Manifold Learning-Based Common Spatial Pattern for EEG Signal Classification.

EEG signal classification using Riemannian manifolds has shown great potential. However, the huge computational cost associated with Riemannian metrics poses challenges for applying Riemannian methods, particularly in high-dimensional feature data. To address these, we propose an efficient ensemble method called MLCSP-TSE-MLP, which aims to reduce the computational cost while achieving superior performance. MLCSP of the ensemble utilizes a Riemannian graph embedding strategy to learn intrinsic low-dimensional sub-manifolds, enhancing discrimination. TSE uses the Euclidean mean as the reference point for tangent space mapping and reducing computational cost. Finally, the ensemble incorporates the MLP classifier to offer improved classification performance. Classification results conducted on three datasets demonstrate that MLCSP-TSE-MLP achieves significant superior performance compared to various competing methods. Notably, the MLCSP-TSE module achieves a remarkable increase in training speed and exhibits much lower test time compared to traditional Riemannian methods. Based on these results, we believe that the proposed MLCSP-TSE-MLP is a powerful tool for handling high-dimensional data and holds great potential for practical applications.

Emerging nonmodel eukaryotes for biofuel production.

Microbial synthesis of biofuels offers a promising solution to the global environmental and energy concerns. However, the main challenge of microbial cell factories is their high fermentation costs. Model hosts, such as Escherichia coli and Saccharomyces cerevisiae, are typically used for proof-of-concept studies of producing different types of biofuels, however, they have a limited potential for biofuel production at an industrially relevant scale due to the weak stability/robustness and narrow substrate scope. With the advancements of synthetic biology and metabolic engineering, nonmodel eukaryotes, with naturally favorable phenotypic and metabolic features, have been emerging as promising biofuel producers. Here, we introduce the emerging nonmodel eukaryotes for the biofuel production and discuss their specific advantages, especially those with the capacity of producing cellulosic ethanol, higher alcohols, and fatty acid-/terpene-derived biofuel molecules. We also propose the challenges and prospects for developing nonmodel eukaryotic as the ideal hosts for future biofuel production.

Binding characteristics of calpastatin domain L to NaV1.5 sodium channel and its IQ motif mutants.

NaV1.5 channel is an integral membrane protein involved in the initiation and conduction of action potentials. IQ motif is located in the C-terminal domain of NaV1.5 sodium channel, which is highly conserved in human sodium channel subtypes. IQ motif is involved in the Ca2+-dependent regulation through interaction with the regulatory proteins such as calpastatin domain L (CSL). Mutations in SCN5A, the gene encoding NaV1.5 channel, have been linked to many cardiac arrhythmias, such as Long QT syndrome type 3 (LQT3) and Brugada syndrome (BRS). LQT3-associated mutations in NaV1.5 IQ motif, IQQ1909R and IQR1913H, have been reported to affect the late INa. A BRS-associated mutation in NaV1.5 IQ motif, IQA1924T, has been reported to affect the peak INa. But the detailed pathogenic mechanisms of LQT3 and BRS remains unclear. To explore the binding properties of CSL to IQ motif and its muants associated with LQT3/BRS, molecular docking and GST pull down assay were performed in this study. As a result, S58 and E59 in CSL activating channel effect region L54-64 were involved in the conformation of the CSL/IQWT complex by protein-protein docking. IQ motif could bind to CSL in a [CSL]-dependent and [Ca2+]-dependent manner by pull down assay. However, the binding affinities of IQQ1909R and IQR1913H to CSL were decreased and its reaction rates with CSL were slower. The binding characteristics of IQA1924T to CSL was opposite in a [Ca2+]-dependent manner and its binding efficacy became smaller. The changes of the binding characteristics of IQmutants to CSL would affect the regulation of NaV1.5 channel, which may be related to LQT3 and BRS.

Nucleosome Assembly and Disassembly in vitro Are Governed by Chemical Kinetic Principles.

As the elementary unit of eukaryotic chromatin, nucleosomes in vivo are highly dynamic in many biological processes, such as DNA replication, repair, recombination, or transcription, to allow the necessary factors to gain access to their substrate. The dynamic mechanism of nucleosome assembly and disassembly has not been well described thus far. We proposed a chemical kinetic model of nucleosome assembly and disassembly in vitro. In the model, the efficiency of nucleosome assembly was positively correlated with the total concentration of histone octamer, reaction rate constant and reaction time. All the corollaries of the model were well verified for the Widom 601 sequence and the six artificially synthesized DNA sequences, named CS1-CS6, by using the salt dialysis method in vitro. The reaction rate constant in the model may be used as a new parameter to evaluate the nucleosome reconstitution ability with DNAs. Nucleosome disassembly experiments for the Widom 601 sequence detected by Förster resonance energy transfer (FRET) and fluorescence thermal shift (FTS) assays demonstrated that nucleosome disassembly is the inverse process of assembly and can be described as three distinct stages: opening phase of the (H2A-H2B) dimer/(H3-H4)2 tetramer interface, release phase of the H2A-H2B dimers from (H3-H4)2 tetramer/DNA and removal phase of the (H3-H4)2 tetramer from DNA. Our kinetic model of nucleosome assembly and disassembly allows to confirm that nucleosome assembly and disassembly in vitro are governed by chemical kinetic principles.

The mathematical expression of damage law of museum lighting on dyed artworks.

