Dynamic analysis, with feedback characterization, of hybrid human musculo-skeletal frameworks by the linegraph-flowgraph procedure.
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Extremities↗
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Memetic algorithms for the unconstrained binary quadratic programming problem.
This paper presents a memetic algorithm, a highly effective evolutionary algorithm incorporating local search for solving the unconstrained binary quadratic programming problem (BQP). To justify the approach, a fitness landscape analysis is conducted experimentally for several instances of the BQP. The results of the analysis show that recombination-based variation operators are well suited for the evolutionary algorithms with local search. Therefore, the proposed approach includes--besides a highly effective randomized k-opt local search--a new variation operator that has been tailored specially for the application in the hybrid evolutionary framework. The operator is called innovative variation and is fundamentally different from traditional crossover operators, since new genetic material is included in the offspring which is not contained in one of the parents. The evolutionary heuristic is tested on 35 publicly available BQP instances, and it is shown experimentally that the algorithm is capable of finding best-known solutions to large BQPs in a short time and with a high frequency. In comparison to other approaches for the BQP, the approach appears to be much more effective, particularly for large instances of 1000 or 2500 binary variables.
Algorithms↗
Eu3+ coordination in an organic/inorganic hybrid matrix with methyl end-capped short polyether chains.
Fourier Transform mid-infrared (FT-IR), Fourier Transform Raman (FT-Raman) and photoluminescence spectroscopies and Two-Dimensional (2D) Correlation Spectroscopic Analysis were employed to examine the anionic and cationic local environments in mono-urethanesils doped with europium triflate (Eu(CF(3)SO(3))(3)). The hybrid host framework of these materials is composed of a siliceous backbone bonded through urethane linkages to CH(3)-terminated polymer chains containing about 7 OCH(2)CH(2) units. Samples with infinity >/= n (composition) >/=5 (where n = OCH(2)CH(2)/Eu(3+)) were studied. In terms of ionic association, the level of complexity of these xerogels is very high. In all the compounds the triflate ions exist "free", weakly coordinated and forming cross-link separated ion pairs. At 20 >/= n >/= 5, in addition to all these species contact ion pairs occur. In agreement with these conclusions, photoluminescence establishes the presence of three distinct cation local sites (Eu(3+)/O=C(urethane cross-links), Eu(3+)/O-C-C(polyether chains) and weakly coordinated Eu(3+)/CF(3)SO(3)(-) ionic pairs).
Journal Article↗
Linear transformations of the payoff matrix and decision criterion learning in perceptual categorization.
The effects of payoff-matrix multiplication, payoff-matrix addition, the presence of long-run gains versus long-run losses, category discriminability, and base rate on decision criterion learning were examined in 2 perceptual categorization experiments. Observers were found to be sensitive to the effects of payoff-matrix multiplication (and category discriminability) on the steepness of the objective reward function in line with predictions from the flat-maxima hypothesis and contrary to the predictions from the payoff-variance hypothesis. Decision criterion learning was best in base-rate conditions, was worst when losses were associated with incorrect responding, and was intermediate when no losses were associated with incorrect responding. This performance profile was well captured by the competition between reward and accuracy (COBRA) hypothesis. A hybrid model framework that instantiates both the flat-maxima and COBRA hypotheses was necessary to account for the data from both experiments.
Attention↗
An embedded network approach for scale-up of fluctuation-driven systems with preservation of spike information.
To address computational "scale-up" issues in modeling large regions of the cortex, many coarse-graining procedures have been invoked to obtain effective descriptions of neuronal network dynamics. However, because of local averaging in space and time, these methods do not contain detailed spike information and, thus, cannot be used to investigate, e.g., cortical mechanisms that are encoded through detailed spike-timing statistics. To retain high-order statistical information of spikes, we develop a hybrid theoretical framework that embeds a subnetwork of point neurons within, and fully interacting with, a coarse-grained network of dynamical background. We use a newly developed kinetic theory for the description of the coarse-grained background, in combination with a Poisson spike reconstruction procedure to ensure that our method applies to the fluctuation-driven regime as well as to the mean-driven regime. This embedded-network approach is verified to be dynamically accurate and numerically efficient. As an example, we use this embedded representation to construct "reverse-time correlations" as spiked-triggered averages in a ring model of orientation-tuning dynamics.
Cerebral Cortex↗
Fast and stable cone-beam filtered backprojection method for non-planar orbits.
We propose a new cone-beam shift-variant filtered backprojection (FBP) method for non-planar orbit data acquisitions. The new method is exact, fast and stable to discretization errors. It is based on the hybrid FBP framework whose key feature is to combine the shift-variant filtering with the ramp filtering to produce the filtered projections. We show that an adequate combination of the two filterings allows us to minimize contributions of the time-consuming and numerically unstable shift-variant filtering. We demonstrate the performances of the new method by simulation studies. We also apply the new method to real x-ray data acquired from our experimental system of monochromatic computed tomography.
Computer Simulation↗
A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.
A truly complete, telomere-to-telomere (T2T), and error-free reference genome remains a foundational resource-and long-standing goal-for unbiased comparative and functional genomics. While recent T2T assemblies of humans and other primates have made substantial progress, most still contain thousands of base-level errors, particularly within highly repetitive regions. Here, we present T2T-MMU8v2.0, a near-perfect T2T assembly of the rhesus macaque (Macaca mulatta), representing the highest base-level accuracy reported in a primate genome to date. By employing an optimized ONT-only assembly strategy, we identify subtelomeric satellite-rich regions as the principal bottleneck to improving assembly quality, owing to technological biases in long-read platforms and limitations in current hybrid assembly frameworks. We discover 268 previously unannotated repeat families and resolve ~8 Mbp of SATR satellite arrays, with over 99-fold enrichment in historically misassembled subtelomeric regions. These satellites form four distinct genomic architectures, each with unique SATR satellite composition, segmental duplication organization, and epigenetic signatures, distinct from the subtelomeric architectures observed in hominid genomes. Notably, in contrast to the largely gene-poor subtelomeric regions in African hominids, the SATR architectures in macaques harbor 58 actively transcribed genes, supported by open chromatin and expression data, suggesting gene innovation within these repetitive regions. Functionally, T2T-MMU8v2.0 improves read mappability and accuracy across sequencing platforms, and results in a 19% improvement of transcription start site enrichment scores and 5,821 additional chromatin accessibility peaks on average, thereby enhancing variant detection, regulatory annotation, and transcriptomic resolution in population genetics or single-nucleus studies. Together, this work establishes a new benchmark for genomics, offers a roadmap for resolving complex repetitive regions, and reveals previously unrecognized features of subtelomeric genome structure and evolution.
Journal Article↗
Adhesion testing of a denture base resin with 5 casting alloys.
PURPOSE: This study compared denture base resin shear bond strengths to silicoated Au-Pd, Au-Pd-Ag, Au-Ag-Pd-Cu, high-Pd, and Ni-Cr-Be alloys used to fabricate frameworks for hybrid implant prostheses. Microleakage between alloy and resin was also compared among groups after specimen fracture. MATERIALS AND METHODS: Twelve cylindrical specimens were cast for each alloy. Each specimen was made from a ring-shaped pattern (diameter [d] = 12 mm and height = 4 mm) and machined to achieve uniform hollow centers (d = 6.5 mm). Castings were abraded with 250-micron aluminum oxide and ultrasonically cleaned in distilled water before silicoating. Denture base resin was processed to the internal surfaces of the silicoated specimens. All specimens were thermocycled (1,000 cycles) between 4 degrees C and 50 degrees C, and placed in basic fuchsin dye for a week. A punch (d = 3.8 mm) driven at a cross-head speed of 0.5 mm/min was used to push out the resin specimens. The force required to cause failure was converted to the nominal shear bond strength for each specimen, and mean shear bond strengths for the 5 groups of specimens (N = 12) were compared using one-way analysis of variance and the Tukey-Kramer HSD multiple range test (alpha = 0.05). Six of the 12 debonded resin samples for each alloy were selected at random and evaluated for dye penetration. Using an 80-square grid, the percentage of dye penetration was evaluated with an optical microscope (x25) to determine the percentage of grid area penetrated by the dye. One-way analysis of variance was used to compare the degree of microleakage among groups. RESULTS: The mean resin-alloy shear bond strengths for the Au-Pd (9.6 +/- 3.7 MPa) and Au-Ag-Pd-Cu (9.2 +/- 1.5 MPa) alloys were significantly greater than mean resin-alloy shear bond strength for the Au-Pd-Ag alloy (5.6 +/- 1.9 MPa). No other significant differences in resin-alloy shear bond strengths were noted among the alloy groups. No significant differences were noted for dye penetration into the resin specimens bonded to any of the 5 alloys. The mean grid area penetrated by the dye was 25% when results for the alloys were pooled. CONCLUSIONS: Alloy type influences the shear bond strength of a denture base resin to silicoated alloys, but no difference in bond strength was found between Au-Pd, Au-Ag-Pd-Cu, high-Pd, and Ni-Cr-Be alloys. In addition, under the conditions of this study, all groups showed a similar degree of microleakage, which penetrated approximately 25% of the bonded specimen surface area.
Air Abrasion, Dental↗
Hidden neural networks.
A general framework for hybrids of hidden Markov models (HMMs) and neural networks (NNs) called hidden neural networks (HNNs) is described. The article begins by reviewing standard HMMs and estimation by conditional maximum likelihood, which is used by the HNN. In the HNN, the usual HMM probability parameters are replaced by the outputs of state-specific neural networks. As opposed to many other hybrids, the HNN is normalized globally and therefore has a valid probabilistic interpretation. All parameters in the HNN are estimated simultaneously according to the discriminative conditional maximum likelihood criterion. The HNN can be viewed as an undirected probabilistic independence network (a graphical model), where the neural networks provide a compact representation of the clique functions. An evaluation of the HNN on the task of recognizing broad phoneme classes in the TIMIT database shows clear performance gains compared to standard HMMs tested on the same task.
Databases as Topic↗
General approach to quantum-classical hybrid systems and geometric forces.
We present a general theoretical framework for a hybrid system that is composed of a quantum subsystem and a classical subsystem. We approach such a system with a simple canonical transformation which is particularly effective when the quantum subsystem is dynamically much faster than the classical counterpart, which is commonly the case in hybrid systems. Moreover, this canonical transformation generates a vector potential which, on one hand, gives rise to the familiar Berry phase in the fast quantum dynamics and, on the other hand, yields a Lorentz-like geometric force in the slow classical dynamics.
Journal Article↗
[2.2]paracyclophane/dehydroannulene hybrids: probing the aromaticity of the dehydro[14]annulene framework.
The synthesis of [2.2]paracyclophane/dehydro[14]annulene hybrids 1 and 2 is reported. Comparison of the proton NMR spectra of 1 and 2 with their open precursors and with related model compounds reveals the pronounced effect of macrocycle formation upon the cyclophane protons H15/H16, which lie above the shielding cone of the diatropic [14]annulene moiety. [structure: see text]
Journal Article↗
Heterogeneous displays for surgery and surgical simulation.
Instruments and procedures continue to become more complex and challenging, but the display environments to which these technologies are connected have not kept pace. Display real-estate (the size and resolution of the display), the configurability of the display, and the ability for display systems to incorporate, fuse and present diverse informational sources are limiting factors. The capabilities of display technologies are far exceeded by the procedures and instruments that rely on them. In this paper we show how to break free from display constraints by moving forward with a hybrid, heterogeneous display framework that preserves key characteristics of current systems (low latency, specialized devices). We have engineered a hybrid display and are currently using it to build a surgical simulation and training environment within which we can evaluate both the technology and the performance of subjects using the technology.
Computer Simulation↗
Selective formation of siloxane-based hybrid cages with methylene groups in the frameworks.
A new class of cage-like oligomers were selectively formed by hydrolysis and polycondensation of a methylene-bridged bistrialkoxysilane precursor in the presence of tetramethylammonium hydroxide, which led to the creation of novel silica-based hybrid materials.
Journal Article↗
An organic-inorganic hybrid material constructed from a three-dimensional coordination complex cationic framework and entrapped hexadecavanadate clusters.
A unique organic-inorganic hybrid compound has been separated under hydrothermal condition, which is constructed from a three-dimensional second metal-organic subunit and entrapped hexadecavanadate clusters.
Journal Article↗
Towards quality control for DNA microarrays.
We present a framework for detecting probes in oligonucleotide microarrays that may add significant error to measurements in hybridization experiments. Four types of so-called degenerate probe behavior are considered: secondary structure formation, self-dimerization, cross-hybridization, and dimerization. The framework uses a well-established model for computing the free energy of nucleic acid sequence hybridization and a novel method for the detection of patterns in hybridization experiment data. Our primary result is the identification of unique patterns in hybridization experiment data that are shown to correlate with each type of degenerate probe behavior. A support function for identifying degenerate probes from a large set of hybridization experiments is given and some preliminary experimental results are given for the Affymetrix HuGeneFL GeneChip. Finally, we show a strong relationship between the Affymetrix discrimination measure for a probe and the free-energy estimate from theoretical models of hybridization. In particular, probes on the HuGeneFL GeneChip with high free-energy estimates (weak hybridization) have almost always approximately zero discrimination. The framework can be applied to any Affymetrix oligonucleotide array, and the software is made freely available to the community.
