-wide DNA methylation patterns revealed 4 clusters among IDH-mutant (MUT) tumors (IDH-MUT-1: mostly ECs and ACTs and some high-grade CSs; IDH-MUT-2: predominantly high-grade CSs; IDH-MUT-3: largely DDCSs; and IDH-MUT-SB: distinct skull base group with a markedly different methylation pattern) and 2 clusters among IDH-wild-type (WT) tumors (IDH-WT-1 and IDH-WT-2: both primarily high-grade CSs, with IDH-WT-2 showing higher tumor grade and more extensive CNVs). Clear cell CSs formed a separate cluster. The amount of CNVs, including loss of CDKN2A, increased with tumor grade, reflecting increased genomic instability during chondrosarcoma progression. Supervised classifiers trained separately, both on methylation and CNV data, and distinguished low-grade and high-grade cartilaginous tumors with area under the curve values of 0.87 to 0.97 and 85% to 90% accuracy. Furthermore, we tested whether DDCSs can be distinguished from metastatic carcinomas and other high-grade sarcomas of the bone. Across 246 reference samples, a supervised classifier achieved 97.2% accuracy (area under the curve, 99.8%) and correctly identified 30 of 32 DDCSs (93.8%). These results indicate that DNA methylation and CNV data analysis provide a valuable tool for distinguishing most low- and high-grade CSs, with additional utility also in differentiating DDCS from morphologic mimics.

cartilaginous tumors↗

PubMed1979

Application of pattern recognition and feature extraction techniques to volatile constituent metabolic profiles obtained by capillary gas chromatography.

The applicability of threshold logic units, a form of nonparametric pattern recognition, to the processing of metabolic profile data obtained by high-efficiency glass capillary column gas chromatography has been investigated. The test data included profiles of the volatile constituents of urine from normal individuals and from individuals with diabetes mellitus. A feature extraction algorithm allowed for dimensionality reduction and indicated the constituents most important in the normal versus pathological distinction. With an optimum number of dimensions, a normal versus pathological prediction rate of 93.75% was achieved. Gas chromatography-mass spectrometry was utilized to identify important profile constituents.

Chromatography, Gas↗

PubMed2026

Genetic heterogeneity affects the risk of incident depression, comorbidity, and response to environment: A prospective trajectory study.

BACKGROUND: Depression exhibits significant heterogeneity in its genetic underpinnings. The role of genetic components in the development of depression and its comorbidities remains insufficiently explored. METHODS: First, depression risk loci from a large-scale genome-wide meta-analysis were annotated to Gene Ontology (GO) terms by functional enrichment. GO-based polygenic risk scores (GO-PRS) were then calculated for individuals in the UK Biobank. Principal component analysis (PCA) was applied for dimensionality reduction, followed by cluster analysis to identify genetic subtypes of depression. Multistate models were applied to assess the impact of genetic patterns on the trajectory from healthy status to incident depression, and depression to 26 subsequent diseases, as well as the associations between environmental factors and disease trajectories across genetic subtypes. RESULTS: Participants were categorized into three genetic subtypes: immune-dominant, neuro-dominant, and comprehensive-risk. Significant differences in risk of depression and subsequent diseases, and susceptibility to environmental factors were observed across subtypes. Comprehensive-risk subtype showed higher risks of depression compared to immune-dominant (HR: 1.10, 95% CI: 1.05-1.15) and neuro-dominant subtype (HR: 1.12, 95% CI: 1.08-1.16). Comprehensive-risk subtype exhibited higher risks of transition from depression to subsequent diseases, such as anemia compared to immune-dominant subtype, and diseases of the digestive system compared to neuro-dominant subtype. Environmental factors were more strongly associated with the transition from depression to subsequent diseases in immune-dominant and comprehensive-risk subtypes, including cardiovascular, respiratory, and metabolic diseases. CONCLUSIONS: Our findings highlight the genetic heterogeneity of depression and comorbidities, and shed light on how genetic components modulate responses to environmental factors.

Humans↗

PubMed2026

Single-Cell Proteomics Reveals Proteome Remodeling and Cellular Heterogeneity During NGF-Induced PC12 Neuronal Differentiation.

Single-cell proteomics enables direct measurement of cellular heterogeneity during dynamic biological processes, but its application to fragile and highly adherent neuronal models remains challenging. Here, we developed and applied an optimized single-cell proteomics workflow to characterize proteome remodeling during nerve growth factor (NGF)-induced differentiation of PC12 cells. To enable reliable single-cell analysis, we implemented gentle dissociation, antiaggregation strategies, and thermal inkjet-based cell dispensing, achieving high accuracy in single-cell isolation. Inclusion of n-dodecyl-β-d-maltoside (DDM) improved recovery of membrane-associated and low-solubility proteins. Coupled with LC-ion mobility-mass spectrometry, this workflow enabled quantification of 2,000-3,000 proteins per cell across the differentiation time course. Single-cell proteomic analysis revealed progressive and heterogeneous proteome remodeling during differentiation. While undifferentiated cells formed a relatively homogeneous population, later stages (Days 4-6) exhibited increased variability, including multimodal protein abundance distributions and separation into distinct subpopulations. Dimensionality reduction, clustering, and non-negative matrix factorization identified multiple coexisting proteomic states within the same time points, reflecting asynchronous differentiation trajectories. These subpopulations were characterized by coordinated differences in pathways related to intracellular trafficking, protein translation, cytoskeletal organization, and neuronal maturation. Comparison with bulk proteomics demonstrated that proteins associated with differentiated neuronal states, including those involved in neurite formation and structural remodeling, are underrepresented in population-averaged measurements but are enriched within specific single-cell subpopulations. Temporal and cluster-resolved analyses further revealed distinct protein expression trajectories, including early decreases in cell cycle and metabolic pathways and later increases in neuronal structural and regulatory proteins. Together, this study establishes an optimized workflow for single-cell proteomics of neuronal systems and demonstrates that NGF-induced PC12 differentiation proceeds through heterogeneous and divergent proteomic states that are not resolved by bulk analysis.

Animals↗

PubMed2025

Association of AGER genetic variants with chronic obstructive pulmonary disease susceptibility in Southern Chinese Han populations.

OBJECTIVE: Chronic obstructive pulmonary disease (COPD) remains a leading cause of disability and mortality among elderly populations. Studies indicate that AGER plays a critical regulatory role in the pathogenesis of respiratory disorders. However, the genetic variations in AGER to COPD susceptibility remain incompletely understood. This study employs a case-control design to investigate associations between AGER genetic variants and COPD risk in the Southern Chinese Han population. METHODS: This study enrolled 270 COPD patients and 271 healthy controls. AGER single-nucleotide polymorphisms (SNPs) were analysed using the MassARRAY iPLEX platform. Logistic regression models evaluated associations between AGER polymorphisms and COPD susceptibility, with false discovery rate (FDR) correction applied to mitigate multiple testing errors. SNP-SNP interactions were investigated through multifactor dimensionality reduction (MDR) analysis. Expression quantitative trait locus (eQTL) data from the GTEx database were further analysed to assess regulatory relationships between SNPs and AGER gene expression levels. RESULTS: This study showed that rs3134941 (G allele, OR = 0.21, 95% CI = 0.10-0.41, p (FDR) = 0.001) and rs3131300 (G allele, OR = 0.32, 95% CI = 0.20-0.49, p (FDR) = 0.0001) were significantly associated with a reduced susceptibility to COPD. MDR indicated that rs3131300 was the optimal predictive model for COPD risk. Additionally, initial mechanistic investigations utilizing the GTEx database identify rs3134941 (C > G) and rs3131300 (A > G) as significant expression quantitative trait loci for AGER mRNA in cell-cultured fibroblasts and whole blood. CONCLUSION: Our study demonstrated that AGER genetic variants might play a protective role in the progression of COPD.

Aged↗