Sequence Arrangement Research Articles

Peptide Amphiphiles as Biodegradable Adjuvants for Efficient Retroviral Gene Delivery.

Retroviral gene delivery is the key technique for in vitro and ex vivo gene therapy. However, inefficient virion-cell attachment resulting in low gene transduction efficacy remains a major challenge in clinical applications. Adjuvants for ex vivo therapy settings need to increase transduction efficiency while being easily removed or degraded post-transduction to prevent the risk of venous embolism after infusing the transduced cells back to the bloodstream of patients, yet no such peptide system have been reported thus far. In this study, peptide amphiphiles (PAs) with a hydrophobic fatty acid and a hydrophilic peptide moiety that reveal enhanced viral transduction efficiency are introduced. The PAs form β-sheet-rich fibrils that assemble into positively charged aggregates, promoting virus adhesion to the cell membrane. The block-type amphiphilic sequence arrangement in the PAs ensures efficient cell-virus interaction and biodegradability. Good biodegradability is observed for fibrils forming small aggregates and it isshown that via molecular dynamics simulations, the fibril-fibril interactions of PAs are governed by fibril surface hydrophobicity. These findings establish PAs as additives in retroviral gene transfer, rivalling commercially available transduction enhancers in efficiency and degradability with promising translational options in clinical gene therapy applications.

Basic notions about gene therapy from the nucleic acid perspective and applications in a pediatric disease: Duchenne muscular dystrophy

Gene therapy involves the introduction of genetic material into cells as a therapeutic molecule to cure a disease. Through the transfer of specific nucleic acid to the target tissue, gene expression can be downregulated, augmented, or corrected thanks to the nucleic acid sequence as a support of gene expression. This is achieved through molecular interactions according to the sequence arrangement or the secondary structure of the molecules or through their catalytic properties. Over the past two decades, the rapid advances of knowledge and technologies in gene therapy have led to the development of different strategies and to the extension of its use to numerous indications, including certain cancers. Major success has been achieved in clinical trials and the field of gene therapy is booming. Several gene therapy products are now on the market in Europe, the United States, and China. In this review, we cover the basic principles of gene therapy and the characteristics of the main vectors used to transfer genetic material into the cell. As an example of applications, we address the various strategies applied to a rare pediatric muscle disease: Duchenne muscular dystrophy. © 2023 Published by Elsevier Masson SAS on behalf of French Society of Pediatrics.

An anisotropic broadband coding metasurface based on ultralight graphene‐assembled film

AbstractAs theoretical research further develops, coding metasurfaces have been widely studied and applied due to their uniqueness in digital characterization and sequence arrangement. In this work, based on highly conductive graphene‐assembled film (GAF), an ultralight anisotropic broadband coding metasurface (ABCM) is proposed. The GAF ABCM consists of 16 units with specific phase responses and enables complete metal substitution. By arranging the unit cells in a specific order, the GAF ABCM realizes the functions of anomalous reflection, polarization conversion, and radar cross‐section (RCS) reduction. Results validate that the GAF ABCM has a measured 10 dB normal incidence backward RCS reduction within the working frequency band of 7–18 GHz, which fully covers the X‐band and Ku‐band for radar application. Furthermore, due to the lightweight property of GAF, the density of the GAF ABCM is only 0.06 g/cm3 (surface mass density of 0.038 g/cm2). All results indicate that the lightweight GAF metasurface is promising in radar stealth and communication fields.

