Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We have identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) that are likely to be associated with the spontaneous tumour formation. Furthermore, we performed the identification of CLE and WOX genes the genomic sequences of the radish inbred lines and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

We use binary string to represent a natural number and show the composite procedure of odd-number and even-number functions, thus we propose full binary directed tree to represent the set of natural numbers and give another partition the natural number set to three sets: pure odd, pure even and mixed number. For the Collatz conjecture we make use of the parity of a natural number to analyse the sequence of iteration (or composite) of Collatz function and reduced Collatz function analog to the inverse function. We give tabular and binary strings to the algebra expression to state the sequence of Collatz, this is the key topic to proof the conjecture: the discrete powers of 2 can be changed to ultimately continuous powers of 2, finally get to pure even number and to the smallest number 1. The sequence created by the infinite iterations of the Collatz function becomes the ultimately periodic sequence if any natural number is the beginning value, proving the conjecture that has been held for 87 years.

We propose a full binary directed tree to represent the set of natural numbers and further divide the set into three sets: pure odd, pure even, and mixed numbers. We utilize a binary string to represent a natural number and demonstrate the composite procedure of odd-number and even-number functions. We analyze the sequence of iteration (or composite) of the Collatz function and reduced Collatz function analog to the inverse function in order to test the Collatz conjecture. We do this by using the parity of a natural number. In order to prove the conjecture, we provide tabular and binary strings to the algebraic formula that states the Collatz sequence. Ultimately, we can convert discrete powers of 2 into continuous powers of 2, ultimately arrive at the smallest natural, 1. If any natural number is the beginning value, the sequence produced by the infinite iterations of the Collatz function becomes the eventually periodic sequence, proving an 87-year-old conjecture.

Originating in the Mediterranean, B. oleracea is grown all over the world and is highly valued for its nutritional value and variety in cooking. Its susceptibility to pests, diseases, and environmental stressors, however, poses significant challenges to sustaining consistent crop quality and productivity. The BASIC PENTACYSTEINE gene significantly impacts plant growth and responses to abiotic stresses. Nevertheless, little is known about its precise role and the underlying biological processes in B. oleracea. Eleven BPC genes in B. oleracea were identified by a thorough genome-wide investigation and categorized into three categories according to their structural traits and gene motifs. There were eight different chromosomes on which these BoBPCs were located. Comparative synteny analysis was used to reveal the evolutionary traits of potatoes, Arabidopsis, and B. oleracea. The BoBPC family genes in B. oleracea were found to have specific cis-elements linked to growth, stress responses, and hormone regulation when their promoter regions were studied. Cuticular wax synthesis expression revealed that all BoBZR1 genes, from wild to mutant, expressed at varied amounts in distinct types. Moreover, distinctive BoBPC gene expression patterns were found in the seven distinct tissues that were studied. Our thorough analysis shows that the BoBPC family is widely involved in B. oleracea developmental processes. The present findings provide an established theoretical basis for further exploration into the composition and roles of BoBPC in B. oleracea.

The evolutionary cancer cell biology ECCB explains the deep homology existent between the life cycle of cancer and protists. Due to their origin and sensitivity to oxygen, all non-gametogenic germ lines and germ stem cells (GSCs), including human adult stem cells (ASCs) and cancer stem cells (CSCs), suffer severe DNADSB damage when exposed to stress oxygen content above 6.0% O2 (Urgermline hyperoxia) as occurring in tissue and bloodstream. As a result, GSCs/ASCs/ CSCs lose their stemness potential and convert from a functional asymmetric cyclic phenotype (ACD phenotype) to a dysfunctional symmetric phenotype capable of defective symmetric proliferation (DSCD) that is, however, unable to repair genomic degradation. Genome reconstruction occurs through evolutionary mechanisms evolved by the common ancestor of amoebozoans, metazoans, and fungi. They complete the cycle by removing the damage, reconstructing the functional genome, and reinstating the ASC phenotype. The stemness life cycle acts not only during carcinogenesis, tumorigenesis, and recurrence but also in the life cycle of protists.

This study delves into a unique binary pattern found within the wellknown 3n+1 problem, or Collatz conjecture. Through careful analysis of the steps in the 3n+1 sequence, we have discovered a special binary representation that captures the behavior of all positive integers undergoing this transformation. With this new understanding, we have provided a solid proof confirming the validity of the 3n+1 problem for all positive integers. Our method goes beyond the need for extensive computational confirmation, providing a simple and elegant resolution to a long-standing mathematical mystery.

Searching over a sorted list is a classical problem in computer science. Binary Search takes at most log2n+1 tries to find an item in a sorted list of size n. Interpolation Search achieves an average time complexity of Ο(loglogn) for uniformly distributed data. Hybrids of Binary Search and Interpolation Search are also available to handle data with unknown distributions. This paper analyzes the computation cost of these methods and shows that interpolation can significantly affect their performance — accordingly, a new method, Interpolation Once Binary Search (IOBS), is proposed. The experimental results show that IOBS outperforms the hybrids of Binary Search and Interpolation Search for nonuniformly distributed data.

Background Homologous recombination deficiency (HRD) evolved into a major diagnostic marker in high grade ovarian cancer (HGOC) predicting the response to poly (Adenosine diphosphate-ribose) polymerase inhibitors (PARPi) and also platinum-based therapy. In addition to HRD, the type of peritoneal tumor spread influences treatment response and patient survival; miliary type tumor spread has poorer predicted outcome than non-miliary type tumor spread. Methods Known methods for HRD assessment were adapted for our technical requirements and the Predictive-value Integrated Genomic Instability Score (PIGIS) for HRD assessment evolved as an outcome. PIGIS was validated in HGOC samples from 122 patients. We used PIGIS to analyze whether the type of tumor spread correlated with HRD status and whether this had an impact on survival. Results We demonstrated that PIGIS can discriminate HRD positive from HRD negative samples. Tumors with miliary tumor spread are HRD negative and have a very bad prognosis with a progression free survival (PFS) of 15.6 months and an overall survival (OS) of 3.9 years. However, HRD negative non-miliary spreading tumors in our cohort had a much better prognosis (PFS 35.4 months, OS 8.9 years), similar to HRD positive tumors (PFS 34.7 months, OS 8.9 years). Conclusions Our results indicate that in a predominantly PARPi naïve cohort the type of tumor spread might be a better predictor of response to platinum sensitivity than HRD. It remains to be determined, whether this also applies for sensitivity to PARPi.

Retired Electric vehicles (EVs) batteries are reused in second life energy storage applications. However, the overall performance of repurposed energy storage system (ESS) is limited by the unevenness of individual batteries use in it. Therefore, battery grading is required for optimal performance of ESS. Electrochemical impedance spectroscopy (EIS) based evaluation of battery aging is a promising way to grade lithium-ion batteries. However, it is not practical to measure impedance of mass retired batteries due to high complexity and slowness. In this paper, a broadband multi-sine binary signal (MSBS) perturbation integrated with multichannel EIS system is presented to measure impedance spectra for high-speed aging evaluation of lithium-ion batteries or modules. The measurement speed is multi-times higher than conventional EIS with single-channel configuration. The broadband MSBS is validated with reference sinusoidal sweep perturbation and corresponding root-mean-square error (RMSE) analysis is performed. Moreover, the accuracy of the presented multichannel EIS system is validated by impedance spectra measurement of Samsung INR18650-29E batteries and comparing it with those measured with commercial EIS instrument. A chi-squared error under 0.641% is obtained for all 8-channels. Since the non-linearity of battery has significant impact on quality of impedance spectra. Therefore, Kronig-Kramer (KK) transform validation is also performed.

κ Draconis is a binary system with a classical Be star as the primary component. Its emission-line spectrum consists of hydrogen lines, notably the Hα line with a peak intensity ratio (V/R) variations phase-locked with the orbital period P = 61.55 days. Among binaries demonstrating the Be phenomenon, κ Dra stands out as one of a few systems with a discernible mass of its secondary component. Based on more than 200 spectra obtained in 2014 − 2023, we verified the physical parameters and constructed the mass function. We used part of these data obtained in 2014 − 2021 to investigate regions in the circumstellar disk of the primary component that emit the Hα line using the Doppler tomography method. The results show that the disk has a non-uniform density distribution with a prominent enhancement at Vy≈ 99 km s−1 and Vx≈−6 km s−1 that corresponds to a cloud-like source of the double-peaked Hα line profile. We argue that this enhancement’s motion is responsible for the periodic variations of the Hα V/R ratio, which is synchronised in orbital phase with the radial velocity (RV) of absorption lines from the atmosphere of the primary component.

Legionella pneumophila can cause a large panel of symptoms beside the classic pneumonia presentation. We present here a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of legionnaires’ disease in the same ward. While the first one was easily assumed as nosocomial based on the date of symptoms onset, the other case needed to rely on clear typing results to be either assigned as nosocomial and related to the same environmental source as the first one, or community acquired. To untangle this specific question, we applied Core-genome MultiLocus Typing (MLST), whole-genome Single Nucleotide Polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large scale epidemiological investigations, NGS typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in environment.

This paper presents an analysis of the number of zeros in the binary representation of natural numbers. The primary method of analysis involves the use of the concept of the fractional part of a number, which naturally emerges in the determination of binary representation. This idea is grounded in the fundamental property of the Riemann zeta function, constructed using the fractional part of a number. Understanding that the ratio between the fractional and integer parts of a number, analogous to the Riemann zeta function, reflects the profound laws of numbers becomes the key insight of this work. The findings suggest a new perspective on the interrelation between elementary properties of numbers and more complex mathematical concepts, potentially opening new directions in number theory and analysis.

INTRODUCTION : In this scoping review, we delve into the transformative potential of artificial intelligence (AI) in addressing challenges inherent in whole genome sequencing (WGS) analysis, with a specific focus on its implications in surgical oncology. METHODS: Scoping review of whole genomic sequencing and artificial intelligence.DISCUSSION : Unveiling the limitations of existing sequencing technologies, the review illuminates how AI-powered methods emerge as innovative solutions to surmount these obstacles. The evolution of DNA sequencing technologies, progressing from Sanger sequencing to next-generation sequencing, sets the backdrop for AI's emergence as a potent ally in processing and analyzing the voluminous genomic data generated by these technologies. Particularly, deep learning methods play a pivotal role in extracting knowledge and discerning patterns from the vast landscape of genomic information. In the context of oncology, AI-powered methods exhibit considerable potential across diverse facets of WGS analysis, including variant calling, structural variation identification, and pharmacogenomic analysis. CONCLUSIONS : This review underscores the significance of multimodal approaches in diagnoses and therapies, highlighting the imperative for ongoing research and development in AI-powered WGS techniques. Integrating AI into the analytical framework empowers scientists and clinicians to unravel the intricate interplay of genomics within the realm of multi-omics research, paving the way for more personalized and targeted treatments in surgical oncology and perhaps beyond.

There are thousands of rare genetic diseases that could be treated with classical gene therapy strategies such as the addition of the defective gene via viral or non-viral delivery or by direct gene editing. However, several genetic defects are too complex for these approaches. These “genomic mutations” include aneuploidies, intra and inter chromosomal rearrangements, large deletions, or inversion and copy number variations. Chromosome Transplantation (CT) refers to the precise substitution of an endogenous chromosome with an exogenous one. By the addition of an exogenous chromosome and the concomitant elimination of the endogenous one, every genetic defect, irrespective of its nature, could be resolved. In the current review, we analyze the state of the art of this technique and discuss its possible application to human pathology. CT might not be limited to the treatment of human diseases. By working on sex chromosomes, we showed that female cells can be obtained from male cells, since chromosome-transplanted cells can lose either sex chromosome, giving rise to 46,XY or 46,XX diploid cells, a modification that could be exploited to obtain female gametes from male cells. Moreover, CT could be used in veterinary biology, since entire chromosomes containing an advantageous locus could be transferred to animals of zootechnical interest without altering their specific genetic background and the need for long and complex interbreeding. CT could also be useful to rescue extinct species if only male cells were available. Finally, the generation of “synthetic” cells could be achieved by repeated CT into a recipient cell. CT is an additional tool for genetic modification of mammalian cells.

The article delves into the intricate phase transitions of 1-Octadecanol and n-Nonadecane within a binary system, unveiling dynamic structural changes under varying conditions. Through Fouri-er-transform infrared (FTIR) analysis, specific molecular vibrations were identified, shedding light on the molecular composition and interactions. The study highlights the challenges in detecting subtle phase transitions and emphasizes the individuality of molecular behaviours in closely related compounds. The findings underscore the complexity of phase transitions in binary systems and advocate for a nuanced approach to studying molecular structures and behaviours. Addi-tionally, the research contributes valuable insights into the molecular dynamics of Organic Polymer Functional Adsorption Materials, offering implications for synthetic waxy layers in plant epidermis.

Axial resolution is one of the most important characteristics of a microscope. In all microscopes, a high axial resolution is desired in order to discriminate information efficiently along the longitudinal direction. However, when studying thick samples that do not contain laterally overlapping information, a low axial resolution is desirable as information from multiple planes can be recorded simultaneously from a single camera shot instead of plane-by-plane mechanical refocusing. In this study, we increased the focal depth of an infrared microscope non-invasively by introducing a binary axicon fabricated on barium fluoride substrate close to the sample. Preliminary results of imaging thick and sparse silk fibers showed an improved focal depth with a slight decrease in lateral resolution and increase in background noise.

Recent advancements in molecular diagnostics have highlighted the potential of circulating cell-free DNA (ccfDNA) as a biomarker in various diseases. This study aims to explore the role of ccfDNA in the early diagnosis, prognosis, and therapeutic monitoring of diseases, with a focus on oncology. We conducted a comprehensive review and analysis of current literature, combined with experimental approaches involving advanced genomic sequencing and bioinformatics techniques. Our research systematically characterizes the molecular composition of ccfDNA, including its origins, size distribution, and methylation patterns, across different disease states. Furthermore, we investigate the dynamics of ccfDNA release and clearance in the bloodstream, elucidating mechanisms that could influence its diagnostic accuracy. In the context of cancer, we analyze the correlation between tumor-derived ccfDNA and disease progression, response to therapy, and overall survival. Our findings indicate that ccfDNA holds promise as a non-invasive biomarker for early disease detection, real-time monitoring of treatment efficacy, and potentially, predicting relapse. This study contributes to the growing field of liquid biopsies and opens new avenues for personalized medicine, emphasizing the need for standardized protocols in ccfDNA analysis to maximize its clinical utility. The implications of our findings extend beyond oncology, suggesting potential applications of ccfDNA in other pathological conditions.

This comprehensive review traces the transformative journey of genomic mapping, ushering in the era of "Genomic Atlas 2.0," characterized by advanced strategies and cutting-edge technologies. Beginning with a historical overview, it highlights the evolution from early linkage analysis to the current landscape shaped by high-throughput sequencing. Key breakthroughs are emphasized, showcasing the pivotal role of platforms such as Illumina and Oxford Nanopore in accelerating the identification of genetic variations. Long-read sequencing technologies, including PacBio and Oxford Nanopore, are explored as transformative elements overcoming limitations associated with short-read sequencing. The review delves into spatial genomics and chromatin conformation capture techniques, revealing the three-dimensional intricacies of the genome, with a particular focus on the revolutionary impact of Hi-C in understanding chromatin interactions. CRISPR technologies emerge as indispensable tools in Genomic Atlas 2.0, enabling targeted genome editing and the generation of precise genetic models. Functional genomics screens, utilizing RNA interference and CRISPR-based techniques, are discussed for their scalable precision in deciphering genome functions. Navigating challenges, the review addresses complexities in data integration and ethical considerations, offering strategies to ensure the robustness and ethical conduct of genetic mapping. Looking optimistically towards the future, it explores opportunities such as improved sequencing accuracy and novel applications of CRISPR technologies. Envisioning the expansion of genomics into personalized medicine, agriculture, and conservation biology, the review serves as a guiding resource for researchers, scientists, and students navigating the intricate terrain of Genomic Atlas 2.0.

The exploration of three-dimensional (3D) DNA structures marks a pivotal shift in genomics, offering unprecedented insights into the intricacies of cellular regulation, disease genesis, and the potential for novel diagnostic and therapeutic strategies. This study delves into the dynamic nature of 3D genome organization, investigating how these structures influence cellular functions in response to environmental changes and over time. Through a combination of real-time imaging and advanced computational models, we aim to unravel the complex interplay between 3D DNA structures, non-coding RNAs, and chromatin organization, and their collective impact on gene expression and cellular differentiation. A significant focus is placed on understanding the role of 3D DNA structures in the development and progression of genetic disorders. By employing comprehensive genomic and epigenomic profiling, this research seeks to identify structural aberrations linked to diseases, paving the way for the development of targeted diagnostics and therapies. Additionally, the study explores the potential of genome editing technologies, such as CRISPR-Cas systems, in correcting these structural abnormalities, while also addressing the ethical, legal, and social implications (ELSI) of such interventions. Integrating data from various genomic analyses, we propose the development of advanced computational models to predict the effects of 3D DNA structures on gene expression and cellular function. This integrative approach not only promises to enhance our understanding of genomic regulation but also sets the stage for groundbreaking advances in genomics-based diagnostics and therapeutics. The findings of this study have the potential to revolutionize our approach to treating genetic disorders, offering a new frontier in personalized medicine.

Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and large extent of non-additive genetic variance associated with its autotetraploid genome. Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as autotetraploid and diploid dosage, plus allele ratios) and SNP marker subsetting (all available SNPs; only genic regions; only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used Genotyping by Sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and onset of flowering, assessed on 143 genotyped plants from a genetically-broad European reference population and their phenotyped half-sib progenies. Results: On average, allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), SNP subsetting offered an advantage compared with any tested subsettings (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting reached better performances. We also released Legpipe2, a SNP calling pipeline tailored for reduced representation (GBS, RAD) medium-sized genotyping experiments.

In 2022, the new WHO Classification of Endocrine and Neuroendocrine Tumors, Fifth Edition (beta version) (WHO 5th) was published. The importance of understanding the molecular genetics of thyroid tumors as revealed by large-scale genomic analyses such as The Cancer Genome Atlas (TCGA). Consequently, the WHO 5th was fundamentally revised, resulting in a systematic classification based on tumor cell-of-origin and clinical risk. This paper outlines following critical points of the WHO 5th. 1. Genetic mutations in follicular cell-derived neoplasms (FDN) highlight the role of mutations in the MAP kinase pathway, including RET, RAS, and BRAF, as drivers of carcinogenesis. Differentiated thyroid cancers such as follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC) have specific genetic alterations that correlate with morphological classifications: RAS-like tumors (RLTs) and BRAF p.V600E-like tumors (BLTs), respectively. 2. The Framework for benign lesions have revised. The WHO 5th introduces new categories such as "developmental abnormalities" and "thyroid follicular nodular disease" in benign FDN. 3. Low-Risk Tumors include NIFTP, TT-UMP, and HTT. 4. PTC histological variants are reclassified as "subtypes" in the WHO 5th. 5. The concept of high-grade carcinomas is introduced, encompassing poorly differentiated thyroid carcinoma (PDTC), differentiated high-grade thyroid carcinoma (DHGTC), and high-grade medullary thyroid carcinoma (MTC). 6. Squamous cell carcinoma is included in anaplastic thyroid carcinoma (ATC) in the WHO 5th due to shared genetic and prognostic features. 7. Hürthle cell adenoma/carcinoma is renamed oncocytic thyroid adenoma/carcinoma. 8. Other miscellaneous tumors are classified into salivary gland-type carcinomas of the thyroid, thyroid tumours of uncertain histogenesis, thymic tumours within the thyroid, and embryonal thyroid neoplasms. The WHO 5th thus emphasizes the importance of classifying tumors based on genetic abnormalities together with histomorphology, aiding in accurate pathological diagnosis and treatment selection, including molecular-targeted therapies.

This article is devoted to the problem of genetically coding of inherited cyclic structures in biological bodies, whose life activity is based on a great inherited set of mutually coordinated cyclic processes. The author puts forward and arguments the idea that the genetic coding system is capable of encoding inherited cyclic processes because it itself is a system of cyclic codes connected with Boolean algebra of logic. In other words, the physiological processes in question are cyclical because they are genetically encoded by cyclic codes. In support of this idea, the author presents a set of his results on the connection of the genetic coding system with cyclic Gray codes, which are one of many known types of cyclic codes. This opens up the possibility of using for modeling inherited cyclic biostructures those algebraic and logical theories and constructions that are associated with Gray codes and have long been used in engineering technologies: Karnaugh maps, Hilbert curve, Hadamard matrices, Walsh functions, dyadic analysis, etc. Additionally, the connections of these constructions with statistical rules of genomic DNAs and binary-genomic numbers are considered.

The Collatz conjecture, a longstanding mathematical puzzle, posits that, regardless of the starting integer, iteratively applying a specific formula will eventually lead to the value 1. This paper introduces a novel approach to validate the Collatz conjecture by leveraging the binary representation of generated numbers. Each transition in the sequence is predetermined using the Collatz conjecture formula, yet the path of transitions is revealed to be intricate, involving alternating increases and decreases for each initial value. The study delves into the global flow of the sequence, investigating the behavior of the generated numbers as they progress toward the termination value of 1. The analysis utilizes the concept of probability to shed light on the complex dynamics of the Collatz conjecture. By incorporating probabilistic methods, this research aims to unravel the underlying patterns and tendencies that govern the convergence of the sequence. The findings contribute to a deeper understanding of the Collatz conjecture, offering insights into the inherent complexities of its trajectories. This work not only validates the conjecture through binary representation but also provides a probabilistic framework to elucidate the global flow of the sequence, enriching our comprehension of this enduring mathematical mystery.

The performance of the presurgical test (preSurg) for temporal lobe epilepsy (TLE) was evaluated via video-electroencephalography (VEEG), electroencephalography (EEG), 99mTc-HmPAO single-photon emission tomography (SPECT) and 1.5 T magnetic resonance imaging (MRI) in a group of 112 men (37.0 ± 1.1 years) and 106 women (39.7 ± 1.1 years) operated on for TLE. The epileptic zone (EZ) was adequately identified to determine whether the patient reached an Engel I grade (EI) at least one year postop. Accuracy was evaluated by the coefficient α, ranging from 3 (when result = EZ) to 2 (result in the same hemisphere as the EZ), 1 (noninformative result) or 0 (EZ in the contralateral hemisphere). The simplicity of diagnosis was defined as the number of preSurg surgeries needed to identify the EZ. EI was obtained in 85.8% of patients even though 42.2% of patients had noninformative MRI results. For preSurg α was (mean ± SEM) = VEEG (2.83 ± 0.04) > MRI (2.14 ± 0.08) > EEG (1.87 ± 0.09) > SPECT (1.71 ± 0.09). The accuracy (combination of sensitivity and specificity) was calculated as follows: VEEG (0.797) > MRI (0.518) > EEG (0.446) > SPECT (0.360). The likelihood positive ratio was greater, and the likelihood negative ratio was lower for VEEG. The most relevant factor for the regression model was VEEG (3.106) > MRI (2.558) > EEG (1.905), and the factors were not significantly related to SPECT. EZs in EI patients with low simplicity were identified mainly by VEEG. A very good postoperative outcome can be obtained even in TLE patients with no lesions on MRI. The VEEG is the most reliable preSurg test and may be the only reliable test for patients with very low simplicity (i.e., difficult).single paragraph of about 200 words maximum. For research articles, abstracts should give a pertinent overview of the work. We strongly encourage authors to use the following style of structured abstracts, but without headings: (1) Background: Place the question addressed in a broad context and highlight the purpose of the study; (2) Methods: briefly describe the main methods or treatments applied; (3) Results: summarize the article’s main findings; (4) Conclusions: indicate the main conclusions or interpretations. The abstract should be an objective representation of the article and it must not contain results that are not presented and substantiated in the main text and should not exaggerate the main conclusions.

Oilseed plants of the Brassicaceae plant family are cultivated for food, feed and industrial purposes on large-scale in Europe. This review gives an overview of current market-oriented applications of new genomic techniques (NGTs) in relevant Brassicaceae oilseed crops based on a literature survey. In this respect, changes in oil quality, yield, growth and resistance to biotic and abiotic stress are goals in oilseed rape (B. napus) and camelina (C. sativa). Environmental risk assessment scenarios are developed for specific NGT applications in Brassicaceae oilseed crops with either a changed oil composition or with fitness related traits. In case of a changed oil composition an increase or decrease of polyunsaturated fatty acids (PUFA) demonstrates risks for health and survival of pollinators. In case of fitness related traits other risks were identified, i. e. an increased risk of spread and persistence of NGT plants. Furthermore, there are indications for potential disturbance of interactions with the environment, involving signalling pathways and reaction to stress conditions. It is shown that for a comprehensive risk assessment the technological potential of NGTs, the plants’ biology and the scale of releases have to be considered in combination. Therefore, the release of NGT plants into the environment for agricultural purposes will require risk assessment and monitoring of single traits as well as of combinatorial and long-term cumulative effects. In addition, risk management should develop concepts and measures to control and potentially restrict the scale of releases. This is especially relevant for NGT Brassicaceae in Europe which is a centre of diversity of this plant family.

