Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “hybrid framework”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

Refined localization and yeast artificial chromosome (YAC) contig--mapping of genes and DNA segments in the 7q21-q32 region.

The chromosome localizations for 159 gene and DNA segments have been refined to one of five intervals in the 7q21-132 region through hybridization analysis with a panel of somatic cell hybrid lines. Seventy-two of these chromosome 7 markers are also mapped on common or overlapping yeast artificial chromosome (YAC) clones. In addition, the breakpoints of chromosome rearrangement contained in five of the somatic cell hybrid lines have been defined by flanking probes within YAC contigs. To provide a framework for further mapping of the 7q21-q32 region, we have established the physical order of a set of reference markers: cen-(COL1A2-D7S15-CYP3A4-PON)-D7S456-(brea kpoint contained in cell hybrid 1EF2/3/K017)-GUSB-D7S186-ASL-(PGY1-PGY3 -GNB2-EPO-ACHE)-D7S238-(proximal breakpoint in GM1059-Rag5)-D7S240-(CUTL1-PLANH1)-(breakp oints in 1CF2/5/K016 and 2068Rag22-2)-(PRKAR2B-D7S13)-LAMB1-(breakpoint in JSR-17S)-DLD-D7S16-MET-WNT2-CFTR-D7S8-tel.

Base Sequence↗

Application of hybridization techniques to genome mapping and sequencing.

Establishment of a variety of hybridization techniques for the analysis of large genomic areas has paved the way for a parallel examination of genomes on many levels within the framework of the various genome projects. Here, I discuss some recent achievements in the application of DNA hybridization techniques, in particular oligomer hybridization.

Base Sequence↗

An Experimental and Theoretical Study of the Substituent Effects on the Redox Properties of 2-[(R-phenyl)amine]-1,4-naphthalenediones in Acetonitrile.

We synthesized and analyzed 19 compounds of 3'- (meta-) and 4'- (para-) substituted 2-[(R-phenyl)amine]-1,4-naphthalenediones (PANs) R = p-MeO, p-Me, p-Bu, p-Hex, p-Et, m-Me, m-Et, H, p-Cl, p-Br, m-F, m-Cl, p-COCH(3), m-CN, m-NO(2), m-COOH, and p-COOH. Despite the fact that the nitrogen atom, which binds the quinone with the meta- and para-substituted ring, interferes with the direct conjugation between both rings, the UV-vis spectra of these compounds show the existence of an intramolecular electronic transfer from the respective aniline to the p-naphthoquinone moiety. In accordance with this donor-acceptor character, the cyclic voltammograms of these compounds exhibit two, one-electron reduction waves corresponding to the formation of radical-anion and dianion, where the half-wave potential values vary linearly with the Hammett constants (sigma(x)). The analysis of the different voltammetric parameters (e.g., voltammetric function, anodic/cathodic peak currents ratio, and the separation between the anodic and cathodic potential peaks) show that with the exception of the carboxylic PAN derivatives, all compounds present the same reduction pathway. We investigated the molecular and electronic structures of these compounds using the semiempirical PM3 method and, within the framework of the Density Functional Theory, using the Becke 3LYP hybrid functional with a double zeta split valence basis set. Our theoretical calculations predict that, with the exception of the p-nitro compound, all the compounds are planar molecules where the conjugation degree of the nitrogen lone pair with the quinone system depends on the position and magnitude of the electronic effect of the substituent in the aniline ring. The Laplacians of the critical points (nabla(2)rho), for the C-O bonds, show that the first reduction wave corresponds to the carbonyl group in alpha-position to the aniline, and that the second one-electron transfer is due to the C(4)-O(2) carbonyl reduction. Thus, the higher reaction constant value (rho) obtained for the second one-electron transfer is due to the fact that the displacement of the nonshared electrons of the amino nitrogen merely modifies the electron density of C(4)-O(2) bond. The positive correlation between the LUMO energy values calculated for these compounds and the E(1/2) potentials corresponding to the C(1)-O(1) carbonyl reduction show that the electron addition takes place at the lowest unoccupied molecular orbital, supporting the fact that this wave is also prone to the substituent effect.

Journal Article↗

Theoretical analysis of structural, energetic, electronic, and defect properties of Li2O.