Enhancing the forming quality of Al2024-T351 sheets in laser peen forming through a novel energy sequence arrangement strategy

Laser peen forming (LPF) employs laser-induced shock waves for shaping and modifying bent structures, exhibiting high flexibility and non-contact advantages. This study investigated the impact of different laser energies, laser peening sequences, and energy sequences on the bending deformation, surface quality, and stress distribution of 4 mm thick sheets, using both experiments and simulations. Increasing laser energy and peening sequences were found to enhance the degree of sheet deformation, while adjusting the energy sequence had an insignificant effect on deformation. Higher laser energy resulted in increased surface roughness in the peened area, whereas increasing the peening sequence reduced surface roughness. The optimal approach for reducing surface roughness in forming sheets was found to be utilizing low-energy peening after high-energy peening (high-then-low). Moreover, compared to single low-energy peening, employing the high-then-low-energy peening strategy decreased the attenuation rate of the compressive stress wave, which led to a 23.5 % increase in the magnitude and 25 % increase in the depth of the final compressive stress. The compressive residual stress (CRS) in the length and width direction of the sheet's surface layer was higher with the high-then-low energy peening strategy compared to other treatment strategies.

Penjadwalan Mata Pelajaran Menggunakan Algoritma Particle Swarm Optimization (PSO) Pada SMPIT Mufidatul Ilmi

Scheduling has a division of time based on a work sequence arrangement plan in the form of a list or table of activities or an activity plan with a detailed division of implementation time which is very necessary in carrying out institutional/company business processes. It is important to note the complexity of the process in scheduling appropriate subjects from various perspectives, both teachers, students and classrooms. Provision of teacher teaching schedules based on abilities in the field of subjects, suitable time each semester is very important to consider for very complex schedule arrangements, the number of classrooms that can be used in teaching activities is relatively small, and preventing teacher teaching conflicts so that the need for optimization of eye scheduling lesson to be made. Furthermore, at the stage of application development using the Waterfall method. The purpose of this research is to build a lesson scheduling application at SMPIT Mufidatul Ilmi by applying the particle swarm optimization (PSO) algorithm to compile lesson schedules. Particle Swarm Optimization is a population-based algorithm that exploits individuals in search. In PSO the population is called a swarm and individuals are called particles. Each particle moves at a speed adapted from the search area and stores it as the best position ever achieved. Design analysis includes Use Case Diagrams, Activity Diagrams, Class Diagrams, Sequence Diagrams, Entity Relationship Diagrams (ERD). The results of this study provide several primary data (service) features, especially features to provide scheduling results from processing with the PSO algorithm

A novel dual-plasmid platform provides scalable transfection yielding improved productivity and packaging across multiple AAV serotypes and genomes

Transient transfection of mammalian cells using plasmid DNA is a standard method to produce adeno-associated virus (AAV) vectors allowing for flexible and scalable manufacture. Typically, three plasmids are used to encode the necessary components to facilitate vector production; however, a dual-plasmid system, termed pDG, was introduced over 2 decades ago demonstrating two components could be combined resulting in comparable productivity to triple transfection. We have developed a novel dual-plasmid system, pOXB, with an alternative arrangement of sequences that results in significantly increased AAV vector productivity and percentage of full capsids packaged in comparison to the pDG dual design and triple transfection. Here, we demonstrate the reproducibility of these findings across seven recombinant AAV genomes and multiple capsid serotypes as well as the scalability of the pOXB dual-plasmid transfection at 50-L bioreactor scale. Purified drug substance showed a consistent product quality profile in line with triple-transfected vectors, except for a substantial improvement in intact genomes packaged using the pOXB dual- transfection system. Furthermore, pOXB dual- and triple-transfection-based vectors performed consistently invivo. The pOXB dual plasmid represents an innovation in AAV manufacturing resulting in significant process gains while maintaining the flexibility of a transient transfection platform.

Coupling photonic quasicrystals with a one-dimensional critical high-temperature superconducting cavity