Dyed artworks are highly sensitive to light and are easily affected by museum lighting, resulting in irreversible permanent color damage such as fading and discoloration. Exposure, light source spectrum and material properties are the three indicators causing damage to artworks. Therefore, it is the basis for effective lighting protection to reveal the quantitative influence of exposure and light source spectrum composition on the damage degree of different pigments and establish a mathematical model that can accurately express the above rules. At present, the color damage calculation model of dyed artworks under three parameters' coupling action is missing. This research established a visual three-dimensional change surface of the color difference values of 23 pigments varying with the spectral wavelength and exposure through experimental methods. The relative responsivity function ΔEn = fn(λ, Q), where n = 1 ~ 23, was obtained for 23 pigments under the coupling effects of exposure and light source spectra. Furthermore, a mathematical model [Formula: see text] calculating the color damage of pigments in the range of visible light was proposed. The proposed model was verified by the experimental method, which realizes the mathematical expression of the damage law of museum lighting on dyed artworks.

Raman spectroscopy-based method for evaluating LED illumination-induced damage to pigments in high-light-sensitivity art.

Because commonly used organic pigments are highly responsive to visible light, high-light-sensitivity art is vulnerable to irreversible illumination-induced damage caused by radiation from light sources. With application of the four primary white light-emitting diodes (fp-WLEDs) in museums, it is urgent to evaluate the illumination-induced damage to high-light-sensitivity art caused by the fp-WLEDs. Four narrowband LEDs with different peak wavelengths of 450, 510, 583, and 650 nm that constitute the spectra of the fp-WLEDs were used to irradiate three commonly used organic pigments: safflower, gamboge, and indigo. Based on the fundamental reason for the illumination-induced damage, that is, photochemical reactions, Raman spectroscopy was introduced into the study. The Raman spectra of pigments were measured before and after illumination. The characteristic Raman peaks corresponding to the functional groups that determine color and structure of pigments were selected, and the variations in their peak intensities were calculated. The illumination-induced damage coefficients of four narrowband LEDs on three organic pigments were obtained, providing a data basis for illumination-induced damage evaluation equation proposed in this study, which was expected to further realize museum admission evaluation of the new fp-WLEDs.

The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro.

Nucleosome positioning along the genome is partially determined by the intrinsic DNA sequence preferences on histone. RRRRRYYYYY (R5Y5, R = Purine and Y = Pyrimidine) motif in nucleosome DNA, which was presented based on several theoretical models by Trifonov et al., might be a facilitating sequence pattern for nucleosome assembly. However, there is not a high conformity experimental evidence to support the concept that R5Y5 motif is a key element for the determination of nucleosome positioning. In this work, the ability of the canonical, H2A.Z- and H3.3-containing octamers to assemble nucleosome on DNA templates containing R5Y5 motif and TA repeats within 10.5-bp periodicity was investigated by using salt-dialysis method in vitro. The results showed that the10.5-bp periodical distributions of both R5Y5 motif and TA repeats along DNA templates can significantly promote canonical nucleosome assembly and may be key sequence factors for canonical nucleosome assembly. Compared with TA repeats within 10.5-bp periodicity, R5Y5 motif in DNA templates did not elevate H2A.Z- and H3.3-containing nucleosome formation efficiency in vitro. This result indicates that R5Y5 motif probably isn't a pivotal factor to regulate nucleosome assembly on histone variants. It is speculated that the regulatory mechanism of nucleosome assembly is different between canonical and variant histone. These conclusions can provide a deeper insight on the mechanism of nucleosome positioning. Communicated by Ramaswamy H. Sarma.

Effects of starches on the textural, rheological, and color properties of surimi-beef gels with microbial tranglutaminase.

In order to evaluate effects of starches (corn starch, potato starch, and tapioca starch) on the characteristics of surimi-beef gels with microbial transglutaminase, the cooking loss, gel strength, color and rheological properties of samples were investigated. Results demonstrated that starches gave negative effects on the cooking loss of surimi-beef gels. The gel with corn starch had the highest cooking loss while that with tapioca starch showed the lowest value. The gel with potato starch obtained the highest gel strength. During the sol-gel transitions, surimi-beef complexes with 3% corn starch exhibited the highest storage modulus value, while that with 3% tapioca starch had the lowest one. The addition of starch caused the increase of L* values of surimi-beef gels. Results showed that the excessive amount of starch resulted in the decrease in gel strength of surimi-beef gels.

Identifying gene clusters within localized regions in multiple genomes.

An important strategy to study genome evolution is to investigate the clustering of orthologous genes among multiple genomes, in which the most popular approaches require that the distance between adjacent genes in a cluster be small. We investigate a different formulation based on constraining the overall size of a cluster and develop statistical significance estimates that allow direct comparison of clusters of different sizes. We first consider a restricted version which requires that orthologous genes are strictly ordered within each cluster and show that it can be solved in polynomial time. We then develop practical exact algorithms for the unrestricted problem that allows paralogous genes within a genome and clusters that may not appear in every genome while considering a general model in which a gene is allowed to appear in more than one orthologous group. We show that our algorithm can identify biologically relevant gene clusters on four bacterial genomes Bacillus subtilis, Streptococcus pyogenes, Streptococcus pneumoniae, and Clostridium acetobutylicum. We also show that our algorithm can identify significantly more functionally enriched gene clusters on four yeast genomes Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces bayanus than previous algorithms. A software program (GCFinder) and a list of gene clusters found on the bacterial and the yeast genomes are available at http://faculty.cse.tamu.edu/shsze/gcfinder .