Sequence Arrangement Research Articles

General metaheuristic-based methodology for computation and decomposition of LMPs

Locational marginal prices (LMPs) are economic signals paramount to the deliberations, policy designs, and planning judgments of most electricity markets. This paper presents a general metaheuristic-based methodology applied in the scope of two subproblems to compute and decompose the LMPs considering the incorporation of a distributed slack bus model in the power flow formulation. The deterministic core of the methodology is governed by a process of sequential setting of maximum number of metaheuristic iterations based on load disharmony indices (LDIs) in the context of the initial subproblem. The metaheuristic crux of the methodology is anchored in a random initialization strategy based on time-traveling parameters in the environment of both subproblems. In the introductory arrangement of the optimization sequence, the chain order of the operating horizon periods is defined based on the LDIs. Due to its notorious merits and the breadth of its applications in power system problems, a particle swarm optimization (PSO) algorithm model is used to solve the mentioned subproblems. For the practical purposes of this paper, in the PSO algorithm model instance the particle coordinates are adopted as time-traveling metaheuristic parameters. Numerical simulations on a 3-bus system and on the IEEE 30-bus test system corroborate the efficiency and adequacy of the proposed methodology.

Analysis of a plasmid encoding botulinum neurotoxin type G gene in Clostridium argentinense

Clostridium argentinense produces botulinum neurotoxin type G (BoNT/G). We sequenced and analyzed the plasmid harboring the bont/G gene, designated pCAG, in C. argentinense strain 2740. The pCAG consisted of 140,070 bp containing the bont/G gene cluster. Although this gene cluster showed high similarities in its DNA sequence and ORF arrangement to those of other bont gene clusters, the other regions of the plasmid did not. A phylogenetic study suggested that pCAG had a unique evolutionary history compared with other clostridial bont-harboring plasmids. This suggests that pCAG is possibly a novel type of plasmid expressing the bont/G gene in C. argentinense.

Generalized Space-Vector-Modulation Method for Soft-Switching Three-Phase Inverters

Three-phase inverters are usually required to output reactive power in electric machine drives, renewable energy generation, static var generators, and other power electronic systems. Therefore, the inverter may operate within wide power factor angle range. However, the traditional zero-voltage-switching space vector modulation (ZVS-SVM) method for three-phase inverters is only applicable when power factor angle is between -π/6 and +π/6. In this article, a general ZVS-SVM method for three-phase inverter with arbitrary output is proposed. The principles for vector selection and vector sequence arrangement are discussed in detail. With only one switching operation of the auxiliary switch in each switching cycle, ZVS of all switches can be achieved. Operation stage analyses and ZVS condition of the inverter with the proposed method are introduced. In addition, the resonant parameters design considerations and loss analyses are investigated. Finally, the proposed ZVS-SVM method is verified by the experiment.

Fast and Flexible Protein Design Using Deep Graph Neural Networks.

Protein structure and function is determined by the arrangement of the linear sequence of amino acids in 3D space. We show that a deep graph neural network, ProteinSolver, can precisely design sequences that fold into a predetermined shape by phrasing this challenge as a constraint satisfaction problem (CSP), akin to Sudoku puzzles. We trained ProteinSolver on over 70,000,000 real protein sequences corresponding to over 80,000 structures. We show that our method rapidly designs new protein sequences and benchmark them in silico using energy-based scores, molecular dynamics, and structure prediction methods. As a proof-of-principle validation, we use ProteinSolver to generate sequences that match the structure of serum albumin, then synthesize the top-scoring design and validate it invitro using circular dichroism. ProteinSolver is freely available at http://design.proteinsolver.org and https://gitlab.com/ostrokach/proteinsolver. A record of this paper's transparent peer review process is included in the Supplemental Information.