The transfer matrix method is used to calculate the transmission spectra in one-dimensional photonic quasicrystal (1D-PQ) coupling via a superconducting cavity. The layers that make up 1D-PQs are barium titanate ferroelectric (BaTiO3) and yttrium dielectric oxide (Y2O3), organized following the Fibonacci sequence. We consider the superconducting cavity to be a critical high-temperature superconductor (YBa2Cu3O7). Based on such proposed heterostructure, a multichannel filter in the near-infrared spectral region is obtained due to the existence of localized modes with an increasing Fibonacci sequence. Such localized modes are found in the null-transmission region named photonic band gaps. We observed that when increasing an incidence angle, the confinement of localized modes augments. Specifically, it is shown that, in 1D-PQs, from ferroelectric and dielectric materials with a Fibonacci sequence arrangement of an order of five (Fb5), two localized modes emerge as part of the PBG localized modes with a quality factor (Q) of Q=155.67 and Q=150.26. In the telecom region, such localized modes are tuned to longer wavelengths as the operating temperatures of the superconducting cavity increase from 10 to 80 K. Finally, we found that an increase in the thickness of the superconducting cavity favors a shift of a localized mode to longer wavelengths. The proposed heterostructure operates in cryogenic temperature environments, and we expect for it to be integrated into the optoelectronic circuit design.

Influence of phase sequence arrangement on the electromagnetic environment of four-circuit AC line on the same tower

The paper predicts the power frequency electric field (PFEF), audible noise (AN), and radio interference (RI) of double-circuit 220kV and double-circuit 110kV four-circuit lines on the same tower erected on the same tower through the numerical calculation method of electromagnetic environment (EME) of AC transmission lines (TLs). Through a typical tower structure, the influence of the phase sequence (PS) on the EME is analysed, and the optimal and worst PSs are obtained. The optimal PS can significantly improve the EME, especially with a good confinement effect on the electric field’s power frequency. In addition, it also focuses on analyzing the influence degree of PS when the phase spacing, conductor-to-ground height and layer spacing change and establishes the applicable range of the optimal PS.

Energy-Efficient Regional Area Metropolitan Optical Access Network (RAMOAN) Using Modified Load Adaptive Sequence Arrangement (M-LASA) Methodology

Energy efficiency in optical networks is one of the important criteria to attain enhanced performance. Better energy efficiency can be attained in optical networks if the resources are properly scheduled. Polling sequences perform resource scheduling based on load requirements, and various methodologies have evolved in recent times for better efficiency. Load adaptive sequence arrangement (LASA) is one of the familiar and efficient methodologies adopted in various methodologies. However, the power consumption and idle time of optical network units are high which should be reduced to attain optimal network performances. Considering this, a modified LASA is presented in this research work for the regional area metropolitan optical access network (RAMOAN). The modified LASA is obtained by integrating the first-in-last-out polling sequence such that the proposed arrangement provides a better coverage radius, minimal power cost, maximum access reach, maximum energy saving, and minimal delay and energy cost. The better performance of the proposed approach is compared with traditional time and wavelength division multiplexed (TWDM), TWDM-protected, and RAMOAN with LASA through simulation analysis to validate the better performances of the proposed model.

Investigation of single-shot high-speed photography based on spatial frequency multiplexing.

The frequency recognition algorithm for multiple exposures (FRAME) is a spatial frequency multiplexing method that enables high-speed videography with high spatial resolution across a wide field of view and high temporal resolution up to femtoseconds. The criterion to design encoded illumination pulses is an essential factor that affects the sequence depth and reconstruction accuracy of FRAME but was not previously discussed. When the spatial frequency is exceeded, the fringes on digital imaging sensors can become distorted. To exploit the Fourier domain for FRAME with deep sequences and avoid fringe distortion, the maximum Fourier map for sequence arrangement was determined to be a diamond shape. The maximum axial frequency should be a quarter of the sampling frequency of digital imaging sensors. Based on this criterion, the performances of reconstructed frames were theoretically investigated by considering arrangement and filtering methods. To ensure optimal and uniform interframe quality, the frames near the zero frequency should be removed and optimized super-Gaussian filters should be employed. Experiments were conducted flexibly with a digital mirror device to generate illumination fringes. Following these suggestions, the movement of a water drip dropping on a water surface was captured with 20 and 38 frames with uniform interframe quality. The results prove the effectiveness of the proposed methods to improve the reconstruction accuracy and promote the development of FRAME with deep sequences.