Porcine sapovirus (PoSaV) is a significant pathogen causing diarrhea with high morbidity and mortality rates. Given its zoonotic characteristics, this study conducts a comprehensive genetic evolutionary analysis of PoSaV. Results confirmed PoSaV as the primary RNA virus in piglet feces (27.54%). Phylogenetic analysis identifies the prevalent PoSaV strain SHCM/Mega2023 in the GIII genogroup, involving a recombinant event with MK962338 and KT922089. The time tree revealed that the GIII genogroup exhibits the widest divergence time span, indicating a high likelihood of viral recombination. Further selective pressure calculations demonstrate that PoSaV was under purifying selection (dN/dS < 1), with seven positively selected sites in VP1 protein which might be related to the antigencity. In conclusion, this study presents a novel genomic evolution of PoSaV, offering valuable insights into antigenicity and vaccine research.

Background: Advancement of next-generation sequencing (NGS) technologies provides opportunities for large-scale Pharmacogenetic (PGx) studies and pre-emptive PGx testing to cover a wide range of genotypes present in diverse populations. However, NGS-based PGx testing is limited by the lack of comprehensive computational tools to support genetic data analysis and clinical decisions. Methods: Bioinformatics utilities specialized for human genomics and the latest cloud-based technologies are used for developing a bioinformatics pipeline for analyzing the genomic sequence data and reporting PGx genotypes. A database was created and integrated in the pipeline for filtering the actionable PGx variants and clinical interpretations. Strict quality verification procedures were conducted on variant calls with whole genome sequencing (WGS) dataset of the 1000 Genomes Project (G1K). The accuracy of PGx allele identification was validated using the whole genome sequencing dataset of the Pharmacogenetics Reference Materials from the Centers for Disease Control and Prevention (CDC). Results: The newly created bioinformatics pipeline, Pgxtools, can analyze genomic sequence data, identify actionable variants in 13 PGx relevant genes, and generate reports annotated with specific interpretations and recommendations based on clinical practice guidelines. Verified with two independent methods, we have found that Pgxtools consistently identifies variants more accurately than the results in the G1K dataset on GRCh37 and GRCh38. Conclusions: Pgxtools provides an integrated workflow for large-scale genomic data analysis and PGx clinical decision support. Implemented with cloud-native technologies, it is highly portable in a wide variety of environments from a single laptop to high performance computing clusters and cloud platforms for different production scales and requirements.

The 2022-2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox infections, particularly among women, to address a notable knowledge gap. This review systematically gathers and analyzes scientific literature and case reports concerning Mpox infections in women, covering a broad geographical spectrum including regions such as Buenos Aires, Brazil, Northern California, Colombia, Nigeria, Europe, Vietnam, Spain, Switzerland, and the United States. The analysis delves into various aspects of Mpox in women, including clinical features, epidemiology, psychological impacts, preparedness strategies, and case studies, with particular attention to pregnant women and those with underlying health conditions. Empirical data from multiple studies underscore the unique epidemiological and clinical patterns of Mpox in women. In the United States, a small percentage of Mpox cases were reported among cisgender women, with a notable portion involving non-Hispanic Black or African American, non-Hispanic White, and Hispanic or Latino ethnicities. The primary transmission route was identified as sexual or close intimate contact, with the virus predominantly manifesting on the legs, arms, and genital areas. Further, a study in Spain highlighted significant disparities in diagnosis delays, transmission modes, and clinical manifestations between genders, indicating a different risk profile and disease progression in women. Additionally, a case from Vietnam linked to a new Mpox sublineage in women emphasizes the role of women in the transmission dynamics and the importance of genomic monitoring. This review emphasizes the necessity for inclusive surveillance and research to fully understand Mpox dynamics across diverse population groups, including women. Highlighting gender and sexual orientation in public health responses is crucial for an effective approach to managing the spread and impact of the disease. The findings advocate for a gender-diverse assessment in health services and further research to explore the nuances of Mpox transmission, behavior, and progression among different groups, thereby enhancing the global response to Mpox and similar public health challenges.

Haemophilus influenzae is one of causative agent of invasive bacterial pathogen that affects both children and adults. Haemophilus influenzae is a pleomorphic gram-negative coccobacillus and it is a common commensal of the upper respiratory tract. It is a human-only pathogen that can cause severe invasive diseases. These bacterial infections can range from mild, such as ear infections, to severe, such as bloodstream infections. The infections typically affect children younger than 5 years old and old age person older than 65 years. They also affect people who are immunocompromised, such as those with certain medical conditions. The highest incidence rates of invasive Haemophilus influenzae disease have recently been discovered in various nations, including North America, Canada, and parts of Europe. In order to monitor the evolving nature of invasive Haemophilus influenzae disease critically reviewed data is required to capture the true status of invasiveness of the Haemophilus influenza diseases. Developing new vaccines against Haemilus influenzae is a potential solution to protect some vulnerable populations against the invasive disease due to this bacterial species. This review article thoroughly investigate recent and up-to-date biomedical science perspective development, innovation, findings, publications and current areas of scientific interest and gap including pathogenicity, diagnosis, multidrug-resistance, Molecular characterization and genetic evolution, epidemiology and immunological characteristics of Haemophilus influenzae, including specific current issues that are affecting the research and development of vaccines to treat Haemophilus influenzae non serotype b diseases and providing insight into how these problems may be overcome.

The saturation properties of symmetric and asymmetric nuclear matter have been computed using the finite range simple effective interaction having Yukawa form-factor. The results of higher order derivatives of the energy per particle and the symmetry energy computed at saturation, namely, Q0, Ksym, Kτ, Qsym, are compared with the corresponding range of values extracted from studies involving theory, experiment and astrophysical observations. The ability of the equations of state computed with this simple effective interaction in predicting the threshold mass for prompt collapse in binary neutron star merger and gravitational redshift have been examined in terms of the compactness of the neutron star and the incompressibility at the central density of the maximum mass star. The correlations existing between neutron star properties with the nuclear matter saturation properties have been analyzed and compared with the predictions of other model calculations.

Abstract Background: Numerous studies have demonstrated that the amalgamation of populations belonging to the same breed or closely related breeds leads to enhanced accuracies in genomic predictions (GP). Extensive experimentation with diverse Bayesian and Genome-enabled best linear unbiased prediction (GBLUP) models has been conducted to explore multi-breed genomic selection (GS) in livestock, ultimately establishing they as successful approaches for predicting genomic estimated breeding value (GEBV). This study aimed to examine the efficacy of BayesR and GBLUP model with different weighted genomic relationship matrices (GRM) in making genomic predictions for three distinct beef cattle breeds. Subsequently, we conducted a comparative analysis of the predictive accuracy pertaining to various marker densities and genetic correlations across three distinct beef cattle breeds. This investigation aimed to identify the optimal approach for enhancing the predictive accuracy of multi-breed genomic selection in beef cattle. Results：Genetic relationship matrices revealed moderate similarities between YL and the other breeds, with a striking genetic similarity of 0.87 between WG and HX. In HX cattle, BayesR demonstrated an enhancement in prediction accuracy, achieving 0.52 with HD and 0.46 with WGS, a marked improvement over 0.41 with HD and 0.42 with WGS in GBLUP. In WG and YL breeds, both methods showed comparable accuracies with HD, but BayesR slightly outperformed GBLUP with WGS. Further, multi-breed GS analysis indicated that BayesR consistently surpassed GBLUP in prediction accuracy, particularly with WGS data. For instance, in a combined HX and WG reference population, BayesR achieved a superior accuracy of 0.53 with WGS in HX cattle, a significant enhancement over GBLUP models. The study also underscores the advantage of incorporating multiple breeds in the reference population, which improved prediction accuracy, underscoring the value of broad-based genomic selection strategies. Conclusion: The results show that accuracy of multi-breed genomic predictions was higher with BayesR than with GBLUP, especially for the distantly genetic relationship between reference and validation breeds. Further improvements of multi-breed accuracy of genomic predictions could be achieved by increasing the density of the SNP marker. These findings underscore that BayesR providing a substantial improvement in genomic prediction and the importance of considering genetic relationships in the development of GS strategies for multi-breed cattle populations. Further research is warranted to optimize GRM construction and to explore alternative models for genomic prediction across breeds.

Background: Atypical teratoid/rhabdoid tumor (AT/RT) is an uncommon and aggressive pediatric central nervous system neoplasm. However, a universal clinical consensus or reliable prognostic evaluation system for this malignancy is lacking. Our study aimed to develop a risk model based on comprehensive clinical data to assist in clinical decision-making. Methods: We conducted a retrospective study by examining data from the Surveillance, Epidemiology, and End Results (SEER) repository, spanning 2000 to 2019. The external validation cohort was sourced from the Children's Hospital Affiliated to Chongqing Medical University, China. To discern independent factors affecting overall survival (OS) and cancer-specific survival (CSS), we applied Least Absolute Shrinkage and Selection Operator (LASSO) and Random Forest (RF) regression analyses. Based on these factors, we structured nomogram survival predictions and initiated a dynamic online risk-evaluation system. To contrast survival outcomes among diverse treatments, we used propensity score matching (PSM) methodology. Molecular data with the most common mutations in AT/RT were extracted from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Results: The annual incidence of AT/RT showed an increasing trend (APC, 2.86%; 95% CI:0.75-5.01). Our prognostic study included 316 SEER database participants and 27 external validation patients. The entire group had a median OS of 18 months (range 11.5 to 24 months) and median CSS of 21 months (range 11.7 to 29.2). Evaluations involving C-statistics, DCA, and ROC analysis underscored the distinctive capabilities of our prediction model. An analysis via PSM highlighted that individuals undergoing triple therapy (integrating surgery, radiotherapy, and chemotherapy) had discernibly enhanced OS and CSS. The most common mutations of AT/RT identified in the COSMIC database were SMARCB1, BRAF, SMARCA4, NF2, and NRAS. Conclusions: In this study, we devised a predictive model that effectively gauges the prognosis of AT/RT and briefly analyzed its genomic features, which might offer a valuable tool to address existing clinical challenges.

Leukemia encompasses diverse blood cancers marked by the unchecked growth and developmental blockage of myeloid or lymphoid precursor cells within the bone marrow and the bloodstream. Treatment traditionally involves intensive chemotherapy or hematopoietic stem cell transplantation, albeit these approaches often yield severe side effects and encounter resistance from leukemia cells. Hence, the quest for novel therapies targeting leukemic cells selectively is paramount to enhancing leukemia outcomes. Exploring natural products is a promising avenue for pursuing effective chemotherapy and preventive measures against leukemia. These compounds serve as a crucial wellspring for drug development and offer a source of biologically active elements for potential therapeutic interventions in leukemia. The enzyme telomerase plays a vital role in stabilizing chromosomes by adding DNA sections to the end of chromosomes during the mitotic cycle. Notably, hTERT mRNA expression strongly correlates with telomerase activity, making it a potential target for therapeutic intervention without adverse systemic effects. Telomerase inhibition is a promising target in cancer therapy, especially in combination with natural ingredients, demonstrating less cytotoxicity than chemotherapies.

