Recognizing the need to enhance immune cells' ability to target and eliminate tumor cells by focusing on tumor-associated antigens is crucial for the success of immunotherapy. Numerous cell-based therapies, such as CAR-T cell therapy, tumor-infiltrating lymphocyte (TIL) therapy, CAR-NK cell therapy, and T-cell receptor (TCR)-based therapies, are currently undergoing clinical and pre-clinical evaluation across various cancer types. However, a significant challenge lies in managing the inflammatory responses that are harmful to cancer patients. To overcome this, developing advanced strategies to target tumor cells precisely while preserving immune balance in cancer patients is imperative. One promising approach involves using modified tumor-associated macrophages (TAMs), which constitute approximately 50% of the tumor microenvironment (TME) and play a pivotal role in tumor progression. CAR-Macrophage (CAR-M) therapy is an emerging potential asset of immunotherapy for a wide range of tumors.

Against the background of the sky, imaging and perception of aircraft are cru- cial. Among these, the location of aircrafts is not a very difficult problem in general, because that deep learning algorithms and object detection models based on convolutional neural network(CNN) are ever-evolving. In order to have a better identification of various aircrafts, or to accurately locate different types of flying targets in the sky, it becomes significant to distinguish and recognize different types of aircrafts. One question is that, distinguishing and recognizing between sub-categories of aircrafts pose great challenges. Although fine-grained recognition focuses on exploring and studying such problems, aircrafts under different sub-categories and granularities lead us to rethink the application of features. We noticed that features in swin-transformer demonstrates the under- standing and processing of images, fully showcasing the encoding and indexing of information. Through this research and proposed approach, we discovered a better understanding of features encoding and use, which are inspired by the feature encoding and computation in swin-transformer. In our paper, our ap- proach has achieved effects on features encoded graphically, manifested from the architecture design and convolutional neural network computation, and outper- forms other famous fine-graiend classification models on this issue. Not only approach we proposed has demonstrated superior performance in fine-grained aicraft classification, but also the mechanisms of the feature encoding under different sample space partitions is revealed for this issue, which provides a re- search for the representation of aircraft fineness characteristics. The relationship between representation orientation of aircraft feature information under various grained divisions, shows that the recognition of different categories according to man-made, such as aircraft, can be achieved by means of the feature represen- tations studied in this paper, for more specific defined classification tasks and various man-made targets partition criteria, which may influences the princi- ple of design for calculation and feature extraction in fine-grained classification models.

Previous studies demonstrate the critical importance of non-coding RNAs interfacing with chromatin-modifying machinery resulting in promoter-enhancer-based gene regulation and raise the possibility that many other enhancer-like RNAs may operate via similar mechanisms. Critically, more than 80% of the disease-linked variations identified in genome-wide studies are located in the non-coding regions of genomes, especially non-coding RNA, suggesting non-coding RNAs are relevant to disease. Thus, a critical path forward for understanding non-coding RNAs' role, especially long non-coding RNAs, is to understand the genomic regions' transcriptional regulation, especially non-coding regions. Here, we developed a user-friendly R package called SomaGene for studying and identifying enhancer-like non-coding RNAs with enriched somatic mutations in the cancer genome. SomaGene accepts different genomic variants (whole genome/exome somatic point mutations, structural variations, copy number variations) to identify those RNAs that significantly mutated in diseases (e.g., cancer). It then uses multiple publicly available genomics and epigenetics datasets including ENCODE epigenomics annotations, FANTOM5 tissue-specific expression profiles, disease-associated genome-wide association SNPs, and tissue-specific eQTL pairs to identify those RNAs with potentially enhancer function. SomaGene, as a powerful R package, can provide the opportunity to cancer scientists to study the roles of non-coding RNAs in different cancer genomes.

Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder characterized by cognitive decline and neuronal loss, representing a most challenging health issue. We present a computational analysis of transcriptomic data of AD tissues vs. healthy controls, focused on elucidation of functional roles played by long non-coding RNAs (lncRNAs) throughout the AD progression. We first assembled our own lncRNA transcripts from the raw RNA-Seq data generated from 527 samples of dorsolateral prefrontal cortex, resulting in the identification of 31,574 novel lncRNA genes. Based on co-expression analyses between mRNAs and lncRNAs, a co-expression network is constructed. Maximal subnetworks with dense connections are identified as functional clusters. Pathway enrichment analyses are conducted over mRNAs and lncRNAs in each cluster, which serve as the basis for the inference of functional roles played by lncRNAs involved in each of the key steps in an AD development model that we have previously build based on transcriptomic data of protein-encoding genes. Detailed information is presented about the functional roles by lncRNAs in activities related to stress response, reprogrammed metabolism, cell-polarity, and development. Our analyses have also revealed that lncRNAs have discerning power in distinguishing between AD samples of each stage and healthy controls. This study represents the first of its kind.

A great deal of studies have assessed the expression of noncoding RNAs (ncRNAs) as well as their relevant molecular functions and biological mechanisms in the individuals of alcohol dependence. Alcohol dependence is one of the most prevalent neuropsychological disorders worldwide, and its pathogenesis is intricate and inadequately understood. There is considerable evidence demonstrating substantial links between multiple genetic factors and the development of alcohol dependence. Critical roles of ncRNAs have been emphasized in the pathophysiology of mental diseases including alcohol dependence. In the comprehension of ncRNAs action and their mechanisms of modification, they have emerged as therapeutic targets for a variety of psychiatric illness including alcohol dependence. Worth mentioning, dysregulated expression of ncRNAs has been regularly detected in individuals of alcohol dependence. An in-depth knowledge of roles of ncRNAs and m6A modification may be valuable for the development of a novel treatment against alcohol dependence. In general, a deeper comprehension of functional roles ncRNAs may make significant contributions to the precise diagnosis and/or actual treatment of alcohol dependence. Here in this review, we mostly focused on the up-to-date knowledge regarding alterations and/or modifications in the expression of ncRNAs in alcohol dependence, and then, presented their prospects for future research and therapeutic application with a novel concept of engram-system.

It has been shown that Human papillomavirus (HPV) infection is associated with several forms of cancer. Additionally, although there are more than 100 types of HPV, more than ten types of it, including types 16 and 18, are considered high-risk. The two proteins that make up the viral capsid of HPV 16 are L1, the major capsid protein, and L2, the minor capsid protein. FDA (The Food and Drug Administration) approved HPV vaccines mostly target L1 and L2 capsid proteins, which facilitate intracellular entry during infection. In this study, it was set out to analyze the creation of phylogenetic relations of L1 nucleic acid sequences of viral isolates. This study also analyzed sequences of three key elements within the amino acid sequences of HPV 16 L1: loops critical for structural stability, nuclear localization signal sequences, and residues implicated in viral attachment. As highlighted by the literature, these elements represent pivotal aspects of viral function. Furthermore, the report highlighted the particular inter-sequence variability within the HPV 16 L1 protein sequences. Overall analysis revealed clustering of sequences primarily due to geographical and characterized by more phylogenetic relatedness within location-specific clusters.

Alignment of picornavirus proteinase/polymerase sequences reveals this family evolved into five ‘supergroups’. Interestingly, the nature of the 2A region of the picornavirus polyprotein is highly correlated with this phylogeny. Viruses within supergroup 4, the Paavivirinae, have complex 2A regions with many viruses encoding multiple 2A^NPGP sequences. In vitro transcription/translation analyses of a synthetic polyprotein comprising green fluorescent protein (GFP) linked to b-glucuronidase (GUS) via individual 2A^NPGPs showed two main phenotypes: highly active 2A^NPGP sequences - similar to Foot-and-Mouth Disease Virus 2A^NPGP and, surprisingly, a novel phenotype of some 2A^NPGP sequences which apparently terminate translation at the C-terminus of 2A^NPGP - without detectable re-initiation of downstream sequences (GUS). Probing databases with the short sequences between 2A^NPGPs did not reveal any potential ‘accessory’ functions. The novel, highly active, 2A-like sequences we identified substantially expands the toolbox for biomedical / biotechnological co-expression applications.

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell Acute Lymphoblastic Leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

This study investigates the possibility of using machine learning models created in DeepLabCut and Create ML to automate aspects of behavioral coding and aid in behavioral analysis. Two models with different capabilities and complexities were constructed and compared to a manually observed control period. The accuracy of the models was assessed before being applied to 7 nights of footage of the nocturnal behavior of two African elephants (Loxodonta africana). The resulting data was used to draw conclusions regarding behavioral differences between the two elephants and between individually observed nights, thus proving that such models can aid researchers in be-havioral analysis. The models were capable of tracking simple behaviors with high accuracy, but had certain limitations regarding detection of complex behaviors, such as the stereotyped behavior sway, and displayed confusion when deciding between visually similar behaviors. Further expansion of such models may be desired to create a more capable aid with the possibility of automating behavioral coding.

Relationships between the Farey sequence and the Riemann hypothesis other than the Franel-Landau theorem are discussed. Whether a function similar to Chebyshev’s second function is square-root close to a line having a slope different from 1 is discussed. The nontrivial zeros of the Riemann zeta function can be used to approximate many functions in analytic number theory. For example, it could be said that the nontrival zeta function zeros and the Möbius function generate in essence the same function - the Mertens function. A different approach is to start with a sequence that is analogous to the nontrivial zeros of the zeta function and follow the same procedure with both this sequence and the nontrivial zeros of the zeta function to generate in essence the same function. A procedure for generating such a function is given.

In Southeast Asia, the incidence of Leukemia, a malignant blood cancer originating from hema-topoietic progenitor cells, is on the rise, marked by a concerning 54% mortality rate. This study focuses on enhancing early-stage prediction to improve patient recovery prospects significantly. Leveraging Machine Learning and Data Science, we employ protein sequential data from frequently mutated genes such as BCL2, HSP90, PARP, and RB to predict Chronic Myeloid Leukemia (CML). Our approach relies on robust feature extraction techniques, namely Di-peptide Composition (DPC), Amino Acid Composition (AAC), and Pseudo amino acid composition (Pse-AAC), with prior attention to addressing outliers and validating feature selection through the Pearson Corre-lation Coefficient. Data augmentation ensures a well-rounded dataset for analysis. Employing a range of Machine Learning models, including Support Vector Machine (SVM), XGBoost, Random Forest (RF), K Nearest Neighbor (KNN), Decision Tree (DT), and Logistic Regression (LR), we achieve accuracy rates spanning from 66% to 94%. These classifiers undergo comprehensive as-sessment using performance metrics such as accuracy, sensitivity, specificity, F1-score, and the confusion matrix. Our proposed solution, encompassing a user-friendly web application dashboard, presents an invaluable tool for early CML diagnosis with profound implications for practitioners, offering a deploy-able asset within healthcare institutions and hospitals.

The aim of this study was to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in the endometrium of individuals with and without EMS during the proliferative (P) and secretory (S) phases of the menstrual cycle. Tissues were obtained from 18 control (CT; P-phase [pCT], n=8; S-phase [sCT], n=13) and 23 EMS patients (P-phase [pEMS], n=13; S-phase [sEMS], n=12). DElncRNAs and DEmRNAs were analyzed using total RNA-sequencing. In P-phase, expression of NONHSAG019742.2 and NONHSAT120701.2 was significantly higher in EMS than control patients, that of while NONHSAG048398.2 and NONHSAG016560.2 was lower in EMS patients. In S-phase, expression of NONHSAT000959.2, NONHSAT203423.1, and NONHSAG053769.2 was significantly increased in EMS patients, while that of NONHSAG012105.2 and NONHSAG020839.2 was lower. In addition, the expression of HSD11B2, THBS1, GPX3, and SHISA6 was similar to that of neighboring lncRNAs in both P- and S-phases. In contrast, ELP3 and NR4A1, respectively, were up- or downregulated in pEMS tissues. In sEMS, expression of LAMB3 and HIF1A was increased, while expression of PAM was reduced. Our findings on lncRNAs and mRNAs encourage not only to explore the potential clinical applications of lncRNAs and mRNAs as prognostic or diagnostic biomarkers for EMS but also to gain valuable insights into its pathogenesis.

End-to-end learned image compression codecs have notably emerged in recent years. These codecs have demonstrated superiority over conventional methods, showcasing remarkable flexibility and adaptability across diverse data domains while supporting new distortion losses. Despite challenges such as computational complexity, learned image compression methods inherently align with learning-based data processing and analytic pipelines due to their well-suited internal representations. The concept of Video Coding for Machines has garnered significant attention from both academic researchers and industry practitioners. This concept reflects the growing need to integrate data compression with computer vision applications. In light of these developments, we present a comprehensive survey and review of lossy image compression methods. Additionally, we provide a concise overview of two prominent international standards, MPEG Video Coding for Machines and JPEG AI. These standards are designed to bridge the gap between data compression and computer vision, catering to practical industry use cases.

The paper presents attribute based characterization of nanomaterials method for computer storage and retrieval as knowledgebase. The knowledgebase permits indepth understanding and comparison between nanomaterials available with the scientists and product developers to satisfy their research and development (R & D) needs. Techniques for order preference by similarity to ideal solution (TOPSIS) is proposed to evaluate nanomaterials in the presence of multiple attributes. The method normalizes attributes to nullify the effect of different units and their values in the range of 0 to 1. The relative importance of different attributes for different applications is considered. The weight vector is derived using Eigen value formulation. The positive and negative benchmark solutions are derived. Euclidean distance of alternatives from these best and worst solution leads to the development of proximity /goodness/suitability index for ranking. Final decision is taken by decision makers by SWOT analysis and short and long term strategies of the organisation. The methodology is illustrated with the help of an example and step-by-step procedure. Results, discussion and conclusion highlights the importance and practical application.

Information molecules of DNA and RNA should obey principles of quantum mechanics where unitary operators in form of unitary matrices have key meanings. Unitary matrices are the basis of calculations in quantum computers. This article presents some author's results, which show that matrix forms of the representation of structured systems of molecular-genetic alphabets can be considered as sets of sparse unitary matrices related with phenomenologic features of the degeneracy of the genetic code. These sparse unitary matrices have orthogonal systems of functions in their rows and columns. A complementarity exists among some unitary genetic matrices in relation each other. Decompositions of numeric genetic matrices into sets of sparse unitary matrices are connected with the logical operation of modulo-2 addition used in quantum computers as well. Tensor (or Kronecker) families of unitary genetic matrices with their fractal-like properties are also considered. The described results are discussed in the frame of development of quantum-information approaches for modeling genetic systems.

Genes encoding regulatory RNAs known as short RNAs (sRNAs) or non-coding sRNAs (ncRNAs), modulate physiological responses through different mechanisms, through RNA-RNA interaction or RNA-protein interaction. These molecules transcribed in trans and in cis relative to the target RNA. They are located between the coding regions of proteins, i.e., in the intergenic regions of the genome and show signals of promoters and termini sequences generally Rho-independent. The size of the ncRNAs genes ranges from ~ 50 to ~ 500 nucleotides and several transcripts are processed by RNase with smaller end products, which modulate physiological responses through different mechanisms, by RNA-RNA interaction or RNA-protein interactions and some interactions may be stabilized by the Hfq chaperone. The Riboswitches constitute another class of ncRNAs, located in the 5'UTR region of an mRNA that promote transcriptional regulation through their interaction with a linker molecule. Recently, in prokaryotes, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regions have described, which repeats of sequences of palindromic bases are. Each replicate consists of short segments of "spacer DNA" from exposures prior to a bacteriophage virus or exogenous plasmid. The CRISPR system consists of an immune system of resistance to exogenous molecules.

The generation of arithmetic sequences involves arithmetic operations. However, is it possible to generate such sequences without being subject to any arithmetic or related operations, all by just hand? The answer may be negative, as the very rule defining these sequences itself relies on arithmetic operations. Nonetheless, this paper presents a few results demonstrating that the exact sequences of $an$, where, $a \in \{ 2,3,\cdots,9,10\}$ and $n \in \mathbb N \cup \{0\}$, can indeed be generated up to any desired number of terms without relying on any arithmetic operations and others derived from such. This is done by the formation of a specialized table that leverages numerical patterns and the notion of concatenation.

In this paper, we define Tetranacci and Tetranacci-Lucas matrix sequences and investigate their properties.

This study aims at highlighting and illustrating innovative actions for achieving and/or improving accurate medical coding within a DRG system. Already grouped DRG cases recorded in the first DRG implementation year in the region of Crete were examined. A sample of 130,000, from a total of 200,000, cases were analyzed and audited, through a process consisting of three stages: i) Digitalization, ii) Auditor training, and iii) Control & consultation. The results indicated that a significant proportion of DRG coding, with a length of stay exceeding one day, were reclassified into different DRG categories. This was not primarily due to errors in the selection of the principal diagnosis, but resulted from coding errors, including omission of secondary diagnoses coding, medical procedures that should have been included and utilization of less specific codes. The findings indicate that medical coding control, consulting services and the adoption of targeted actions can be instrumental for proper implementation of the DRG coding system, and for ensuring transparent allocation of resources within hospitals. Ultimately, this shortens the coding learning curve, from four years typically reported in the international literature, to a more efficient duration of two years, leading to rational and documented clinical and financial management of hospitals.

Digital gait monitoring is increasingly used to assess locomotion and fall risk. The aim of this work is analyzing the changes in the foot-floor contact sequences of Parkinson’s Disease (PD) patients in the year following the implant for deep brain stimulation (DBS). During their best-ON condition, 30 PD patients underwent gait analysis at baseline (T0), at 3 months (T1), and 12 months (T2) after the DBS neurosurgery for bilateral high-frequency subthalamic nucleus stimulation. Thirty age-matched controls underwent gait analysis once. Each subject was equipped with bilateral foot-switches and a 5-minute walk was recorded, including both straight-line and turnings. The walking speed, turning time, stride time variability, percentage of atypical gait cycles, stance, swing, and double support duration were estimated. Overall, the gait performance of PD patients improved after DBS, as also confirmed by the decrease in the UPDRS-III score from 19.4±1.8 to 10.2±1.0 points (T0 vs. T2) (p < 0.001). In particular, the percentage change of atypical gait cycles of PD more affected side decreased at T1 (Straigh-line: -72%; Turnings: -43%) and at T2 (Straigh-line: -54%; Turnings: -20%). The percentage of atypical gait cycles proved an informative digital biomarker for quantifying PD gait changes after DBS, both in straight-line paths and turnings.

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark Prionace glauca from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high confidence lncRNAs were identified with 8,984 and 3,067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations.

Recombinant laboratory plasmids (RLPs) are common in biological research and freely shared among academic research laboratories (ARLs), a practice required by many research funding agencies. However, the generation of accurate, reproducible results in experiments utilizing RLPs can be hampered by a lack of accompanying sequence information and metadata. This culture of RLP sharing without knowledge of sequence or etiology is accepted by publishers, not regulated by governments, and outside the realm of bio-industry. In addition, no centralized infrastructure currently exists to collate such data, which at the moment is fragmented across companies, non-profits, and governments and thus is not easily accessed or enacted toward threat assessment. The ubiquity, free exchange, and dual-use risk of RLPs exemplifies a biosecurity threat and elevates the need to characterize their composition to facilitate improved biorisk management by the academic community. A number of common sense solutions are available to create a culture that addresses the biosecurity gap posed by RLP sharing. Culture shift in RLP management will require new norms, effective data management for collation of RLP sequences and metadata, and an incentive structure that encourages sequencing by stakeholders. The next generation of researchers must initiate and champion this shift with support from funding agencies and endorsement from governments and international organizations. Coordination of efforts and stakeholders will require international public/private collaboration, a structure that will be critical to ensure widespread utility as well as the ability of lower-resourced partners to participate, contribute, and benefit.

In this letter, we advocate that it is possible to mitigate Pilot Contamination in Massive MIMO systems by scrambling the pilot sequences with a Base Station (BS) scrambling sequence. It is possible if a set of sequences is carefully designed to meet the orthogonality property defined in this letter. Each BS possesses its own scrambling sequence that can be reused the same way frequency reuse is applied to cell deployment. The main advantage of the prosed pilot generation scheme is that the frequency reuse factor can be set to 1, the most aggressive one, while the scrambling sequences can be reused with much less aggressive reuse factors (e.g. 4, 7, 9, 12, etc.), which in consequence results in pilot contamination mitigation and increased system's performance.

We obtain two generalizations of a known theorem of A. Alam and M. Imdad (Fixed Point Theory Appl. 17 (2015) 693–702) showing that some standard proofs can be obtained involving only Cauchy sequences of the successive approximations instead of the usual successive approximations sequences. Suitable examples prove the effective generalization of our results in metric spaces not necessarily complete.

Let an odd integer \(\mathcal{X}\) be expressed as $\left\{\sum\limits_{M > m} b_M 2^M\right\} + 2^m - 1,$ where $b_M \in \{0, 1\}$ and $2^m - 1$ is referred to as the Governor. In Collatz-type functions, a high index Governor is eventually reduced to $2^1 - 1$. For the $3\mathcal{Z} + 1$ sequence, the Governor occurring in the Trivial cycle is $2^1 - 1$, while for the $5\mathcal{Z} + 1$ sequence, the Trivial Governors are $2^2 - 1$ and $2^1 - 1$. Therefore, in these specific sequences, the Collatz function reduces the Governor $2^m - 1$ to the Trivial Governor $2^{\mathcal{T}} - 1$. Once this Trivial Governor is reached, it can evolve to a higher index Governor through interactions with other terms. This feature allows $\mathcal{X}$ to reappear in a Collatz-type sequence, since $2^m - 1 = 2^{m - 1} + \cdots + 2^{\mathcal{T} + 1} + 2^{\mathcal{T}} + (2^{\mathcal{T}} - 1).$ Thus, if $\mathcal{X}$ reappears, at least one odd ancestor of $\left\{\sum\limits_{M > m} b_M 2^M\right\} + 2^{m - 1} + \cdots + 2^{\mathcal{T} + 1} + 2^{\mathcal{T}} + (2^{\mathcal{T}} - 1)$ must have the Governor $2^m - 1$. Ancestor mapping shows that all odd ancestors of $\mathcal{X}$ have the Trivial Governor for the respective Collatz sequence. This implies that odd integers that repeat in the $3\mathcal{Z} + 1$ sequence have the Governor $2^1 - 1$, while those forming a repeating cycle in the $5\mathcal{Z} + 1$ sequence have either $2^2 - 1$ or $2^1 - 1$ as the Governor. Successor mapping for the $3\mathcal{Z} + 1$ sequence further indicates that there are no auxiliary cycles, as the Trivial Governor is always transformed into a different index Governor. Similarly, successor mapping for the $5\mathcal{Z} + 1$ sequence reveals that the smallest odd integers forming an auxiliary cycle are smaller than $2^5$. Finally, attempts to identify integers that diverge for the $3\mathcal{Z} + 1$ sequence suggest that no such integers exist.

Let $S=\left(s_1, \ldots, s_n\right)$ be a finite sequence of integers. Then $S$ is a Gilbreath sequence of length $n$, $S\in\mathbb{G}_n$, iff $s_1$ is even or odd and $s_2, \ldots, s_n$ are respectively odd or even and $\min\mathbb{K}_{\left(s_1, \ldots, s_m\right)}\leq s_{m+1}\leq\max\mathbb{K}_{\left(s_1, \ldots, s_m\right)}\forall m\in\left[\left.1, n\right)\right.$. This, applied to the order sequence of prime number $P$, defines Gilbreath polynomials and two integer sequences A347924 \cite{oeisA347924} and A347925 \cite{oeisA347925} which are used to prove that Gilbreath conjecture $GC$ is implied by $p_n-2^{n-1}\leqslant\mathcal{P}_{n-1}\left(1\right)$ where $\mathcal{P}_{n-1}\left(1\right)$ is the $n-1$-th Gilbreath polynomial at 1.

Early diagnosis of paroxysmal atrial fibrillation (PAF) could suggest patients to receive timely interventions in clinical practice. Various PAF onset prediction algorithms might benefit from accurate heart rate variability (HRV) analysis and machine learning classification but to be challenged in real-time monitoring scenarios. The aim of this study is to present an end-to-end deep learning based PAFNet model that integrates a sliding window technique on raw R-R interval of electrocardiogram (ECG) segments to achieve a real-time prediction of PAF onsets. This integration enable the deep convolutional neural network (CNN) to be customized as a light-weight architecture that accommodates the size of sliding windows simply by altering the input layer, specifically its effectiveness in making a new prediction with each new heartbeat. Catering to potential influence of input sizes, three CNN models were trained using 50, 100, and 200 R-R intervals, respectively. For each model, the performance of automated algorithms was evaluated for PAF prediction using a ten-fold cross-validation. As a results, a total of 56,381 PAFN-type and 56,900 N-type R-R interval segments was collected from publicly accessible ECG databases, and a promising prediction performance of the automated algorithm with a 100 R-R intervals was achieved in terms of the sensitivity of 97.12%, the specificity of 97.77%, and the accuracy of 97.45%, respectively. Importantly, the automated algorithm with a sliding windows step of 1 could process one sample in only 23.1 milliseconds and identify the onset of PAF at least 45 minutes in advance. The present results suggest that the sliding window technique on raw R-R interval sequences along by deep learning based algorithms may offers the possibility of providing an accurate, real-time, and end-to-end clinical tool for mass monitoring of PAF.

Hypoxia contributes to tumor progression and metastasis, and hypoxically dysregulated RNA molecules may thus be implicated in poor outcomes. Canine oral melanoma (COM) has a par-ticularly poor prognosis, and some hypoxia-mediated miRNAs are known to exist in this cancer; however, equivalent data on hypoxically dysregulated other non-coding RNAs (ncRNAs) are lacking. Accordingly, we aimed to elucidate non-miRNA ncRNAs that may be mediated by hy-poxia, targeting primary-site and metastatic COM cell lines and clinical COM tissue samples in next generation sequencing (NGS), with subsequent qPCR validation and quantification in COM primary and metastatic cells, plasma and extracellular vesicles (EVs) for any identified ncRNA of interest. Findings suggested that a number of non-miRNA ncRNA species are hypoxically up- or downregulated in COM. We identified one ncRNA, the long ncRNA fragment EN-SCAFT00000084705.1, as a molecule of interest due to its consistent downregulation in COM tissues, hypoxically and normoxically cultured primary and metastatic cell lines, when compared to the oral tissues from healthy dogs. However, this molecule was undetectable in plasma and plasma EVs, suggesting that its expression may be tumor tissue-specific and it has little potential as a biomarker. Here, we provide evidence of hypoxic transcriptional dysregulation for ncRNAs other than miRNA in COM for the first time, and suggest that ncRNA ENSCAFT00000084705.1 is a molecule of interest for future research on the role of the transcriptome in hypoxia-mediated progression of this aggressive cancer.

This study aims at providing a climatological analysis of annual and long-term variability of dry periods in the Polish Carpathians in the period of 35 years between 1986 and 2020. Aside days with precipitation, dry periods, namely sequences of days with no precipitation, constitute an inherent characteristic of the climate. The input data for the research was formed by daily precipitation totals from 17 meteorological stations acquired from the Institute of Meteorology and Water Management - National Research Institute, and T. Niedźwiedź catalogue of circulation types over southern Poland. Frequency of dry periods of different duration has been presented. The incidence of long-term periods has been related to the atmospheric circulation. An analysis was performed regarding the change of the average quantity and average length of dry sequences in the 35-year period covered. At most stations, there were no statistically significant trends with respect to the analysed dry day characteristics. This is an obvious result of high variability year-to-year, which means that exclusively large changes may achieve statistical significance. Dry days have been evidenced to related to circulation types. A vast majority of dry days is related to anti-cyclonal systems, particularly the anti-cyclonal wedge (Ka) and western anti-cyclonal (Wa) situations.

The early elongation events in transcription or translational control in the N-terminal of genes are assuming critical roles in their heterologous expression. The secretory expression of the alkaline pectin lyase APL in B. subtilis were studied to explore the effects of the N-terminal 5-7 amino acids sequences of different signal peptides on gene transcription and protein secretion in this study. The first 5 amino acid sequences of the N-terminal of the signal peptide LipA were identified to play an important role in promoting the expression of APL for the first time. Meanwhile, it also revealed that the signal peptide LipA could lead to higher secretory expression than other signal peptides not because of its sequence structure associated with secretion is stronger but because the N-terminal sequences showed greater advantages in gene transcription. At this basis, the recombinant strain structed in this work showed a new record for the highest extracellular yields (12 295 U/ml) of APL in B. subtilis which was 1.9 times higher than that expressed in the recombinant Escherichia coli strain we had reported before. The novel theories revealed in this study would assuming significance roles for improving expression of foreign proteins in or out of the cells.

In this paper, it is proved that s-iteration with error and Picard-Mann iteration with error iterative processes converge strongly to the unique fixed point of Lipschitzian strongly pseudo-contractive map. This convergence is almost -stable and -stable. Applications of these results to the operator equations, where is a strongly accretive and accretive mappings of into itself.

B chromosomes are supernumerary chromosomes which are found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several types of repeats. Although the evolution of B chromosomes has been subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences is not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.

Alzheimer´s Disease (AD) has currently no effective treatment; however, preventive measures can significantly delay the progress/onset of the disease. Thus, accurate and early prediction of risk is an important strategy to alleviate the AD burden. Neuroinflammation is a major factor prompting the onset of the disease. Inflammation exerts its toxic effect via multiple mechanisms. Amongst others, it is affecting gene expression via modulation of non-coding RNAs (ncRNAs), such as miRNAs. Recent evidence supports that inflammation can also affect long non-coding RNAs (lncRNAs) expression. While the association between miRNAs and inflammation in AD has been extensively studied, the role of lncRNAs in neurodegenerative diseases has been less explored. In this review, we focus on lncRNAs and inflammation in the context of AD. Furthermore, since plasma-isolated extracellular vesicles (EVs) are increasingly recognized as an effective monitoring strategy of brain pathologies, we have focused on the studies reporting dysregulated lncRNAs in EVs isolated from AD patients and controls. The revised literature shows a positive association between pro-inflammatory lncRNAs and AD. However, the reports evaluating lncRNAs alterations in EVs isolated from plasma of patients and controls, although still limited confirm the value of specific lncRNAs associated with AD as reliable biomarkers. This is an emerging field that will open new avenues to improve risk prediction, patients’ stratification and may lead to the discovery of potential novel therapeutic targets for AD

For decades since the central dogma, cancer biology research has been focusing on the involvement of genes encoding proteins. It has been not until more recent times that a new molecular class has been discovered, named non-coding RNA (ncRNA), which has been shown to play crucial roles in shaping the activity of cells. An extraordinary number of studies into shown that ncRNAs represent an extensive and prevalent group of RNAs, including both oncogenic or tumor suppressive molecules. Henceforth, various clinical trials involving ncRNAs as extra ordinary biomarkers or therapies have started to emerge. In this review, we will focus on the prognostic and diagnostic role of ncRNAs for breast cancer.

Although Shannon mutual information has been widely used, its effective calculation is often difficult for many practical problems, including those in neural population coding. Asymptotic formulas based on Fisher information sometimes provide accurate approximations to the mutual information but this approach is restricted to continuous variables because the calculation of Fisher information requires derivatives with respect to the encoded variables. In this paper, we consider information-theoretic bounds and approximations of the mutual information based on Kullback--Leibler divergence and Rényi divergence. We propose several information metrics to approximate Shannon mutual information in the context of neural population coding. While our asymptotic formulas all work for discrete variables, one of them has consistent performance and high accuracy regardless of whether the encoded variables are discrete or continuous. We performed numerical simulations and confirmed that our approximation formulas were highly accurate for approximating the mutual information between the stimuli and the responses of a large neural population. These approximation formulas may potentially bring convenience to the applications of information theory to many practical and theoretical problems.

The switching game Lights Out and its variants were studied extensively as recreational mathematics problems. The game board of the ordinary Lights Out is a rectangular grid of lights, where each light is either on or off. By clicking a light, the clicked light and its adjacent rectilinear neighbors are toggled. Given an arbitrary initial configuration of lights, the final mission is to “solve” this game by switching off all the lights. Most studies on Lights Out and its variants focused on the solvability of given games or the number of solvable games, but when the game is viewed in a coding-theoretical perspective, more interesting questions with special meanings in coding theory will naturally pop up, such as finding the minimal number of lit lights among all solvable games except the solved game, or finding the minimal number of lit lights that the player can achieve from a given unsolvable game, etc. However, these problems are usually hard to be solved in general in terms of algorithmic complexity. This study considers a natural extension of the Lights Out game, which enlarges the toggle pattern in a way that all the lights in the same row and those in the same column of the clicked light are toggled. This variant of Lights Out is a two-state version of a switching game called Alien Tiles. In this paper, we investigate the properties of the two-state Alien Tiles, and discuss several coding-theoretical problems about this game. Then, we apply this game as an error correction code and investigate its optimality. We also give a brief overview on algorithmic complexity and coding theory for readers who are not familiar with these topics. The purpose of this paper is to propose ways of playing switching games in a think-outside-the-box manner, which benefit the recreational mathematics community.

Network coding approaches typically consider an unrestricted recoding of coded packets in the relay nodes for increased performance. However, this can expose the system to pollution attacks that cannot be detected during transmission, until the receivers attempt to recover the data. To prevent these attacks while allowing for the benefits of coding in mesh networks, the Cache Coding was proposed. This protocol only allows recoding at the relays when the relay has received enough packets to decode an entire generation of packets. At that point, the relay node recodes and signs the recoded packets with its own private key allowing for the system to detect and minimize the effect of pollution attacks and make relays accountable for changes on the data. This paper analyzes the delay performance of Cache Coding to understand the security-performance trade-off of this scheme. We introduce an analytical model for the case of two relays in an erasure channel relying on an Absorbing Markov Chain and a approximate model to estimate the performance in terms of the number of transmissions before successfully decoding at the receiver. We confirm our analysis using simulation results. We show that Cache Coding can overcome security issues of unrestricted recoding with only a moderate decrease in system performance.

Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3’ UTR, 5’ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved, and how sRNAs integrate with complex regulatory networks.

Background and Objectives To compare navigator-gated three-dimensional T1-weighted gradient-echo sequences (NG-3D T1W-GRE) with standard breath-hold T1W-GRE (BH T1W-GRE) for the detection of HCC nodules in patients with chronic viral hepatitis which undergo at magnetic resonance imaging (MRI) using gadoxetic acid. Methods and materials We evaluated 58 patients with hepatic nodules at least 1 cm in diameter detected by ultrasound who underwent liver MRI including NG-3D T1W-GRE sequences and breath hold T1-weighted gradient-echo sequences with different flip angles(FA) at 10-25-40° after contrast administration of gadoxetic acid at magnetic scanner operating at1.5 Tesla. Image quality and relative hepatic and nodular enhancement were evaluated by three blinded reviewers. Results In these patients, image quality of NG-3D T1W-GRE was assessed significantly better than quality of BHT1W- GRE (P < 0.005) and relative enhancement was significantly higher than that of BH- T1W-GRE ( P

Optical motion capture systems are prone to the errors connected with markers recognition – occlusion, leaving the scene or mislabelling – all these errors are then corrected in the software, but still, the process is not perfect, resulting in artifact distortions. In the article, we examine four existing types of artifacts, then propose the method for detection and classification of the distortions. The algorithm is based on the derivative analysis, low-pass filtering, mathematical morphology and loose predictor. The tests involved multiple simulations using synthetically distorted sequences, comparison of performance to the human operators on real life data and applicability analysis for the distortion removal.

Protein molecules show varying degrees of flexibility throughout their three-dimensional structures. This flexibility is associated with the fluctuation of the torsion angle in proteins. The protein backbone can be defined mainly by two torsion angles, phi (φ) and psi (ψ). The fluctuation of torsion angles is derived from different NMR models’ variations in backbone torsion angles. The angle fluctuations in the cartesian coordinate space are used to characterize the protein’s structural flexibility. Fluctuation of torsion angle is useful in predicting protein function and structure when the torsion angles are used as restraints. This study aims to develop a machine learning method to predict torsion angle fluctuations directly from protein sequences. It explores various useful features such as disorder probability, position-specific scoring matrix profiles, secondary structure probabilities, monograms, bigram, position-specific estimated energy, half-sphere exposures, etc. Likewise, it explores well-known machine learning methods and proposes an optimized Light Gradient Boosting Machine Regressor (LightGBM) method, named TAFPred, to predict torsion angle fluctuations with the selected features. The proposed method achieves ten-fold cross-validated correlation coefficients of 0.746 and 0.737 and mean absolute errors of 0.114 and 0.123 for the angle fluctuation of φ and ψ, respectively, and attains an improvement of 10.08% in MAE, 24.83% in PCC in the phi angle, and 9.93% in MAE, 22.37% in PCC in psi angle compared to the state-of-the-art method proposed by Zhang et al.

The purpose of this study is to provide an accurate formula for calculating entropy for short DNA sequences and to demonstrate how to use it to examine leukemia patient surviving. We used IDIBAPS leukemia patient’s data base with 117 anonymized records. The generalized form of the Robust Entropy Estimator (EnRE) for short DNA sequences was proposed and key EnRE futures was showed. The Survival Analysis has been done using statistical package IBM SPSS. Entropy EnRE were calculated for leukemia patients for two samples: A. 2 groups divided by median EnRE and B. 2 groups of patients were formed according to their belonging to 1st and 4th quartiles of EnRE. The result of survival analysis are statistically significant: A. p &lt; 0.05; B. p &lt; 0.005. The death hazard for a patient with EnRE below median is 1.556 times that of a patient with EnRE over median and that the death hazard for a patient of 1st quartile (lowest EnRE) is 2.143 times that of a patient of 4th quartile (highest EnRE). The transition from median to quartile patients’ groups with more EnRE differentiation confirmed the unique significance of the entropy of DNA sequences for leukemia patients surviving.

In this paper, we introduce and study the notion of rough I₂-lacunary statistical convergence of double sequences in normed linear spaces. We also introduce the notion of rough I₂-lacunary statistical limit set of a double sequence and discuss about some properties of this set.

Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia and an increased risk for evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review will present a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS.

Thyroid cancer is the most prevalent malignancy of the endocrine system and the ninth most common cancer globally. Despite the advances in the management of thyroid cancer, there are critical issues with the diagnosis and treatment of thyroid cancer that result in the poor overall survival of undifferentiated and metastatic thyroid cancer patients. Recent studies have revealed the role of different non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) that are dysregulated during thyroid cancer development or the acquisition of resistance to therapeutics, and may play key roles in treatment failure and poor prognosis of the thyroid cancer patients. Here, we systematically review the emerging roles and molecular mechanisms of ncRNAs that regulate thyroid tumorigenesis and drug response. We then propose the potential clinical implications of ncRNAs as novel diagnostic and prognostic biomarkers for thyroid cancer.

RNA polymerase II (RNAPII) frequently transcribes non-protein coding DNA sequences in eukaryotic genomes into long non-coding RNA (lncRNA). Here, we focus on the impact of the act of lncRNA transcription on nearby functional DNA units. Distinct molecular mechanisms linked to the position of lncRNA relative to the coding gene illustrate how non-coding transcription controls gene expression. We review the biological significance of the act of lncRNA transcription on DNA processing, highlighting common themes, such as mediating cellular responses to environmental changes. This review presents the background in chromatin signaling to appreciate examples in different organisms where we can interpret functions of non-coding DNA through the act of RNAPII transcription.

Exponential increase in mobile video delivery will continue with the demand for higher resolution, multi-view and large-scale multicast video services. Novel fifth generation (5G) 3GPP New Radio (NR) standard will bring a number of new opportunities for optimizing video delivery across both 5G core and radio access network. One of the promising approaches for video quality adaptation, throughput enhancement and erasure protection is the use of packet-level random linear network coding (RLNC). In this work, we discuss the integration of RLNC into the 5G NR standard, building upon the ideas and opportunities identified in 4G LTE. We explicitly identify and discuss in detail novel 5G NR features that provide support for RLNC-based video delivery in 5G, thus pointing out to the promising avenues for future research.

With the advancement of next generation sequencing in past several years, a rising number of non-coding RNAs have been found as new actors to regulate gene expression. Non-coding RNAs not only play important roles in carcinogenesis, but also affect the clinical treatment strategies. They have been proved to be deeply correlated with chemoresistance in several cancers. Ovarian cancer is the leading cause of death in gynecological malignancy, with low 5-year survival rate. Most patients are identified when they have late-stage disease. This review mainly makes a compilation of the most relevant research literature in this field with the purpose of shedding light on the relation between ncRNAs and chemoresistance in ovarian cancer.

Abstract: Antimicrobial peptides (AMPs) are short peptides, usually made up of less than 100 amino acid residues. They are found in many living organisms and are an important factor in their innate immune systems. AMPs can be extracted from various living sources including bacteria, plants, animals and even humans. They are usually cationic peptides with an amphiphilic structure, which allows them to easily bind and interact with the cellular membranes of viruses, bacteria, fungi and other pathogens. They can act against both Gram-negative and Gram-positive pathogens and have various modes of action against them. Some attack the pathogens membrane, while others target their intracellular organelles as well as their nucleic acids, proteins and metabolic pathways. A crucial area of use of AMPs is in their ability to help with emerging antibiotic resistance: some AMPs are active against resistant strains and are susceptible to peptide engineering. This review considers AMPs from three key sources: plants, animals and humans, as well as their modes of action and some AMPs sequences.

One of creators of quantum mechanics P. Jordan in his work on quantum biology claimed that life's missing laws were the rules of chance and probability of the quantum world. The article presents author’s results of studying frequencies (or probabilities) of nucleotides on so-called epi-chains of long DNA sequences of various eukaryotic and prokaryotic genomes. DNA epi-chains are algorithmically constructed subsequencies of DNA nucleotide sequences. According to the algorithm of construction of any epi-chain of the order n, the epi-chain is such nucleotide subsequence, in which the numerations of adjacent nucleotides differ by natural number n (n = 1, 2, 3, 4,…). Correspondingly each epi-chain of order n ≥ 2 contains n times less nucleotides than the original DNA sequence. The presented results unexpectedly discover that in long single-stranded and double-stranded DNA of any tested genome its DNA epi-chains of different orders n (values n are not too large) have practically identical frequencies (or probabilities) of each kind of nucleotides. These data allow considering DNA as a regular rich set of epi-chains, which can play a certain role in genetic and epigenetic phenomena as the author belives. Appropriate rules of nucleotide frequencies on epi-chains of long DNA sequences are formulated for further their tests on a wider set of genomes. These results testify on existence of long-range coherence in long DNA and remind the Fröhlich's theory of long-range coherence in biological systems. The phenomenological data are discussed from different standpoints: the DNA double helices and helical antennas with circular polarizations of electromagnetic waves; relations with the Fröhlich's theory; numerical analysis of DNA epi-chains under binary representations of nucleotides. Results are useful for developing quantum and algebraic biology.

Water is essential to all life-forms including various ecological, geological, hydrological, and climatic processes/activities. With changing climate, associated El Nino/Southern Oscillation (ENSO) events appear to stimulate highly uncertain patterns of precipitation (P) and evapotranspiration (EV) processes across the globe. Changes in P and EV patterns are highly sensitive to temperature variation and thus also affecting natural streamflow processes. This paper presents a novel suite of stochastic modelling approaches for associating streamflow sequences with climatic trends. The present work is built upon a stochastic modelling framework HMM_GP that integrates a Hidden Markov Model with a Generalised Pareto distribution for simulating synthetic flow sequences. The GP distribution within HMM_GP model is aimed to improve the model's efficiency in effectively simulating extreme events. This paper further investigated the potentials of Generalised Extreme Value Distribution (EVD) coupled with an HMM model within a regression-based scheme for associating impacts of precipitation and evapotranspiration processes on streamflow. The statistical characteristic of the pioneering modelling schematic has been thoroughly assessed for their suitability to generate/predict synthetic river flows sequences for a set of future climatic projections. The new modelling schematic can be adapted for a range of applications in the area of hydrology, agriculture and climate change.

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

In industry 4.0 era, video applications such as surveillance visual systems, video conferencing, or video broadcasting have been playing a vital role. In these applications, for manipulating and tracking objects in decoded video, the quality of decoded video should be consistent because it largely affects to the performance of the machine analysis. To cope with this problem, we propose a novel perceptual video coding (PVC) solution in which a full reference quality metric named Video Multimethod Assessment Fusion (VMAF) is employed together with a deep convolutional neural network (CNN) to obtain the consistent quality while still achieving the high compression performance. First of all, to achieve the consistent quality requirement, we propose a CNN model with an expected VMAF as input to adaptively adjust the quantization parameters (QP) for each coding block. Afterwards, to increase the compression performance, a Lagrange coefficient of Rate-Distortion optimization (RDO) mechanism is adaptively computed under Rate-QP and Quality-QP models. Experimental results show that the proposed PVC has achieved two targets simultaneously: the quality of video sequence is kept consistently with an expected quality level and the bit rate saving of the proposed method is higher than traditional video coding standards and relevant benchmark, notably with around 10% bitrate saving in average.

Long non-coding RNAs (LncRNAs) are mRNA-like molecules that do not encode for proteins and that are longer than 200 nucleotides. LncRNAs play important biological roles in normal cell physiology and organism development. Therefore, deregulation of their activities is involved in disease processes such as cancer. Lung cancer is the leading cause of cancer-related deaths due to late stage at diagnosis, distant metastasis, and high rates of therapeutic failure. LncRNAs are emerging as important molecules in lung cancer for their oncogenic or tumor suppressive functions. LncRNAs are highly stable in circulation, presenting an opportunity for use as non-invasive and early-stage cancer diagnostic tools. Here, we summarize latest works providing in vivo evidence available for LncRNAs role in cancer development, therapy-induced resistance, and their potential as biomarkers for diagnosis and prognosis, with a focus on lung cancer. Additionally, we discuss current therapeutic approaches to target LncRNAs. The evidence discussed here strongly suggests that investigation of LncRNAs in lung cancer in addition to protein-coding genes will provide a holistic view of molecular mechanisms of cancer initiation, development, and progression, and could open a new avenue for cancer treatment.

An adaptor signature can be viewed as a signature concealed with a secret value and, by design, any two of the trio yield the other. In a multiparty setting, an initial adaptor signature allows each party create additional adaptor signatures without the original secret. Adaptor signatures help address scalability and interoperabity issues in blockchain. They can also bring some important advantages to cryptocurrencies, such as low on-chain cost, improved transaction fungibility, and less limitations of a blockchain’s scripting language. In this paper, we propose a new two-party adaptor signature scheme that relies on quantum-safe hard problems in coding theory. The proposed scheme uses a hash-and-sign code-based signature scheme introduced by Debris-Alazard et al. and a code-based hard relation defined from the well-known syndrome decoding problem. To achieve all the basic properties of adaptor signatures formalized by Aumayr et al., we introduce further modifications to the aforementioned signature scheme. We also give a security analysis of our scheme and its application to the atomic swap. After providing a set of parameters for our scheme, we show that it has the smallest pre-signature size compared to existing post-quantum adaptor signatures.

The operations of digitization, transmission and storage of medical data, particularly images require increasingly effective encoding methods not only in terms of compression ratio and flow of information but also in terms of visual quality. At first, there was DCT (discrete cosine transform) then DWT (discrete wavelet transform) and their associated standards in terms of coding and image compression. After that, the 2nd generation wavelets seeks to be positioned and confronted to the image and video coding methods currently used. It is in this context that we suggested a method combining bandelets and SPIHT (set partitioning in hierarchical trees) algorithm. There are two main reasons for our approach: the first lies in the nature of the bandelet transform to take advantage by capturing the geometrical complexity of the image structure. The second reason stems in the suitability of encoding the bandelet coefficients by the SPIHT encoder. Quality measurements shows that in some cases (for low bit rates) the performances of the proposed coding compete with the well-established ones and opens up new application prospects in the field of medical imaging.

This article presents an analysis of monthly precipitation totals based on the Global Precipitation Climatology Centre database and monthly mean temperatures based on National Oceanic and Atmospheric Administration data for 377 catchments located around the world. Data sequences covering 110 years from 1901 to 2010 were analysed. The long-term sequences of precipitation and temperature were used to assess the variability of climate extremes, referred to here as polarisation. Measures of polarisation used in the natural sciences are discussed. A simple measure of polarisation was presented and applied to long-term sequences of monthly precipitation totals and monthly mean temperatures. Due to the nature of the proposed polarisation measure, other characteristics of precipitation and temperature sequences are also presented as a background for the discussion of the polarisation index. The study showed the existence of trends related to the polarisation of temperature and precipitation phenomena. As a result of the analysis, trends of polarisation factors in the area of precipitation and temperature were identified in 11 catchments out of the 377 analysed catchments. The trend analysis used Mann-Kendall tests at a level of significance of 5%. The Pettitt test was used to determine the point of trend change for precipitation and temperature data. The whole investigation is supported by rich graphical analyses, and the results are presented in tabular form.

The article is devoted to biological models using recurrence sequences, which are connected with the harmonic progression 1, 1/2, …, 1/n, and some cooperative properties of genomes. The harmonic progression is itself one of the recurrence sequences based on the harmonic mean. This progression appears in the hyperbolic rules of oligomer cooperative organization in eukaryotic and prokaryotic genomes. This allows thinking that the harmonic progression is also related to inherited physiological systems, which must be structurally consistent with the genetic coding system for their transmission to descendants and survival in evolution. The harmonic progression is one of historically known mathematical series, whose features were studied by Pythagoras, Leibniz, Newton, Euler, Fourier, Dirichlet, Riemann. It is widely used in many known algorithms and is closely related to some other important mathematical objects, for example, the function of the natural logarithm and harmonic numbers. Accordingly, the article describes the possibilities of using these interrelated mathematical objects to model biological structures, including logarithmic spirals and some other. Modeling inherited spiral configurations seems to be a particularly urgent task, since they are extremely common at all levels of organization of living bodies and, according to Goethe, are lines of life. The principle of a recurrence similarity, that is a special similarity of parts and transformations presented in recurrence sequences of numbers and matrix operators (the scale similarity and scale transformations are only particular cases of such similarity), is considered as one of the key principles of structural organization of living bodies.

Attention-Deficit/Hyperactivity Disorder (ADHD) is traditionally conceptualized within a framework emphasizing deficits in attention regulation and executive function. However, emerging evidence from the fields of predictive coding and active inference offers a novel lens through which to understand ADHD not merely as a disorder of attention but as a distinctive mode of neurodevelopmental variation. This article synthesizes current research and theoretical models to propose a redefined understanding of ADHD. By integrating insights from Ryan Smith, Paul B. Badcock, and Karl J. Friston (2020), we explore the premise that individuals with ADHD exhibit unique differences in how their brains generate and update predictions about the environment, leading to the characteristic behavioral patterns observed in ADHD. We argue that ADHD involves a divergence in the brain's predictive models and its ability to minimize prediction error, impacting sensory processing, attention allocation, and motor control. This perspective illuminates the adaptive aspects of ADHD, suggesting that what are often labeled as deficits could also reflect an adaptive fit to certain environmental contexts, underscoring the role of neurodiversity in human evolution. Furthermore, we discuss the implications of this reconceptualization for clinical practice, including diagnosis, treatment, and support for individuals with ADHD, emphasizing approaches that align with their unique neurocognitive profiles. This article calls for a shift in the narrative surrounding ADHD, advocating for a model that appreciates the complexity and adaptiveness of neurodevelopmental diversity.

How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis. So, it requires some form of chemical free energy to drive it. Amino acid activation and acyl-transfer are also slow and call for catalysis. All living things must thus also convert free energy and synchronize cellular chemistry. Most importantly, functional proteins occupy only small, isolated regions of sequence space. Nature evolved heritable symbolic data processing to seek out and use those sequences. That system has three parts: a memory of how amino acids behave in solution and inside proteins, a set of code-keys to access that memory, and a scoring function. The code-keys themselves are the genes for cognate pairs of tRNA and aminoacyl-tRNA synthetases, AARS. I outline the surprising links between all these questions and the structural duality of the base-pairing that holds genes together and how those links arise from the experiments.

Perinatal brain injury is a major public health problem burdened with high morbidity, mortality and severe neurological sequelae. Despite advances in neonatal life-saving technologies, neonatal encephalopathy lacks specific and effective treatment. Therefore, mechanisms of central nervous system changes associated with perinatal brain injury have been a hot topic of neonatology research. In recent years, researchers have shifted more focus from neurons themselves to perineuronal cells and intercellular interactions. As a member of the nervous system network, astrocytes are one of the dominant glial cells that regulate ion homeostasis, blood flow, and antioxidant function in the brain. Their changes in molecular mechanisms (e.g., alterations in RNA regulatory networks) during brain injury storms deserve further attention. Non-coding RNAs participate in and promote reactive pathophysiologic changes in astrocytes. The review summarizes and discusses the role of non-coding RNAs in astrocytes in recent years in studies of neonatal brain injury. It focuses on the most studied disease-related ncRNAs: miRNAs, lncRNAs and circRNAs, and hopes to provide possible directions for pathophysiological studies and therapeutic approaches of neonatal brain injury.

In the coded pulse scanning light detection and ranging (LIDAR) system, the number of laser pulses used at a given measurement point changes depending on the modulation and the method of spreading used in optical code-division multiple access (OCDMA). The number of laser pulses determines the pulse width, output power, and duration of the pulse transmission of a measurement point. These parameters determine the maximum measurement distance of the laser and the number of measurement points that can be employed per second. In this paper, we evaluate the performance and characteristics of combinations of modulation and spreading technology that can be used for OCDMA, and study optimal combinations according to varying operating environments.

Prime period sequences can serve as the fundamental tool to construct arbitrary composite period sequences. This is a review study of prime period perfect Gaussian integer sequence (PGIS). When cyclic group {1,2,…,N−1} can be partitioned into k cosets, where N=kf+1 is an odd prime number, the construction of a degree-(k+1) PGIS can be derived from either matching the flat magnitude spectrum criterion or making the sequence with ideal periodic autocorrelation function (PACF). This is a systematic approach of prime period N=kf+1 PGIS construction, and is applied to construct PGISs with degrees 1, 2, 3 and 5. However, for degrees larger than 3, matching either the flat magnitude spectrum or achieving the ideal PACF encounters a great challenge of solving a system of nonlinear constraint equations. To deal with this problem, the correlation and convolution operations can be applied upon PGIS of lower degrees to generate new PGIS with degree-4 and other higher degrees, e.g., 6, 7, 10, 11, 12, 14, 20 and 21 in this paper. In this convolution based scheme, both degree and pattern of a PGIS vary and can be indeterminant, which is rather nonsystematic compared with the systematic approach. The combination of systematic and nonsystematic schemes contributes the great efficiency for constructing abundant PGISs with various degrees and patterns for the associated applications.

Optical motion capture is a mature contemporary technique for the acquisition of motion data, alas it is non-error-free. Due to technical limitations and occlusions of markers, gaps might occur in such recordings. The article reviews various neural network architectures applied for gap filling problem in motion capture sequences within FBM framework providing the representation for body kinematic structure. The results are compared with interpolation and matrix completion methods. We found out, that for longer sequences simple linear feedforward neural networks can outperform the other, sophisticated architectures. We were also able to identify, that acceleration and monotonicity of input sequence are the parameters that have a notable impact on the obtained results.

Multi-receiver encryption enables a sender to encrypt a message and transmit the ciphertext to a set of authorized users, while no one out this group of authorized users can decrypt the message. Multi-receiver encryption is of great importance in many sectors such as broadcast communication, cloud computing, wireless communications, networking applications, e-voting, lottery, and medical applications. This paper proposes an efficient multi-receiver public key encryption scheme based on Lucas sequences. The results of the computational analysis show that, projected scheme is better against renown attacks and prevailing anonymous multireceiver algorithms

Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.

DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair

Vibrotactile displays have been reported effective in enhancing awareness of flight attitude for pilots and releasing other heavily loaded sensory channels. Although some work have been done on vibrotactile coding of flight altitude, there is lack of a systematic investigation into coding methods with combination of multiple coding parameters. In this paper, seven coding methods with combinations of multiple coding parameters (location, rhythm, intensity, and mode) were systematically studied to cue flight attitude for pilots with a vibrotactile vest. We conducted two psychophysical experiments in a static tactile sensory environment in which the attitude commands in the form of vibrotactile feedback are presented randomly, and quantitatively evaluated the effectiveness of the vest according to the users’ recognition accuracy, reaction time and information transfer rate. The results show that vibrotactile vest is effective to cue attitude information. The preferred coding method with combinations of location, rhythm and mode allowed users to perform with lowest reaction time and highest recognition accuracy and yield about 255 bits/min of information transfer rate. Overall, the presented work provides valuable insights and guidance for the design of haptic displays for vibrotactile aids for the pilots.

Cleomaceae is an important group that is medicinally and economically important. However, its systematic position has been controversial. In this study, we have obtained three chloroplast genomes sequencing results of Cleomaceae species. The genome sizes ranged from 157,073 bp (Sieruela rutidosperma) to 158,152 bp (Gynandropsis gynandra). These chloroplast genomes have a typical quadripartite formation with a large single-copy (LSC) region (86,422-87,242bp), a small single-copy (SSC) region (18,485-18,548bp), and a pair of inverted repeat (IR) regions (26,083-26,184bp). The chloroplast genomes encoded 131-132 genes, comprising 8 rRNA genes, 37 tRNA genes, and 79-84 protein-coding genes. The overall GC contents of the three chloroplast genomes are almost identical (35.81%-36.02%). The phylogenetic trees concluding 8 Cleomaceae plants were constructed based on ML and BI methods. The results showed that Gynandropsis gynandra and Sieruela rutidosperma were in the same branch, with Corynandra viscosa as their sister. Six hypervariable areas were identified, containing clpP, matK, ndhF, atpH-atpI, atpF-atpH and petN-psbM which could be used in species identification and population genetics studies. This study provides valuable information for further species identification, evolutionary and genetic studies of Cleomaceae in the future.

In this work, we present a new way to study the genetic code mathematical and chemical structure, based on the use of mathematical computations involving some few recently designed Fibonacci-like sequences, the “seeds” (“initial conditions”) of which are chosen according to the chemical and physical data of the three amino acids serine, arginine and leucine, playing a prominent role in a recent symmetry classification scheme of the genetic code. It appears that these mathematical sequences, of the same kind as the famous Fibonacci series, apart from their usual recurrence relations, are highly interwinned by many useful linear relationships. Using these sequences and also various sums or linear combinations of them, we derive several physical and chemical quantities of interest, as the number of total coding codons, 61, obeying various degeneracy patterns, the detailed number of hydrogen atoms, the detailed number of atoms (H/CNOS) and the integer molecular mass (or nucleon number), in the side chains of the 61 “amino acids”, also in various degeneracy patterns, in agreement with those described in the literature. Also, unexpectedly but interestingly, we find, as a by-product, an accurate description of the very chemical structure of the four ribonucleotides uridine monophosphate (UMP), cytidine monophosphate (CMP), adenosine monophosphate (AMP) and guanosine monophosphate (GMP), the building blocks of RNA whose groupings, in three units, constitutes the triplet codons. In summary, we find a full mathematical and chemical connection with the “ideal sextet’s classification scheme” mentioned above as well as with several others, notably, the Findley-Findley-McGlynn symmetrical classification. We organize the content of the text in such a way that, besides the presentation of several new research results, it has also an educational dimension. The paper could therefore be read and the computations easily worked out, also by non-experts with mathematical background.

The article presents an analysis of monthly precipitation totals based on the GPCC database, and monthly mean temperatures (NOAA data) for 377 catchments distributed across the globe. The analysis included 110-year data sequences from 1901 to 2010 calculated from grid data with a spatial resolution of 0.5°x 0.5° longitude and latitude. Long-term sequences of precipitation and temperature were used to assess the polarization of climatic phenomena. The noticeable impact of polarization in the area of extreme changes in temperature and precipitation is related to anthropogenic factors such as greenhouse gas emissions, deforestation and pollution, which affect ecosystem functioning, biodiversity, water resources and economies. The paper demonstrates the existence of trends related to the polarization of temperature and precipitation phenomena. The measures of polarization used in science are discussed. A simple measure of polarization was proposed and applied to both long-term sequences of monthly precipitation totals and monthly mean temperature. Due to the nature of the proposed polarization measure, other characteristics of the precipitation and temperature sequences are also presented as background for the discussion of the polarization index. The paper presents, for a selection of several hundred catchments from around the world, analyses of the assessment of precipitation and temperature trends using non-parametric tests. The trend analyses use Mann -Kendall tests at the 5% significance level. A Pettitt test was used to determine the trend change point for precipitation and temperature data. The whole is supported by rich graphical analyses and the results are presented tabularly.

Inherited mutations in BRCA1 and BRCA2 genes increase risks for breast, ovarian, and other cancers. Both genes encode proteins for accurately repairing chromosome breaks. If mutations inactivate this function, broken chromosomes may not be restored correctly, allowing breaks to persist or rearrange chromosomes. These abnormalities are potentially catastrophic events that can originate from viral infections. I used bioinformatic analyses of publicly available breast cancer patient data to show that the distribution of chromosome breaks in hereditary breast cancers differs markedly from sporadic breast cancers. Then I tested hereditary breast cancer sequence data around chromosome breaks for DNA similarity to all known viruses. Human DNA flanking breakpoints usually had decisive matches to Epstein-Barr virus (EBV / HHV4) tumor variants HKHD40 and HKNPC60. Many breakpoints were near EBV genome anchor sites, human EBV tumor-like sequences, EBV-associated epigenetic marks, and some fragile sites. On chromosomes 2 and 12, sequences near EBV genome anchor sites accounted for 90% and 88% of breakpoints (p<0.0001), respectively. On chromosome 4, 51/52 inter-chromosomal breakpoints were close to EBV-like sequences in 19 hereditary breast cancers. In contrast, 19 sporadic breast cancers only had 12 interchromosomal breakpoint regions on chromosome 4 near EBV-like sequences. On various other chromosomes, five EBV genome anchor sites were near hereditary breast cancer breakpoints at precisely defined, disparate gene or LINE locations. Independent evidence further implicating EBV in hereditary breast cancer breakpoints is that 25 breast cancer break positions are within 1.25% of breakpoints in model EBV cancers. In addition to BRCA1 or BRCA2 mutations, all the hereditary breast cancers had mutated genes essential for immune responses. This compromise facilitates reactivation of herpes viruses which produce nucleases capable of breaking chromosomes. EBV also causes other deleterious effects: anchored EBV episomes can interfere with normal replication and obstruct DNA break repairs; even very early infection causes massive transcription changes. The results, therefore, imply proactive treatment and prevention of herpes viral infections may prevent some chromosome breaks and benefit BRCA mutation carriers.

Inherited mutations in BRCA1 and BRCA2 genes increase risks for breast, ovarian, and other cancers. Both genes encode proteins for accurately repairing chromosome breaks. If mutations inactivate this function, chromosome fragments may not be restored correctly. Resulting chromosome rearrangements can become critical breast cancer drivers. Because I had data from thousands of cancer structural alterations that matched viral infections, I wondered whether infections contribute to chromosome breaks and rearrangements in hereditary breast cancers. There are currently no interventions to prevent chromosome breaks because they are thought to be unavoidable. However, if chromosome breaks come from infections, they can be treated or prevented. I used bioinformatic analyses to test publicly available breast cancer sequence data around chromosome breaks for DNA similarity to all known viruses. Human DNA flanking breakpoints usually had the strongest matches to Epstein-Barr virus (EBV) tumor variants HKHD40 and HKNPC60. Many breakpoints were near sites that anchor EBV genomes, human EBV tumor-like sequences, EBV-associated epigenetic marks, and fragile sites. On chromosome 2, sequences near EBV genome anchor sites accounted for 90% of breakpoints (p<0.0001). On chromosome 4, 51/52 inter-chromosomal breakpoints were close to EBV-like sequences. Five EBV genome anchor sites were near breast cancer breakpoints at precisely defined, disparate gene or LINE locations. Breakpoint flanking regions resembled known EBV-cancers. Twenty-five breakpoints in breast cancers were within 1.25% of EBV cancer breakpoints. In addition to BRCA1 or BRCA2 mutations, all the breast cancers had mutated genes essential for immune responses. Because of this immune compromise, herpes viruses can activate and produce nucleases that break chromosomes. Alternatively, anchored viral episomes can obstruct break repairs, whatever the cause. The results, therefore, imply proactive treatment and prevention of herpes viral infections may prevent some chromosome breaks and benefit BRCA mutation carriers.

In this article/review, the selective interactions of several berberine and palmatine derivatives with various DNA G-quadruplex structures are reported. These derivatives were constructed starting from two natural compounds, berberine and palamatine, through specific synthetic passages following two different schemes for each of them and using several substituents. The details of these synthesis are also described. Indeed, the study of the interactions of these derivative compounds with various G-quadruplex forming sequences was carried out by means of various structural and biochemical techniques. The results show that the presence of suitable side chains are very useful to improve the interaction of the ligands with G-quadruplex structures. Thus, since G-quadruplex formation is promoted by these compounds, which have never been reported before, these may be tested as potential anticancer drugs.

Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.

Diabetic retinopathy (DR) is a progressive blinding disease that affects vision and quality of life of patients and severely impacts society. This complication, caused by abnormal glucose metabolism, leads to structural, functional, molecular, and biochemical abnormalities in the retina. Oxidative stress (OS) and inflammation also play pivotal roles in the pathogenic process of DR, leading to mitochondrial damage and decrease in the mitochondrial function. DR causes retinal degeneration in glial and neural cells, while the disappearance of pericytes in retinal blood vessels leads to modifications in vascular regulation and stability. Clinical changes include dilatation and blood flow alterations in response to the reduce in retinal perfusion in retinal blood vessels, leading to vascular leakage, neovascularization and neurodegeneration. Thus, DR is a highly complex disease with various biological factors that contribute to its pathogenesis. The interplay between biochemical pathways and non-coding RNAs (ncRNAs) is essential for understanding the development and progression of DR. Abnormal expression of ncRNAs has been confirmed to promote the development of DR, suggesting that ncRNAs such as miRNAs, lnc-RNAs and circ-RNAs have potential as diagnostic biomarkers and theranostic targets in DR. This review provides an overview of interactions between abnormal biochemical pathways and dysregulated expression of ncRNAs under the influence of hyperglycemic environment in DR.

The non-coding RNAs (ncRNAs) are indispensable for controlling genes and genetic programming during development, as well as for health and cardiovascular diseases. Cardiac arrhythmia is a frequent cardiovascular disease, which has a complex pathology. Recent studies have shown that ncRNAs are also associated with cardiac arrhythmias. Many non-coding RNAs and/or genomes have been reported as a genetic background for cardiac arrhythmias. Arrhythmias may be affected by several functional and structural changes in the myocardium. Therefore, ncRNAs might be indispensable regulators of gene expression in cardiomyocytes, which could play a dynamic role in regulating the stability of cardiac conduction and/or in the remodeling process. Although it remains almost unclear how ncRNAs regulate the expression of molecules for controlling the cardiac conduction and/or in the remodeling process, gut microbiota and immune system within the intricate networks might be involved in the regulatory mechanisms. This study would discuss them and provide a research basis for ncRNAs modulation, which might support the development of emerging innovative therapies against cardiac arrhythmias.

Diversification of cropping sequences has a positive impact on soil organic carbon, while improving nutrient cycling and crop yields. The objective of this research was to assess amylase and cellulase activity, C and N dynamics, and maize yield on a low fertility Oxisol in the Brazilian Cerrado. The experiment was conducted under field conditions during three maize crop succession cycles. Treatments consisted of cultivating maize during the summer, after sorghum and lablab cropped as green manure and fallow during the winter. Higher maize yields were achieved by sorghum-maize succession compared to monocropping, due to higher N fertilizer and biomass in-puts to topsoil. Sorghum-maize succession also provided a higher proportion of stable C and N compared to other successions. Maize yields declined as tropical soil fertility intrinsically de-creased along three crops succession cycles. Cellulase activity decreased over time, whereas amylase activity increased as the plant residues were already in advanced stages of decomposition. The sorghum-maize crop succession stood out compared to lablab and fallow as it provided the high-est maize yields, while, maintaining higher C and N levels, and amylase activity. This better performance was likely due to larger amounts of incorporated biomass and better mineral N fertilizer management.

Well-annotated gene and genomic sequences serve as a foundation for making inferences in molecular biology and evolution, and can directly impact public health. The first SARS-CoV-2 genome was submitted to GenBank and used to develop the two successful vaccines. Conserved protein domains are often chosen as targets for developing antiviral medicines or vaccines. Mutation and substitution patterns provide crucial information not only on functional motifs and genome/protein interactions but also for characterizing phylogenetic relationships among viral strains. These patterns, together with the collection time of viral samples, serve as the basis for addressing the question of when and where the host-switching event occurred. Unfortunately, viral genomic sequences submitted to GenBank undergo little quality control, and critical information in the annotation is frequently changed without being recorded. Researchers often have no choice but to hold blind faith in the accuracy of the sequences. There have been reports of incorrect genome annotation but no report that casts doubt on the genomic sequences themselves because it seems theoretically impossible to identify genomic sequences that may not be authentic. This paper takes an innovative approach to show that some SARS-CoV-2 genomes submitted to GenBank cannot be possibly authentic. Specifically, some SARS-CoV-2 genomic sequences deposited in GenBank with collection time in 2023 and 2024, isolated from saliva, nasopharyngeal, sewage, and stool are identical to the reference genome of SARS-CoV-2 (NC_045512). The probability for such occurrence is effectively 0. I also compile SARS-CoV-2 genomes with changed sample collection time. One may led astray in bioinformatic analysis without being aware of errors in sequences and sequence annotation.

In the context of all-digital radar systems, phase-modulated continuous wave (PMCW) based on pseudorandom binary sequences (PRBSs) appears a prominent candidate modulation scheme for applications such as autonomous driving. Among the reasons for that are its simplified transmitter architecture and lower linearity requirements, e.g., compared to orthogonal-frequency division multiplexing radars, as well as its high velocity unambiguity and multiple-input multiple-output operation capability that are characteristic of digital radars. For appropriate operation of a PMCW radar, choosing a PRBS whose periodic autocorrelation function (PACF) has low sidelobes and high robustness to Doppler shifts is paramount. In this sense, this article performs an analysis of Doppler shift tolerance of the PACFs of typically adopted PRBSs in PMCW radar systems supported by simulation and measurement results. To accurately measure the Doppler-shift-induced degradation of PACFs, peak power loss ratio (PPLR), peak sidelobe level ratio (PSLR), and integrated-sidelobe level ratio (ISLR) were used as metrics. Furthermore, to account for effects on targets whose ranges are not multiples of the range resolution, oversampled PACFs are analyzed.

The aim of this survey is to review some recent developements in devising efficient preconditioners for sequences of linear systems A x = b. Such a problem arise in many scientific applications, such as discretization of transient PDEs, solution of eigenvalue problems, (Inexact) Newton method applied to nonlinear systems, rational Krylov methods for computing a function of a matrix. Full purpose preconditioners such as the Incomplete Cholesky (IC) factorization or approximate inverses are aimed at clustering eigenvalues of the preconditioned matrices around one. In this paper we will analyze a number of techniques of updating a given IC preconditioner (which we denote as P0 in the sequel) by a low-rank matrix with the aim of further improving this clustering. The most popular low-rank strategies are aimed at removing the smallest eigenvalues (deflation) or at shifting them towards the middle of the spectrum. The low-rank correction is based on a (small) number of linearly independent vectors whose choice is crucial for the effectiveness of the approach. In many cases these vectors are approximations of eigenvectors corresponding to the smallest eigenvalues of the preconditioned matrix P0 A. We will also review some techniques to efficiently approximate these vectors when incorporated within a sequence of linear systems all possibly having constant (or slightly changing) coefficient matrices. Numerical results concerning sequences arising from discretization of linear/nonlinear PDEs and iterative solution of eigenvalue problems show that the performance of a given iterative solver can be very much enhanced by the use of low-rank updates.

Aim: Streptococcus pneumoniae and influenza H1N1 virus are common organisms associated with human infections. These infections could play a significant role in immune regulation. The study was performed to analyse the genome sequences of these organisms with human genome and study its functional significance. Methods: The study was performed to analyse the overlapping of genome sequences in Streptococcus pneumoniae and Influenza (H1N1) virus against human genome sequences by BLASTn sequence analysis. The alignments are studied against the corresponding genes for their functional significance with DAVID and NDEx software.Results: Several hits or overlapping nucleotide segments were identified. Between streptococcus and homo sapiens 287 overlaps were identified, and among influenza and homo sapiens 124 hits were identified. A wide range of functional significance of these genes were identified, and the results are presented in this study. The results show insights into functional pathways and biological activities associated with the respective vaccinations or infections by these microorganisms. Conclusion: The common organisms like Streptococcus pneumoniae and Influenza H1N1 virus actively interact with the immune system and result in a wide range of immune regulations.

Physical roots, exemplifications and consequences of periodic and aperiodic ordering (represented by Fibonacci series) in biological systems are discussed. The role and physical and biological roots of symmetry and asymmetry appearing in biological patterns is addressed. Generalization of the Curie-Neumann Principle as applied to biological objects is presented, briefly summarized as: “asymmetry is what creates a biological phenomenon”. The “up-bottom approach” and “bottom up” approaches to the explanation of symmetry in organisms are presented in detail. The “up-bottom approach”, implies that the symmetry of the biological structure follows the symmetry of media in which this structure is functioning; the “bottom-up” approach, in turn, adopt that the symmetry of biological structures emerges from the symmetry of molecules constituting the structure. A diversity of mathematical measures applicable for quantification of ordering in biological patterns is introduced. The continuous, Shannon and Voronoi measures of symmetry/ordering and their application to biology objects are addressed. The fine structure of the notion of “ordering” is discussed. Informational/algorithmic roots of ordering inherent for the biological systems are considered. Ordered/symmetrical patterns provide economy of biological information, necessary for algorithmic description of a biological entity. Application of the Landauer principle bridging physics and theory of information to the biological systems is discussed.

Non-coding RNA regions have long been considered the "dark matter" of the genome, with their significance in gene regulation remaining enigmatic. However, recent advances in genomics and molecular biology have illuminated the pivotal role that non-coding RNA regions play in the fine-tuned orchestration of hemoglobin expression. Hemoglobin, the oxygen-carrying protein vital for life, is tightly regulated, and any disruption in its production can lead to severe medical conditions, such as hemoglobinopathies. This review delves into the intricate world of non-coding RNA regions, exploring how they act as master conductors in controlling hemoglobin gene expression. We will discuss various classes of non-coding RNAs, including long non-coding RNAs, microRNAs, and circular RNAs, and their specific mechanisms in fine-tuning hemoglobin levels. Additionally, we will highlight emerging therapeutic approaches that target non-coding RNA regions to ameliorate hemoglobin-related disorders. Understanding the critical role of non-coding RNA regions in hemoglobin regulation opens new avenues for precision medicine and gene therapies, offering hope for those affected by hemoglobinopathies and related conditions. This comprehensive review sheds light on the significance of these non-coding RNA regions, demonstrating that the "silent" players in the genome are, in fact, the conductors of harmony in the symphony of hemoglobin regulation.

miRNA regulatory axes in blood of MCI patients, which includes lncRNA-SNHG16, lncRNA-H19 and lncRNA-NEAT1. Microarray investigations have demonstrated modifications in the expression of long non-coding RNAs (lncRNA) in blood of patients with MCI compared with control samples. This is the first study to explore lncRNA profiles in Mild Cognitive Impairment blood. Our study proposes RNAs targets involved in molecular pathways connected to the pathogenesis of MCI.

A definitive transcriptome atlas for the non-coding expressed elements of pathogenic mycobacteria does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g. Mycobacterium tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasising the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non- coding transcriptome with experiments that can help refine and confirm these predictions.

In this contribution, we present a high-speed multiplex grating spectrometer based on a spectral coding approach that is founded on principles of compressive sensing. The spectrometer employs a single-pixel InGaAs detector to measure the signals encoded by an amplitude spatial light modulator (digital micromirror device, DMD). This approach leads to a speed advantage and multiplex sensitivity advantage atypical for standard dispersive systems. Exploiting the 18.2 kHz pattern rate of the DMD, we demonstrate 4.2 ms acquisition times for full spectra with a bandwidth of 450 nm (5250 cm-1 – 4300 cm-1; 1.9 µm – 2.33 µm). Due to the programmability of the DMD, spectral regions of interest can be chosen freely, thus reducing acquisition times further, down to the sub-millisecond regime. The adjustable resolving power of the system accessed by means of computer simulations is discussed, quantified for different measurement modes, and verified by comparison with a state-of-the-art Fourier-transform infrared spectrometer. We show measurements of characteristic polymer absorption bands in different operation regimes of the spectrometer. The theoretical multiplex advantage of 8 was experimentally verified by comparison of the noise behavior of the spectral coding approach and a standard line-scan approach.

The world is facing a major health crisis, the global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus, for which no approved antiviral agents or vaccines are currently available. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available via Addgene. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

Peer-to-peer (P2P) content distribution or file sharing system aims to facilitate the dissemination of large files over unreliable networks. Network coding is a new transmission technique that has captured the interest of researchers because of its ability to increase throughput and robustness of the network, and decrease the download time. In this survey paper, we extensively summarize, assess, compare, and classify the most recently used techniques to improve P2P content distribution systems performance using network coding. To the best of our knowledge, this survey is the first comprehensive survey that specifically focuses on the performance of network coding based P2P file sharing systems.

Mammalian genomes encode tens of thousands of long-noncoding RNAs (lncRNAs), which are capable of interactions with DNA, RNA and protein molecules, thereby enabling a variety of transcriptional and post-transcriptional regulatory activities. Strikingly, about 40% of lncRNAs are expressed specifically in the brain in precisely regulated temporal and spatial expression patterns. In stark contrast to the highly conserved repertoire of protein-coding genes, thousands of new lncRNAs have appeared during primate nervous system evolution with hundreds of human-specific lncRNAs. Their evolvable nature and the myriad of potential functions make lncRNAs ideal candidates for drivers of human brain evolution. The human brain displays the largest relative volume of any animal species and the most remarkable cognitive abilities. In addition to brain size, structural reorganization and adaptive changes represent crucial hallmarks of human brain evolution. LncRNAs are increasingly reported to be involved in neurodevelopmental processes including proliferation, neurite outgrowth and synaptogenesis, as well as in neuroplasticity, suggested to underlie human brain evolution. Hence, evolutionary human brain adaptations are proposed to be essentially driven by lncRNAs, which will be discussed in this review.

This article presents a rigorous approach to the Collatz Conjecture, focusing on fundamental properties of Collatz sequences. We establish key properties of the Collatz function and its inverse, including surjectivity and injectivity. The structure of Collatz sequences is analyzed in depth, proving important results such as the Bounded Subsequence Property and the uniqueness of cycles. Central theorems on the properties of Collatz sequences, including the boundedness of all sequences and the nature of the unique cycle, are presented and proved. These results culminate in a complete resolution of the Collatz Conjecture, demonstrating that all Collatz sequences eventually reach the cycle {1, 4, 2}. We provide a rigorous proof of the conjecture, while emphasizing the need for thorough peer review and verification by the mathematical community given the significance of this long-standing problem.

The steel damper column is an energy-dissipating member that is suitable for reinforced concrete (RC) buildings, and those used for multistory housing in particular. However, the effectiveness of steel damper columns may be affected by the behavior of surrounding members, and this effect can be severe in the case of seismic sequences. This article investigates the nonlinear response of building models having an RC moment-resisting frame (MRF) with and without steel damper columns under seismic sequences. The applicability of the concept of the momentary energy input to the prediction of the peak response of RC MRFs with damper columns under seismic sequences is also investigated. The main findings of the study are summarized as follows. (1) The peak response of RC MRFs with damper columns subjected to sequential accelerations is similar to the peak response obtained considering only the mainshock, whereas the cumulative strain energy of RC MRFs accumulates more for sequential accelerations. (2) The steel damper column is effective in reducing the peak and cumulative responses of RC MRFs in the case of sequential seismic input. (3) The relation of the hysteretic dissipated energy during a half cycle of the structural response and the peak displacement of the first modal response can be properly evaluated using the simple model proposed in this study.

A study of curvature along the contour provides important sources of information about the shape of an object. Knowledge of contour curvature allows for the perception of and interaction with 3D objects. In this review, we will explore the value of contour curvature in the field of neurophysiology, psychophysics, computer vision, and psychology. The serial consolidation of disjoint edges, oriented in a particular manner, into composited curves allows building of identifiable shapes in occluded natural environments [Hess1999, Wertheimer1923, Zucker1989, Feldman2001]. Examples are our ability to pick objects, sort and manage shapes otherwise hidden or confounded by occlusion in messy natural environments. Contour curvature has been intensively studied in psychology as it forms the first steps in 2D shape building which eventually becomes 3D object recognition in the human brain.

Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5'end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5’ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I or MDA5 receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host-cell interactions driving the development of acute or persistent EV-B infections.

After the increasing number of SARS-CoV-2 infections all over the world, researchers and clinicians are struggling to find a vaccine or innovative therapeutic strategies to treat this viral infection. The SARS-CoV infection that occurred in 2002, MERS and other more common infectious diseases such as HCV, led to the discovery of many RNA-based drugs. Among them, siRNAs and antisense LNAs have been demonstrated to have effective antiviral effects both in animal models and humans. Owing to the high genomic homology of SARS-CoV-2 and SARS-CoV (80-82%) the use of these molecules could be employed successfully also to target this emerging coronavirus. Trying to translate this approach to treat COVID-19, we analyzed the common structural features of viral 5’UTR regions that can be targeted by non-coding RNAs and we also identified miRNAs binding sites suitable for designing RNA-based drugs to be employed successfully against SARS-CoV-2.

In this paper, inspired by recent articles of G. Anatriello and G. Vincenzi (see \cite{Ana}), and G. Cerda-Morales (see \cite{Cer1,Cer2}), we will introduce the third-order $\overline{h}$-Jacobsthal and third-order $\overline{h}$-Jacobsthal--Lucas sequences and their associated quaternions. The new results that we have obtained extend most of those obtained in \cite{Cer2}.

We hypothesize that the first ancestral "ante-cell" molecular structures, i.e., first RNAs and peptides which gradually transformed into real cells once the Earth had cooled sufficiently for organic molecules to appear there, have leaved traces in RNAs and genes of present cells. We propose a circular RNA which could have been one of these ancestral structures whose vestigial pentameric subsequences would mark the evolution from this key moment when the ante-cells have begun to join the living organisms. In particular, we propose that in present RNAs (ribosomal or messenger) playing an important role in the metabolism of current cells, we look for traces of the proposed primitive structure in the form of pentamers (or longer fragments) belonging to their nucleotide sequence. The result obtained can be summarized in the existence of a gradient of occurrence of such pentamers, with a high frequency for the most vital functions (protein synthesis, nucleic synthesis, cell respiration, etc.). This gradient is also visible between organisms, from the oldest (Archaea) to the most recent (Eukaryotes) in evolution of species.

We extend Ziv and Lempel's model of finite-state encoders to the realm of lossy compression of individual sequences. In particular, the model of the encoder includes a finite-state reconstruction codebook followed by an information lossless finite-state encoder that compresses the reconstruction codeword with no additional distortion. We first derive two different lower bounds to the compression ratio that depend on the number of states of the lossless encoder. Both bounds are asymptotically achievable by conceptually simple coding schemes. We then show that when the number of states of the lossless encoder is large enough in terms of the reconstruction block-length, the performance can be improved, sometimes significantly so. In particular, the improved performance is achievable using a random-coding ensemble that is universal, not only in terms of the source sequence, but also in terms of the distortion measure.

In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences enriched with thymine bases represent the signal inducing abortive transcription. On the other hand, certain repetitive sequence elements broadly embedded in promoter regions constitute the signal inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we also suggest that repetitive sequence elements of promoter DNA modulate the rigidity of its double-stranded form, which profoundly influences the reaction coordinates of the productive initiation via pausing.

This paper presents the design of a new neuro-generator of pseudorandom number type PRNG Pseudorandom Number Generator, which produces complex sequences with an adequate bit distri-bution. The circuit is connected to a neuronal module with six impulse neurons with different be-haviors: spike frequency adaptation, phasic spiking, mixed mode, phasic bursting, tonic bursting and tonic spiking. This module aims to generate a non-periodic signal that becomes the clock sig-nal for one of the LFSRs Linear Feedback Shift Register that the neuro-generator has. To verify its correct operation, the neuro-generator was subjected to a series of tests where the frequencies of the impulse neurons were modified. This modification allows generating a greater number of pulses at the output of the neuronal module, to obtain sequences with different characteristics that pass different NIST statistical tests National Institute of Standards and Technology of U.S. The results show that the new neuro-generator maintains pseudo-randomness in the sequences obtained with different frequencies and it can be implemented on reconfigurable FPGA Field Programmable Gate Array Virtex 7 xc7vx85t-2ffg1761 device. Therefore, it can be used for applications such as biologi-cal systems.