The altitude correction term of the corona loss on alternating-current transmission lines

The increase in mobility of charged particles causes high-voltage alternating-current (AC) transmission lines in high-altitude areas to be more likely to undergo severe corona discharge and associated losses, to the detriment of the economic efficiency of power transmission. Evaluating the corona loss on transmission-line conductors in high-altitude areas is conducive to conductor selection, parameter optimization, transmission-line tower arrangement, and optimization of the phase sequence arrangement. The altitude correction factor K of 3.33 dB/km recommended by the Bonneville Power Administration (BPA) in the United States is commonly used in engineering design, however, measured data indicate that the correction method may be subject to significant error, so the altitude correction factor is discussed under different weather conditions. K is suggested to be 4.5 and 1.5 dB/km separately under dry and rainy conditions, the better to evaluate the coronal loss.

Русский голос в «своей» загранице

The Russian-language press in Finland became noticeably more active in March 1917, after the February Revolution. The emerged newspapers and magazines, being often publications of local departments of various parties, reflected as a rule their political aspirations. The proclamation of Finland’s independence in December 1917 intensified the nationalist movement in the country and sharp increase of Russophobia, which were reflected in the pages of the Russian-language press. In the article is considered the newspaper “Voice of the Russian Colony” (1918), which was published in Helsingfors by university professor, writer Konstantin Arabazhin. The problems and structure of the newspaper as a whole, as well as the themes and genre originality of a number of journalistic texts in particular, are characterized. The editorial office of the newspaper positioned itself as an organ of independent non-partisan thought; directed its efforts to unite all layers of the Russian population of Helsingfors on the basis of national cultural values; expressed confidence that she would be able to correctly reflect the interests of her compatriots in Finland and thus become the voice of the Russian colony in the broadest sense of the word. The article describes in detail the materials of the first issue of the newspaper “Voice of the Russian Colony”. As follows from the analysis, the constituent components of the newspaper are thematically interconnected, and their arrangement in a certain sequence makes it possible to read the issue as a single text, aimed to convince the Russian-speaking reader of the significance and usefulness of the new periodical.

A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences.

New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.

DeePromClass: Delineator for Eukaryotic Core Promoters Employing Deep Neural Networks.

Computational promoter identification in eukaryotes is a classical biological problem that should be refurbished with the availability of an avalanche of experimental data and emerging deep learning technologies. The current knowledge indicates that eukaryotic core promoters display multifarious signals such as TATA-Box, Inr element, TCT, and Pause-button, etc., and structural motifs such as G-quadruplexes. In the present study, we combined the power of deep learning with a plethora of promoter motifs to delineate promoter and non-promoters gleaned from the statistical properties of DNA sequence arrangement. To this end, we implemented convolutional neural network (CNN) and long short-term memory (LSTM) recurrent neural network architecture for five model systems with [-100 to +50] segments relative to the transcription start site being the core promoter. Unlike previous state-of-the-art tools, which furnish a binary decision of promoter or non-promoter, we classify a chunk of 151mer sequence into a promoter along with the consensus signal type or a non-promoter. The combined CNN-LSTM model; we call "DeePromClass", achieved testing accuracy of 90.6%, 93.6%, 91.8%, 86.5%, and 84.0% for S. cerevisiae, C. elegans, D. melanogaster, Mus musculus, and Homo sapiens respectively. In total, our tool provides an insightful update on next-generation promoter prediction tools for promoter biologists.

Analysis and treatment of current unbalance abnormal situation of 750 kV double-circuit parallel transmission line

At present, the biggest problem faced by short-distance double-circuit parallel lines is the three-phase parameter asymmetry problem caused by non-transposition. This leads to three-phase current asymmetry, especially during heavy load performance is more prominent. Take a 750 kV double circuit parallel erection line in actual operation as an example, use EMTPE electromagnetic transient simulation software to simulate and analyze the current imbalance phenomenon. This paper studies the influence of phase sequence arrangement, distance between loops, distance between wires, line length, equivalent impedance, ground wire conditions and line power flow on current imbalance, and puts forward reasonable restraining measures. The simulation results show that when the line power flow is heavy, the double circuit lines are arranged in the same phase sequence and the distance between circuits is relatively short, there will be a large amplitude of zero sequence current on the line, mainly circulation current. If it is not suitable to adjust the protection measures, it can be considered to adjust the double-circuit lines to reverse phase sequence operation mode. The research results can provide reference for the engineering design of double-circuit parallel transmission lines.