THE EXTENT OF INCLUSION OF KNOWLEDGE ECONOMY'S CONCEPTS AND SKILLS IN THE EDUCATIONAL POLICY DOCUMENTS IN THE SULTANATE OF OMAN

The study aimed to identify the extent to which the contents of the general educational policy documents in the Sultanate of Oman contain the concepts and skills of the knowledge economy, as the concepts were divided into the four knowledge economy indicators, which are: First: the information and communication technology system (ICT), second: the research, development and innovation system, and third: the institutional system For countries, and fourth: the system of research, development and innovation, While the skills consisted of five general skills, namely: basic knowledge skills, digital skills, knowledge production skills, professional and life skills, followed by a set of basic and then sub-skills. The results showed that the highest percentage of inclusion was for the concepts of the fourth Indicator (The Education and Training System) in the National Education 2040 Strategy, and that the lowest percentage of inclusion was for the concepts of the first indicator: the information and communication technology system. The results also indicated that the concepts of the fourth Indicator: The Education and Training System are the concepts most included in all general educational policy documents and that the concepts of the first indicator: the information and communication technology system are the concepts that are the least included in all these documents. In addition, the results indicated that the highest coverage rate was for basic knowledge skills in the educational evaluation document for the social studies curriculum, and that the lowest coverage rate was for digital skills in the educational philosophy document, and the results indicated that basic knowledge skills are the highest inclusion among all skills and digital skills are considered the least inclusion among all knowledge economy skills. The study recommended the necessity of a kind of sequence and logical arrangement in including knowledge economy skills in these documents according to their importance and their inclusion from the general to the specific. Furthermore, there is a need for updating inclusion of these concepts and skills constantly in line with the developments and changes of the age and undertaking more renewed and continuous research. Article visualizations:

Pedestrian Walkways for Health in Shiraz, Iran, the Contribution of Attitudes, and Perceived Environmental Attributes

Walking is important for improving physical activity and public health. The pedestrian walkways called Walkways for Health in Shiraz, Iran, present a high standard of aesthetic and design features which attract many people for the purpose of recreation. In addition, a significant percentage of Iranians suffer from mental disorders. The contribution of aesthetic and design features toward walking for recreation as well as mental health has been demonstrated in previous studies, which have focused on either one or the other of these aspects. This interdisciplinary research study aims to evaluate both of these aspects simultaneously. A quantitative approach including a survey questionnaire and multiple regression analysis was used to examine the objectives. The contributions of walking attitudes and several perceived environmental attributes to the attractiveness for walking and to general/mental health were determined, which suggested the need for new arrangements of the visual sequences and social setting along these walkways. In addition, the observation that younger people suffer are more affected by mental health disorders was one of the most challenging findings. The policy makers of this city could apply the findings of this study to these pedestrian walkways in order to improve the attractiveness for walking as well as general and mental health.

Integration of ion-tuned oligonucleotide structural motifs and DNA-templated copper nanoclusters as a manipulable logic device

Molecular logic gates possess great potential for multi-parameter sensing, intelligent diagnostics, and molecular computation. One remaining challenge was to construct novel new logic gates based on smart nanomaterials and functional nucleic acids. In this study, two novel new logic devices were constructed utilizing ion-tuned DNA/copper nanoclusters (CuNCs), which were dual-responsive to K+ and H+. By merely altering the arrangement of a specific sequence of the DNA stabilizer, two kinds of well-designed DNA probes permuted by G-tracts, C-tracts, and poly-T were designed as the building blocks of the logic device. Poly-T acted as the template for the formation of CuNCs. G-tracts and C-tracts enabled a K+/H+-responsive conformational switch into G-quadruplex (G4) and i-motif structures. Such a conformational conversion significantly modulated the fluorescence behaviors of CuNCs. This study discovered the unique interaction between the logic device and graphene oxide (GO). The logic devices were implemented for the analysis of K+ and microRNA.

Identification, molecular characterization, expression analysis and wound-healing ability of multifunctional calreticulin from big-belly seahorse Hippocampus abdominalis

