Search Results (13)

Extra edge connectivity is an important parameter for measuring the reliability of interconnection networks. Given a graph G and a non-negative integer h, the h-extra edge connectivity of G, denoted by ${\lambda }_h\left(G\right)$, is the minimum cardinality of a set of edges in G (if it exists) whose deletion disconnects G such that each remaining component contains at least $h+1$ vertices. In this paper, we obtain the h-extra edge connectivity of Cayley graphs generated by transposition trees for $h\le 5$. As byproducts, we derive the h-extra edge connectivity of the star graph $S_n$ and the bubble-sort graph $B_n$ for $h\le 5$. Full article

This paper describes the E-Sense Artificial Intelligence system. It comprises a memory model with two levels of information and then a more neural layer above that. The lower memory level stores source data in a Markov (n-gram) structure that is unweighted. Then, a middle ontology level is created from a further three aggregating phases that may be deductive. Each phase re-structures from an ensemble to a tree, where the information transposition is from horizontal set-based sequences into more vertical, typed-based clusters. The base memory is essentially neutral, but bias can be added to any of the levels through associative networks. The success of the ontology typing is open to question, but the results suggested related associations more than direct ones. The third level is more functional, where each function can represent a subset of the base data and learn how to transpose across it. The functional structures are shown to be quite orthogonal, or separate, and are made from nodes with a progressive type of capability, including unordered to ordered. Comparisons with the columnar structure of the neural cortex can be made and the idea of ordinal learning, or just learning relative positions, is introduced. While this is still a work in progress, it offers a different architecture to the current frontier models and is probably one of the most biologically inspired designs. Full article

White spot syndrome virus (WSSV) has emerged as a significant threat to global shrimp aquaculture, causing economic losses because of its rapid spread and high mortality rates. This study aims to elucidate the genetic and evolutionary dynamics of WSSV through a comprehensive genome analysis. Utilizing 27 complete genome sequences sourced from public databases, this study investigates the genetic variability, potential recombination events, and evolutionary patterns of WSSV. Our results identified multiple genomic deletions, 14 novel single-nucleotide polymorphism sites, and variable number tandem repeats across different strains, underscoring the virus’s genetic diversity. A recombination event between freshwater and marine strains highlights a complex transmission pathway, potentially facilitated by aquaculture practices. A phylogenetic tree constructed using ancestral genes suggests that WSSV originated in Southeast Asia and subsequently globally spread, influenced by both natural and anthropogenic factors. Genomic shrinkage of the virus occurred in time series, while the host’s viral infection induced transposon transposition and insertion into the earlier virus genome to provide a basis for genomic shrinkage. Our research emphasizes the importance of advanced molecular characterization and evolutionary models of the virus in understanding the spread of viral pathogens in aquaculture environments. Full article

The thymidylate kinase (tmk) gene is indispensable for the proliferation and survival of phytoplasma. To reveal the molecular variation and phylogeny of the tmk genes of Candidatus phytoplasma ziziphi, in this study, the tmk genes of 50 phytoplasma strains infecting different resistant and susceptible jujube cultivars from different regions in China were amplified and analyzed. Two sequence types, tmk-x and tmk-y, were identified using clone-based sequencing. The JWB phytoplasma strains were classified into three types, type-X, type-Y, and type-XY, based on the sequencing chromatograms of the tmk genes. The type-X and type-Y strains contained only tmk-x and tmk-y genes, respectively. The type-XY strain contained both tmk-x and tmk-y genes. The type-X, type-Y, and type-XY strains comprised 42%, 12%, and 46% of all the strains, respectively. The type-X and type-XY strains were identified in both susceptible and resistant jujube cultivars, while type-Y strain was only identified in susceptible cultivars. Phylogenetic analysis indicated that the tmk genes of the phytoplasmas were divided into two categories: phylo-S and phylo-M. The phylo-S tmk gene was single-copied in the genome, with an evolutionary pattern similar to the 16S rRNA gene; the phylo-M tmk gene was multi-copied, related to PMU-mediated within-genome transposition and between-genome transfer. Furthermore, the phylogenetic tree suggested that the tmk genes shuttled between the genomes of the Paulownia witches’ broom phytoplasma and JWB phytoplasma. These findings provide insights into the evolutionary and adaptive mechanisms of phytoplasmas. Full article

