Sequence Elements Research Articles

Graphical edge-weight-function indices of trees

<p>Consider a tree graph $ G $ with edge set $ E(G) $. The notation $ d_G(x) $ represents the degree of vertex $ x $ in $ G $. Let $ \mathfrak{f} $ be a symmetric real-valued function defined on the Cartesian square of the set of all distinct elements of the degree sequence of $ G $. A graphical edge-weight-function index for the graph $ G $, denoted by $ \mathcal{I}_\mathfrak{f}(G) $, is defined as $ \mathcal{I}_\mathfrak{f}(G) = \sum_{st \in E(G)} \mathfrak{f}(d_G(s), d_G(t)) $. This paper establishes the best possible bounds for $ \mathcal{I}_\mathfrak{f}(G) $ in terms of the order of $ G $ and parameter $ \mathfrak{p} $, subject to specific conditions on $ \mathfrak{f} $. Here, $ \mathfrak{p} $ can be one of the following three graph parameters: (ⅰ) matching number, (ⅱ) the count of pendent vertices, and (ⅲ) maximum degree. We also characterize all tree graphs that achieve these bounds. The constraints considered for $ \mathfrak{f} $ are satisfied by several well-known indices. We specifically illustrate our findings by applying them to the recently introduced Euler-Sombor index.</p>

Exploring the Function of Gene Promoter Regulatory Elements Using CRISPR Tools.

Gene promoters serve as pivotal regulators of transcription, orchestrating the initiation, rate, and specificity of gene expression, resulting in cellular diversity found among distinct cell types within multicellular organisms. Identification of the sequence and function of promoters' regulatory elements and their complex interaction with transcription factors, enhancers, silencers, and insulators is fundamental to coordinated transcriptional processes within cells. Identifying these regulatory elements and scrutinizing their functions and interactions through the use of synthetic promoters can pave the way for researchers in various fields ranging from uncovering the origins of diseases associated with promoter mutations to harnessing these regulatory components in biotechnological applications.In this chapter, we describe the manipulation of regulatory elements within promoters, with a specific focus on the use of CRISPR technology on enhancers and silencer elements of the Ovalbumin gene promoter. We explain and discuss processes for the deletion of/interference with regulatory elements within the promoter, employing CRISPR-based approaches. Furthermore, we demonstrate that a CRISPR/Cas-manipulated promoter can activate gene transcription in cell types where it is normally inactive. This confirms that CRISPR technology can be effectively used to engineer synthetic promoters with desired characteristics, such as inducibility, tissue-specificity, or enhanced transcriptional strength. Such an approach provides valuable insights into the mechanisms and dynamics of gene expression, thereby offering new opportunities in the fields of biotechnology and medicine.

ON STYLISTIC DIFFERENTIATION IN UKRAINIAN POETIC SPEECH BASED ON THE SYNTACTIC STRUCTURE OF SENTENCES

Background. The article is devoted to the stylistic differentiation of syntactic structures of Ukrainian-language poetic texts of the Ukrainian language corpus. The goal is to study the idiostyle on models of syntactic structures, graphically presented in the form of dependency trees, with the establishment of parameters for characterizing the author's style. The properties of the linear structure of 7,752 Ukrainian-language sentences in the verse style were studied. An "averaged" dependency graph was built for each author as a generalization of the syntactic parameters of dependency trees. Methods. Applied methods of structural linguistics included quantitative methods and modeling methods, distributive analysis, direct component method, method of constructing dependency trees (DT) and direct components in linguistic analysis modules: automatic morphological (distributive) and automatic syntactic (direct component and dependency tree method). Results. As a result of the study, it was established that the architecture of the phrase is important, that is, a scheme in the form of a graph that reflects the real sequence of syntactic elements of the statement. If the author has developed his individual writing style, this will inevitably affect the originality of the graphic drawings for the structures of his typical phrases. It is in syntactic stylistics that dependence graphs as a research method will find an unlimited field of application. Eight graph parameters are proposed, the choice of which is determined by the fact that they have stylistic distinguishing power. Conclusions. To justify the applied method of statistical analysis, it can be said that in stylistics each analysis gives only what it can give; the overall research picture consists of a comprehensive review of the results of all analyses. Qualitative methods can describe what is perceived from the text through its symbolic character, but only quantitative methods can explain why the text is constructed in the way it is. Qualitative characteristics consist of precisely those quantitative characteristics that cannot be seen by the average reader, and their detection is the task of science.

Whatever You Bestow on Him, You Will Bestow on Me: Key Motifs of Early Byzantine Letters of Recommendation

The letter of recommendation was known in Antiquity as a separate genre of letter writing for which a certain set of compositional techniques and formulae were developed. In Byzantium, too, the letter of recommendation was in great demand: letters in which the author presents his protégé to the addressee and, as a rule, asks him to perform something for him are not difficult to find in the epistolary collections of many authors from the 4th to the 15th century. Meanwhile, while the ancient letter of recommendation is well studied, the etiquette of this genre in the Byzantine tradition has hardly been investigated yet. The purpose of this piece is to characterize the etiquette norms of Greek letter of recommendation in the early Byzantine period (4th — early 7th centuries). The subject of the study are, first of all, literarische Privatbriefe, belonging to Libanius, Basil the Great, Gregory of Nazianzus, John Chrysostom, Synesius of Cyrene, Theodoret of Cyrrhus, Procopius of Gaza and others, but also private papyrus letters. Their analysis leads to the conclusion that there is a wide variability of the canons of the letter of recommendation, the absence of any rigid scheme that presupposes a clear sequence of structural elements. At the same time, it reveals six recurrent etiquette motifs, all of which are subordinated to a single goal — to persuade the addressee to patronize the recommended person. These motifs are analyzed in detail, and stable formulas are indicated for some of them. An attempt is made to determine to what extent the canons of Greek letters of recommendation of the 4th–7th centuries go back to the ancient tradition. The letters of recommendation of Cicero and Pliny the Younger, as well as letters preserved on late antique papyri, are used as material for comparative analysis.

A case of primary ciliary dyskinesis with DRC1 deletion and literature review: Additional evidence on the founder effect.

Primary ciliary dyskinesia (PCD) is a rare genetic disease caused by defects in various genes affecting ciliary function. It is currently unclear why DRC1 gene variants are a relatively frequent cause of disease in Japanese and Korean patients. A 12-year-old Japanese girl with bronchiectasis was suspected of PCD and examined using whole-exome sequencing (WES). The breakpoint region was confirmed by Sanger sequencing and evaluation of transposable elements. Whole-exome sequencing revealed a deletion of DRC1 exons 1-4 in the patient, followed by validation with Sanger sequencing. A DRC1 exon 1-4 deletion is recurrently observed in Japanese and Korean patients with PCD. All reported patients carry the same breakpoint region, which shows signs of Alu-mediated recombination. Intriguingly, common haplotypes were observed around the DRC1 gene in Japanese and Korean patients. The recurrent DRC1 exon 1-4 deletion is therefore likely to be a founder variant and should be considered a major genetic cause of PCD in Japanese and Korean patients with PCD.

An Analysis of the Application of Motion Capture Technology in the Creation of Contemporary Dance with the Integration of Fibonacci Sequences

Abstract This paper combines the existing development of Fibonacci sequence aesthetics in art creation for the aesthetic planning of the Fibonacci sequence on music rhythm, proposes to design a new modern dance creation method by combining the diversified rotation methods of the Fibonacci sequence, and builds a process framework for generating Fibonacci sequence dance score based on motion capture. The wavelet transform is employed to determine the start of the dance movement, and the gradient descent algorithm is utilized to analyze the time coordinates and refine the dance movement. Recognize the segmented elemental action sequences using the DTW method, propose three basic actions from the dataset, and test the recognition rate of the DTW algorithm for each action. Generate a Fibonacci sequence dance score by combining human gestures. Combined with the research scoring, analyze the artistic talent of the Fibonacci sequence-generated dance. According to the data results, it can be seen that the action feature vector of the two-handed waving image is P=[0.8968, 0.9925, 0.9124, 1.0243, 1.0198, 1.2438, 1.4596, 1.3698, 1.5868, 1.6596, 1.5029] with 98.67% of the two-handed waving recognition rate (with a standard deviation of 0.25). The evaluation of Fibonacci sequence generation dance by research users tends to be moderate.

Predição da capacidade última de elementos em concreto armado usando metodologias de análises não linear

Abstract This work aims to investigate the ultimate capacity of reinforced concrete elements in terms of cracking and stiffness loss. Nonlinear finite element analysis (NLFEA) was performed in the ATENA software and compared with a proposed numerical simulation of nonlinear static analysis (NLSA), where material cracking is evaluated based on the loss of tangent stiffness of the elements. The analysis was applied to a low-rise reinforced concrete frame with constant axial loads in the columns, and monotonic lateral load applied at the top beam level. Both methodologies showed good agreement regarding the capacity curve and crack patterns, and the numerical simulation NLSA allowed the identification of the sequence of elements' stiffness loss. The results indicated a substantial similarity between the numerical simulation NLFEA and NLSA and the experimental test, indicating a high potential in predicting the nonlinear behavior of reinforced concrete.

Prediction of mitochondrial targeting signals and their cleavage sites.

In this chapter we survey prediction tools and computational methods for the prediction of amino acid sequence elements which target proteins to the mitochondria. We will primarily focus on the prediction of N-terminal mitochondrial targeting signals (MTSs) and their N-terminal cleavage sites by mitochondrial peptidases. We first give practical details useful for using and installing some prediction tools. Then we describe procedures for preparing datasets of MTS containing proteins for statistical analysis or development of new prediction methods. Following that we lightly survey some of the computational techniques used by prediction tools. Finally, after discussing some caveats regarding the reliability of such methods to predict the effects of mutations on MTS function; we close with a discussion of possible future directions of computer prediction methods related to mitochondrial proteins.

Molecular characteristics and pathogenic mechanisms of KPC-3 producing hypervirulent carbapenem-resistant Klebsiella pneumoniae (ST23-K1).

This study aimed to comprehensively investigate hypervirulent carbapenem-resistant Klebsiella pneumoniae (CR-hvKP) in the Ningbo region. Importantly, we sought to elucidate its molecular characteristics and pathogenic mechanisms. This information will provide evidence-based insights for preventing and controlling nosocomial infections and facilitate improved clinical diagnosis and treatment in this region. 96 carbapenem-resistant Klebsiella pneumoniae strains were collected from the Ningbo region between January 2021 and December 2022. Whole genome sequencing and bioinformatic methods were employed to identify and characterize CR-hvKP strains at the molecular level. The minimum inhibitory concentrations (MICs) of common clinical antibiotics were determined using the VITEK-2 Compact automatic microbiological analyzer. Plasmid conjugation experiments evaluated the transferability of resistance plasmids. Finally, mouse virulence assays were conducted to explore the pathogenic mechanisms. Among the 96 strains, a single CR-hvKP strain, designated CR-hvKP57, was identified, with an isolation frequency of 1.04%. Whole-genome sequencing revealed the strain to be ST23 serotype with a K1 capsule. This strain harbored three plasmids. Plasmid 1, a pLVPK-like virulence plasmid, carried multiple virulence genes, including rmpA, rmpA2, iroB, iucA, and terB. Plasmid 2 contained transposable element sequences such as IS15 and IS26. Plasmid 3, classified as a resistance plasmid, harbored the bla KPC-3 carbapenem resistance gene. Mouse virulence assays demonstrated a high mortality rate associated with CR-hvKP57 infection. Additionally, there was a significant increase in IL-1β, IL-6, and TNF-α levels in response to CR-hvKP57 infection, indicating varying degrees of inflammatory response. Western blot experiments further suggested that the pathogenic mechanism involves activation of the NF-κB signaling pathway. This study confirms the emergence of hypervirulent CR-hvKP in the Ningbo region, which likely resulted from the acquisition of a pLVPK-like virulence plasmid and a bla KPC-3 resistance plasmid by the ST23-K1 type Klebsiella pneumoniae. Our findings highlight the urgent need for more judicious use of antibiotics to limit the emergence of resistance. Additionally, strengthening infection prevention and control measures is crucial to minimize the spread of virulence and resistance plasmids.

CONCEPTUAL PREMISES FOR SKETCHING A RATIONALE FOR THE INSTITUTION OF PRESCRIPTION

The author observes that the concerns of substantiating the institution of prescription belong to the theory of civil law and that the presentations of the civil model are made separately for the two forms of prescription (extinctive and acquisitive). This, in a context where criminal jurisprudence faces one of the most intense debates on how to apply the criminal rules regarding the prescription of criminal liability, a debate which, however, omits the idea of substantiating the institution. The thesis is updated according to which time - movement in sequence of events, external and unavoidable natural element of subjective rights - is presented as a modality of obligations, a concept that can be used both in the scope of civil and criminal norms. Time with the stated legal meaning can be accepted as the basis of prescription. The model offers a consistent methodological potential for the hypotheses in which the legal norm - whatever its origin - finds its meaning with difficulty. Hence the consequence: the subjective rights - interests with high legal protection of the subjects in the relationship - placed in time, can be understood in a unitary way and applied to all branches of law.

Analisis Deret Vokal Dalam Cerpen “Cerita Si Kancil Dan Buaya”

This study discusses the vocal series as a sequence of elements in a series of sounds. This abstract reviews the concept of vocal series from a theoretical and practical point of view, focusing on the analysis of vocal series in the short story "the story of the mouse deer and the crocodile". This study aims to investigate the properties of vocal series and their potential in providing new insights related to understanding and application of vocal series in sound processing technology. explore the use of vowel series in language and understand their role in creating nuance in stories. Qualitative analysis methods are used to explore the meaning contained in vowel series, explain the relationship between vowel use and characters, and identify linguistic patterns that enrich the narrative. The findings from this study may provide additional insight into the use of language in short stories and the contribution of vocal series to the formation of the story's atmosphere.

Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.

Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3' end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA polymerase II at the end of a gene, and faster cleavage leads to quicker degradation of downstream readthrough RNA. Our findings shed light on the features important for efficient 3' end cleavage and the regulation of transcription termination.

A fundamental sequences method with time-reduction for one-dimensional lateral Cauchy problems

A fundamental sequences method is derived for the numerical solution of an ill-posed one-dimensional lateral Cauchy problem for a hyperbolic damped wave equation, including as a special case the parabolic heat equation. Either the Laguerre transform or the Houbolt finite difference scheme is applied to reduce the time-dependent lateral Cauchy problem to a sequence of second-order ordinary differential equations (ODEs) with function values and derivatives specified at the right endpoint of a finite space interval. A set of fundamental solutions is constructed, termed a fundamental sequence, to the differential equations. The solution of the obtained ODEs is approximated by a linear combination of elements in the fundamental sequence. Source points are placed outside of the solution interval in space, and by collocating at the endpoints of this interval a sequence of linear equations is obtained for finding the unknown coeficients. Tikhonov regularization is used to render a stable solution to the obtained systems of linear equations. Numerical results both for the parabolic and hyperbolic case confirm the efficiency of the proposed method including noisy data. The presented results complement the higher-dimensional case initiated in our previous researches.

Novel chaotic image cryptosystem using dynamic DNA coding

This study aims to solve the problem of small key space in image cryptosystems based on logistic mapping. First, a new one-dimensional (1D) chaotic system, with a wide continuous chaotic interval, a large Lyapunov exponent and obvious chaotic characteristics are presented. Subsequently, a novel image encryption algorithm based on the new 1D chaotic system and dynamic DNA encoding is designed. Compared with other DNA coding methods, the proposed image encryption algorithm encodes chaotic sequences and ensures that the sequence elements at different positions correspond to different DNA coding schemes. This will help to overcome the fixity of DNA coding and make the proposed dynamic DNA coding easy to operate and implement. Finally, the cipher image is obtained by scrambling and bit XOR operation based on the chaotic sequences. The fixed DNA coding method is compared with other chaotic image encryption schemes, and the experimental results indicate that the image encryption algorithm has higher security and can resist common attacks.

Towards utility-driven contiguous sequential patterns in uncertain multi-sequences

In data mining, high-utility sequential pattern mining (HUSPM) focuses more on the specific values of items than on their frequency, making it more practical in real-life scenarios. HUSPM with the contiguous constraint can be used to solve some applications requiring the sequence elements to occur consecutively. Due to device, environment, privacy issues, and other factors, the data is often not accurate, and traditional algorithms for mining high-utility continuous sequence patterns (HUCSPs) do not perform well in handling uncertain data. To address this challenge, this paper presents a new algorithm named uncertain utility-driven contiguous pattern mining (UUCPM), which is able to discover HUCSPs in the uncertain database efficiently and correctly. The algorithm is designed to obtain results from sequence data with uncertain probability set on the item or itemset level. Two tighter upper bounds on utility and corresponding pruning strategies are also proposed, which can effectively process and reduce the number of candidate patterns generated during pattern mining, thereby improving the performance of the mining process. The proposed UUCPM algorithm has been verified for accuracy and performance through extensive experiments, demonstrating its advanced properties. The source code and datasets are available at GitHub https://github.com/DSI-Lab1/UUCPM.

Study on the evolution law and stage response relationship between meteorological elements and hydrological drought in Xiangtan area

Studying the propagation law and response relationship between meteorological elements and hydrological drought is conducive to exploring the propagation mechanism and transmission time of drought, and providing a basis for reasonable and efficient drought relief work. In this paper, the area above Xiangtan station is taken as the research area, and the temperature and precipitation are selected as the meteorological elements. The standardized flow index (SDI) is used to characterize the hydrological drought. The linear regression method and Mann-Kendall trend test are used to analyze the evolution sequence of meteorological elements and hydrological drought at different scales. The characteristics and laws of drought propagation are revealed, and the hydrological drought is divided into stages by combining the ordered cluster analysis method and the sliding t-test method. The Pearson correlation analysis method is used to analyze the stage correlation degree between meteorological elements and hydrological drought, reflecting the response relationship between meteorological elements and hydrological drought under different types and different scales, and the response period of hydrological drought to meteorological elements at different time scales is obtained. Studying the development trend and evolution law of meteorological elements and hydrological drought, and deeply exploring the phased response relationship are conducive to improving the drought resistance ability and drought disaster reduction management ability of Xiangtan area.

Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits.

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.

Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics.

Extreme environments provide unique challenges for life, and the study of extremophiles can shed light on the mechanisms of adaptation to such conditions. Pyrococcus furiosus, a hyperthermophilic archaeon, is a model organism for studying thermal stress response mechanisms. In this study, we used an integrated analysis of RNA-sequencing and mass spectrometry data to investigate the transcriptomic and proteomic responses of P. furiosus to heat and cold shock stress and recovery. Our results reveal the rapid and dynamic changes in gene and protein expression patterns associated with these stress responses, as well as the coordinated regulation of different gene sets in response to different stressors. These findings provide valuable insights into the molecular adaptations that facilitate life in extreme environments and advance our understanding of stress response mechanisms in hyperthermophilic archaea.

Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer

Genomic hypomethylation has recently been identified as a determinant of therapeutic responses to immune checkpoint blockade (ICB). However, it remains unclear whether this approach can be applied to cell-free DNA (cfDNA) and whether it can address the issue of low tumor purity encountered in tissue-based methylation profiling. In this study, we developed an assay named iMethyl, designed to estimate the genomic hypomethylation status from cfDNA. This was achieved through deep targeted sequencing of young LINE-1 elements with > 400,000 reads per sample. iMethyl was applied to a total of 653 ICB samples encompassing lung cancer (cfDNA n = 167; tissue n = 137; cfDNA early during treatment n = 40), breast cancer (cfDNA n = 91; tissue n = 50; PBMC n = 50; cfDNA at progression n = 44), and ovarian cancer (tissue n = 74). iMethyl-liquid predicted ICB responses accurately regardless of the tumor purity of tissue samples. iMethyl-liquid was also able to monitor therapeutic responses early during treatment (3 or 6 weeks after initiation of ICB) and detect progressive hypomethylation accompanying tumor progression. iMethyl-tissue had better predictive power than tumor mutation burden and PD-L1 expression. In conclusion, our iMethyl-liquid method allows for reliable noninvasive prediction, early evaluation, and monitoring of clinical responses to ICB therapy.

The bacterial replication origin BUS promotes nucleobase capture

Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaAATP assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).