Background: Chronic Myeloid Leukemia (CML) is initiated in the bone marrow due to the chromosomal translocation t(9;22), resulting in the fusion oncogene BCR-ABL. Tyrosine kinase inhibitors (TKIs) targeting BCR-ABL have transformed fatal CML into an almost curable disease. However, TKIs lose efficacy during disease progression, and the mechanism of CML progression remains to be fully understood. Additionally, common molecular biomarkers for CML progression are lacking. Our studies previously detected ANKRD36 (c.1183_1184 delGC and c.1187_1188 dupTT) associated exclusively with advanced phase CML. However, clinical validation of this finding was pending. Therefore, this study aimed to clinically validate mutated ANKRD36 as a novel biomarker of CML progression. Materials and Methods: The study enrolled 124 patients in all phases of CML, recruited from Mayo Hospital and Hameed Latif Hospital in Lahore, Punjab, between January 2020 and September 2023. All response criteria were adopted from the European LeukemiaNet guideline 2020. Informed consent was obtained from all study subjects. The study was approved byscientific and ethical review committees of all participating centers. Sanger sequencing was employed to detect ANKRD36mutations in CML patients in accelerated phase (AP) (n=11) and blast crisis (BC) (n=10), with chronic-phase CML (CP-CML) patients as controls (n=103). Samples were processed using Big Dye Terminator Cycle Sequencing Ready Reaction kits and sequenced using ABI Prism 3730 Genetic Analyzer, and sequencing using forward and reverse primers for ANKRD36.Results: During our study, 17% of CML patients progressed to advanced phases AP-CML n= 11 (8.9%) and BC-CML n=10(8.1%). The chronic- and advanced-phase patients showed significant difference with respect to male-to-female ratio, hemoglobin level, WBC count, and platelet count. Sanger sequencing detected ANKRD36 mutations c.1183_1184 delGC and c.1187_1185 dupTT exclusively in all AP- and BC-CML patients but in none of the CP-CML patients. Nevertheless, mutations status was not associated with male-to-female ratio, hemoglobin level, WBC count, and platelet count, which makes ANKRD32 as an independent predictor of early and terminal disease progression in CML. Conclusions: The study confirms ANKRD36 as a novelgenomic biomarker for early and late CML progression. Further prospective studies should be carried out in this regard. ANKRD36, although fully uncharacterized in humans, shows the highest expression in bone marrow, particularly myeloid cells. Functional integrated genomic studies are recommended to further explore the role of ANKRD36 in the biology and pathogenesis of CML.

Background: To describe epidemiological characteristics and perform a SARS-CoV-2 genomic surveillance in the southeastern region of São Paulo state. Methods: During the first months of 2022, we compared weekly SARS-CoV-2 infection prevalence considering age, Ct value and variants lineages. Results: An increase in the number of SARS-CoV-2 positive cases until the fourth epidemiological week were observed. From the 4th epidemiological week onwards, the number of tests for SARS-CoV-2 diagnosis began to decrease, but the number of positive samples for SARS-CoV-2 remained high, reaching its most expressive level with a rate of 60% of infected individual cases. In this period, we observed a growing increase in SARS-CoV-2 infection within the age group 0-10 throughout the epidemiological weeks, from 2.8% in the 1st epidemiological week to 9.2% in the 8th epidemiological week. We further observed significantly higher Ct values within younger patients samples compared to other older age groups. According to lineage assignment, SARS-CoV-2 (BA.1) was the most prevalent (74.5%) in the younger group, followed by BA.1.1 (23%), BA.2 (1.7%) and Delta (1%). Phylogenetic analysis showed that BA.2 sequences clustered together, indicating sustained transmission of this Omicron VOC sublineage by that time. Our results suggest the initial dissemination steps of the Omicron’s sublinage BA.2 into the younger group, due specific genomic features of the detected sequences. Conclusion: These data provide interesting results related to the spread, emerging and evolution of the Omicron variant in the Southeast Brazilian population.

The COVID-19 pandemic caused by the RNA virus SARS-CoV-2, has had a significant impact not only on bodily metabolism but also at the genomic level. This study utilizes a bibliometric approach to map and identify the relationship between COVID-19 and DNA damage, genomic instability, and cell cycle deregulation. The research began with the development of in-depth research questions and conducted two rounds of literature search in the Scopus database with stringent filters to ensure relevance and accuracy. From an initial 1098 documents, 576 relevant documents were selected for further analysis. The collected data was then visualized using bibliometric methods, enabling the identification of important patterns, trends, and relationships among the research variables. Key findings indicate that DNA damage, which can induce apoptosis, is the worst impact of the infection on cells. Term frequency analysis and science mapping revealed a close relationship between "DNA damage" and "apoptosis". Furthermore, discussions on genomic instability highlight telomere regulation issues, while cell cycle deregulation during virus replication in mammalian cells indicates the importance of maintaining cell membrane integrity.This study confirms the importance of bibliometric analysis in detecting and understanding the impact of COVID-19 at the genomic level, proposing several potential research targets and enhancing our understanding of the biological response to viral infection.

This study provides an in-depth examination of the binary system of n-Nonadecane and 1-Octadecanol, representative of plant cuticular waxes. It emphasizes the crystallization and phase transitions in this hydrocarbon mixture. Using Differential Scanning Calorimetry (DSC) and Fourier Transform Infrared (FTIR) spectroscopy, the research uncovers detailed thermal properties and phase behaviors. The findings reveal the distinct phase transitions and enthalpy changes of each component in the binary system. This research is significant for its implications in under-standing the structural properties of plant waxes. Such insights are crucial for enhancing the effi-ciency of fertilizer and pesticide absorption in plant leaves, with broad applications in bionics and materials science. This study not only furthers the understanding of identifying specific phase transitions for each compound, facing challenges in detecting subtle changes using DSC. The re-search enhances understanding of plant cuticle waxes through FTIR analysis, revealing intricate molecular interactions and structural complexities. but also opens avenues for improved agri-cultural practices and material engineering, potentially influencing future innovations in these fields.

The purpose of this study is to analyze the causes of cost variation in natural disaster prevention projects (NDPP) in Gyeongsangbuk-do and to develop effective cost and risk management strategies. The study collected data by conducting an online survey of 244 stakeholders. Binary logistic regression was used to analyze the impact of various variables on cost deviation, in-cluding project management risk (PMR), project costing and execution risk (PCER), project exe-cution strategy risk (PESR), construction project risk (CPR), project cost and schedule risk (PCSR), project management challenges (PMC), and construction project subcontractor and safety man-agement (CPSSM). The results showed that PMR (OR=3.744, 95% C.I. [1.657, 8.457]), PCER (OR=5.068, 95% C.I. [2.236, 11.484]), PESR (OR=3.447, 95% C.I. [1. 853, 6.413]), CPR (OR=2.292, 95% C.I. [1.020, 5.151]), PCSR (OR=4.817, 95% C.I. [2.250, 10.317]), PMC (OR=2.954, 95% C.I. [1.452, 6. 013]), and CPSSM (OR=2.419, 95% C.I. [1.297, 4.515]) had statistically significant effects on cost deviation. In particular, PMR, PCER, and PESR were identified as the main causes, and the effects of additional factors such as CPSSM were also important. The developed predictive model plays an important role in helping stakeholders of NDPP to manage risks in advance and take appro-priate preventive measures to ensure the success of the project. This study empirically supports the theoretical hypotheses of previous studies and provides a clear understanding of the causes of cost deviation in NDPP, which provides important insights for strategic decision-making and provides a new perspective on risk management.

The author previously reported an experimental result of evolutionary reinforcement learning of neural network controllers for the pendulum task. In the previous work, a conventional multilayer perceptron was employed in which connection weights were real numbers. In this study, the author experimentally applies an evolutionary algorithm to the reinforcement training of binary neural networks. In both studies, the same task and the same evolutionary algorithm are utilized, i.e. the pendulum control problem and Evolution Strategy respectively. The only differences lie in the memory size per connection weight and the model size of the neural network. The findings from this study are (1) the performance of the binary MLP with 32 hidden units was inferior to that of the real-valued MLP with 16 hidden units; however, this difference was not statistically significant (p >.05); (2) the trained binary MLP successfully swung the pendulum swiftly into an inverted position and maintained its stability after inversion, as the real-valued MLP had done; and (3) the memory size required to record the binary MLP with 32 hidden units is 3.1% or 6.2% of the memory size required to record the real-valued MLP with 16 hidden units.

Chronic Myeloid Leukemia, resulting due to chromosomal aberration t(9;22) through formation of oncogenic BCR-ABL fusion oncogene. Modern BCR-ABL inhibitors, called TKIs, have revolutionized CML treatment. CML has three stages: chronic, accelerated, and blast crisis. TKIs work well in CP-CML, where patients survive as long as the normal population, but they don't work in AP- and BC-CML. Even with advances in treatment, BC-CML has an average overall survival of less than a year, giving oncologists little time to clinically intervene. Oncologists can delay or prevent CML advancement by detecting patients at risk of disease progression early and making timely treatment decisions, especially with third and fourth generation TKIs. However, no universal molecular biomarkers exist to diagnose CML patient groups at risk of disease progression. A recent study found that all BC-CML patients have mutant FANCD2. Our study was designed to detect mutant FANCD2 in AP-CML (early progression phase) to investigate its potential as a novel biomarker of early CML progression from chronic phase to accelerated phase due to the urgent need for such a biomarker. Our study comprised of 123 CP-CML (control group) and 60 AP-CML patients (as experimental group) from Hayatabad Medical Complex, Peshawar, Pakistan, from Jan 2020 to July 2023. DNA was extracted from the patients and FANCD2 gene was sequenced using Illumina next generation sequencer (NGS) Illumina MiSeq sequencer. NGS analysis revealed a unique splice site mutation in FANCD2 gene (c. 2022-5C>T). This mutation was detected in all CP-CML patients but in none of CP-CML. The mutation was confirmed by Sanger sequencing. FANCD2 is member of Fanconi anemia (FA-) pathway gene involved in DNA repair and genomic instability. Therefore, our studies show that FANCD2 (c. 2022-5C>T) mutation as a very specific molecular biomarker for early CML progression. We recommend to clinical validate this biomarker is prospective clinical trials.

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of hybrid (F1) and its parents (w30 and 082). Analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above parental expression level, more actively expressed genes and up-regulated DEGs in F1. Further study revealed that the DEGs detected in F1 and its parents were mainly involved in response to auxin, plant hormone signal transduction, DNA metabolic process, Purine metabolism, starch and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of B. rapa. The analysis of 3D genome data revealed that hybrid F1 tend to contain more transcriptionally active A compartments after hybridization. Additionally, F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change of activated TAD was higher than repressed TAD. More specific TAD boundaries were detected between parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. Among them, we found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggest that genomic structural variants, such as TADs and A/B compartments, may affect gene expression and contribute to heterosis in B. rapa. This study provides further insight into the molecular mechanism of heterosis in B. rapa.

During geomagnetic storms, which are a result of solar wind interaction with the Earth’s magnetosphere, geomagnetically induced currents (GICs) begin to flow in the long-distance high-voltage power grids on the Earth’s surface. It causes a number of negative phenomena that affect the normal operation of the entire electric power system. To investigate the nature of the phenomenon and its possible effects on transformers, a GIC monitoring system was created in 2011, the devices of which were installed at five substations of the Kola-Karelian power transit in northwestern Russia. Over 12 years of operating the system a large amount of data has been accumulated, which cannot be analyzed manually within a reasonable amount of time. To analyze the constantly growing volume of recorded data effectively, a method for automatic classification of GIC in autotransformer neutral was proposed. The method is based on a continuous wavelet transform of the neutral current data combined with a convolutional neural network (CNN) to classify the obtained scalogram images. As the result of comparing four CNNs with different architectures, a model that showed excellent GIC classification performance on the validation set (100.00% accuracy and loss of 0.0115) was chosen.

We consider boundary value problems for a nonlinear mass transfer model, which generalizes the classical Boussinesq approximation, under inhomogeneous Dirichlet boundary conditions for the velocity and the substance’s concentration. It is assumed that the leading coefficients of viscosity and diffusion and the buoyancy force in the model equations depend on concentration. We develop mathematical apparatus of studying inhomogeneous boundary value problems under consideration. It is based on using of a weak solution of the boundary value problem and construction of liftings of the inhomogeneous boundary data. They remove the inhomogeneity of the data and reduce original problems to equivalent homogeneous boundary value problems. Based on this apparatus we will prove the theorem of the global existence of a weak solution to boundary value problem under study and establish important properties of the solution. In particular, we will prove the validity of the maximum principle for the substance’s concentration. We will also establish sufficient conditions for the problem data, ensuring the local uniqueness of weak solutions.

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease- and species-specific and contingent upon a multitude of factors. The field of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favourable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate to high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems, AI algorithms, and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

During the COVID-19 pandemic, immunosuppressed patients showed prolonged SARS-CoV-2 infections, with several studies reporting the accumulation of mutations in the viral genome. The weakened immune system present in these individuals, along with the effect of antiviral thera-pies, are thought to create a favourable environment for intra-host viral evolution and have been linked to the emergence of new viral variants, which strongly challenged the containment measures and some therapeutic treatments. To assess whether an impaired immunity could lead to an increased instability of viral genomes, longitudinal nasopharyngeal swabs were collected from eight immunocompromised patients and fourteen non-immunocompromised subjects, all undergoing SARS-CoV-2 infection. Intra-host viral evolution was compared between the two groups through deep sequencing, exploiting a probe-based enrichment method to minimize the possibility of artefactual mutations commonly generated in amplicon-based methods, which heavily rely on PCR amplification. Although, as expected, immunocompromised patients expe-rienced significantly longer infections, the acquisition of novel intra-host viral mutations was similar between the two groups. Moreover, a thorough analysis of viral quasispecies showed that the variability of viral populations in the two groups is comparable not only at the consensus level, but also when considering low frequency mutations. This study suggests that a compro-mised immune system alone does not affect SARS-CoV-2 within-host genomic variability.

Furunculosis, caused by Aeromonas salmonicida, poses a significant threat to both salmonid and non-salmonid fish in diverse aquatic environments. This study explores the genomic intricacies of re-emergent A. salmonicida outbreaks in Atlantic salmon (Salmo salar). Previous clinical cases have exhibited pathological characteristics, such as periorbital hemorrhages and gastrointestinal abnormalities. Genomic sequencing of three Chilean isolates (ASA04, ASA05, and CIBA_5017) and 25 previously described genomes determined the pan-genome, phylogenomics, insertion sequences, and restriction-modification systems. Unique gene families have contributed to an improved understanding of the psychrophilic and mesophilic clades, while phylogenomic analysis has been used to identify mesophilic and psychrophilic strains, thereby further differentiating between typical and atypical psychrophilic isolates. Diverse insertion sequences and restriction-modification patterns have highlighted genomic structural differences and virulence factor predictions can emphasize exotoxin disparities, especially between psychrophilic and mesophilic strains. Thus, a novel plasmid was characterized, which emphasized the role of plasmids in virulence and antibiotic resistance. The analysis of antibiotic resistance factors revealed resistance against various drug classes in Chilean strains. Overall, this study elucidates the genomic dynamics of re-emergent A. salmonicida and provides novel insights into their virulence, antibiotic resistance, and population structure. However, rigorous monitoring and control in aquaculture remain crucial to mitigate the spread of antibiotic resistance.

In this research a neccessary and sufficient condition for the proof of the Binary Goldbach conjecture is established. It is established that the square of all natural numbers greater or equal to 2 have an additive partition equal to the sum of the square of a natural number greater or equal to zero and a Goldbach partition semiprime. All Goldbach partition semiprimes are odd except 4. This finding is in itself proof all composite even numbers have at least Goldbach partition. The result of the proof of the Binary Goldbach conjecture is used to prove the Andrica and Legendre conjectures. The Riemann hypothesis is examined and sources of non trivial zeroes outside the critical strip are discussed. An example example of a non-trivial zero outside the critical strip is given

The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called ‘the clones of high risk’ often drive the spread of resistance within particular species. Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. In this dataset, we present the results of a comprehensive genomic epidemiology analysis of 17,546 genomes of a dangerous bacterial pathogen Acinetobacter baumannii. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic blaOXA-51-like gene variants, capsular (KL) and oligosaccharide (OCL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to nine known international clones of high risk. The presence of antimicrobial resistance genes within the genomes is also reported. These data will be useful for researchers in the field of A. baumannii genomic epidemiology, resistance analysis and prevention measure development.

The groundbreaking Advanced Forest-Based Tagging Framework (AFTF) represents a paradigm shift in the domain of information extraction from medical texts. AFTF introduces a novel dual-binary tree structure that redefines how entity-relation triples are extracted. This innovative approach directly tackles the limitations of traditional linear and graph-based methods, effectively addressing challenges related to overlapping triples and computational efficiency. The AFTF model stands as a beacon of excellence, surpassing established baselines by significant margins in comprehensive evaluations on two pivotal medical datasets. Notably, AFTF achieves remarkable improvements in F1 scores, showcasing its prowess in accurate information extraction from complex medical narratives. Beyond its exceptional performance in the medical domain, AFTF exhibits remarkable versatility. This adaptability is vividly demonstrated through its robust performance across three diverse public datasets, further affirming its position as a versatile and reliable solution for information extraction tasks. This paper provides a comprehensive exposition of the AFTF architecture, shedding light on its innovative design principles and its efficient handling of intricate medical texts. AFTF represents a groundbreaking step forward in the realm of information extraction, promising enhanced accuracy, efficiency, and adaptability for a wide range of applications.

Fat has a high energy density and excessive fatness has been recognized as a problem for egg production and the welfare of chickens. The identification of a genetic polymorphism controlling fat deposition would be helpful to select against excessive fatness in the laying hen. This study aimed to estimate genomic heritability and identify the genetic architecture of abdominal fat deposition in a population of chickens from a Dongxiang blue-shelled local breed crossbred with the White Leghorn. A genome-wide association study wase conducted on abdominal fat percentage, egg production and body weights using a sample of 1534 hens genotyped with a 600K Chicken Genotyping Array. The analysis yielded a heritability estimate of 0.19 ± 0.04 for abdominal fat percentage, 0.56 ± 0.04 for body weight at 72 weeks, 0.11 ± 0.03 for egg production and 0.24 ± 0.04 for body weight gain. The genetic correlation of abdominal fat percentage with egg production between 60 and 72 weeks of age was 0.35 ± 0.18. This implies a potential trade-off between these two traits related to allocation of resource. Strong positive genetic correlations were found between fat deposition and weight traits. A promising locus close to COL12A1 on chromosome 3, associated with abdominal fat percent, was found in the present study. The other region located around HTR2A on chromosome 1, where allele substitution was predicted to be associated with body weight gain, accounted for 2.9% of phenotypic variance. Another region located on chromosome 1, but close to SOX5, was associated with egg production. These results may be used to influence the balanced genetic selection for laying hens.

The quadratic unconstrained binary optimization (QUBO) is a classic NP-hard problem with an enormous number of applications. Local search strategy (LSS) is one of the most fundamental algorithmic concepts that has been successfully applied to a wide range of hard combinatorial optimization problems. One LSS that has gained the attention of researchers is the r-flip (also known as r-Opt) strategy. Given a binary solution with n variables, the r-flip strategy ‘flips’ r binary variables to get a new solution if the changes improve the objective function. The main purpose of this paper is to develop several results for implementation of r-flip moves in QUBO, including a necessary and sufficient condition that when a 1-flip search reaches local optimality, the number of candidates for implementation of the r-flip moves can be reduced significantly. The results of the substantial computational experiments are reported to compare an r-flip strategy embedded algorithm and a multiple start tabu search algorithm on a set of benchmark instances and three very-large-scale QUBO instances. The r-flip strategy implemented within the algorithm makes the algorithm very efficient, very high-quality solutions within a short CPU time.

Recent dramatic reductions in the timeframe in which genomic sequencing can deliver results means its application in time-sensitive screening programs such as newborn screening (NBS) is becoming a reality. As genomic NBS (gNBS) programs are developed around the world, there is an increasing need to address the ethical and social issues that such initiatives raise. This study therefore aimed to explore the Australian public’s perspectives and values regarding key gNBS characteristics and preferences for service delivery. We recruited English-speaking members of the Australian public over 18 years of age via social media; 75 people aged 23-72 participated in one of 15 focus groups. Participants were generally supportive of introducing genomic sequencing into newborn screening, with several stating that adoption of such revolutionary and beneficial technology was a moral obligation. Participants consistently highlighted receiving an early diagnosis as the leading benefit, which was frequently linked to the potential for early treatment and intervention, or access to other forms of assistance, such as peer support. Informing parents about the test during pregnancy was considered important. This study provides insights into the Australian public’s views and preferences to inform the delivery of a gNBS program in the Australian context.

This research identifies the resilience factors of tax centers in Cameroon. To do so, we use binary logistic regression on data collected from tax revenue mobilization centers (TRMC). the results show that the digitization of the tax system and leadership are factors in absorbing the crisis. Access to electricity and staff at the center are the recovery factors for the level of revenue after the crisis. We recommend that public institutions improve the digitalization processes of tax administrations. The transmission channels of digitization such as access to electricity and telecommunications networks must be ensured in the tax centers. Furthermore, we propose to increase the number of tax centers or to build tax kiosks to reduce the distance between taxpayers and their centers of attachment.

Cotton is the most important natural fiber cash crop, which has high commodity economic benefits and provides an important material foundation for China's construction. With the improvement of textile technology and living standard, higher requirements are put forward for raw cotton quality. Traditional cotton breeding methods need typing and selection. With the development of biotechnology and the research of genomics, genomic selection has been widely used in cotton breeding. Genomic selection is a new breeding method, which can be selected and bred by constructing a prediction model and using high-density molecular markers covering the whole genome. In this study, the application of various genomic selection models in cotton fiber quality was explored, which provided more reliable information for genetic breeding improvement in the future, thus helping to improve the efficiency of actual cotton breeding.

Published in July 2018, TAILORx aimed to establish non-inferiority of endocrine therapy (ET) compared to addition of chemotherapy (CHT-ET) in hormone receptor positive, human epidermal receptor 2 negative (HR+/HER2-) breast cancer (BC) patients with a 21-gene intermediate (11-25) recurrence score (RS). While this hypothesis proved correct, the study did show benefit of addition of chemotherapy (CHT) in a subgroup of women under 50 years of age, and particularly in the RS 16-25. The aim of this present study was to look at how TAILORx findings, including changes in RS categories, impacted CHT implementation at one oncologic center in Basel, Switzerland, and to identify main factors leading to these changes. Methods: We conducted a retrospective study on HR+/HER2-, BC patients who underwent 21-gene genomic testing between 2010-2021, at our center. Patients with metastatic disease were not included. We identified 326 eligible patients, of which 165 had a BC diagnosis before TAILORx (cohort A) and 161 after TAILORx publication (cohort B). Results: Demographic and tumor characteristics were similar in the two cohorts, although cohort B included significantly more women under the age of 50 when compared to A (34% vs. 24%, p<0.001). Median age and mean RS results were comparable 59 (IQR 16) in A and 58 (IQR 19) years in B and 17.72 (SD9.59) in A and 17.89 (SD9.53) in B, respectively. Patients in cohort A were slightly more overweight when compared to B (55% vs. 40% respectively, p<0.001). Most patients had stage II tumors of NST histologic type. Tumors in cohort B had higher Ki-67 than cohort A (39% vs. 32%, p=0.010). When compared based on manufacturer’s and based on TAILORx thresholds there were no significant differences in RS distribution. However, changes in score category led to shifts in patient population distribution, leading to a 40% drop in the low RS (from 60% to 20%), a doubling in the intermediate RS (from 30% to 60%) and an increase of 5% in the high RS (from 8-10% to 15%). Most patients had conservative surgery, adjuvant radiotherapy (RT) and ET. Overall CHT recommendation and application did not differ significantly in B vs. A. There was a reduction of 1% in the intermediate RS (11-25) and an increase of 13% CHT-ET application in the high RS (>26) category. In cohort B we noticed an increase in CHT-ET application among women <50 years old (by 12.5%), in lobular carcinomas (by 10%), grade 3 tumors (by 2%), node positive BC (by 3%) and node negative (by 2%). Tumor board recommendation for CHT dropped by 1% in the post TAILORx era, with a notable reduction of 5% in the intermediate RS (11-25) category. However, overall CHT administration rate was 19% in cohort A and 22% in B (p=0.763). Tumor Board recommended CHT for 90% of the BC patients that would have otherwise been assigned to CHT according to new RS guidelines in A and for 85% in B, showing a trend for undertreatment. Logistic regression analysis showed significance of age in both cohort A (OR 1.05, 95% CI 1.01-1.11, p=0.03) and cohort B (OR 0.89, 95% CI 0.84-0.94), p<0.001), and of nodal status in both cohort A (=R 3.32 95% CI 1.09-10-06, p=0.034) and cohort B (OR 3.31, 95% CI 1.29-8.53, p=0.013), while intermediate and high RS seem to be more relevant in cohort A (OR 0.12, 95% CI 0.03-0.43, p=0.01 and OR 0.04, 95% CI 0.01-0.21, p<0.01). Overall logistic regression analysis showed relevance of age (OR 0.93, 95% CI 0.08-0.97, p=0.001), pN (OR 4.77, 95% CI 2.03-11.22, p<0.001) and RS categories (RS 11-25: OR 0.02, 95% CI 0.01-0.07, p<0.001; RS>26: OR 617.93, 95% CI 57.97-6587.16, p<0.001). Conclusion: Our findings are similar to those reported across several studies: while tumor board recommendation for CHT decreases in the intermediate RS category, there is an increase being reported in the high RS category, leading to overall minor changes in CHT application. Administration of CHT-ET seems to be increasing among younger women, with unfavorable histo-pathological factors, such as lobular carcinoma and G3 histologic grade. Before TAILORx there is a tendency for undertreatment (-10%), especially among older BC patients, which seems to be maintained and even deepened (-15%) in the post TAILORx era, pointing to a personalized decision-making approach among Swiss oncologists.

The methods used to introduce CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out of target genes in different fruit trees species including tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses have been firstly described in this review. The application of this gene editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits in elite cultivars without changing other traits. However, at this moment, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are the genotype-dependent or the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, latest news on the legislation and regulations about the use of plants modified through CRISPR/Cas systems has been also discussed.

The port environments have some structures that still need regular control. However, the nature of these environments presents a number of challenges in determining an accurate vehicle position and consequently performing successful image similarity detection. These scenarios, however, can have poor visibility conditions and are highly dynamic, making place recognition difficult because the appearance of a place can change over time. Under these operational conditions, imaging sonars are a promising solution. There are some factors that affect the quality of the captured images, but the fact that they do not suffer from haze is a plus. Therefore, in this paper, a purely acoustic similarity detection method based on forward-looking sonar (FLS) data is proposed to overcome the inherent perceptual problems in a port scenario. Considering the lack of available data in this context and to facilitate the variation of environmental parameters and sensor configurations, a port scenario was simulated using the Stonefish simulator. Experiments were conducted on predefined trajectories near structures. The place recognition approach performs better compared to the results obtained with optical imagery. In general, it provides a good compromise in terms of distinctiveness and achieves a performance of 87.5% when appropriate constraints and assumptions are made.

Imaginary dimensions in physics require an imaginary set of base Planck units and some negative parameter $c_n$ corresponding to the speed of light in vacuum $c$. The second, negative fine-structure constant $\alpha_2^{-1} \approx -140.178$ present in Fresnel coefficients for the normal incidence of electromagnetic radiation on monolayer graphene leads to the imaginary Planck units. Furthermore, it sets $c_n \approx -3.06 \times 10^8~\text{[m/s]}$. It follows that electric charges are the same in real and imaginary dimensions. Neutron stars and white dwarfs, objects emitting perfect black-body radiation, need energy exceeding their mass-energy equivalence ratios. Complex energies are defined in terms of real and imaginary Planck units. Their imaginary parts, inaccessible for direct observation, store the excess of these energies. It follows that black holes are fundamentally uncharged, charged micro neutron stars and white dwarfs with masses lower than $5.7275 \times 10^{-10}~[\text{kg}]$ are unphysical, and the radii of white dwarfs' cores are limited to $R_{\text{WD}} < 6.7933~G M_{\text{WD}}/c^2$. It is conjectured that the maximum atomic number $Z=238$. A black-body object is in the equilibrium of complex energies of masses, charges, and wavelengths if its radius $R_\text{eq} \approx 2.7665~G M_{\text{BBO}}/c^2$, which corrects the value of the photon sphere radius $R_{\text{ps}}=3G M/c^2$, taking into account the value(s) of the fine-structure constant(s), which is otherwise neglected in general relativity.

The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection across all studied breeds. Both of these genes are associated with muscular development in pigs and other species. Furthermore, in the Large White breed a number of genes were detected by the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In Duroc breed a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain and other similar traits. Overall, our results have identified a number of genomic regionsthat are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.

Understanding the genetic architecture of a disease is crucial for development of valid diagnostic and therapeutic interventions. The analysis of genomic variations associated with pathological conditions is the starting point for uncovering disease-causing pathways (candidate processes). However, the complexity of intergenic and genetic-environmental interactions hinders the identification of pathogenic values of genomic changes. Furthermore, heredity, epigenetics and somatic mosaicism make the interpretation of genomic data even more sophisticated. To succeed, a variety of bioinformatic techniques are applied. Here, reviewing own and literature data, knowledge-based prioritization of genomic variations is described. Theoretical basis of the knowledge-based prioritization is given with a special regard to gene ontology, heuristics, hermeneutics (genomic hermeneutics) and analytics. Practical and methodological issues of prioritization using ontology- or pathway-based systems analysis are considered in the light of optimistic and realistic scenarios of cumulative phenotypic effects of the variome (the whole set of genomic variations in an individual or specific set of genomic variations for a phenotypic outcome). In the present communication, copy number variants (CNVs) in children with neurodevelopmental diseases are used as a practical foundation for the prioritization, inasmuch as these genome variations are systematically overlooked in the so-called NGS era. Nonetheless, it is highly likely that the prioritization is applicable to almost all types of genomic variations (e.g. chromosome abnormalities, gene mutations, functional synonymous variants etc.). The present methodology seems to be a valuable addition to current biomedical science widening the opportunities for medical genomics and genetics.

The dengue virus (DENV) is an arbovirus belonging to the Flaviviridae family; the species comprises four antigenically distinct serotypes (DENV–1, DENV–2, DENV–3, and DENV–4), which are further subdivided into genotypes. The virus is transmitted to humans through mosquito bites, primarily from the Aedes spp. genus. Dengue is endemic in various parts of the world, including tropical and subtropical regions of Asia, Latin America, Africa, and Oceania. In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of arboviral disease cases, particularly dengue. This study aimed to monitor DENV circulation within the state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. During this period, both DENV-1 and DENV-2 serotypes were identified. Our findings confirm the circulation of DENV serotypes 1 and 2 in Tocantins, affecting males and females equally, with younger age groups (4 to 43 years old) being the most susceptible. Phylogenetic analysis revealed that the circulating viruses belong to DENV–1 genotype V American and DENV–2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 Genotype V sequenced here is closely related to genomes previously sequenced in the state of São Paulo. Regarding DENV-2 genotype III genomes, these are clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. In both cases, our results suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the significant impact of major population centers in Brazil on virus dispersion, including other Latin-American countries and the USA. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here reveal the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of the DENV and the ongoing significance of surveillance efforts in supporting public health policies.

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and quantitative trait loci (QTLs) for grain length, co-detected by all GAPIT models on (Chr) 1–3, 5, 7, and 11), were qGL1-1BFSG (AX-95918134, Chr1: 3820526 bp) explains 65.2%–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1BFSG (AX-273945773, Chr1: 5623288 bp) for grain width explains 15.5%–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1Blink, AX-279261704, Chr1: 18023142 bp) and 54.9% (qGT2-1Farm, AX-154787777, Chr2: AX-154787777 bp) of the observed PVE. For t length-to-width ratio, the qLWR2BFSG (AX-274833045, Chr2: 10000097 bp) explains nearly 15.2%–32% of PVE for LWR. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6BFSG, AX-115737727, 28484619 bp) and explains 32.8%–54% of PVE. The qTGW6BFSG QTL coincides with qGW6-1Blink for grain width and explained 32.8%–54% of PVE. Putative Candidate genes pooled from major QTLs for each grain traits have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs.

We have identified a new human voltage-gated potassium channel (hKv1.3) blocker, NnK-1, in the jellyfish Nemopilema nomurai, based on its genomic information. The gene sequence encoding NnK-1 contains 5,408 base pairs, with five introns and six exons. The coding sequence of the NnK-1 precursor is 894 nucleotides long and encodes 297 amino acids, containing five presumptive ShK-like peptides. An electrophysiological assay demonstrated that the chemically synthesized fifth peptide, NnK-1, is an effective hKv1.3 blocker. A multiple sequence alignment with cnidarian Shk-like peptides, which have Kv1.3-blocking activity, revealed that four residues (3Asp, 25Lys, 33Lys, and 34Thr) of NnK-1, together with six cysteine residues, are conserved. Therefore, we hypothesize that these four residues are crucial for the binding of the toxins to voltage-gated potassium channels.

The two main strategies used in this study are the binary representation and the decomposition of a natural number into many compound functions of odd function and even function. The Collatz conjecture regarding odd even numbers in number theory can be examined and discussed using them in this way: The sequence created by the finite iterations of the Collatz function becomes the ultimately periodic sequence if any natural number is the beginning value, proving the conjecture that has been held for 85 years.

The Influenza A virus (IAV) is a highly infectious virus that poses a significant threat to global public health and food supplies. The current subtype of avian influenza virus (AIV), H5N1, is being closely monitored worldwide due to its unprecedented spread from Europe to North America and now to Central and South America. This review summarizes recent updates on the evolution of the different IAV subtypes in birds and mammals including humans, in Chile. The distribution and spread of AIV H5N1 in Chile indicated a complex interplay between ecological and human factors in that it was negatively correlated with distance to the closest urban center and precipitation and temperature seasonality. It is evident that highly pathogenic avian influenza (HPAI) H5N1 in Chile was introduced from North America via the Atlantic migratory flyways as opposed to local transmission from other countries in South America. The presence of these viruses in Chile underscores the need for increased biosecurity on poultry farms and continuous genomic surveillance approaches to understand and control AIVs in both wild and domestic bird populations in Chile.

The black-necked crane is the only species that lives in the plateau. At present, there is little re-search on viral diseases of the black-necked crane. In this study, a virus metagenomics approach was employed to investigate the viral composition of black-necked cranes in Saga County, Shi-gatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly in-clude Genomoviridae, Parvoviridae, and Picornaviridae. Among them, one picornavirus genome is characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvoviruses genome were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomoviruses ge-nome were also acquired and identified as members of three different species including Ge-mykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable in-formation for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet and for monitoring, preventing, and treating black-necked cranes viral diseases.

In recent, Chae found that, at weak gravitational acceleration g_N≲10⁻⁹ms⁻², the observed orbit of the wide binary stars is not accordant with current theory of binary star. Here, we present, this finding should be an observational evidence for that Newtonian theory of orbit perturbation is still valid in galactic scale.

Recently a measure termed F* was described, as an interpretable transformation of the F measure, also known as the Dice coefficient. Using elementary mathematical methods, it is shown that F* is in fact identical to a previously described measure, monotonically related to the F measure, and variously termed in previous publications, dating from the late 19^th to the late 20^th century, as the ratio of verification, the Jaccard similarity measure or index, the threat score, the Tanimoto index, and the critical success index. The origins of these different terms in different disciplines (weather forecasting, ecology, machine learning) may explain the repeated independent redescription of this measure.

An investigation of pair partial radial distribution functions and molecular pair potentials within a system has established that the existing potential functions are rooted in the assumption of a static arrangement of atoms, overlooking their distribution and vibration. In this study, Hill’s proposed radial distribution function polynomials are applied for the pure gaseous state to a binary liquid alloy system to derive the pair potential energy. The partial radial distribution functions of 36 binary liquid alloy systems reported in literature were examined and then validated using four thermodynamic models. Results show that the molecular interaction volume model (MIVM) and regular solution model (RSM) outperform other models when an asymmetric method is used to calculate the partial radial distribution function. The MIVM exhibits a mean standard deviation (SD) of 0.095 and a mean absolute relative difference (ARD) of 32.2%. Similarly, the RSM demonstrates a mean SD of 0.078 and an ARD of 32.2%. The Wilson model yields a mean SD of 0.124 and a mean ARD of 226%. The nonrandom two-liquid (NRTL) model exhibits a mean SD of 0.225 and a mean ARD of 911%. On applying the partial radial distribution function symmetry method, the MIVM and RSM outperform the other approaches, with a mean SD of 0.143 and a mean ARD of 165.9% for the MIVM. The RSM yields a mean SD of 0.117 and an ARD of 208.3%. The Wilson model exhibits the mean values of 0.133 and 305.6% for SD and ARD, respectively. The NRTL model shows an average SD of 0.200 and an average ARD of 771.8%. Based on this result, the influence of the symmetry degree on the thermodynamic model is explored by examining the symmetry degree as defined by the experimental activity curves of the two components.

The life cycle of cancer follows the life cycle of the common ancestor of amoebozoans, metazoans, and fungi (AMF) and its systemic germline, which serves as a blueprint for all germlines capable of asymmetric cell division (ACD) and stem cell differentiation. Consequently, the oxygen sensitivity of the ancient non-gametogenic germline (Urgermline) was inherited by all germ and stem cell lines including the cancer germline. They all respond to Ugermline’s hyperoxia with loss of stemness and ACD ability and a dysregulated phenotype with irreparable DNA defects and defective symmetric cell divisions (DSCD). In protists, defective DSCD cells undergo an ancient MGRS repair program involving cell and nuclear fusion and hyperploid giant nuclei that restores the damaged genome to its former pre-DSCD state, with ACD potential and stemness. Human and metazoan DSCD use the same MGRS repair program inherited from the AMF ancestor. Ectopic DSCDs and DSCD-like phenotypes can survive in humans for many years in suitable niches. Under favorable environmental conditions, they also have access to the ancient MGRS repair mechanism including the ancient gene regulatory network (aGRN) and all other AMF genes. The aGRN takes control of cancer’s hybrid genome and represses human genes. It installs a G+S cancer life cycle of AMF imprinting that shapes the differentiation of naïve cancer stem cells (CSCs). CSCs are deeply homologous to the aGSCs of the AMF ancestor. Reprogramming of the DSCD genome by MGRS paves the way for oncogenesis. In this light, cancer is not a mutational or genetic disease, but a non-mutational genome-altering disease.

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pangenomes of several crops. The pan-genomes of crops constructed from various cultivars/accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novels genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding for mitigating the impact of global climate change. Here we summarize the tools used for pangenome assembly and annotations, web-portals hosting plant pangenomes. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and its future potential.

Over the past several decades, the extensive use of pyrethroids has led to the development of resistance in many insect populations, including the economically damaging pest tarnished plant bug (TPB), Lygus lineolaris on cotton. To manage TPB resistance, several commercially formulated pyrethroid-containing binary mixtures, in combination with neonicotinoids or avermectin are recommended for TPB control and resistance management in the Mid-south USA. This study aimed to evaluate the toxicity and resistance risks of four formulated pyrethroid-containing binary mixtures (Endigo, Leverage, Athena, and Hero) on one susceptible and two resistant TPB populations which were field-collected in July (Field-R1) and October (Field-R2), respectively. Based on LC50 values, both resistant TPB populations displayed variable tolerance to the four binary mixtures, with Hero showing the highest resistance and Athena the lowest. Notably, the Field-R2 exhibited 1.5-3-fold higher resistance compared to the Field-R1 for all four binary insecticides. Moreover, both resistant TPB populations demonstrated significantly higher resistance ratios toward Hero and Leverage compared to their corresponding individual pyrethroid, while Endigo and Athena showed similar or lower resistance. This study also utilized the calculated additive index (AI) and co-toxicity coefficient (CTC) analysis, which revealed that the two individual components in Leverage exhibited antagonist effects against the two resistant TPB populations. In contrast, the two individual components in Endigo, Hero and Athena displayed synergistic interactions. Considering that Hero is a mixture of two pyrethroids which can enhance the development of TPB resistance, our findings suggest that Endigo and Athena are likely superior products for slowing down resistance development in TPB populations. This study provides valuable insight for selecting the most effective mixtures to achieve better TPB control through synergistic toxicity analysis, while simultaneously reducing economic and environmental risks associated with resistance development in the insect pest.

Genome-based testing in oncology is a rapidly expanding area of health care which is the basis of the emerging area of precision medicine. Efficient and considered adoption of novel genomic medicine testing is hampered in Canada by the fragmented nature of health care oversight as well as by lack of clear and transparent processes to support rapid evaluation, assessment and implementation of genomic tests. This article provides an overview of some key barriers and proposes approaches to addressing these challenges as a potential pathway to developing a national approach to genomic medicine in oncology.

Rotavirus is a major cause of diarrhea globally in animals and young children under 5 years. Here, molecular detection and genetic characterization of porcine rotavirus in smallholder and commercial pig farms in the Lusaka Province of Zambia were con-ducted. Screening of 148 stool samples by RT-PCR targeting the VP6 gene revealed a prevalence of 22.9 % (34/148). Further testing of VP6-positive samples with VP7-specific primers produced 12 positives, which were then Sanger-sequenced. BLASTn of the VP7 positives showed sequence similarity to porcine and human rota-virus strains with identities ranging from 87.5% to 97.1%. By next-generation se-quencing, the full-length genetic constellation of the representative strains RVA/pig-wt/ZMB/LSK0137 and RVA/pig-wt/ZMB/LSK0147 were determined. Geno-typing of these strains revealed a known Wa-like genetic backbone and their genetic constellations were G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1, respectively. Phylogenetic analysis revealed that these two viruses might have their ancestral origin from pigs, though some of their gene segments were related to human strains. The study shows evidence of reas-sortment and possible interspecies transmission between pigs and humans in Zambia. Therefore, the “One Health” surveillance approach for rotavirus A in animals and humans is recommended to inform the design of effective control measures.

In recent years, there has been a notable rise in the incidence of breast cancer among young patients, who exhibit worse survival outcomes and distinct characteristics compared to the intermediate and elder patients. Therefore, it’s imperative to identify identify the specific features unique to young patients, which could offer insights into potential therapeutic strategies and improving survival outcomes. In our study, we performed an integrative analysis of bulk transcriptional and genomic data from extensive clinical cohorts to identify prognostic factors. Additionally, we analyzed the single-cell transcriptional data and conducted in vitro experiments. Our work confirmed that young patients exhibited higher grading, worse disease-free survival (DFS), a higher frequency of mutations in TP53 and BRCA1, a lower frequency of mutations in PIK3CA, and upregulation of eight metabolic pathways. Notably, galactose metabolism pathway showed upregulation in young patients and was associated with worse DFS. Further analysis and experiments indicated that galactose metabolism pathway may regulate the stemness of cancer cells and ultimately contribute to worse survival outcomes. In summary, our finding identified distinct clinicopathological, transcriptional, and genomics features and revealed a correlation between galactose metabolism pathway, stemness, and poor disease-free survival of breast cancer in young patients.

When two black holes form a binary system, each black hole observes an event horizon and a curved distorted space-time region around the other black hole. In this space-time, two such regions are formed, and another black hole forms in the second region from the initial black hole, which may be termed the “image” of the first black hole. The same event occurs for the other black hole also, and an extra image of it is formed. In these conditions, the energy of the system divides between the two black holes and their images. These four new black holes that are formed interact with each other again and produce new horizons and new distorted regions. Each black hole produces an image of all the other black holes and detects the background of six black holes instead of three. Consequently, for four black holes, 24 new black holes arise. The energy of the system will be divided amongst all 24 black holes. This story continues and black holes interact with one another and produce new images. Finally, very light black holes are formed each of which is so weak that it cannot produce strong distortions of space-time. The radiated gravitational waves from these weak black holes could be detected by LIGO as well as the signature of these binary black holes. However, detected waves are only a part of very strong gravitational waves. Each time a part of these waves escapes from the system and reaches the earth, they may be regarded as emitted waves from a new binary black hole. The time between radiated signals decreases, and it may be interpreted that a new supermassive binary black hole is radiating. If radiated signals combine, an explosion of the very strong binary system could be detected.

The recently discovered Gaia BH1 binary system, a Sun-like star and a dark object (presumably a black hole), may significantly change our understanding of the population of low-q binaries. The paper presents the components mass ratio distributions of binary systems of different observational classes. They all demonstrate a significant shortage of low-q systems. It is shown that this shortage can be filled with the help of search and study of objects like Gaia BH1.

Recently, some authors have claimed that we may live in one of a pair of universes in which one is expanding receding from the Big Bang and its partner is contracting and moving towards the Big Bang. We show that near a black hole binary system, this event may be occurring. If we suppose that there is a N dimensional brane which contains many smaller k dimensional branes and black holes, there is a possibility that the curved space times near black holes act like mirrors. This is because these space-times contain two regions such that the branes in the one region have opposite quantum numbers with respect to the branes in the other region. Also, if branes in one region are expanding and go away from a point state and the Big Bang, anti-branes in the other region are contracting and moving towards the point state and the Big Bang. If black holes join and form a binary system, then their states become similar to two mirrors that are facing each other and producing many images themselves of smaller branes and even black holes in the binary system. Summing over all branes and images give the CPT system. Dark energy could be a result of the images of observed matter. Comparing the masses of the observed objects and dark energy, the angle between cosmic mirrors like black hole binary systems could be determined.

Next generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion between ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last 3 aminoacids of ORF8. Interestingly, the deleted region was flanked by 2 small repeats, likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, 7 out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nuclotides deletion. It is noteworthy that 3 out of 6 cases were detected in patients with immunodeficiency and is conceivable that this clinical condition could promote the replication and selection of these mutations.

Histoplasmosis is one of the most underdiagnosed and underreported endemic mycoses in the United States. Histoplasma capsulatum is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of H. capsulatum in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of H. capsulatum in the United States and how genomic sequencing can be applied for surveillance and outbreak investigation of histoplasmosis.

In any region of a space, the gravitational field cannot be eliminated. The speed of light in a vacuum has never been observed and cannot be observed with current technology. Till now, only the speed of light in a gravitational field has been observed. It results in that all the observed speed of light are always being varied by the gravity. Here, it is presented that light could be dispersion in a gravitational field analogous to the dispersion of light in the Newtonian prism experiment. The relativistic mass density on the surface of a neutron star is on the level of 10¹⁷kg/m³ while on the surface of the Earth is only 10^-7kg/m³, the effect of the gravitational field acting on the speed of light by a neutron star is much larger than that by the Earth. Therefore, the dispersion of light in strong gravitational field could be generally observed from the image of a star and it should have been observed through the double-image gravitational lensing and the spectroscopic binary system. And, it should affect the observed numbers, spectrogram, size and distance of the celestial objects.

The production of plants and crops is influenced by environmental stress, which is a serious scientific issue. Cotton is an essential crop for producing natural fibers that are used to make biofuel and edible oils. Salinity is the main element that influences cotton growth during the beginning of germination. The type of salt and the growth stage affects how sensitive a plant is to salt stress. Developing ways to enhance cotton performance in salty circumstances can be aided by an understanding of the response of cotton to salt, its mechanism of resistance, and its management methods. Osmotic and ionic imbalances originate due to the deposition of soluble salts under salinity stress in the plant's root zone. Soil salinity significantly reduces plant growth due to several factors, such as nutritional ion imbalance, which reduces K+, PO4-, and NO- absorption, excessive salt chloride concentrations, and osmotic stress, which hinders water availability. Research has revealed that compared to subsequent stages, the germination, emergence, and seedling phases are more vulnerable to salinity stress, which ultimately affects the seed cotton yield by delaying blooming, reducing fruiting positions, shedding fewer fruits, and reducing boll weight. The morphology, growth of cotton roots, shoots, yield, and fiber quality are all strongly impacted by salinity stress. It slows down plant feeding, cellular metabolism, and photosynthesis. The soil, water, and climate all affect how the plant responds to salinity stress. During salt stress, excessive exclusion of sodium or its compartmentalization is the key adaptation process in cotton. A major adaptive potential to create cotton types that can withstand salt is provided by the up-regulation of both physicochemical and non-enzymatic antioxidant genes. A successful strategy to increase cotton germination in saline soils is seed priming. Moreover, the transgenic strategy might be a viable choice for improving cotton yield in saline environments. Our review focuses on the impacts of salinity on cotton productivity as well as how plants react to salt stress. It also clarifies recent genetic advancements and molecular breeding for cotton's resistance to soil salt. To create salt-tolerant cultivars, a combination of traditional breeding and novel molecular approaches will be useful.

Background: The incidence of prostate cancer (PC) has been risen annually. Despite the diagnosis is made mainly with non-metastatic PC, mortality is explained by the metastatic disease (mPC). Without a doubt there is an intermediate scenario in which patients have no mPC but will have initiated a metastatic cascade through an epithelial-mesenchymal transition. There is indeed a need for more and better tools to predict what patients will progress in the future to non-localized clinical disease or already have micrometastatic disease, and therefore, will clinically progress after primary treatment. Biomarkers for predicting mPC are still under development; there are few studies and not much evidence of their usefulness. Summary: This review is focused on tissue-based genomic biomarkers (TBGB) for predicting metastatic disease. We developed four main research questions that will attempt to answer according to the current evidence. Why is important to predict metastatic disease? Which tests are available to predict metastatic disease? What impact should there be on clinical guidelines and clinical practice in predicting metastatic disease? What are current prostate cancer treatments? Key Messages: Knowing useful predict tools could help determine which patients may need multimodal or adjuvant treatment even with a localized disease, and in consequence, what patients do not need more than a single modality of treatment. The importance of predicting metastasis is fundamental, given that once metastasis is diagnosed, the quality of life (QoL) and survival drop dramatically.

Hyperspectral image and LiDAR image fusion plays a crucial role in remote sensing by capturing spatial relationships and modeling semantic information for accurate classification and recognition. However, existing methods, like Graph Convolutional Networks (GCNs), face challenges in constructing effective graph structures due to variations in local semantic information and limited receptiveness to large-scale contextual structures. To overcome these limitations, we proposed a invariant attribute-driven binary bi-branch classification (IABC) method which is a unified network that combines binary Convolutional Neural Network (CNN) and GCN with invariant attributes. Our approach utilizes a joint detection framework that can simultaneously learn features from small-scale regular regions and large-scale irregular regions, resulting in an enhanced structured representation of HSI and LiDAR images in the spectral-spatial domain. This approach not only improves the accuracy of classification and recognition but also reduces storage requirements and enables real-time decision-making, which is crucial for effectively processing large-scale remote sensing data. Extensive experiments demonstrates the superior performance of our proposed method in hyperspectral image analysis tasks. The combination of CNNs and GCNs allows for accurate modeling of spatial relationships and effective construction of graph structures. Furthermore, the integration of binary quantization enhances computational efficiency, enabling real-time processing of large-scale data. Therefore, our approach presents a promising opportunity for advancing remote sensing applications using deep learning techniques.

Genome-wide sequencing data play an important role in evaluating the genomic level differences between superior and poor-quality crop plants and improving our understanding of molecular association with desired traits. We analyzed the obtained 92,921,066 raw reads from genome-wide resequencing of Cucumis sativus var. hardwickii through in-silico approaches and mapped to the reference genome of Cucumis sativus to identify the genome-wide single nucleotide polymorphisms (SNPs) and Single nucleotide variations (SNV). Here, we report 19, 74,213 candidate SNPs including 1,33,468 insertions and 1,43,237 deletions and 75 Indels genome-wide. A total of 2228224 identified variants were classified into four classes including 0.01% sequence alteration, 5.94% insertion, 6.37% deletion and 87.66% SNV respectively. These variations can be a major source of phenotypic diversity and sequence variation within the species. During the present study these variants were also utilized to resolve orthologous relationships among the genomes of C. melo and C. sativus var. hardwickii. Overall, the discovery of SNPs and genomic variants may help predict the plant response to certain environmental factors and can be utilized to improve crop plants' economically important traits.

Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lip-idomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.

Transitional waters are fragile ecosystems with high ecological values, representing the breeding and resting sites for rare and threatened species. They deserve particular concern for protection, undergoing numerous threats from anthropogenic nature. The present review aims to analyze the recent literature on Aphanius fasciatus, nowadays considered one of the most strictly estuarine-dependent fish species, and as such affected by the degradation of lagoon habitats, and to discuss its suitability as sentinel species of the quality of transitional water environments. The analysis and discussion highlight the potential applicability of the molecular, cellular, and physiological responses of this species as diagnostic tools for detecting the subtle effects induced by environmental pollution on the biota in transitional water environments. Moreover, the suitability of the responses of this species is suggested in the wider framework of the One Health Perspective which considers human and animal health and the environmental state highly interconnected, sharing common aspects. To date, omics technologies show very great potential in reacquiring novel knowledge on the responses of the organisms to environmental changes and to the alterations of the environmental health status. Therefore, considering the relevant potential of this species as sentinel species, many efforts are needed in the next future to improve the quantity and quality of the -omics tools that refer to A. fasciatus.

The safety of a pedestrian crossing may depend on infrastructure, vehicular and pedestrian traffic characteristics. This research portrays the safety challenges caused by vehicles on crosswalk in the City of Kigali. Through observing the stopping of drivers in pedestrian crossing events, the study aims to evaluate driver’s behaviors against traffic flow parameters. 10 collection sites were finally selected purposively and randomly to suit observations for data recording. A total of 10,259 crossing events were recorded within 280 hours. Statistical analysis, tests and Binary logistic regression model were used to evaluate the behaviors. Sadly,82.4% drivers violate crosswalks, endangering crossing. Motorcyclists exhibit the most aggressive behavior. Car drivers are relatively less aggressive,60% managed to brake in the events. Buses and bicycles share a negligible collective of 2%, being aggressive and would not stop. Cars are 10.389 times more likely to stop compared to bicycles. Having more vehicles in a row is safer to cross, for each unit increase on the vehicle density scale, there were 1.956 more chances that every driver would stop.13% to 21% of traffic variables predict the variance in stopping behaviors model.

In the article, we are trying to find a general law that describes the physical properties of a complex compound through the same physical properties of compound elements. For metal alloys operated under extreme conditions - neutron and proton irradiations and thermal heating, the mechanical properties of these alloys and their elements have been studied. It turned out that the ultimate tensile strength of tantalum alloys used in the design of space reactors can be expressed in terms of the weighted sum of the ultimate tensile strengths of its elements in the range of neutron doses: (0 - 0.96) displacement per atom (dpa) for Ta–10W alloy and (1.4 - 1.7) dpa for T–111 alloy with a neutron energy of more than 0.1 MeV. For tungsten binary alloys used in the design of fusion reactors, the Vickers hardness can also be expressed in terms of the weighted sum of the Vickers hardnesses of the alloy elements in the range of proton irradiation doses: (0 - 0.05) dpa for W-1%Re alloy, (0.05 - 0.2) dpa for W-3%Re alloy and (0.05 - 1) dpa for W-1%Ta with a proton energy of 1 MeV.

(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: to achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3,704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains.

Ovarian tissue cryopreservation (OTC) or testicular tissue cryopreservation (TTC) are effective and often the only options for fertility preservation in female or male patients due to oncological, medical, or social aspects. While TTC and resumption of spermatogenesis, either in vivo or in vitro, has still be considered an experimental approach in humans, OTC and autotransplantation has been applied increasingly to preserve fertility with more than 200 live births worldwide. However, the cryopreservation of reproductive cells followed by the resumption of gametogenesis, either in vivo or in vitro, may interfere with sensitive and highly regulated cellular processes. In particular, the epigenetic profile, which includes not just reversible modifications of the DNA itself but also post-translational histone modifications, small non-coding RNAs, gene expression and availability, and storage of related proteins or transcripts, have to be considered in this context. Due to complex reprogramming and maintenance mechanisms of the epigenome in germ cells, growing embryos, and offspring, OTC and TTC are carried out at very critical moments early in the life cycle. Given this background, the safety of OTC and TTC taking into account the epigenetic profile has to be clarified. Cryopreservation of mature germ cells (including Metaphase II oocytes and mature spermatozoa collected via ejaculation or more invasively after testicular biopsy) or embryos has been used successfully for many years in Medically Assisted Reproduction (MAR). However, tissue freezing followed by in vitro or in vivo gametogenesis has become more attractive in the past, while few human studies have analysed the epigenetic effects, with most data deriving from animal studies. In this review, we highlight the potential influence of the cryopreservation of immature germ cells and subsequent in vivo or in vitro growth and differentiation on the epigenetic profile in humans and animals.

An attempt to investigate the effect of binary composite activators on the microstructure of fly ash-based geopolymers is conducted through the comparison of 24 experiments, which consisted of Na2SiO3•9H2O, Na2CO3, K2CO3, NaOH, and KOH through a facile preparation technique. The results show that the activator of Na2SiO3•9H2O+KOH presents the highest mechanical strength, due to the synergy activation between the inherent ≡Si-O-Si≡ chains derived from Na2SiO3 and K+’s catalysis. It reveals that the K+ plays a crucial role in Na2SiO3-activated fly ash geopolymer, which is the rate-determining step of the enhanced crosslinking and propagation of N-(C)-A-S-H chains, leading to an increase in weight loss temperatures of specimens from TG/DTG results. Furthermore, the adding silica fume facilitates as-formed amorphous silicates, which also could fill into the pores of N-(C)-A-S-H amorphous gels and present a uniform and compact morphology, leading to an increase in the pore volume of the pore diameter less than 100 nm. It explores an efficient and cost-effective preparation of fly ash-based geopolymer for developing solid-waste recycling techniques.

The fight against suicide is highly challenging as it may be one of the most complex and at the same time most threatening among all psychiatric phenomena. In spite of its huge impact, and despite advances in neurobiology research, understanding and predicting suicide remains a major challenge for both researchers and clinicians. To be able to identify those patients who are likely to engage in suicidal behaviors and identify suicide risk in a reliable and timely manner, we need more specific, novel biological and genetic markers/indicators to develop better screening and diagnostic methods, and in the next step to utilize these molecules as intervention targets. One such potential novel approach is offered by our increasing understanding of the involvement of neuroinflammation based on multiple observations of increased proinflammatory states underlying various psychiatric disorders including suicidal behavior. The present paper overviews our existing understanding of the association between suicide and inflammation including peripheral and central biomarkers, genetic and genomic markers, and our current knowledge of intervention in suicide risk using treatments influencing inflammation, also overviewing the next steps to be taken and obstacles to be overcome before we can utilize cytokines in the treatment of suicidal behavior.

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of a first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: 1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; 2) a comprehensive variant calling pipeline; 3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequenc-ing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of the variant calling pipeline are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusion: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of up-to-date list of mutations, which can be incorporated into global efforts to sustainably prevent or treat infections.

This article is devoted to the results of in-depth analysis of the system of binary-oppositional structures in DNA n-plet alphabets and their algebraic-matrix representations. These results show that the molecular complementary replication of DNA strands is accompanied by the presence of an algebraic version of the principle "like begets like" in matrix representations of DNA alphabets having internal structures. This algebraic version is based on binary-oppositional structures in the genetic molecular system, which can be represented by binary numbers and corresponding matrices of DNA alphabets. The received results allow thinking that the phenomenon "like begets like" (or a complementary replication in a wide sense) is systemic in the genetic organization and is connected with algebraic features of biological organization. Correspondingly, the biological principle "like begets like" can be additionally modeled by algebraic-matrix methods and approaches. Such algebra-matrix modeling of the genetic coding system gives new ways for studying and understanding the key role of the named principle in genetic and other inherited physiological complexes. On this way, the author discovered general rules of stochastic organization of information binary sequences of genomic DNAs of eukaryotes and prokaryotes. The presented rules are connected with information dichotomies of probabilities and corresponding fractal-like trees of probabilities, which fundamentally differ from constructional dichotomies in biological bodies. The received phenomenological data and rules lead to new biological ideas.

The following is the Collatz Conjecture: Suppose we begin with a positive number, multiply it by 3 and add 1 if it is odd, and divide it by 2 if it is even. Then continue doing this as long as you can. Will it matter where you start, whether you end up at the number 1? The Collatz conjecture has been studied for around 85 years. We transform the Collatz function from decimal to binary, then use the binary string's character to prove the Collatz conjecture. In addition, we use mathematics to give another interpretation to chaos, which is the ultimately periodic positive integer sequence.

Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

Dairy cattle predicted by genomic breeding values to be heat tolerant are known to have less milk production decline and lower core body temperature increases in response to elevated temperatures. In a study conducted at the University of Melbourne’s Dookie Robotic Dairy Farm during summer, we identified the most 20 heat-susceptible and 20 heat-tolerant cows in a herd of 150 Holstein Friesian lactating cows based on their phenotypic responses (changes in respiration rate, surface body temperature, panting score, and milk production). Hair samples were collected from the tip of the cows' tail following standard genotyping protocols. The results indicated variation in feed saved and HT genomic estimated breeding values (GEBVs) (P≤0.05) across age, indicating a potential for their selection. As expected, the thermotolerant group had higher GEBVs for HT and feed saved but lower for milk production. In general, younger cows had superior GEBVs for Balanced Performance Index (BPI), Type Weighted Index (TWI) and Australian Selection Index (ASI), whilst older cows were superior in fertility, feed saved (FS) and HT. The study demonstrated highly significant (P≤ 0.001) negative correlations (-0.28 to -0.74) between HT and GEBVs for current Australian Dairy cattle selection indices (BPI, TWI, ASI, HWI) and significant (P≤ 0.05) positive correlations between HT and GEBVs for traits like FS (0.45) and fertility (0.25). Genomic selection for HT will help improve cow efficiency and sustainability of dairy production under hot summer conditions. However, a more extensive study involving more lactating cows across multiple farms is recommended to confirm the associations between the phenotypic predictors of HT and GEBVs.

In the American Mathematical Monthly there is a problem that related to the governmental inspection of coins in the Lower Slobbovia, where it is desirable to classify and correct counterfeit coins by using a minimum number of measurements, but the article only proves the existence of the solution, which does not give a practical solution to the problem. In this article, we provide an effective method to achieve the identification of coin heaps using Dirac delta functions, Singularity functions and their selectivity, unit-order construction of continuum mappings and construction of discretization of unique basis vectors without attempted expansions in S-binary space.

Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species have not been studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding on the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1,038 –2,826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, are positively correlated with the genome size (r=0.86, p-value=0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signal with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified a total of 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of HTT events caused by a Gypsy transposon might have caused the recent expansion of Gypsy subfamily in the S.exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events had substantial impacts on the Noctuidae genome evolution.