With applications in computer networks, robotics, genetics, data center network optimization, cryptocurrency exchange, transportation and logistics, cloud computing, and social network analysis, the problem of sorting permutations on transposition trees under various operations is highly relevant. The goal of the problem is to sort or rearrange the markers in a predetermined order by swapping them out at the vertices of a tree in the fewest possible swaps. Only certain classes of transposition trees, like path, star, and broom, have computationally efficient algorithms for sorting permutations. In this paper, we examine the so-called $n-broom$ transposition trees. A single broom or simply a $broom$ is a spanning tree formed by joining the center of the star graph with one end of the path graph. A generalized version of a broom known as an $n-broom$ is created by joining the ends of n brooms to one vertex, known as the $n-broom$ center. By using the idea of clear path markers, we present a novel algorithm for sorting permutations on an $n-broom$ for $n>2$ that reduces to a novel $2-broom$ algorithm and that further reduces to two instances of a $1-broom$ algorithm. Our single-broom algorithm is similar to that of Kawahara et al.; however, our proof of optimality for the same is simpler. Full article

Ramshorn snails from the family Planorbidae are important freshwater snails due to their low trophic level, and some of them act as intermediate hosts for zoonotic trematodes. There are about 250 species from 40 genera of Planorbidae, but only 14 species from 5 genera (Anisus, Biomphalaria, Bulinus, Gyraulus, and Planorbella) have sequenced complete mitochondrial genomes (mitogenomes). In this study, we sequenced and assembled a high-quality mitogenome of a ramshorn snail, Polypylis sp. TS-2018, which represented the first mitogenome of the genus. The mitogenome of Polypylis sp. TS-2018 is 13,749 bp in length, which is shorter than that of most gastropods. It contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA). We compared mitogenome characteristics, selection pressure, and gene rearrangement among all of the available mitogenomes of ramshorn snails. We found that the nonsynonymous and synonymous substitution rates (Ka/Ks) of most PCGs indicated purifying and negative selection, except for atp8 of Anisus, Biomphalaria, and Gyraulus, which indicated positive selection. We observed that transpositions and reverse transpositions occurred on 10 tRNAs and rrnS, which resulted in six gene arrangement types. We reconstructed the phylogenetic trees using the sequences of PCGs and rRNAs and strongly supported the monophyly of each genus, as well as three tribes in Planorbidae. Both the gene rearrangement and phylogenetic results suggested that Polypylis had a close relationship with Anisus and Gyraulus, while Bulinus was the sister group to all of the other genera. Our results provide useful data for further investigation of species identification, population genetics, and phylogenetics among ramshorn snails. Full article

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the “poneroid” clade and the “formicoid” clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the “formicoid” clade. Full article

Phytochrome-interacting factors (PIFs) are transcription factors with the basic helix–loop–helix (bHLH) domain. As integration factors between different signal pathways, members of the PIF protein family regulate many aspects of plant growth and development, such as seed germination, photomorphogenesis, thermomorphogenesis, rhythm regulation, flowering response, stomatal development, and stress responses. Our previous studies have shown that the BpSPL2 gene may regulate plants’ adventitious root development through PIF genes. Within the Betula platyphylla genome, we identified eight PIF (BpPIFs) genes. We analysed and named them based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that transposition or segmental duplication events played a minor role in the expansion of BpPIFs. The comparative syntenic analysis combined with phylogenetic analysis provided a deep insight into the phylogenetic relationships of BpPIF genes, suggesting that BpPIF proteins are closer to PtPIF than to AtPIF. The analysis of cis-acting elements in promoter regions of BpPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. In addition, we found that these promoters have the transcription factor of B. platyphylla SPL2 (BpSPL2) binding motif GTAC. Expression analysis demonstrated that BpPIF genes, especially BpPIF4, BpPIF9b, and BpPIF10, might be the potential target genes of BpSPL2 in the process of adventitious root formation. Besides providing a comprehensive understanding of the BpPIF family, we propose a hypothetical gene network regulatory model for adventitious root formation. Full article

Pesticides are commonly used to protect plants against various pests and to preserve crops, but their residues can be harmful for human health. They are the third most widely reported hazard category in the European Rapid Alert System for Food and Feed (RASFF). The purpose of the study was to identify the most frequently notified pesticides in the RASFF in 1981–2020, considering: year, notification type, product category, origin country, notifying country, notification basis, distribution status and action taken. The data from the RASFF database was processed using: filtering, transposition, pivot tables and then subjected to cluster analysis: joining (tree clustering) and two-way joining methods. Pesticides were most commonly reported in fruits and vegetables and herbs and spices following border controls and rejections. The products usually came from India or Turkey and were not placed on the market or were not distributed and then destroyed. The effectiveness of the European Union border posts in terms of hazards detection and mutual information is important from the point of view of protecting the internal market and ensuring public health. It is also necessary to increase the awareness of pesticide users through training and the activity of control authorities in the use of pesticides. Full article

Sorting permutations with various operations has applications in genetics and computer interconnection networks where an operation is specified by its generator set. A transposition tree $T=(V,E)$ is a spanning tree over n vertices $v_1,v_2,\dots v_n$. T denotes an operation in which each edge is a generator. A value assigned to a vertex is called a token or a marker. The markers on vertices u and v can be swapped only if the pair $(u,v)\in E$. The initial configuration consists of a bijection from the set of vertices $v_1,v_2,\dots ,v_n$ to the set of markers $(1,2,\cdots ,n-1,n)$. The goal is to sort the initial configuration of T, i.e., an input permutation, by applying the minimum number of swaps or moves in T. Computationally tractable optimal algorithms to sort permutations are known only for a few classes of transposition trees. We study a class of transposition trees called a broom and its variation a double broom. A single broom is a tree obtained by joining the centre vertex of a star with one of the two leaf vertices of a path graph. A double broom is an extension of a single broom where the centre vertex of a second star is connected to the terminal vertex of the path in a single broom. We propose a simple and efficient algorithm to obtain an optimal swap sequence to sort permutations with the transposition tree broom and a novel optimal algorithm to sort permutations with a double broom. We also introduce a new class of trees named millipede tree and prove that $D^{*}$ yields a tighter upper bound for sorting permutations with a balanced millipede tree compared to $D^{\prime }$. Algorithms $D^{*}$ and $D^{\prime }$ are designed previously. Full article

A connected graph $\Gamma$ is k-extendable for a positive integer k if every matching M of size k can be extended to a perfect matching. The extendability number of $\Gamma$ is the maximum k such that $\Gamma$ is k-extendable. In this paper, we prove that Cayley graphs generated by transposition trees on $\{1,2,\dots ,n\}$ are $(n-2)$-extendable and determine that the extendability number is $n-2$ for an integer $n\ge 3$. Full article

In this work, a strategy for scheduling a battery energy storage system (BESS) in a renewable energy community (REC) is proposed. RECs have been defined at EU level by the 2018/2001 Directive; some Member States transposition into national legislation defined RECs as virtual microgrids since they still use the existing low voltage local feeder and share the same low-medium voltage transformer. This work analyzes a REC which assets include PV generators, BESS and non-controllable loads, operating under the Italian legislative framework. A methodology is defined to optimize REC economic revenues and minimize the operation costs during the year. The proposed BESS control strategy is composed by three different modules: (i) a machine learning-based forecast algorithm that provides a 1-day-ahead projection for microgrid loads and PV generation, using historical dataset and weather forecasts; (ii) a mixed integer linear programming (MILP) algorithm that optimizes the BESS scheduling for minimal REC operating costs, taking into account electricity price, variable feed-in tariffs for PV generators, BESS costs and maximization of the self-consumption; (iii) a decision tree algorithm that works at the intra-hour level, with 1 min timestep and with real load and PV generation measurements adjusting the BESS scheduling in real time. Validation of the proposed strategy is performed on data acquired from a real small-scale REC set up with an Italian energy provider. A 10% average revenue increase could be obtained for the prosumer alone when compared to the non-optimized BESS usage scenario; such revenue increase is obtained by reducing the BESS usage by around 30% when compared to the unmanaged baseline scenario. Full article

Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs. Full article