Research on the construction of rural interface style based on aesthetic rules

Abstract The form and overall style of rural settlements are the carrier of the rural regional context and aesthetics. At present, China’s rural areas are facing a disorderly style and urbanisation. This study is based on similarity aesthetic regularity and visual aesthetic regularity; on the one hand, this work researches the method of building interface coordination from the aspects of form, material and colour, and puts forward the interface construction method of strong contrast, medium contrast and weak contrast according to the rural areas. On the other hand, this study analyses people’s perception characteristics of the style from the visual psychological level, explains the skills for the rural interface and sequence arrangement based on the relationship between visual matching and the bottom of the picture and constructs the aesthetic image under the new overall relationship of the place. Finally, this study puts forward a series of strategies for rural style construction, such as symbol concatenation, contrast reconstruction and aesthetic conflict transformation, to constructing a new aesthetic image of place so as to provide ideas and methods for the development of the rural style in the future.

Time-resolved strand displacement amplification enables G-quadruplex-amplified detection of type 2 diabetes mellitus-related circulating microRNA-146a

DNA has proven to be exquisite molecules for the design of artificial analytical tools in molecular diagnosing of human diseases. In this work, we constructed a time-resolved strand displacement amplification (TR-SDA) for molecularly determination of microRNA-146a (miR-146a), a potential biomarker of Type 2 diabetes mellitus (T2DM). Such an amplification strategy makes use of a multi-functionalized cytosine-rich hairpin probe (C-HP). Unlike conventional amplifications that relying on exogenous primer-directed strand polymerization, the hybridization of target miR-146a with C-HP causes a C-HP based intramolecular replication in parallel with an miR-146a/C-HP based intermolecular replication. This feature leads to a time-resolved amplification pattern responsible for controlling C-HP with a cascaded signal amplification ability. Without requirement of any assist probes or complex sequence arrangements, the method enables efficiently accumulate numbers of G-quadruplexes at a constant temperature. After intercalated with thioflavin T (ThT), the complex of G-quadruplex/ThT immediately becomes fluorescence-emissive for detecting of the miR-146a concentration. We demonstrated the successful detection of miR-146a with a high sensitivity and also measured miR-146a from healthy donors and T2DM patients with different expression level. As a proof-of-concept study, the TR-SDA acting as a powerful molecular diagnostic method might provide promising opportunities to meet future clinical needs in biomedicine.

Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery.

Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent nonspecific DNA-binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.

SVPWAM modulation strategy for back-to-back converters to reduce harmonic and common mode voltage

ABSTRACT This paper presents a new switching strategy by combining space vector modulation (SVM) and pulse amplitude modulation (PAM) techniques. The proposed method can eliminate harmonics and reduce power loss, leading to efficiency increment. Moreover, as one of the significant challenges in any modulation technique, the common-mode voltage is investigated. Accordingly, applying the proposed method in a conventional back-to-back two-level converter results in a substantial reduction of the common-mode voltage as well as the harmonic content of the systems’ input current fed by the power grid. Also, easy implementation regardless of the converter’s rating is the other advantage of using this method. Furthermore, applying this strategy does not add to the converter’s volume, weight, and cost. The appropriate selection of the active vectors, the arrangement of the switching sequences for the inverter and rectifier, as well as the modulation index of the converter are key factors in this technique. The performance of the proposed strategy is investigated through both simulations and experimentations on a back-to-back two-level converter prototype. The experimental results show that the proposed method reduces the common-mode voltage by more than 50%, reaching 87.2% efficiency, making the proposed method suitable for industrial applications.

Migration of repetitive DNAs during evolution of the permanent translocation heterozygosity in the oyster plant (Tradescantia section Rhoeo)

Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture.