The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures and for this propose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanism leading to the creation of genomic heterogeneity by altering the number of chromosomes as well as changing their structures. In this review we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, human genome shows induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as whole genome doubling to more discrete changes as indels as well as the recent discovered complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double strand breaks (DSB) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar pattern observed during tumorigenesis. Then, we will also list several diseases associated to CIN resulting in fertility issue, miscarriage, genetic rare diseases and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.

In this work we looked for a stable and accurate procedure to perform feature selection in datasets with a much higher number of predictors than individuals, as in Genome-Wide Association Studies. Due to the instability in feature selection when many potential predictors are measured, a variable selection procedure is proposed that combines several replications of shrinkage regression models. A weighted formulation is used to define the final predictors. The procedure is applied to investigate Single Nucleotide Polymorphisms (SNPs) predictors associated to Alzheimer’s disease in the Alzheimer’s disease Neuroimaging Initiative (ADNI) dataset. Two data scenarios are investigated: one considering only the set of SNPs and another with the covariates age, sex, educational level and APOE4 genotype. The SNP rs2075650 and the APOE4 genotype are given as risk factors for AD, which is in line with the literature, and other four new SNPs are pointed, opening new hypotheses for in vivo analyses. These experiments demonstrate the potential of the new method for stable feature selection.

Cercospora beticola Sacc. is an ascomycete pathogen that causes Cercospora leaf spot in sugar beets (Beta vulgaris L.) and other related crops. The disease symptoms are characterized by circular lesions with an ash-gray centre and dark brown to purple margins on the leaves. It can lead to significant yield losses if not effectively managed. This study aims to characterize and assess the impact of bacterial biological control agents against C. beticola. Following a dual-culture screening, 18 bacteria exhibiting over 50% inhibition were selected, with six of them demonstrating more than 80% control. Identification of the bacteria was carried out through sequencing of the16S rDNA, revealing potentially 12 species belonging to six genera including Bacillus which was represented by four species. Additionally, the bacteria underwent in-depth characterization of biochemical and molecular properties, as well as plant-growth promotion. PCR detection of genes responsible for producing antifungal metabolites revealed that 83%, 78%, 89%, and 56% of the selected bacteria possessed the bacillomycin, iturin, fengycin, and surfactin encoding genes, respectively. Infrared spectroscopy analysis confirmed the presence of lipopeptide structure in the bacteria supernatant filtrate. Subsequently, the bacteria were assessed for their effect on sugar beet plants in controlled conditions. The bacteria exhibited notable capabilities, promoting growth in both roots and shoots, resulting in significant increases in root length, weight, and shoot length. The field experiment with four bacterial candidates demonstrated good performance against C. beticola compared to difenoconazole fungicide. These bacteria played a significant role in disease control, achieving a maximum efficacy of 77.42%, slightly below the 88.51% efficacy attained by difenoconazole. Additional field trials are necessary to verify the protective and growth-promoting effects of these candidates, whether applied individually, combined in consortia, or integrated with chemical inputs in sugar beet crop production.

Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.

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.

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes.” Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness.

Scientists can use the Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system, which is a powerful and flexible tool for changing the genome, to change only certain parts of the genome. This has helped researchers figure out how target genes work in biology and disease. CRISPR/Cas9 is made up of a sequence-specific CRISPR RNA (crRNA) set and a generic Cas9 nuclease. The crRNA set tells Cas9 where to cut DNA and cause double-strand breaks. In the next step of cellular DNA repair, insertions, deletions, and swaps are made at specific spots. For CRISPR/Cas9-mediated DNA cleavage to be specific, the target sequences must match the crRNA, and a protospacer nearby motif must be placed after the target sequences. In this article, we talk about how CRISPR/Cas9 works at the molecular level, what it can be used for, what it can't do, and what its future clinical treatment promise might be.

This paper investigates the effect of the Internet on tax revenue instability, notably through the international trade channel. It has used a sample of 142 countries over the period 1995-2017, and relied primarily on the two-step system Generalized Methods of Moments (GMM) estimators (but also incidentally on the Error Component Two-Stage Least Squares estimator). Tax revenue instability is primarily measured by the instability of non-resource tax revenue, but also by the instability of total tax revenue (for robustness check). The findings indicate that the Internet exerts a negative effect on tax revenue instability. Interestingly, this effect genuinely translates through the international trade channel, regardless of the measure of tax revenue instability considered. Countries enjoy a higher negative effect of the Internet on tax revenue instability as they enjoy a greater participation in international trade. These findings, therefore, add to the potential benefits of the Internet adoption (e.g., strengthening countries' participation in international trade, enhance their tax revenue performance and promote tax reform, including in developing countries) by showing that it could also help to stabilize tax revenue, particularly through the degree of countries' participation in international trade.

Genetic engineering has become an essential element in developing climate-resilient crops and environmental sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition rich, disease resistant, stress-tolerant “crops” fruits and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign DNA free or non-transgenic crops that could be easily regulated for commercialization in most countries.

Diacylglycerol kinase (DGK) is a lipid kinase that phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Based on converting one important signaling molecule (DAG) to another (PA), DGK plays an important role in plant responses to abiotic stress including waterlogging stress. However, no studies have been reported on the characterization of the DGK gene family in the waterlogging-tolerant kiwifruit germplasm, Actinidia valvata Dunn. Here, we identified 18 AvDGK genes in the A. valvata genome. The phylogenetic analysis showed that AvDGKs can be classified into three clusters, and members within the same cluster have similar domain distribution, exon-intron structures and conserved motif compositions. Chromosome localization analysis revealed that all the AvDGK genes are located across 18 different chromosomes. There were 29 duplicated gene pairs in kiwifruit and all had undergone purifying selection during evolution. Promoter cis-element analysis revealed that the cis-elements within AvDGK genes are associated with multiple functions, including phytohormone signal transduction, stress response, and plant growth and development. The expression pattern analyses indicated that AvDGK play an important role in the fruit development and plant response to waterlogging stress. AvDGKs gene family in the tetraploid A. valvata genome might promote PA synthesis and subsequent signal transduction both under short-term and long-term waterlogging stress. These results provide information regarding the structural characteristics and potential function of DGK genes within kiwifruit and lay a fundamental basis for further research into breeding for enhancing the kiwifruit’s tolerance to waterlogging stress.

An entropic origin of gravity is re-visited. Isothermal self-gravitating cloud seen as an ideal gas is analyzed. Gravitational attraction within the isothermal cloud in equilibrium is balanced by the pressure, which is of a pure entropic nature. The notion of the Jeans entropy of the cloud corresponding to the entropy of the self-gravitating cloud in mechanical and thermal equilibrium is introduced. Balance of the gravitational compression and the entropic repulsion yields the scaling relation hinting to the entropic origin of the gravitational force. The analysis of the Jeans instability enables elimination of the “holographic screen” or “holographic principle” necessary for grounding of the entropic origin of gravity.

Understanding the subtle signs of carpal instability and other unique injury patterns in the wrist is a critical skill for radiologists. Proper patient management and outcomes are directly dependent on the accurate interpretation of wrist imaging studies. This review will provide a detailed overview of typical imaging features of carpal trauma and instability, management, and complications, using multimodality imaging and original medical illustrations. A detailed overview of the osseous, ligamentous, arterial anatomy of the wrist, arcs of Gilula, and zones of vulnerability will be provided. Carpal fractures, dislocations, special radiographic views, and imaging pearls will be discussed. Instability patterns and the myriad of associate abbreviations (CID, CIND, CIC, CIA, VISI, DISI, SLD, LTD, MCI, SLAC, SNAC) will be clarified. Expected outcomes, potential complications, and management will be reviewed.

Chemical instability of liquid-repellent surfaces is one of the nontrivial hurdles that hinders their real-world applications. Although much efforts have been made to prepare chemically durable liquid-repellent surfaces, few attentions have been paid to exploit the instability for versatile use. Herein, we propose to create hydrophilic patterns on superhydrophobic surface by taking advantage of its chemical instability induced by acid solution treatment. Superhydrophobic Cu(OH)2 nanoneedles covered Cu plate that shows poor stability towards HCl solution (1.0 M) is taken as an example. Results show that 2.5 min of HCl solution exposure leads to the etching of Cu(OH)2 nanoneedles and partial removal of self-assembled fluoroalkyl silane molecular layer, resulting in the wettability transition from superhydrophobocity to hydrophilicity, and the water contact angle decreases from ~160° to ~30°. Hydrophilic dimples with different diameters are then created on the superhydrophobic surfaces by depositing HCl droplets with different volumes. Afterwards, the hydrophilic dimple patterned superhydrophobic surfaces are used for water droplet manipulations, including controlled transfer, merging and nanoliter droplets deposition. The results thereby verify the feasibility of creating wettability patterns on superhydrophobic surfaces by using their chemical instability towards corrosive solutions, which broadens the fabrication methods and applications of functional liquid-repellent surfaces.

Elbow dislocation and instability present significant clinical challenges, necessitating a thorough understanding of the underlying bio-mechanical mechanisms. In this study, a quasi-static three-dimensional finite element model of the human elbow joint is developed to investigate stress distribution and stages of dislocation in the human elbow under various loading conditions. The model simulates the elbow joint in different degrees of flexion (30°, 45°, 60°, and 90°) and forearm positions (pronation and supination), providing detailed insights into the progression of dislocation. Significant findings include the identification of high stress concentrations on the humerus at 90° flexion and on the radial and coronoid processes at 30°, 45°, and 60° flexion. Three reproducible stages of dislocation were observed, particularly in flexed positions with forearm pronation or supination. These stages align with experimental observations and highlight the initial occurrence of bony failures, such as radial head and ulnar coronoid fractures, preceding soft tissue tears. Clinically, the study underscores that early-stage low-impact posterior elbow dislocations retain enough stability to be managed with closed reduction and early mobilization. However, as dislocations progress, significant damage to the medial and lateral collateral ligaments is expected, necessitating more invasive treatments. This research provides valuable bio-mechanical insights into elbow dislocation, aiding in the development of improved treatment strategies and enhancing patient outcomes through precise and timely clinical interventions. The validated FEM serves as a powerful tool for pre-surgical planning offering a comprehensive understanding of elbow joint mechanics.

The management of shoulder instability in children and adolescents is a challenging field of orthopaedics. There are several complicating factors which originate from the variable underlying cause that is often a unique combination of traumatic factors, ligamentous laxity, and the pattern of muscle contractility. As the cause is often multifactorial, this makes interpretation of the literature difficult as nomenclature is variable. The purpose of this review is to shed light on the nuances of paediatric and adolescent shoulder instability.

Chromosomal instability (CIN), defined by variations in the number or structure of chromosomes from cell to cell, is recognized as a distinctive characteristic of cancer, associated with the ability of tumors to adapt to challenging environments. CIN has been recognized as a source of genetic variation that leads to clonal heterogeneity (CH). Recent findings suggest a potential association between CIN and CH with the prognosis of BC patients, particularly in tumors expressing the epidermal growth factor receptor 2 (HER2+). In fact, information on the role of CIN in other BC subtypes, including luminal B BC, is limited. Additionally, it remains unknown whether CIN in luminal B BC tumors, above a specific threshold, could have a detrimental effect on the growth of human tumors, or if low or intermediate CIN levels could be linked to a more favorable BC patient prognosis when contrasted with elevated levels. Clarifying these relationships could have a substantial impact on risk stratification and the development of future therapeutic strategies aimed at targeting CIN in BC. This study aimed to assess CIN and CH in tumor tissue samples from ten patients with luminal B BC, and compared them with established clinicopathological parameters. The results of our study show that luminal B BC patients exhibit intermediate CIN and stable aneuploidy, both of which correlated with lymphovascular invasion. These findings suggest that evaluating CIN, CH and aneuploidy could improve risk stratification, the prediction of clinical outcomes and future therapeutic approaches in luminal B BC patients.

Keywords: Amorphous-precipitate, Nitride, Morphological stability, Diffusion, Internal stresses, Modelling, Simulation

In this study, we deal with a nonlinear system of neutral Volterra integro-differential equations (NVIDEs) with infinite delay. We study stability, uniform stability and instability of zero solution of the system of NVIDEs with infinite delay. We obtain three new results with regard to these concepts via two new Lyapunov– Krasovskii functionals (LKFs), respectively. As the main contributions of this work, we improve and generalize some earlier results in the relevant database from the linear case to more general nonlinear cases.

Genetic activation of the class I PI3K pathway is very common in cancer. This mostly results from oncogenic mutations in PIK3CA, the gene encoding the ubiquitously expressed PI3Kα catalytic subunit, or from inactivation of the PTEN tumour suppressor, a lipid phosphatase which opposes class I PI3K signalling. The clinical impact of PI3K inhibitors in solid tumours, aimed at dampening cancer-cell-intrinsic PI3K activity, has thus far been limited. Challenges include poor drug tolerance, incomplete pathway inhibition and pre-existing or inhibitor-induced resistance. The principle of pharmacologically targeting cancer-cell-intrinsic PI3K activity also assumes that all cancer-promoting effects of PI3K activation are reversible, which might not be the case. Emerging evidence suggests that genetic PI3K pathway activation can induce and/or allow cells to tolerate chromosomal instability, which – even if occurring in a low fraction of the cell population – might help to facilitate and/or drive tumour evolution. While it is clear that such genomic events cannot be reverted pharmacologically, a role for PI3K in the regulation of chromosomal instability could be exploited by using PI3K pathway inhibitors to prevent those genomic events from happening and/or reduce the pace at which they are occurring, thereby dampening cancer development or progression. Such an impact might be most effective in tumours with clonal PI3K activation and achievable at lower drug doses than the maximum-tolerated doses of PI3K inhibitors currently used in the clinic.

The patellofemoral joint (PFJ) is a complex articulation between the patella and the femur, in-volved in the extensor mechanism of the knee. Patellofemoral disorders can be classified into ob-jective patellar instability, potential patellar instability, and patellofemoral pain syndrome. An-atomical factors such as trochlear dysplasia, patella alta, and tibial tuberosity-trochlear groove (TT-TG) distance contribute to instability. Patellofemoral instability can result in various types of dislocations, and the frequency of dislocation can be categorized as recurrent, habitual, or per-manent. Primary patellar dislocation requires diagnostic framing, including physical examina-tion and imaging. Magnetic resonance imaging (MRI) is essential for assessing the extent of damage, such as bone bruises, osteochondral fractures, and medial patellofemoral ligament (MPFL) rupture. Treatment options for primary dislocation include urgent surgery for oste-ochondral fragments or conservative treatment for cases without lesions. Follow-up after treat-ment involves imaging screening and assessing principal and secondary factors of instability. Detecting and addressing these factors is crucial for preventing recurrent dislocations and opti-mizing patient outcomes.

Abstract: Fanconi anemia (FA), a chromosomal instability syndrome, is caused by inherited pathogenic variants in any of 22 FANC genes, that cooperate in the FA/BRCA pathway. This pathway regulates the repair of DNA interstrand crosslinks (ICLs) through homologous recombination. In FA proper repair of ICLs is impaired, and accumulation of toxic DNA double strand breaks occurs. In order to repair this type of DNA damage, FA cells activate alternative error-prone DNA repair pathways, that may lead to the formation of gross structural chromosome aberrations of which radial figures are the hallmark of FA and their segregation during cell division are the origin of subsequent aberrations like translocations, dicentrics and acentric fragments. The deficiency in DNA repair has pleiotropic consequences in the phenotype of patients with FA, including developmental alterations, bone marrow failure and an extreme risk to develop cancer. The mechanisms leading to the physical abnormalities during embryonic development have not been clearly elucidated, however FA has features of premature aging with chronic inflammation mediated by pro-inflammatory cytokines, that results in tissue attrition, selection of malignant clones and cancer onset. Moreover, the effect of the FA/BRCA pathway in germinal cells, evidenced by infertility in patients with FA attests of chromosomal instability and cell death also occurring in the germinal compartment.

The feasibility of using full ion kinetics, instead of gyrokinetics, in simulating low-frequency Ion-Temperature-Gradient (ITG) instabilities in tokamaks has recently been demonstrated by Sturdevant et al. [Physics of Plasmas 24, 081207 (2017)]. In that work, a variational integrator was developed to integrate the full orbits of ions in toroidal geometry, which proved to be accurate in capturing both the short-time scale cyclotron motion and long time scale drift motion. The present work extends that work in three aspects. First, we implement a relatively simple full orbit integrator, the Boris integrator, and demonstrate that the accuracy of this integrator is also sufficient for simulation of ITG instabilities. Second, the equilibrium magnetic configuration is extended to general toroidal configuration specified numerically, enabling simulation of realistic equilibria reconstructed from tokamak experiments. Third, we extend that work to the nonlinear regime and investigate the nonlinear saturation of ITG instabilities. To verify the new numerical implementation of the orbit integrator and magnetic configuration, the linear electrostatic ITG frequency and growth rate are compared with those given in Sturdevant's work and good agreement is found.

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

Opossums, native to the Americas, are unique marsupials with over 100 species. The Common Opossum and Virginia Opossum are notable species. They are nocturnal, omnivorous, and adapt to various habitats. Their reproduction involves a short gestation and marsupial pouch development. Despite their ecological benefits like seed dispersal and insect control, their proximity to human habitats exposes them to pathogens, posing public health risks. These include protozoa, helminths, and arthropods that can spread zoonotic parasites and vector-borne diseases. The marsupial immune system, including opossums, is complex, rivaling eutherian mammals. Key immune genes were identified in the grey short-tailed opossum genome. CD1 protein and VpreB surrogate light chain were also found. Marsupials are proposed as ideal models for studying developmental immunology. A West Indian opossum (Didelphis marsupialis) was found and examined. Blood tests revealed abnormalities, including a low white blood cell count and signs of anemia. The results contribute to understanding the species’ health and adaptability in the wild.

Balance requires constant adjustments in muscle activation to attain force steadiness. Creating appropriate training can be challenging. The purpose of this study was to examine the effects of two weeks front squat instability training using a water-filled training tube on force steadiness during an instability challenge. Control (CON, n= 13) and experimental (EXP, n=17) subjects completed pre and post testing for EMG variability by completing one set of 10 repetitions with a stable and unstable training tube. Electrodes were placed bilaterally on the anterior deltoid, paraspinal and vastus lateralis muscles. CON subjects completed 2 weeks of training using a stable training tube, while EXP subjects trained with a water-filled instability tube. EMG data were integrated for each contraction and force steadiness computed using the natural log of coefficient of variation. CON results showed no changes in force steadiness for any condition. EXP showed significant reductions in EMG activation variability across all muscles. These results indicate a significant training effect in reducing muscle activation variability in subjects training with a water-filled instability training device. Improvements seen in these healthy subjects supports development of training implements for a more clinical population to help improve force steadiness.

Papillary thyroid carcinoma (PTC) has two main histologic variants: classical-PTC (CL-PTC) and follicular variant PTC (FV-PTC). Recently, due to its similar features to benign lesions, the encapsulated FV-PTC variant was reclassified as noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP). Nonetheless, specific molecular signatures are not yet available. It is well known that telomere-related genome instability is caused by inappropriate DNA repair of dysfunctional telomeres and that mechanisms involved in the damaged telomere repair processing may led to detrimental outcomes, altering the 3D nuclear telomere and genome organization in cancer cells. This pilot study aimed to evaluate whether a specific nuclear telomere architecture might characterize NIFTP, potentially distinguishing it from other PTC histologic variants. Our findings demonstrate that 3D telomere profiles of CL-PTC and FV-PTC were different from NIFTP and that NIFTP more closely resembles follicular thyroid adenoma (FTA). NIFTP has longer telomeres than CL-PTC and FV-PTC samples and telomere length overlaps in NIFTP and FTA. There was no association between BRAF expression and telomere length in all tested samples. Our data showing that 3D nuclear telomere organization is altered differently in thyroid cancer variants, suggest that this parameter might guide clinical management of NIFTP. Although further investigations in a larger cohort of patients are necessary to corroborate our observations, telomere-related genomic instability might be of value in the diagnosis of NIFTP and allow for a more appropriate selection of the correct treatment.

The purpose of this paper is to simulate a two-dimensional Rayleigh-Taylor instability problem using the classical method of Finite Element analysis of a multiphase model using ANSYS FLUENT 19.2. The governing equations consist of a system of coupled nonlinear partial differential equations for conservation of mass, momentum and phase transport equations. The study focuses on the transient state simulation of Rayleigh Taylor waves and subsequent turbulent mixing in the two phases incorporated in the model. The Rayleigh Taylor instability is an instability of an interface between two fluids of different densities which occurs when the lighter fluid is pushing the heavier fluid in a gravitational field. The problem was governed by the Navier-Stokes and Cahn-Hilliard equations in a primitive variable formulation. The Cahn- Hilliard equations were used to capture the interface between two fluids systems. The objective of this article is to perform grid dependency test on Rayleigh Taylor Instability for 2 different mesh size and compare the results for the variation in Atwood Number. The results were validated with the observations from previous published literatures.

Emergence of zoonotic-human pathogens is proven to be a lethal threat to public health, and RNA virus including influenza viruses, severe acute respiratory syndrome coronavirus, middle east respiratory syndrome coronavirus, Wuhan coronavirus (COVID-19), plays a pivotal role. As those viruses as airborne microorganisms spread mainly by tiny airborne particles, it is important to de-active those airborne particles before their entry into human bodies. In this study, we investigated the effect of far infrared (FIR) radiation on inhibition of airborne microorganisms. The result confirmed that double stand DNA from airborne microorganisms were stable under mild FIR radiation. However, single strand RNA from them was found to be sensitive to FIR radiation, indicating that RNA virus in airborne particles is instable under FIR radiation. Based on this observation, two models on usage of FIR radiation to prevent RNA virus transmission and cure RNA virus infection were proposed, implying that FIR radiation might be a cheap, convenient, and efficient method in clinic to treat RNA virus.

Behavioral instability is a new concept used for indicating environmental stress based on behavioral traits. This study investigates the possibility of using behavioral instability as a tool for assessing personality in captive animals. The understanding of personality in captive animals can be a resourceful tool in the development of enrichment programs in order to improve animal welfare. In this study it is examined how an olfactory stimulus affects the behavior of two individuals of the species Ursus maritimus in captivity. When using continuous focal sampling throughout the day it was for many behaviors found that the individuals responded differently to stimuli, indicating that there was a difference in personality. This is shown using multiple approaches. One approach used traditional methods for behavioral analyses and the other approach used the concept of behavioral instability as a new quantitative method. This study proves use of behavioral instability as a new quantitative method for investigating personality, expanding the possibility of comparing personality between species. Moreover, it is shown that outliers, which cause asymmetric distributions, should not be removed in behavioral analysis without careful consideration.

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called “-omics”, have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated.

Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are incompletely understood. During SNP-array molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n=612), we observed colocalizaion of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n=47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either to partial/whole chromosome loss (e.g. aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g. prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything” like the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.

The occurrence of chaotic instability of oscillations at the output of a single-stage amplifier on a powerful bipolar microwave transistor when a biharmonic signal is amplified is considered. It has been established that at a high level of the input signal at the output of the amplifier, the signal contains a significant chaotic component. Cases were experimentally studied when the frequency distance between the partial frequency components of a biharmonic signal is close to the gain band and when it is much smaller than this band. It has been established that in the first case, the chaos in oscillations is associated with the emergence of a sequence of trains of a forced oscillatory process with arbitrary initial phases and durations. In the second case, the appearance of a chaotic pedestal is associated with the chaos in the passive underexcited mode of the nonlinear circuit formed by the capacitance of the p-n junction and the input matching circuits of the amplifier stage.

Classifications of AAFD/PCFD have evolved with an increased understanding of the pathology involved. A review of classification systems helps identify deficiencies and respective contributions to the evolution in understanding the classification of AAFD. Using multiple electronic database searches (Medline, PubMed) and Google search, original papers classifying AAFD were identified. Nine original articles were identified that met the inclusion criteria. Johnson's original classification and multiple variants provided a significant leap in understanding and communicating the pathology but remained tibialis posterior tendon focussed. Drawbacks of these classifications include the implication of causality, linearity of progression through stages, an over-simplification of stage 2 deformity and a failure to understand multiple tendons react, not just tibialis posterior. Later classifications, such as the PCFD classification, are deformity-centric. Early instability in non-cavus feet and all stages of cavus feet can present pain and instability with minor/no deformity. These may not be captured in deformity-based classifications biased to planus feet.' The authors developed the 'Triple Classification' (TC) understanding that primary pathology is a progressive ligament failure/instability that presents as tendon reactivity, deformity, and painful impingement. There is a variable manifestation dependent on starting foot morphology. This review has identified deficiencies within classification systems used in AAFD/PCFD and, as a result, was used to help develop a more comprehensive 'Triple classification'. Advantages of the TC include representing foot types with no deformity, defining complex secondary instabilities, delinking of foot types, tendon reactivity/ligament instability and deformity to represent these independently in a more comprehensive classification system.

Ballasted railway tracks can be modelled using reduced/simplified models composed of several layers of discrete components. This paper deals with the two-layer model, which is very popular due to its computational efficiency. In order to provide some recommendations for track design, it is necessary to identify which set of parameters leads to some irregular/unexpected behavior. Such irregularity is investigated at three levels, such as: (i) critical velocity of moving constant force; (ii) instability of a single moving mass; (iii) instability of two moving masses. All results are presented in dimensionless form to cover a wide range of real parameters. Irregular cases are identified by sets of parameters leading to them and then general conclusions are drawn. Regarding the method, all results are obtained analytically or semianalytically, where “semi” refers to solving the roots of a given polynomial by predefined numerical procedures in symbolic software. No numerical integration is involved in all results presented. This means that the results are highly accurate and refer to exact values, so any kind of parametric or sensitivity analyses is readily possible.

Interaction of an electromagnetic field with matter in a laser cavity without the assumption of a fixed direction of the transverse electric field, described by the two-level Maxwell-Bloch equations, is studied. By using a perturbative nonlinear analysis, performed near the laser threshold, we report on the derivation of the laser (3+1)D vectorial complex cubic-quintic complex Ginzburg-Landau equation. Furthermore, we study the modulational instability of the plane waves both theoretically using the linear stability analysis, and numerically, using direct simulations via the split-step Fourier method. The linear theory predicts instability for any amplitude of the primary waves. Our numerical simulations confirm the theoretical predictions of the linear theory as well as the threshold of the amplitude of perturbations. The system understudy shows a deep dependence on the laser cavity parameters, for which there appear wave patterns in accordance with the predictions from the gain spectrum.

In this paper, an analytical investigation of the combined effect of through flow and magnetic field on the convective instability in an electrically conducting fluid layer, bounded in a Hele-Shaw cell is presented within the context of linear stability theory. The Galarkin method is utilized to solve the eigenvalue problem. The outcome of the important parameters on the stability of the system is examined analytically as well as graphically. It is observed that the through flow and magnetic field have both stabilizing effects, while the Hele-Shaw number has destabilizing effect on the stability of system. It is also found that the oscillatory mode of convection possible only when the magnetic Prandtl number takes the values less than unity.

Abstract: The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes isolated from cattle farms, cattle abattoirs, and retail outlets in Gauteng province, South Africa. The isolates' sequence types (STs), clonal complexes (CCs), and lineages were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were 7 STs, 6 CCs, 44 putative virulence factors, 2 resistance genes, 1 plasmid with AMR genes and 3 with conjugative genes, 1 CRISPR gene, and all 60 isolates were positive for proviruses. Among the 7 STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p<0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (P<0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in 3 (5%) isolates. A CRISPR-Cas system was detected in 6 (10%), and all the isolates carried proviruses. Significant differences were detected in the frequencies of STs and virulence factors regarding the source and sample type of the L. monocytogenes isolates. The presence of both fosX and vga(G) genes in all the isolates from the three industries (cattle farms, abattoirs, and retail outlets) can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain in the country, provides the first evidence of the distribution of the pathogen with potential food safety and therapeutic implications.

The issue of monitoring and early warning of rock instability has received increasing critical attention in the study of rock engineering. To investigate the damage evolution process of granite under triaxial compression tests, acoustic emission (AE) tests were performed simultaneously. This study firstly introduced two novel parameters, i.e., the coefficient of variation (CoV) of the information entropy and correlation dimension of the amplitude data from the AE tests, to identify the precursor of the failure of granite. Then the relationship between the changes in these parameters and the stress-time curve was compared and analyzed. The results of this study show that: (1) There is a strong correlation between the CoV of the information entropy and the failure process of granite. The granite failed when the CoV curve raised to a plateau. (2) The fluctuation of the correlation dimension indicates the different stages of the loading process, i.e., the initial compaction stage, the linear elastic stage, the yield stage, and the failure stage. Each stage contains a descending and a rising process in the correlation dimension curve, which indicates that this parameter could be used to identify the precursor of the failure as well. (3) The combined analysis of the two can improve the accuracy of rock instability prediction. This study provides new insights into the prediction of rock instability, which has theoretical implications for the stability of subsurface engineering rock masses.

The modulation instability of surface capillary-gravity water waves is analysed in a shear flow model with a tangential discontinuity of velocity. It is assumed that air blows along the surface of the water with a uniform profile in the vertical direction. Such a model, despite its simplicity, plays an important role in hydrodynamics as the reference model for investigating basic physical phenomena of wave-current interactions and acquiring insights into a series of complex phenomena. In certain cases where the wavelength of interfacial perturbations is much bigger than the width of the shear fow profile, the model with the tangential discontinuity in the velocity is adequate for describing physical phenomena at least within limited spatial and temporal frameworks. A detailed analysis of the air-flow conditions under which modulation instability sets in is presented. It is also shown that the interfacial waves are subject to dissipative or radiative instability when negativeenergy waves appear at the interface.

Whole genome alignment (WGA) is a critical process in comparative genomics, facilitating the detection of genetic variants and aiding our understanding of evolution. This paper offers a detailed overview and categorization of WGA techniques, encompassing suffix tree-based, anchors-based, and graph-based methods. It elaborates on the algorithmic properties of these tools, focusing on performance and methodological aspects. The paper underscores the latest progress in WGA, emphasizing the increasing capacity to manage the growing intricacy and volume of genomic data. However, the field still grapples with computational and biological hurdles affecting the precision and speed of WGA. We explored these challenges and potential future solutions. This paper aims to provide a comprehensive resource for researchers, deepening our understanding of WGA tools and their applications, constraints, and prospects.

Recently, there have been revolutions in the development of both gene therapy and genome surgical treatments for inherited diseases. Much of this progress has been centered around hereditary retinal dystrophies, because the eye is an immune-privileged and anatomically ideal target. Gene therapy treatments, already demonstrated to be safe and efficacious in numerous clinical trials, are benefitting from the development of new viral vectors, such as dual and triple AAVs. CRISPR/Ca9, which revolutionized the field of gene editing, is being adapted into more precise “high fidelity” and catalytically dead variants. New CRISPR endonucleases, such as CjCas9 and Cas12a, are generating excitement in the field as well. Stem cell therapy has emerged as a promising alternative, allowing human embryo derived stem cells and induced pluripotent stem cells to be edited precisely in vitro and then reintroduced into the body. This article highlights recent progress made in gene therapy and genome surgery for retinal disorders, and it provides an update on precision medicine FDA treatment trials.

First, a recently developed eigenfunction expansion technique, based in part on separation of the thickness-variable and partly utilizing a modified Frobenius type series expansion technique in conjunction with the Eshelby-Stroh formalism, is employed to derive three-dimensional singular stress fields in the vicinity of the front of an interfacial crack weakening an infinite bicrystalline superlattice plate, made of orthorhombic (cubic, hexagonal and tetragonal serving as special cases) phases, of finite thickness and subjected to the far-field extension/bending, in-plane shear/twisting and anti-plane shear loadings, distributed through the thickness. Crack-face boundary and interface contact conditions as well as those that are prescribed on the top and bottom surfaces of the bicrystalline superlattice plate are exactly satisfied. It also extends a recently developed concept of lattice crack deflection (LCD) barrier to a superlattice, christened superlattice crack deflection (SCD) energy barrier for studying interfacial crack path instability, which can explain crack deflection from a difficult interface to an easier neighboring cleavage system. Additionally, the relationships of the nature (easy/easy, easy/difficult or difficult/difficult) interfacial cleavage systems based on the present solutions with the structural chemistry aspects of the component phases (such as orthorhombic, tetragonal, hexagonal as well as FCC (face centered cubic) transition metals and perovskites) of the superlattice are also investigated. Finally, results pertaining to the through-thickness variations of mode I/II/III stress intensity factors and energy release rates for symmetric hyperbolic sine distributed load and their skew-symmetric counterparts that also satisfy the boundary conditions on the top and bottom surfaces of the bicrystalline superlattice plate under investigation, also form an important part of the present investigation.

Sediment cores were collected from a mudflow lobe (80 m water depth) offshore of the Mississippi River’s Southwest Pass in 2017 to better understand the sedimentology near the lobe entraining the SS Virginia shipwreck (sunk by a German U-Boat in 1942) and surrounding Mississippi River Delta Front. Core analyses included 210Pb/137Cs geochronology, granulometry, and X-radiography. Sediment accumulation rates (SAR) calculated from excess 210Pb activity in multicores are 0.22–0.29 cm/yr at seabed depths less than 20 cm and 0.29–0.51 cm/year at depths greater than 20 cm. 137Cs accumulation rates are ~0.15 to ~ 0.37 cm/year since 1954 and 1963 respectively. Sediment accumulation rates from 210Pb and 137Cs geochronology and indicators of relative sedimentation and bioturbation from X-radiographs suggest that rates of sediment accumulation near Virginia have declined since ca. the mid-20th century. This may be explained by the multi-decade downslope mass transport of the mudflow lobe in which the shipwreck is embedded, and decreases in sediment supply delivered offshore from the Mississippi River. Mass-transport calculations of the Virginia lobe derived from core properties and published lobe advection rates suggest downslope mass transport is far higher than sediment resupply from the Mississippi River, consistent with recent studies of delta retreat.

With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.

The goal of this study was to analyze the instability during stepping of young and older adults at fast and spontaneous speed. To this aim, the anteroposterior and the mediolateral distances between the body center of mass (COM) and the minimum moment axis (MMA) were computed. A total of 15 young adults (25y.o. [19-29]) and 15 older adults 68.7y.o. [63-77] volunteered for this study. For the computation of the distances, a complete biomechanical protocol combining two force platforms and a 3D motion capture analysis system was setup. The subjects were equipped with 47 reflective markers and were modeled as a frictionless multibody with 19 segments, 18 joints and 42 degrees of freedom and were asked to perform a stepping at both speeds. The stepping was divided in 5 phases with successive swing and double stance phases. The greater instability was observed during the swing phases. The distances indicate a significant higher instability at fast speed for both groups (p < 0.001) for all the phases. The anteroposterior distance also increases significantly for older adults highlighting greater instability while no differences were observed for the mediolateral distance all along the 5 phases suggesting higher risks of backward of forward falls during stepping.

The onset of the thermal instability is investigated in a porous channel with plane parallel boundaries saturated by a non–Newtonian shear–thinning fluid and subject to a horizontal throughflow. The Ellis model is adopted to describe the fluid rheology. Both horizontal boundaries are assumed to be impermeable. A uniform heat flux is supplied through the lower boundary, while the upper boundary is kept at a uniform temperature. Such an asymmetric setup of the thermal boundary conditions is analysed via a numerical solution of the linear stability eigenvalue problem. The linear stability analysis is developed for three–dimensional normal modes of perturbation showing that the transverse modes are the most unstable. The destabilising effect of the non-Newtonian shear–thinning character of the fluid is also demonstrated as compared to the behaviour displayed, for the same flow configuration, by a Newtonian fluid.

A linear stability analysis of the parallel uniform flow in a horizontal channel with open upper boundary is carried out. The lower boundary is considered as an impermeable isothermal wall, while the open upper boundary is subject to a uniform heat flux and it is exposed to an external horizontal fluid stream driving the flow. An eigenvalue problem is obtained for the two-dimensional transverse modes of perturbation. The study of the analytical dispersion relation leads to the conditions for the onset of convective instability as well as to the determination of the parametric threshold for the transition to absolute instability. The results are generalised to the case of three-dimensional perturbations.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.

Enterovirus A71 (EV-A71) infection is a major cause of hand, foot and mouth disease (HFMD) which may be occasionally associated with severe neurological complications. There are currently a lack of treatment options for EV-A71 infection. The Raf-MEK-ERK signaling pathway, in addition to its critical importance in the regulation of cell growth, differentiation and survival, has been shown to be essential for virus replication. In this study, we investigated the anti-EV-A71 activity of vemurafenib, a clinically approved B-Raf inhibitor used in the treatment of late stage melanoma. Vemurafenib exhibits potent anti-EV-A71 effect in cytopathic effect inhibition and viral load reduction assays, with half maximal effective concentration (EC50) at nanomolar concentration. Mechanistically, vemurafenib interrupts both EV-A71 genome replication and assembly. These findings expand the list of potential antiviral candidates of anti-EV-A71 therapeutics.

The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence is a major factor influencing the position of nucleosomes on genomes. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

Cardiomyopathies are diseases of heart muscle, a significant percentage of which are genetic in origin. Cardiomyopathies can be classified as dilated, hypertrophic, restrictive, arrhythmogenic right ventricular or left ventricular non-compaction, although mixed morphologies are possible. A subset of neuromuscular disorders, notably Duchenne and Becker muscular dystrophies, are also characterized by cardiomyopathy aside from skeletal myopathy. The global burden of cardiomyopathies is certainly high, necessitating further research and novel therapies. Genome editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as increasingly important technologies in studying this group of cardiovascular disorders. In this review, we discuss the applications of genome editing in the understanding and treatment of cardiomyopathy. We also describe recent advances in genome editing that may help improve these applications, and some future prospects for genome editing in cardiomyopathy treatment.

Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes.

An interesting physical phenomenon was recently observed when a fresh-water basin is covered by a thin ice film that has properties similar to that of a rubber membrane. Surface waves can be generated under the action of wind on the air-water interface that contains an ice film. The modulation property of hydro-elastic waves (HEWs) in deep water covered by thin ice film blown by the wind with a uniform vertical profile is studied here in terms of the air-flow velocity versus a wavenumber. The modulation instability of HEWs is studied through the analysis of coefficients of the nonlinear Schrödinger (NLS) equation with the help of the Lighthill criterion. The NLS equation is derived using the multiple scale method in the presence of airflow. It is demonstrated that the potentially unstable hydro-elastic waves with negative energy appear for relatively small wind speeds, whereas the Kelvin–Helmholtz instability arises when the wind speed becomes fairly strong. Estimates of parameters of modulated waves for the typical conditions are given.

An innovative wireless sensor network (WSN) based on Ultra-Wide Band (UWB) technology for 3D accurate superficial monitoring of ground deformations, as landslides and subsidence, is proposed. The system has been designed and developed as part of an European Life+ project, called Wi-GIM (Wireless Sensor Network for Ground Instability Monitoring). The details of the architecture, the localization via wireless technology and data processing protocols are described. The flexibility and accuracy achieved by the UWB two-way ranging technique is analysed and compared with the traditional systems, such as robotic total stations (RTSs), Ground-based Interferometric Synthetic Aperture Radar (GB-InSAR), highlighting the pros and cons of the UWB solution to detect the surface movements. An extensive field trial campaign allows the validation of the system and the analysis of its sensitivity to different factors (e.g., sensor nodes inter-visibility, effects of the temperature, etc.). The Wi-GIM system represents a promising solution for landslide monitoring and it can be adopted in conjunction with traditional systems or as an alternative in areas where the available resources are inadequate. The versatility, easy/fast deployment and cost-effectiveness, together with the good accuracy, make the Wi-GIM system a possible solution for municipalities that cannot afford expensive/complex systems to monitor potential landslides in their territory.

A signal analysis of the genoma sequenced of coronavirus variants: B.1.1.7, B.1.135, B.1.429-B.1.427, B.1.525 and P1 is presented. We deal with a certain type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases A,C,G,T. This method provides additional information to conventional Similarity comparisons and Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of genomic sequences according to its progression along the nucleotide bases position. Hence, the method could be useful for survelliance of genoma variants.

Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type. This paper includes a broad and comparative review of the most recent short-read, long-read and hybrid assembly techniques. In this review, we provide (1) an algorithmic description of the important processes in the workflow that introduces fundamental concepts and improvements; (2) a review of existing software that explains possible options for genome assembly; and (3) a comparison of the accuracy and the performance of existing methods executed on the same computer using the same processing capabilities and using the same set of real and synthetic datasets. Such evaluation allows a fair and precise comparison of accuracy in all aspects. As a result, this paper identifies both the strengths and weaknesses of each method. This comparative review is unique in providing a detailed comparison of a broad spectrum of cutting-edge algorithms and methods.

Ankle sprains are exceedingly common injuries in both athletes and general population. They account for 10 to 30% of all sports injuries. Although the vast majority of lateral ankle ligamentous injuries respond successfully to conservative management, the absolute number of those that progress to chronic lateral ankle instability (CLAI) remains considerably important. This condition is characterized by persistent symptoms and may be associated with short-term and long-term complications and functional deficits. There is still a lack of ideal postoperative management of CLAI patients. Furthermore, an evidence-based rehabilitation phasing does not exist and most of the published studies regarding this subject suggest some protocols based on a wide variety of functional assessment scores and other modalities which are not accurate enough. Moreover, the literature that assesses the ability to return to work (RTW) and return to sport (RTS) in general population and athletes operated for CLAI shows most commonly aggregated results with global rates of RTW or RTS without describing a detailed timeline based on the readiness of patients to return to each level of activity. Although stress radiographs and MRI have been assessed as potential tools to improve postoperative management of CLAI patients, the first modality is limited by its low sensitivity to detect laxity and the second one by its static character and its inability to predict the healing process phase nor the mechanical properties of the repaired/reconstructed ligaments. Bioelectrical impedance, mechanical impedance and near-infrared spectroscopy are non-invasive methods of measurement that could be potential assessment tools to help surgeons improve the postoperative management of patients after CLAI surgery.

Mapping forest composition using multiseasonal optical time series is still challenging. Highly contrasted results are reported from one study to another suggesting that drivers of classification errors are still under-explored. We evaluated the performances of single-year Formosat-2 time series to discriminate tree species in temperate forests in France and investigated how predictions vary statistically and spatially across multiple years. Our objective was to better estimate the impact of spatial autocorrelation in the validation data on measurement accuracy and to understand which drivers in the time series are responsible for classification errors. The experiments were based on ten Formosat-2 image time series irregularly acquired during the seasonal vegetation cycle from 2006 to 2014. Due to lot of clouds in the year 2006, an alternative 2006 time series using only cloud-free images has been added. Thirteen tree species were classified in each single-year dataset based on the SVM algorithm. The performances were assessed using a spatial leave-one-out cross validation (SLOO-CV) strategy, thereby guaranteeing full independence of the validation samples, and compared with standard non-spatial leave-one-out cross-validation (LOO-CV). The results show relatively close statistical performances from one year to the next despite the differences between the annual time series. Good agreements between years were observed in monospecific tree plantations of broadleaf species versus high disparity in other forests composed of different species. A strong positive bias in the accuracy assessment (up to 0.4 of Overall Accuracy) was also found when spatial dependence in the validation data was not removed. Using the SLOO-CV approach, the average OA values per year ranged from 0.48 for 2006 to 0.60 for 2013, which satisfactorily represents the spatial instability of species prediction between years.

Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r²≥0.8, while 2961 pairs of markers showed complete LD (r²=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

An 8-month-old, 3.4 kg, castrated male Toy Poodle was referred for progressive tetraparesis and respiratory disorder without a history of trauma. Diagnostic imaging, including dynamic CT and MRI, revealed concurrent atlanto-occipital dislocation (AOD) and atlantoaxial instability (AAI) with spinal cord compression. This case was unique due to its congenital nature and the absence of trauma. The surgical intervention involved precise removal of the C1 vertebra's ventral articular facet, which was compressing on the spinal cord, attributed to its fixed and malaligned position within the atlantooccipital joint. Following facetectomy, the stabilization of the occipital bone to the C2 vertebra was achieved by screws, wire, and polymethyl methacrylate. Postoperative recovery was monitored with CT and radiographs, showing successful decompression and gradual improvement in gait, despite mild residual ataxia. The dog experienced postoperative complications with screw loosening at 114 days, which was managed successfully by extracting the problematic screws. Postoperatively, the dog showed a near-normal gait and experienced no pain through 21 months of monitoring. This case represents the first report of concurrent congenital AOD and AAI treated with ventral surgical approach, contributing new insights to the understanding and management of such complex cranio-cervical junction disorders in veterinary neurosurgery.

The art work of this present paper is to show properly conditions and aspects to reach stability in the process control, as also to avoid instability, by using digital PID controllers, with the intention of help the industrial community. The discussed control strategy used to reach stability is to manipulate variables that are directly proportional to their controlled variables. To validate and to put the exposed principles into practice, it was done two simulations of a continuous fermentation tank process start-up with the yeast strain S. Cerevisiae NRRL-Y-132, in which the substrate feed stream contains different types of sugar derived from cane bagasse hydrolysate. These tests were carried out through the resolution of conservation laws, more specifically mass and energy balances, in which the fluid temperature and level inside the tank were the controlled variables. The results showed the facility in stabilize the system by following the exposed proceedings.

With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.

Entamoeba histolytica, like other Organismes, is characterized by diversity and heterogeneity in its genetic content, which is one of the most important reasons for survival, and the increase in susceptibility to infection.Non-condensation of chromosomes during the process of cell division and the ambiguity of the chromosomal ploidy makes predicting the exact chromosomal number difficult. Genes distributed across 14 chromosomes as well as many extra-chromosome elements. Most Genes composed of one axon only, with Introns in 25% of Genes. This genome is characterized by the presence of Polymorphic internal repeat regions, and several gene families, one of these large families encoding Transmembrane kinas, Cysteine protease (CP), SREHP protein, and others.

Translational rockslides caused by toe excavation are one of the commonly seen geohazards in mountainous regions due to line traffic construction. Quantifying their failure extension length (FEL) and travel distance are of significant interest as well as huge challenges in landslide hazard assessment. In this paper, a simple criterion is proposed for predicting these two factors based on the principles of rigid body limit equilibrium and kinetic energy theorem. Further, the proposed criterion is validated against the field observations and numerical results with a practical case of the Xinjianan landslide, a medium-sized translational rockslide that occurred in 2013 in Nanchuan District, Chongqing. The findings indicate that a tiny discrepancy can be found in FEL between the field observations and the proposed criteria, while this discrepancy could be considerable in travel distance between different methods. However, the relative discrepancies all fall within 20%, deemed acceptable.

Functional ankle instability (FAI) results from multiple ankle sprains, causing a perceived sense of joint instability due to muscle and ligament imbalances. Neuromuscular training (NMT) is employed to enhance ankle stability in individuals with FAI. The study included 24 male university students with FAI, who underwent ankle NMT on three surfaces. OpenSim musculoskeletal model analyzed the effects on ankle muscle activity, kinetics, and kinematics. Utilizing repeated measures analysis of variance (ANOVA) and one-dimensional statistical non-parametric mapping (SNPM1d) to identify distinctions between training surfaces. NMT on foam cushion (FC) significantly enhanced tibialis anterior (TA) and gastrocnemius medial (GM) activation during walking compared to level-ground (LG) and artificial turf (AT) (p<0.05). However, no differences observed for peroneus longus (PL), gastrocnemius lateral (GL), and peak ankle plantarflexion (PF). During jogging and fast running, post FC training increased TA, PL, GM, GL activation, and peak ankle PF moment (p<0.05). Additionally, post FC training, subtalar mobility was significantly reduced (p<0.05), and ankle joints exhibited greater dorsiflexion (DF) angles during jogging and fast running (p<0.05). Consequently, selecting FC for short-term ankle NMT proves more advantageous in enhancing ankle stability among individuals with FAI, yielding a more positive impact on FAI improvement.

: Two-dimensional instability of a horizontal layer of boiling liquid with a finite height is experimentally studied. In this layer, “vapor columns” rose at the corners of a square rectangular grid. The symmetry of “vapor column” location on the heating surface is considered. The model considers the approach to the boiling crisis in terms of both developed nucleate boiling and transitional boiling (the Zuber problem). When dealing with developed nucleate boiling, the layer of boiling liquid is considered in calculations as an isotropic homogeneous system (foam). It is shown how the conditions on the heating surface (capillary-porous coating) affect external hydrodynamics of the liquid layer and, ultimately, the value of the critical heat flux. The calculation ratio obtained by approaching the boiling crisis with regard to developed nucleate boiling takes into account the dependence of the critical heat flux on the void fraction of the boiling liquid layer. A new solution to the boiling crisis problem is proposed when approaching the crisis from the point of transitional boiling (the Zuber problem). This new solution eliminates some shortcomings of the classical problem (in particular, the void fraction of the layer corresponds to the experiments).

Mandatory fortification of food with the synthetic folic acid (FA) was instituted in 1998 to reduce the incidence of neural tube defects. Adequate folate status is correlated with numerous health benefits. However, elevated consumption of FA is controversially associated with deleterious effects on health. We previously reported that excess FA mimicked folate depletion in a lymphoblastoid cell line. To explore the impact of FA intake from fortified food, we conducted an observational human study on 33 healthy participants aged 18-40 not taking any supplements. Food intake, anthropomorphic measurements, and blood samples were collected and analyzed. Our results show that individuals belonging to the highest tertile of folic acid intake, as well as ones with the highest folic acid to total folate intake ratio (FAR), display a significantly greater incidence of lymphocyte genomic damage. A decrease in global DNA methylation is observed in the highest tertile of FAR compared to the lowest (P=0.055). A downward trend in the overall gene expression of select DNA repair and one carbon cycle genes (MGMT, MLH1, UNG, MTHFR, MTR) is noted with increased folate status and FA intake. These results provide supporting evidence that high consumption of FA from fortified foods can precipitate genomic instability in peripheral lymphocyte in-vivo.

Postural instability (PI) in Parkinson’s disease (PD) exposes patients to increased risk of falls (RF). Although dopaminergic therapy and deep brain stimulation (DBS) improve motor performance in advanced PD patients, their effects on PI and RF are not clear. PI and RF were assessed by a stabilometric platform in 6 advanced PD patients. Patients were evaluated on and off dopaminergic medication and four DBS conditions: bilateral-DBS, DBS of the more- or less-affected side and DBS-off. Dopaminergic medication alone worsened PI and RF, DBS alone worsened RF, and no medication/DBS combination produced an improvement in postural control with respect to the OFF-medication/DBS-off condition. When ON-medication, PI and RF significantly improved after turning the DBS on, regardless of medication condition. Among DBS conditions, bilateral-DBS provided the maximal improvement of PI and RF when ON medication, and minimal worsening of PI and RF when OFF medication, whereas patients performed worse when in most-affected side DBS condition. These results can help in developing the best therapeutic strategy for postural disorders in patients with advanced PD.

In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species.

The Oriental ratsnake Ptyas mucosa is a common non-venomous snake of the colubrid family, with a wide geographic range spanning much of South and Southeast Asia. P. mucosa is widely cultivated dut to it used in traditional medicine, scientific research, and handicrafts. Therefore, genome resources could play an important role in the efficacy of traditional medicine and the analysis of the living environment of the species. We collected a snake sample in Hezhou, Guangxi, China, which was identified as P. mucosa by morphological identification. Here we present a highly continuous P. mucosa genome with a genome size of 1.74Gb. The scaffold N50 length is 9.57Mb and the maximal length of scaffold is 78.3Mb, the P. mucosa genome has a CG content of 37.9% and the integrity of the gene reached 86.6%.Assembled using long-reads, the total length of the repeat sequence in the genome reached 735 Mb, and its repeat content was as high as 42.19%. A total of 24,869 functional genes were annotated. This study will assist in the understanding of the P. mucosa, and also provide a basis for medicinal research.

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

The analysis of curated genomic, metagenomic, and proteomic data are of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw form in free international repositories, its access requires plenty of computing, storage, and processing capacities for the domestic user. The purpose of the study is to offer a comprehensive set of genomic and proteomic reference data, in an accessible and easy-to-use form to the scientific community. A representative type material set of genomes, proteomes and metagenomes were directly downloaded from the site: https://www.ncbi.nlm.nih.gov/assembly/ and from Genome Taxonomy Database, associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy raw reduced representations, by using Mash software. Our dataset contains near to 100 GB of space disk reduced to 585.78 MB and represents 87,476 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with computational resources. Potential uses of this dataset include but are not limited to, microbial species delimitation, estimation of genomic distances, genomic novelties, paired comparisons between proteomes, genomes, and metagenomes.

The growing population meet the challenge for agricultural production. CRISPR/Cas9 technology is based on plant research for the development of the new varieties as well as disease resistance crops. In addition the deletion of significant characters makes the new alleles from the CRISPR/Cas9. Recent and reliable molecular scissor for genetic engineering. The review is focused on the various application of the CRISPR/Cas9 technology in plant enhancement of plant disease resistance, stress burden in plant, nutritional improvement, and quality of crops from the CRISPR/Cas9 system. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (cas9) is adopted from the prokaryotic type II system. CRISPR/Cas9 is simplicity and efficiency than ZENs and TALENs for the genome engineering. Due to rapid growing of the CRISPR/Cas9 system has been formulate the adaptation of many plant species. The current advancement of plants and future schemes of improve of CRISPR technology has been presented in contest of multiplex editing, knowledge on induced mutation whether the factor effect in CRISPR/Cas9 technology in plant. Remarkable perspective and challenges of CRISPR/Cas9 technology in significance of plant genetic modification.

Single-stand selective monofunctional uracil DNA glycosylase 1 (SMUG1) works to remove uracil and certain oxidized bases from DNA during base excision repair (BER). This review provides a historical characterization of SMUG1 and 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) one important substrate of this enzyme. Biochemical and structural analyses provide remarkable insight into the mechanism of this glycosylase revealing SMUG1 has a unique helical wedge which influences damage recognition during repair. Rodent studies suggest that, while SMUG1 shares substrate specificity with another uracil glycosylase UNG2, loss of SMUG1 can have unique cellular phenotypes. This review highlights the multiple roles SMUG1 may play in preserving genome stability, and how the loss of SMUG1 activity may promote cancer. Finally, we discuss recent studies indicating SMUG1 has moonlighting functions beyond BER, playing a critical role in RNA processing including the RNA component of telomerase.

Background/Objectives Recurrent shoulder instability following Bankart lesion repair often necessitates surgical revision. Identified risk factors include young age, glenoid bone loss, and off-track Hill-Sachs lesions. This systematic review aims to understand failure rates of arthroscopic revision Bankart repair and if these aforementioned factors influence its success. Methods Following PRISMA guidelines, this systematic review, registered on PROSPERO, included twenty-four articles. Two independent reviewers assessed eligibility across three databases, focusing on recurrent instability as the primary endpoint, while also noting functional measures, adverse events, revision operations, and return-to-sport rates when available. Results Key surgical techniques for recurrent instability post-Bankart repair were identified, with revision arthroscopic Bankart being the most common (685/1032). Despite generally endorsed effectiveness, recurrence rates have increased over the past four years. Comparative analysis revealed significantly lower recurrence for open Latarjet compared to revision arthroscopic Bankart (p

Emergency control load-shedding is a key solution to prevent blackouts in the power system. This paper proposed a new model of emergency controls load shedding based on the fast identification of the unstable state of the power system. K-means clustering algorithm divided the instability mode into the clusters. The results of analysis of this cluster were used as the basis for classification control. Building load shedding strategies is consisted of the pre-designed rules based on AHP algorithm. When the recognition of the power system “instability” is detected, the signal of load shedding control is triggered immediately, therefore the decision time is greatly shortened comparing to the traditional methods. The effectiveness of the proposed method was tested on the IEEE 39-bus to overcome the limitations of the last traditional methods.

Climate change poses a serious threat to global agricultural activity and food production. To address this issue, plant genome editing technologies have been developed to provide an alternative solution for crop improvement. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome to produce crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and possible gaps in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.

Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 genomes in Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species and performed a phylogenetic analysis to determine their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasica and Apis mellifera mellifera and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD30D/Tigger, DD33D/Tigger and DD34D/mariner may have experienced horizontal transfer events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under conditions of relaxed selection, and results in a balance between rates of mutation and rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the tree of life, and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.

During the progression of cancer cells, the degree of genome instability increases leading to genome chaos in populations of malignant cells. While normally chaos is associated with er-godicity, i.e., the state when the time averages of relevant parameters is equal to their phase space averages, the situation with cancer propagation is more complex. Chromothripsis, a catastrophic massive genomic rearrangement, is observed in many types of cancer leading to increased mu-tation rates. We present an entropic model of genome chaos and ergodicity and experimental evidence that increasing the degree of chaos beyond the non-ergodic threshold may lead to the self-destruction of the tumor cells. We study time and population averages of chromothripsis frequency in cloned rhabdomyosarcoma from rat stem cells. Clones with frequency above 10% result in cell apoptosis possibly due to mutations in the BCL2 gene. Potentially this can be used for suppressing cancer cells by shifting them into a non-ergodic proliferation regime.

Concatemeric viral DNA is packaged into Bacteriophage P22 procapsids via a headful packaging mechanism mediated by a molecular machine consisting of small (gp3) and large (gp2) terminase subunits. Although a negative stain reconstruction exists for the terminase holoenzyme, it is not clear how this complex binds dodecameric portal protein located at a 5-fold mismatch vertex. Herein, we describe new assemblies for the holoenzyme. Both native mass spectrometry and transmission electron microscopy reveal that the P22 terminase complex adopts three main assemblies, which include a nonameric S-terminase bound to two L-terminase 1(gp3)9:2(gp2), two nonameric S-terminase bound to five L-terminase 2(gp3)9:5(gp2), and three nonameric S-terminase bound to seven L-terminase 3(gp3)9:7(gp2). Native agarose gel electrophoresis shows that the terminase complex interacts with procapsid with mild crosslinking. These results herein illustrate the P22 terminase complex can adopt a variety of confirmations and assembly states.

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.

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during plant growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula. Background and Objectives: The cell cycle factors not only influence cell cycle progression together, but also regulate accretion, division and differentiation of cells, and then regulate growth and development of plant. In this study, we identified the putative cell cycle genes in B. pendula genome, based on the annotated cell cycle genes in A. thaliana. It could serve as a foundation for further functional studies. Materials and Methods: The transcript abundance was determined for all the cell cycle genes in xylem, root, leaf and flower tissues using RNA-seq technology. Results: We identified 59 cell cycle gene models in the genome of B. pendula, 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1 and BpWEE1. Conclusions: We identified 17 core cell cycle genes in the genome of birch by combining phylogenetic analysis and tissue specific expression data.

We are in a new chapter of crop and livestock improvement with the emergence of genome editing. This latest generation of molecular tools can be used to make targeted changes in a genome including insertions, deletions, and mutations. With new advances comes new risks for unintended changes and impacts, thus the need for appropriate risk assessment for product development and to inform regulatory measures. Though CRISPR/Cas has arisen as the predominant technology, there are multiple types of genome editing tools each with pros and cons depending on the organism and desired outcome. Furthermore, each editing tool differs in specificity as they may edit non-intended sites, referred to as off-target edits. The consensus of the agricultural editing community is to avoid off-target editing through design and detection, instead of determining whether off-target editing in each case is detrimental. The design of a targeting component, the tool chosen, and the identification of the edit(s) made are the critical factors in avoiding off-target edits and confirming intended edits in final products that are released commercially. The limited amount of head-to-head comparisons of genome editing tools in diverse crops and livestock make it difficult to develop broad conclusions and best practices, which is further compounded by the diversity of techniques, targets, and processes. Developers and breeders should consult the literature and test as needed to determine which editing technology will be the most effective for their purposes, especially as more tools with altered efficiency and specificity become available. Yet, the lack of off-target edits in studies that employed careful design of targeting components followed by wide testing for on- and off-target edits bodes well for the use of genome editing with proper precautions of target selection and screening.

The development of CRISPR associated proteins, such as Cas9, has led to increased accessibility and ease of use in genome editing. However, additional tools are needed to quantify and identify successful genome editing events in living animals. We developed a method to rapidly and quantitatively monitor gene editing activity non-invasively in living animals that also facilitates confocal microscopy and nucleotide level analyses at the end of study. Here we report a new CRISPR “footprinting” approach to activate luciferase and fluorescent proteins in mice as a function of gene editing. This system is based on experience with our prior Cre-detector system and is designed for Cas editors able to target LoxP including gRNAs including SaCas9 and ErCas12a [1, 2]. These CRISPRs cut specifically within LoxP, an approach that is a departure from previous gene editing in vivo activity detection techniques that targeted adjacent stop sequences. In this sensor paradigm, CRISPR activity was monitored non-invasively in living Cre reporter mice (FVB.129S6(B6)-Gt(ROSA)26Sortm1(Luc)Kael/J and Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J, which will be referred to as LSL and mT/mG throughout the paper) after intramuscular or intravenous hydrodynamic plasmid injections, demonstrating utility in two diverse organ systems. The same genome-editing event was examined at the cellular level in specific tissues by confocal microscopy to determine the identity and frequency of successfully genome-edited cells. Further, SaCas9 induced targeted editing at efficiencies that were comparable to Cre recombinase demonstrating high effective delivery and activity in a whole animal. This work establishes genome editing tools and models to track CRISPR editing in vivo non-invasively and to fingerprint the identity of targeted cells. This approach also enables similar utility for any of the thousands of previously generated LoxP animal models.

Conventional plant breeding has contributed enormously towards feeding the world and has played crucial roles in the development of modern society. The conventional method creates variation by transferring genes between or within the species. In general, these methods are more expensive and takes more time, to overcome these limitations, new technology is required. Genome editing is a powerful tool for biotechnology applications, with the capacity to alter the function of any gene. With the availability of gene information for the majority of the traits, genome editing emerged as a potential to create a new variation with the introduction of any transgene. The important genome editing tools used nowadays are ZFNs, TALEN, Pentatricopeptide repeats protein, adenine base editor, RNA interference, and CRISPR/Cas9. These tools have opened a new era for crop improvement. Due to the complex genetic architecture of most traits, it is challenging to edit genes controlling them. To overcome these challenges, genome editing provides a broader perspective. Among the above-mentioned tools, CRISPR/Cas9 is the most powerful tool for gene editing. These technologies are being used to create abiotic and biotic resistance crop varieties.

The instability of traveling pulses in nonlinear diffusion problems is inspected on the example of Gunn domains in semiconductors. Mathematically the problem is reduced to the calculation of the "energy" of the ground state in Schrödinger equation with a complicated potential. A general method to obtain the bottom-part spectrum of such equations based on the approximation of the potential by square wells is proposed and applied. Possible generalization of the approach to other types of nonlinear diffusion equations is discussed.

In this study, the multi-relaxation-time lattice Boltzmann method is applied to investigate the oscillatory instability of lid-driven flows in two-dimensional semi-elliptical cavities with different vertical to horizontal aspect ratios K in the range of 1.0--3.0. The program implemented in this study is parallelized using CUDA (compute unified device architecture), a parallel computing platform, and computations are carried out on NVIDIA Tesla K40c GPU. To carry out precise calculations, the CUDA algorithm is extensively investigated, and its parallel efficiency indicates that the maximum speedup is 47.6 times faster. Furthermore, the steady--oscillatory Reynolds numbers are predicted by implementing the CUDA-based programs. The amplitude coefficient is defined to quantify the time-dependent oscillation of the velocity magnitude at the monitoring point. The simulation results indicate that the transition Reynolds numbers correlate negatively with the aspect ratio of the semi-elliptical cavity, and are smaller than those of the rectangular cavity at the same aspect ratio. In addition, the detailed vortex structures of the semi-elliptical cavity within a single period are also investigated when the Reynolds number is larger than the steady--oscillatory value to determine the effects of periodic oscillation of the velocity magnitude.

The Particle-In-Cell (PIC) method has been developed in order to investigate microscopic phenomena, and with the advances of computing power, newly developed codes have been used for several fields such as astrophysical, magnetospheric, and solar plasmas. PIC applications have grown extensively with large computing powers available on supercomputers such as Pleiades and Blue Waters in the US. For astrophysical plasma research PIC methods have been utilized for several topics such as reconnection, pulsar dynamics, non-relativistic shocks, relativistic shocks, relativistic jets, etc. PIC simulations of relativistic jets have been reviewed with the emphasis on the physics involved in the simulations. This review summarizes PIC simulations, starting with the Weibel instability in slab models of jets, and then focuses on global jet evolution in helical magnetic field geometry. In particular we address kinetic Kelvin-Helmholtz instabilities and mushroom instabilities.

Advanced genomics, transcriptomics and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids, and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research, the principles of genomics, transcriptomics and epigenomics, alongside their most advanced technologies (like single cell omics and spatial omics), which allows to investigate the molecular events that occur at single cell resolution retaining the spatial information.

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

Hallux valgus deformity (HVD) involves subluxation of the first metatarsophalangeal joint. While HVD is primarily considered a forefoot condition, midfoot instability may play a significant role in its development and severity. Therefore, this review had a particular focus on understanding midfoot instability based upon weightbearing imaging assessments of the TMT joint. This review followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and searched five databases for studies on midfoot instability in HVD patients. Severity of HVD was defined by hallux valgus angle (HVA) and distal metatarsal articular angle (DMAA). Data was extracted, and articles were graded using the Methodological Index for Non-Randomized Studies (MINORS). Of 547 initially retrieved articles, 23 met inclusion criteria. Patients with HVD showed higher HVA and DMAA on weight-bearing radiographs (WBRG) and weight-bearing computed tomography (WBCT) compared to healthy individuals. Midfoot instability was assessed through intermetatarsal angle (IMA) and tarsometatarsal angle (TMT angle). Patients with HVD exhibited greater IMA and TMT angles on both WBRG and WBCT. This review highlights the importance of weight-bearing imaging assessments for midfoot instability in HVD. IMA and TMT angles can differentiate between healthy individuals and HVD patients, emphasizing the significance of midfoot assessment in understanding HVD pathology.

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.

Zanthoxylum armatum is an forest tree with apomixis characteristic, and RWP-RKs are plant-specific transcription factors known to regulate nitrogen response and embryonic development. However, the genome-wide analysis of RWP-RK family genes in Z.armatum is unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z.armatum, among which 15 genes were belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed close phylogenetic relationship between Z.armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of embryonic development of Z.armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z.armatum.

The ZIPs (ZRT/IRT-like proteins) play critical roles in the absorption, transport, and intracellular balance of metal ions essential for various physiological processes in plants. However, little is known about the pan-genomic characteristics and properties of ZIP genes in cucumber (Cucumis sativus L.). In this study, we identified 10 CsZIP genes from the pan-genome of 13 C. sativus accessions. Among them, only CsZIP10 showed no variation in protein sequence length. We analyzed the gene structure, conserved domains, promoter cis-elements, and phylogenetic relationships of these 10 CsZIP genes derived from "9930". Based on phylogenetic analysis, the CsZIP genes were classified into three branches. Amino acid sequence comparison revealed the presence of conserved histidine residues in the ZIP proteins. Analysis of promoter cis-elements showed that most promoters contained elements responsive to plant hormones. Expression profiling in different tissues showed that most CsZIP genes were expressed at relatively low levels in C. sativus leave, stem, and tendril, and CsZIP7 and CsZIP10 were specifically expressed in root, indicating their potential involvement in the absorption and transport of metal ions. Transcriptomic data indicated that these 10 ZIP genes displayed responses to both downy mildew and powdery mildew, and CsZIP1 were significantly downregulated after both salt and heat treatments. In conclusion, this study deepens our understanding of the ZIP gene family and enhances our knowledge of the biological functions of CsZIP genes in C. sativus.

Dendrobium Sw have multiple photosynthetic pathways but due to the lack of identification, the influence of CAM pathway on the plastid genomic evolution of Dendrobium and the origin of CAM pathway are still poorly understood. In this study, based on the results of δ13C, net photosynthetic rates (Pn) and titratable acid value, we identified Dendrobium species into three photosynthetic pathways. Then the chloroplast whole genome characteristics of 10 Dendrobium species were analyzed with next-generation sequencing technology. The quadripartite-structure plastomes ranged from 151,673 bp to 160,375 bp and included 127 to 132 genes. Five noncoding mutational hotspots (rbcL-accD, atpB-rbcL, rbcL, trnLUAA, accD, Pi > 0.10) were identified. A total of 41–60 SSRs were recognized, the average trinucleotide content was only about 4%, which is probably due to a more conserved SSR. Among multiple photosynthetic pathways, the apparent differences in IR junctions of SSC/IRB junctions (JSBs) were measured within chloroplast genomes, and the chloroplast genome size of constitutive CAM plants is shorter because of their ndh gene loss or pseudogenization, and this phenomenon accounts for a decreasing proportion of constitutive CAM, facultative CAM, and obligate C3 plants, so that the loss of the ndh gene may be speculated to be closely related to the CAM pathway. Phylogenetic analyses showed that there are multiple independent CAM origins in selected Dendrobium species, and the ancestral Dendrobium plastome possessed full ORFs for all ndh genes. The study aims to clarify the chloroplast genomic features of different photosynthetic pathways, enrich the genomic data of CAM plants, and provide genetic information from different perspectives for further systematic study of Dendrobium.

Brown-Spotted Pit viper (Protobothrops mucrosquamatus), also known as the Chinese habu, is a widespread and highly venomous snake distributed from from northeastern India to eastern China. Genomics research can help provide much insight in understanding venom components and natural selection in vipers. Here, we collected, sequenced and assembled the genome of a male P. mucrosquamatus individual from China, producing a highly continuous reference genome, with the length of 1.53 Gb and 41.18% repeat element content. From this 24,799 genes were identified, and 97.97% genes could be annotated. Nuclear genome single-copy genes phylogenetic tree including 6 species verified the validity of our genome assembly and annotation process. This research will contribute to further study on Protobothrops biology and the genetic basis of the snake venom.

Recent developments in artificial nucleic acid and drug delivery systems (DDS) present possibilities for the symbiotic engineering of oligonucleotide therapeutics, such as antisense oligonucleotides (ASOs), and small interfering RNA (siRNA). These technologies can also be applied for triplex-forming oligonucleotides (TFOs) to develop symbiotic genome-targeting tools and a new class of oligonucleotide drugs. Many reports have described the functionalization of TFOs and the enhancement of TFO activities. In particular, the tethering of crosslinking groups to TFOs enables irreversible triplex formation and is frequently exploited for antigene and genome-editing experiments. These crosslinkable TFOs have shown considerable potential for therapeutic application. In this review, we revisit these crosslinking techniques and explore the combination of these techniques with recent artificial oligonucleotide and DDS technologies.

Staphylococcus aureus is a high-priority pathogen causing severe infections with high morbidity and mortality worldwide. Many S. aureus strains are methicillin-resistant (MRSA) or even multi-drug resistant. It is one of the most successful and prominent modern pathogens. An effective fight against S. aureus infections requires novel targets for antimicrobial and antistaphylococcal therapies. Recent advances in whole-genome sequencing and high-throughput techniques facilitate the generation of genome-scale metabolic models (GEMs). Among the multiple applications of GEMs is drug-targeting in pathogens. Hence, comprehensive and predictive metabolic reconstructions of S. aureus could facilitate the identification of novel targets for antimicrobial therapies. This review aims at giving an overview of all available GEMs of multiple S. aureus strains. We downloaded all 114 available GEMs of S. aureus for further analysis. The scope of each model was evaluated, including the number of reactions, metabolites, and genes.Furthermore, all models were quality-controlled using Mᴇᴍᴏᴛᴇ, an open-source application with standardized metabolic tests. Growth capabilities and model similarities were examined. This review should lead as a guide for choosing the appropriate GEM for a given research question. With the information about the availability, the format, and the strengths and potentials of each model, one can either choose an existing model or combine several models to create models with even higher predictive values. This facilitates model-driven discoveries of novel antimicrobial targets to fight multi-drug resistant S. aureus strains.

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.