Calreticulin (CRT) is a multifunctional ubiquitous protein that is widely presented in all cells in eukaryotes except erythrocytes. CRT is well known for diverse cellular functions such as endoplasmic reticulum (ER)-specialized protein quality control during protein synthesis and folding, in-vivo Ca2+ homeostasis, antigen presentation, phagocytosis, wound-healing, proliferation, adhesion, and migration of cells. In the current study, we identified CRT from Hippocampus abdominalis (HaCRT) and analyzed expression profiles and functional properties. The cDNA sequence of HaCRT was identified with an open reading frame of 1226 bp. The molecular weight of HaCRT was estimated as 49 kDa. The in-silico study revealed conserved sequence arrangements such as two CRT signature motifs (5′-KHEQSIDCGGGYVKVF-3′ and 5′-LMFGPDICG-3′), triplicate repeats (5′-IKDPEAKKPEDWD-3′, 5′-IPDPDDTKPEDWD-3′, 5′-IPDPDAKKPDDWD-3′), signal peptide and an ER-targeting 5′-KDEL-3′ sequence of HaCRT. Close sequence similarity of HaCRT was observed with Hippocampus comes from phylogenetic analysis and pairwise sequence comparison. From quantitative polymerase chain reaction (qPCR) results, HaCRT was ubiquitously distributed in all tested tissues and expression levels of HaCRT were significantly modulated in blood, liver and gill tissues after stimulation with Streptococcus iniae, Edwardsiella tarda, polyinosinic:polycytidylic acid, and lipopolysaccharides. Bacterial- and pathogen-associated molecular patterns-binding activities were observed with recombinant HaCRT (rHaCRT). The treatment of murine macrophages with rHaCRT induced the expression of immune genes, such as tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6), inducible nitric oxide synthase (iNOS), and interleukin-1β (IL-1β). Furthermore, rHaCRT exhibited wound-healing ability. Based on the results from the above study, we suggest that HaCRT play an indispensable role in the immunity of big-belly seahorses by recognition and elimination of pathogens as well as the tissue repairing process.

Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays.

In eukaryotes, transcription factors (TFs) orchestrate gene expression by binding to TF-binding sites (TFBSs) and localizing transcriptional co-regulators and RNA polymerase II to cis-regulatory elements. However, we lack a basic understanding of the relationship between TFBS composition and their quantitative transcriptional responses. Here, we measured expression driven by 17,406 synthetic cis-regulatory elements with varied compositions of a model TFBS, the c-AMP response element (CRE) by using massively parallel reporter assays (MPRAs). We find CRE number, affinity, and promoter proximity largely determines expression. In addition, we observe expression modulation based on the spacing between CREs and CRE distance to the promoter, where expression follows a helical periodicity. Finally, we compare library expression between an episomal MPRA and a genomically integrated MPRA, where a single cis-regulatory element is assayed per cell at a defined locus. These assays largely recapitulate each other, although weaker, non-canonical CREs exhibit greater activity in a genomic context.

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies.

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

Change in Cropping Pattern In Nalanda District

Cropping pattern is a dynamic concept because it changes over space and time. The adoption of crops in any area can be understood by the physical characteristics and the socio-economic conditions of the people in the concerned area. Cropping pattern can be defined as the proportion of area under various crops at a point of time. In other words, it is a yearly sequence and spatil arrangement of sowing and fallow on a given area. In India, the cropping is determined by rainfall, climate, temperature, soil type and technology and so does in Nalanda District of Bihar.

An Enhanced Adaptive Perturb and Observe Technique for Efficient Maximum Power Point Tracking Under Partial Shading Conditions

In this paper, we propose enhanced adaptive step size Perturb and Observe (P&O) maximum power point tracking (MPPT) with properly organized comparison sequences which lead to achieving the actual maximum power point (MPP) effectively in the presence of partial shading conditions, taking into account the optimization of all aspects of high-performance MPPT to be novel, simpler, fast, and accurate, with the best efficiency reaching up to almost 100%. In this study, the proposed algorithm, along with a boost converter, was designed and simulated in MATLAB/Simulink to validate the performance of the suggested technique. Four different levels of partial shading conditions were considered for system examination: weak, moderate, and two different levels of strong shading. Each case was applied separately first and then combined in a sequence arrangement to provide robust and comprehensive testing which can provide a guaranteed assessment of the proposed algorithm. The performance of the suggested technique is discussed and compared with that of conventional P&O and conventional incremental conductance (IC) MPPT techniques. The failure of the conventional techniques to work efficiently in the presence of partial shading conditions was observed from the simulation results. Meanwhile, the success of the proposed technique and its high performance were clearly confirmed under partial shading conditions with no increase in complexity or convergence time.

Chain-End Modifications and Sequence Arrangements of Antimicrobial Peptoids for Mediating Activity and Nano-Assembly.