Base Sequence↗
Development of a deer mouse whole-genome radiation hybrid panel and comparative mapping of Mus chromosome 11 loci.
A 5000-rad whole-genome radiation hybrid cell panel (BW5000) was developed for mapping the deer mouse (Peromyscus maniculatus bairdii) genome. The panel consists of 103 cell lines and has an estimated marker retention frequency of 63.9% (range, 28%-88%) based on PCR typing of 30 Type I (coding gene) and 25 Type II (microsatellite) markers. Using the composite Mus map, Type I markers were selected from six Mus chromosomes, 22 of which are on Mus Chr 11. Fifteen of the Mus Chr 11 markers were simultaneously mapped on an interspecific (P. maniculatus x P. polionotus) backcross panel to test the utility of the radiation hybrid panel, create a framework map, and help establish gene order. The radiation hybrids have effectively detected linkage in the deer mouse genome between markers as far apart as 6.7 cM and resolved markers that are, in the Mus genome, as close as 0.2 Mb. Combined results from both panels have indicated a high degree of gene order conservation of the telomeric 64 cM of Mus Chr 11 in the deer mouse genome. The remaining centromeric portion also shows gene order conservation with the deer mouse but as a separate linkage group. This indicates a translocation of that portion of Mus Chr 11 in P. maniculatus and is consistent with rearrangement breakpoints observed between Mus and other mammalian genomes, including rat and human. Furthermore, this separate linkage group is likely to reside in a chromosomal region of inversion polymorphism between P. maniculatus and P. polionotus.
Animals↗
Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts.
Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because both parental alleles are measured in a shared trans-regulatory environment. Here, we analyzed RNA sequencing data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrid. Among the 4,164 genes with sufficient allele-specific support for strict classification, 2,134 (51.2%) showed detectable cis and/or trans regulatory divergence. However, hybrid expression remained largely conserved, with 81.5% of genes not significantly different from either parent. Compensatory cis-trans divergence predominated over reinforcing divergence; cross-replicate estimation reduced the apparent magnitude of this excess, but opposite-sign effects remained predominant in all 20 non-overlapping replicate comparisons. To connect gene expression to genome sequence, we analyzed the strongly cis-diverged locus LYS2 and found species differences in promoter architecture, including an S. cerevisiae-specific AT-rich insertion, altered spacing among candidate regulatory features, and a promoter-proximal TATA-like element unique to S. cerevisiae. Sequence-based nucleosome prediction suggests that these differences create a broader promoter-proximal nucleosome-depleted region in S. cerevisiae than in S. paradoxus. We also quantified allele-resolved intron retention and found that allele-resolved intron retention was broadly conserved, with only rare locus-specific hybrid-associated shifts. Together, these results show that regulatory divergence is widespread but often buffered in the hybrid, whereas intron-retention divergence is comparatively limited.
Saccharomyces↗
Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts.
Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because both parental alleles are measured in a shared trans-regulatory environment. Here, we analyzed RNA sequencing data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrid. Regulatory divergence was widespread, with 61.3% of tested orthologs showing significant divergence in at least one cis or trans component. However, hybrid expression remained largely conserved, with 81.6% of genes not significantly different from either parent. Compensatory cis-trans divergence predominated over reinforcing divergence, consistent with widespread buffering of transcript abundance. To connect genome-wide patterns to mechanism, we analyzed the strongly cis-diverged locus LYS2 and found species differences in promoter architecture, including an S. cerevisiae-specific AT-rich insertion, altered spacing among candidate regulatory features, and a promoter-proximal TATA-like element unique to S. cerevisiae. Sequence-based nucleosome prediction suggests that these differences create a broader promoter-proximal nucleosome-depleted region in S. cerevisiae than in S. paradoxus. We also quantified allele-resolved intron retention and found that splicing was broadly conserved, with only rare locus-specific hybrid-associated shifts. Together, these results show that regulatory divergence is widespread but often buffered in the hybrid, whereas post-transcriptional divergence is comparatively limited.
Gene expression↗