The structural, energetic, and electronic properties of stoichiometric and defective Li(2)O were studied theoretically. The reliability of the Perdew-Wang method in the framework of density functional theory (DFT), and of two DFT/Hartree-Fock hybrid methods (PW1PW and B3LYP), was examined by comparison of calculated and available experimental data. Atom-centered orbitals and plane waves were used as basis functions for the crystalline orbitals. For both cases, the basis set dependence of calculated properties was investigated. With most of the methods, good agreement with the experimental Li(2)O lattice parameter and cohesive energy was obtained. In accordance with experiment, the analysis of electronic properties shows that Li(2)O is a wide gap insulator. Among the considered methods, the hybrid methods PW1PW and B3LYP give the best agreement with experiment for the band gap. The formation of an isolated cation vacancy defect and an F center in Li(2)O were studied. The effect of local relaxation on the calculated defect formation energies and the defect-induced changes of electronic properties were investigated and compared to available experimental results. The migration of a Li(+) ion in Li(2)O bulk was investigated. The activation energy for the migration of a Li(+) ion from its regular tetrahedral site to an adjacent cation vacancy was calculated, including the effect of local relaxation. The calculated activation barriers, 0.27-0.33 eV, are in excellent agreement with experiment.

Journal Article↗

High accuracy calculations of the optical gap and absorption spectrum of oxygen contaminated Si nanocrystals.

We report accurate high level calculations of the optical gap and absorption spectrum of small Si nanocrystals, with hydrogen and oxygen at the surface. Our calculations have been performed in the framework of time dependent density functional theory (TDDFT) using the hybrid nonlocal exchange and correlation functional of Becke and Lee, Yang and Parr (B3LYP). The accuracy of these calculations has been verified by the high level multi-reference second order perturbation theory. The effect of oxygen contamination is studied by considering several different bonding configurations of the surface oxygen atoms. We show that for nanocrystals of sizes smaller than 20 angstroms, the widening of the gap due to quantum confinement facilitates the stabilization of Si[double bond, length as m-dash]O double bonds. For this type of bonding, the oxygen related states determine the value of the optical gap and make it significantly lower compared to the corresponding gap of oxygen-free nanocrystals. For diameters larger than 20 angstroms, the double bonds delocalize inside the valence band. We find that for small amounts of oxygen, the size of the optical gap depends strongly on their relative distribution and bonding type, while it is practically insensitive to the exact number of oxygen atoms.

Journal Article↗

Somatic diversification in the heavy chain variable region genes expressed by human autoantibodies bearing a lupus-associated nephritogenic anti-DNA idiotype.

Monoclonal anti-DNA antibodies bearing a lupus nephritis-associated idiotype were derived from five patients with systemic lupus erythematosus (SLE). Genes encoding their heavy (H)-chain variable (VH) regions were cloned and sequenced. When compared with their closest VH germ-line gene relatives, these sequences exhibit a number of silent (S) and replacement (R) substitutions. The ratios of R/S mutations were much higher in the complementarity-determining regions (CDRs) of the antibodies than in the framework regions. Molecular amplification of genomic VH genes and Southern hybridization with somatic CDR2-specific oligonucleotide probes showed that the configuration of the VH genes corresponding to VH sequences in the nephritogenic antibodies is not present in the patient's own germ-line DNA, implying that the B-cell clones underwent somatic mutation in vivo. These findings, together with the characteristics of the diversity and junctional gene elements utilized to form the antibody, indicate that these autoantibodies have been driven through somatic selection processes reminiscent of those that govern antibody responses triggered by exogenous stimuli.

Amino Acid Sequence↗

MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.

Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.

Metagenomics↗

N6-methyladenine identification using deep learning and discriminative feature integration.

N6-methyladenine (6 mA) is a pivotal DNA modification that plays a crucial role in epigenetic regulation, gene expression, and various biological processes. With advancements in sequencing technologies and computational biology, there is an increasing focus on developing accurate methods for 6 mA site identification to enhance early detection and understand its biological significance. Despite the rapid progress of machine learning in bioinformatics, accurately detecting 6 mA sites remains a challenge due to the limited generalizability and efficiency of existing approaches. In this study, we present Deep-N6mA, a novel Deep Neural Network (DNN) model incorporating optimal hybrid features for precise 6 mA site identification. The proposed framework captures complex patterns from DNA sequences through a comprehensive feature extraction process, leveraging k-mer, Dinucleotide-based Cross Covariance (DCC), Trinucleotide-based Auto Covariance (TAC), Pseudo Single Nucleotide Composition (PseSNC), Pseudo Dinucleotide Composition (PseDNC), and Pseudo Trinucleotide Composition (PseTNC). To optimize computational efficiency and eliminate irrelevant or noisy features, an unsupervised Principal Component Analysis (PCA) algorithm is employed, ensuring the selection of the most informative features. A multilayer DNN serves as the classification algorithm to identify N6-methyladenine sites accurately. The robustness and generalizability of Deep-N6mA were rigorously validated using fivefold cross-validation on two benchmark datasets. Experimental results reveal that Deep-N6mA achieves an average accuracy of 97.70% on the F. vesca dataset and 95.75% on the R. chinensis dataset, outperforming existing methods by 4.12% and 4.55%, respectively. These findings underscore the effectiveness of Deep-N6mA as a reliable tool for early 6 mA site detection, contributing to epigenetic research and advancing the field of computational biology.

Deep Learning↗

High-resolution landmark framework for the sequence-ready mapping of Xq23-q26.1.

We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover approximately 15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.

Blotting, Southern↗

HyLnc: a hybrid deep learning and feature-based approach for long non-coding RNA prediction.

Long non-coding RNAs (lncRNAs) play important roles in gene regulation, development and disease, yet accurate identification of lncRNAs from transcriptomic data remains a major computational challenge. Existing methods often rely either on handcrafted sequence features or deep learning approaches, each with their inherent limitations in capturing the full complexity of RNA sequences. In this study, we proposed HyLnc, a computational framework that integrates transformer-based contextual embeddings with biologically meaningful sequence features for improved lncRNA prediction. A custom BERT-based model was first pre-trained on a large corpus of metazoan RNA sequences using a masked language modelling strategy to learn contextual nucleotide dependencies. The model was subsequently fine-tuned on curated datasets of lncRNAs and protein-coding transcripts and 256-dimensional deep sequence embeddings were extracted. Parallelly, 348 handcrafted features, including ORF characteristics, untranslated region (UTR) properties, nucleotide composition and Fickett scores, were computed. A multi-stage feature selection strategy was applied to identify the most informative features, resulting in optimized hybrid feature sets. Multiple machine learning classifiers were evaluated, with the RF model achieving the best performance. The proposed framework attained an accuracy of 91.30%, F1-score of 91.23% and MCC of 82.60 on an independent validation dataset, outperforming several existing lncRNA prediction tools. Thus, HyLnc demonstrates that integrating deep contextual representations with biologically interpretable features enhances lncRNA prediction. This approach provides a robust and scalable solution for large-scale transcriptome annotation and can be extended to other sequence-based prediction.

RNA, Long Noncoding↗

Heterogeneity in the human Ig VH locus.

We have used synthetic oligonucleotides corresponding to human VH sequences to analyze sequence variation in human genomic DNA. By using probes 20 to 24 bp long and conditions of hybridization and washing under which identity in 17 to 21 consecutive bp is required for hybridization, it has been possible to dramatically reduce the complexity of hybridization patterns. We have been able to identify unambiguously individual VH elements. Concomitant with the reduction in overall complexity of hybridization patterns has been a marked increase in the variation between hybridization patterns when different individuals are compared. Variation between individuals was detected using probes corresponding to both framework and complementarity determining regions and depended in part on the complexity of the corresponding VH gene family. Probes corresponding to a cDNA clone belonging to the single-member VH6 family, hybridized to a single, invariant, band in all individuals tested. An oligonucleotide probe corresponding to CDR2 of one member of the VH3 family also detected a single, invariant, band in all individuals tested. However, an oligonucleotide probe corresponding to framework region 2 revealed variants of more than 40% of the 22 VH elements it detects. In addition, a panel of 5 oligonucleotide probes corresponding to a second member of the VH3 family revealed variants of 10 of 14 elements detected. The patterns of variation suggest that some VH elements have multiple alleles, whereas some elements are remarkably conserved. The number of variant elements we have detected is evidence that the haplotype arrangement of the human VH locus is probably extremely complex. Importantly, this heterogeneity may contribute directly to disease susceptibility in man.

Antibody Diversity↗

A radiation hybrid map of the human genome.

We have developed a panel of whole-genome radiation hybrids by fusing irradiated diploid human fibroblasts with recipient hamster cells. This panel of 168 cell lines has been typed with microsatellite markers of known genetic location. Of 711 AFM genetic markers 404 were selected to construct a robust framework map that spans all the autosomes and the X chromosome. To demonstrate the utility of the panel, 374 expressed sequence tags (ESTs) previously assigned to chromosomes 1, 2, 14 and 16 were localized on this map. All of these ESTs could be positioned by pairwise linkage to one of the framework markers with a LOD score of greater than 8. The whole genome radiation hybrid panel described here has been used as the starting material for the Genebridge4 panel that is being made widely available for genome mapping projects.

Animals↗

Experimental design and error detection for polyploid radiation hybrid mapping.

In this paper we consider issues of experimental design and error detection and correction for polyploid radiation hybrid mapping. Using analytic methods and computer simulation, we first consider the combinations of fragment retention rate, ploidy, and marker spacing that provide the best chance to order markers. We find that in general, combinations of ploidy and chromosome-specific retention rates that lead to a per-hybrid retention rate of approximately 50% result in the greatest power to order markers. We also find that analyzing polyploid radiation hybrids as if they were haploid does not compromise the ability to order markers but does result in less accurate intermarker distance estimates. Second, we examine the effect of typing errors on two-locus information, ability to order multiple loci, and estimation of intermarker distances and total map length. Even low levels of error result in large losses of information about breakage probabilities, markedly reduce ability to order loci, and inflate estimates of intermarker distances and total map length. We compare the ordering accuracy that results from duplicate typing of hybrids to that of single typing twice as many hybrids and find that duplicate typing results in a higher probability of identifying the true order as one of the best orders, but that single typing of twice as many hybrids results in stronger support for the true order. For low error rates, framework maps constructed from the larger single-typed panels are only slightly less likely to be correct and include substantially more markers than the smaller double-typed panels. Third, we develop a method to calculate the distribution of the number of obligate chromosome breaks for a polyploid radiation hybrid under a given locus order and discuss how this method may be used to identify hybrids with suspiciously large numbers of chromosome breaks.

Animals↗

An alternate treatment method for a fixed-detachable hybrid prosthesis: a clinical report.

The inability to consistently achieve a passive fit with screw-retained implant prostheses is well documented in the literature. Cement-retained implant frameworks have been advocated for implant-retained fixed partial dentures. However, cement retention has not been routinely advocated for fixed-detachable hybrid prostheses. This article describes a method for fabricating a cement-retained fixed-detachable hybrid prosthesis. The advantages and disadvantages are discussed.

Cementation↗

From two dimensional (2D) to three dimensional (3D) analysis by confocal microscopy.

The confocal microscope is becoming increasingly important as an apparatus to analyze the 3-D topography of the cell. Main reasons are the high resolution optical sectioning capacity, the non-invasiveness which leaves the object intact, and the imaging capabilities. This chapter introduces a description of the confocal principle, the basic concepts of confocal fluorescence microscopy and some criteria for cell preservation. Optimization of in situ immunofluorescence, hybridization and detection procedures in combination with new digital microscope techniques can fully express their capacities only if the preparation of biological specimens is accurate for 3-D analysis. Some applications of confocal microscopy to the study of intranucleolar antigens, enzyme translocations and fluorescence in situ hybridization, are described in association with 3-D software image processing, as a useful framework for the study of the 3-D visualization of proteins and chromatin domains.

Histocytological Preparation Techniques↗

Cytonuclear theory for haplodiploid species and X-linked genes. I. Hardy-Weinberg dynamics and continent-island, hybrid zone models.

We develop models that describe the cytonuclear structure for either a cytoplasmic and nuclear marker in a haplodiploid species or a cytoplasmic and X-linked marker in a diploid species. Sex-specific disequilibrium statistics that summarize nonrandom cytonuclear associations in such systems are defined, and their basic Hardy-Weinberg dynamics and admixture formulae are delimited. We focus on the context of hybrid zones and develop continent-island models whereby individuals from two genetically differentiated source populations migrate into and mate within a single zone of admixture. We examine the effects of differential migration of the sexes, assortative mating by pure type females, and census time (relative to mating and migration), as well as special cases of random mating and migration subsumed under the general models. We show that pure type individuals and nonzero cytonuclear disequilibria can be maintained within a hybrid zone if there is continued migration from both source populations, and that females generally have a greater influence over these cytonuclear variables than males. The resulting theoretical framework can be used to estimate the rates of assortative mating and sex-specific gene flow in hybrid zones and other zones of admixture involving haplodiploid or sex-linked cytonuclear data.

Animals↗

Short KIR haplotypes in pygmy chimpanzee (Bonobo) resemble the conserved framework of diverse human KIR haplotypes.

Some pygmy chimpanzees (also called Bonobos) give much simpler patterns of hybridization on Southern blotting with killer cell immunoglobulin-like receptor (KIR) cDNA probes than do either humans or common chimpanzees. Characterization of KIRs from pygmy chimpanzees having simple and complex banding patterns identified nine different KIRs, representing seven genes. Five of these genes have orthologs in the common chimpanzee, and three of them (KIRCI, KIR2DL4, and KIR2DL5) also have human orthologs. The remaining two genes are KIR3D paralogous to the human and common chimpanzee major histocompatibility complex A- and/or -B-specific KIRs. Within a pygmy chimpanzee family, KIR haplotypes were defined. Simple patterns on Southern blot were due to inheritance of "short" KIR haplotypes containing only three KIR genes, KIRCI, KIR2DL4, and KIR3D, each of which represents one of the three major KIR lineages. These three genes in pygmy chimpanzees or their corresponding genes in humans and common chimpanzees form the conserved "framework" common to all KIR haplotypes in these species and upon which haplotypic diversity is built. The fecundity and health of individual pygmy chimpanzees who are homozygotes for short KIR haplotypes attest to the viability of short KIR haplotypes, indicating that they can provide minimal, essential KIRs for the natural killer and T cells of the hominoid immune system.

Amino Acid Sequence↗