Poly(N-substituted glycine) “peptoids” are an interesting class of peptidomimics that can resist proteolysis and mimic naturally found antimicrobial peptides (AMPs), which exhibit wide spectrum activity against bacteria. This work investigates the possibility of modifying peptoid AMP mimics (AMPMs) with aliphatic lipid “tails” to generate “lipopeptoids” that can assemble into micellar nanostructures, and evaluates their antimicrobial activities. Two families of AMPMs with different distributions of hydrophobic and cationic residues were employed—one with a uniform repeating amphiphilicity, the other with a surfactant-like head-to-tail amphiphilicity. To further evaluate the interplay between self-assembly and activity, the lipopeptoids were variously modified at the AMPM chain ends with a diethylene glycol (EG2) and/or a cationic group (Nlys-Nlys dipeptoid) to adjust amphiphilicity and chain flexibility. Self-assembly was investigated by critical aggregation concentration (CAC) fluorescence assays and dynamic light scattering (DLS). The structure of a key species was also verified by small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM). To screen for antibacterial properties, we measured the minimum inhibitory concentrations (MIC) against S. aureus, E. coli, and P. aeruginosa. We found that certain combinations of lipid tail and AMPM sequences exhibit increased antibacterial activity (i.e., decreased MICs). Perhaps counter-intuitively, we were particularly interested in increased MICs in combination with low CACs. Concealing antimicrobial interactions due to packing of AMPMs in nano-assemblies could pave the way to AMPMs that may be “inert” even if unintentionally released and prevent microbes from gaining resistance to the lipopeptoids. Overall, incorporation of EG2 significantly improved lipopeptoids packing while the hydrophobic tail length was found to have a major influence over the MIC. One particular sequence, which we named C15-EG2-(kss)4, exhibited a very low CAC of 34 μM (0.0075 wt.%) and a significantly increased MIC above values for the unmodified AMPM. With the sequence design trends uncovered from this study, future work will focus on discovering more species such as C15-EG2-(kss)4 and on investigating release mechanisms and the potency of the released lipopeptoids.

Optimization on the melting performance of triplex-layer PCMs in a horizontal finned shell and tube thermal energy storage unit

This paper numerically investigates the melting performance of triplex-layer phase change materials (PCMs) in a horizontal shell and tube latent thermal energy storage (LTES) unit. The paraffin wax with different melting temperatures (i.e., RT42, RT50, and RT60) are selected as PCMs. To accelerate the heat transfer, metal fins are adopted in the unit. Considering the heat transfer enhancement and thermal energy storage capacity loss by metal fins, a comprehensive storage density evaluation (CSDE) criterion was innovatively proposed to assess the melting performance of the LTES unit with triplex-layer PCMs. Based on CSDE, the effects of partition walls and fin arrangements were firstly discussed in a transient two-dimensional model. It was found that the natural convection of liquid PCMs was significantly suppressed by partition walls. Compared with Case 1 (no fins), gradual fin additions in triplex-layer PCMs significantly saved the melting time by 55.3% (Case 2), 66.1% (Case 3), and 71.0% (Case 4). The uniform radial fin arrangement in each PCM layers (Case 4) presents the maximum value of CSDE. Subsequently, the uniformity of PCM melting rates was optimized by different arrangements of metal fins, PCM sequences and space ratios, respectively. Finally, the optimum case was achieved and the value of CSDE further increased 36.2% with the comparison of Case 4. The criterion of CSDE can be used to optimize the design of the horizontal shell and tube LTES unit with metal fins for heat transfer enhancement, and provides a guidance for the further experimental study.

The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri.

Gene copy number variation is a predominant mechanism used by organisms to respond to selective pressures from the environment. This often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity in Amaranthus palmeri: a massive, ∼400-kb extrachromosomal circular DNA (eccDNA) that harbors the 5-ENOYLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) gene and 58 other genes whose encoded functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of these 59 genes, with high expression of EPSPS, as well as genes coding for aminotransferases, zinc finger proteins, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is composed of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and waterhemp (Amaranthus tuberculatus) suggests that higher order chromatin interactions contribute to the genomic origins of the A. palmeri eccDNA replicon structure.

Production of an antibody Fab fragment using 2A peptide in insect cells

Antibody Fab fragments consist of heavy chain (Hc) and light chain (Lc) polypeptides assembled with a disulphide bond. The production of a recombinant Fab fragment requires the simultaneous expression of two genes encoding both an Hc and an Lc in the same host cell. In the present study, we investigated the production of Fab fragments in lepidopteran insect cells using a bicistronic plasmid vector carrying the Hc and Lc genes linked with a 2A self-cleaving peptide sequence from the porcine teschovirus-1. We also examined the arrangement of a GSG spacer sequence and a furin cleavage site sequence with the 2A sequence. Western blot analysis and enzyme-linked immunosorbent assay (ELISA) of culture supernatants showed that Trichoplusia ni BTI-TN-5B1-4 (High Five) cells transfected with a plasmid in which the Hc and Lc genes were joined by the 2A sequence successfully secreted Fab fragments with antigen-binding activity after self-cleavage of the 2A peptide. The GSG linker enhanced 2A cleavage efficiency, and the furin recognition site was useful for removal of 2A residues from the Hc. Transfection with a single plasmid that contained sequences for GSG, the furin cleavage site, GSG, and the 2A peptide between the Hc and Lc genes exhibited a higher productivity than co-transfection with a set of plasmids separately carrying the Hc or Lc gene. These results demonstrate that bicistronic expression with the appropriate combination of a furin recognition site, GSG linkers, and a 2A peptide may be an effective way to efficiently produce recombinant antibody molecules in insect cells.

The complete mitochondrial genome and phylogenetic analysis of Phaneroptera falcata (Orthoptera: Tettigoniidae)

In the present study, we determined the complete mitochondrial genome sequence of Phaneroptera falcata by next-generation sequencing. The complete mitogenome of P. falcata is 15,672 bp in length, and has the typical gene arrangement of the ancestral sequence. The P. falcata mitogenome contained 37% A, 17.6% C, 10.7% G, and 34.7% T bases, with an AT bias of 71.8%, and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop. We constructed Bayesian inference tree using mitogenomes of 49 species from Tettigoniidae including P. falcata, and the results of this study provided basis for the study of the phylogenetic evolution of the genus Phaneroptera.

Simulation and characterization of circular hexagonal braiding fabricstructure

Hexagonal braiding technology is a kind of state-of-the-art braiding method, which uses hexagonal horngears to driveyarn carriers and make yarns intertwined into fabrics. In terms of hexagonal braiding principles, the braiding parameterslike initial arrangement of yarn carriers, yarn number and horngears sequence were defined, and then the movementpaths of yarn carriers in hexagonal braiding process and stitch length were obtained, which could be converted intocoordinates on the xoy plane and the coordinates along z-axis. In that case, a group of spatial coordinates were got tocreate the yarn trajectories and fabric structures in Matlab. And then, B-spline curve was utilized to fit the yarntrajectories. Considering the compactness of hexagonal fabric, the coordinates conversion algorithm and conversionmatrix were utilized to optimize the fabric structure, so a more compact fabric structure was established. The braidingangle variation and volume fraction of fabric showed that after coordinates conversion the braiding angles became morestable than original fabric model, and the fiber volume fraction of fabric was improved too. So the fabric structure modelwas available to describe hexagonal fabric structure, which can offer the reference for the further study on properties ofhexagonal braiding technology and application of hexagonal braided fabric

Проблематизация информации как важнейшего понятия современности

The notion of information tends to become blurred within the contemporary discourse not only due to its polysemy, but due to its paradoxical nature. Analysing the generally accepted definitions of “information” and relying on examples from the spheres of scientific cognition and personal choice, the author identifies essential features of information: finite sequence (arrangement) of elements within the given environment, systematicity, necessary existence of information receiver, level of logical (not ethical) choice. Originality of the study includes developing an onto-gnoseological approach to information, which is considered not just as a philosophical category but as a modern world vision.

DNA Sequence-Directed Cooperation between Nucleoid-Associated Proteins

Nucleoid associated proteins (NAPs) are a class of highly abundant DNA binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilising higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding-site arrangements. We find that spatial organisation of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction, as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome.