Number Of Changes Research Articles

Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression

Genomic heterogeneity has largely been overlooked in single-cell replication timing (scRT) studies. Here, we develop MnM, an efficient machine learning-based tool that allows disentangling scRT profiles from heterogenous samples. We use single-cell copy number data to accurately perform missing value imputation, identify cell replication states, and detect genomic heterogeneity. This allows us to separate somatic copy number alterations from copy number changes resulting from DNA replication. Our methodology brings critical insights into chromosomal aberrations and highlights the ubiquitous aneuploidy process during tumorigenesis. The copy number and scRT profiles obtained by analysing >119,000 high-quality human single cells from different cell lines, patient tumours and patient-derived xenograft samples leads to a multi-sample heterogeneity-resolved scRT atlas. This atlas is an important resource for cancer research and demonstrates that scRT profiles can be used to study replication timing heterogeneity in cancer. Our findings also highlight the importance of studying cancer tissue samples to comprehensively grasp the complexities of DNA replication because cell lines, although convenient, lack dynamic environmental factors. These results facilitate future research at the interface of genomic instability and replication stress during cancer progression.

Modeling Trends and Projections of Riding with Alcohol-Impaired Drivers in Fatal Crashes among Young Adults: A System Dynamics Approach.

The purpose of the study was to investigate factors contributing to the decline in the number of passengers riding with alcohol-impaired drivers involved in fatal crashes since 1982, and to examine the impact of simulated interventions on this group through 2050. Historical data were obtained from the Fatality Analysis Reporting System. We applied linear regression to analyze changes in the average numbers of passengers per alcohol impaired young driver involved in fatal crashes between 1982 and 2020 by age and sex. We also extended our existing system dynamics simulation model developed to examine driving while impaired (DWI) behaviors of U.S. male and female drivers aged 15 to 24 and explored riding with an impaired driver (RWI) behaviors and corresponding interventions. We conducted sensitivity analyses to examine the likely trajectories of alcohol impaired drivers' passengers in fatal crashes across multiple scenarios through 2050. Our findings show that the decline in passengers of alcohol impaired drivers in fatal crashes primarily stems from a decrease in the number of impaired drivers, rather than a change in average number of passengers per impaired drivers. The simulation model replicated historical trends from 1982 to 2020, and the sensitivity analyses show that the policies reducing DWI trips also decrease RWI trips. Wide adoption of a comprehensive strategy, combining increased enforcement, an alcohol truth campaign, the provision of alternative transportation, and the enactment of a new DWI restrictive law, could significantly reduce the number of passengers in fatal crashes involving alcohol-impaired drivers, while minimizing possible unintended consequences.

Sector-differences in Adults' Dental Care Service Utilisation: 11-year Register-based Observations.

This register-based study evaluated sector-specific differences in adults' utilisation of dental care services in Helsinki, Finland in 2007-2017. The target population comprised all inhabitants aged 20+ years in Helsinki over an 11-year period, from 2007 to 2017. The data, aggregated into 5-year age groups by treatment year and type of treatment, included inhabitants with at least 1 visit to a dentist in the private or public sector. In 2007-2017, the numbers of all patients ranged between 229,772 and 261,488. The patient age groups were analysed for periodontal, restorative, endodontic, and oral surgery treatment received. Attendance rates (%) refer to the number of patients per number of inhabitants. Proportions (%) of patients receiving various treatment types refer to numbers of patients per all patients. Comparisons between the age groups included percentual change in absolute numbers and percentage points in rates. The treatment-year trends were analysed by applying linear regression models. Attendance rate for all adult patients was 49.5% in 2007 and 48.8% in 2017. During the 11-year period, adults' attendance to private service decreased (31.4%-24.9%) but increased to public service (18.1%-23.9%). Patients receiving periodontal care increased in both the private (67%-72%) and public (36%-45%) sectors, while patients with restorative care decreased in both sectors private (67%-58%) and public (58%-48%). Further, fewer private- than public-sector patients received oral surgery or endodontic treatment. Sector-specific differences in patient treatments may indicate over- or undertreatment choices in restorative and periodontal care.

Stutzerimonas stutzeri culture enhances microbial community structure and tomato seedling growth in saline soil.

Plant growth-promoting rhizobacteria (PGPR) improve microbial community structure, promote crop growth, and reduce greenhouse gas emissions in agricultural soils; however, the effects of PGPR fermentation on the growth and salt tolerance of tomato plants remain unclear. In this study, we aimed to investigate the effects of the PGPR Stutzerimonas stutzeri NRCB010 on the microbial communities, tomato growth, and nitrous oxide (N2O) emissions in saline soil by performing a greenhouse pot experiment. The experiment was conducted under two soil salt concentrations (0 and 3 g kg-1 NaCl) and three treatments (LSFJ broth, NRCB010 cells, and NRCB010 culture). Both salt stress and NRCB010 treatments significantly affected the physicochemical properties and microbial community structure of tomato rhizosphere soil. Treatment with 3 g kg-1 NaCl significantly reduced the shoot and root dry weights of the plants compared with those of the control plants. Application of NRCB010 cells as well as that of culture promoted the growth of tomato seedlings and alleviated salt stress. The copy number changes in the nosZⅠ gene on day 3 and amoA gene on day 25 demonstrated that NRCB010 cells significantly reduced soil N2O emissions when treated with 0 g kg-1 NaCl. Furthermore, soil physicochemical properties, plant biomass, and soil microbial diversity were correlated with each other. The results emphasize the enormous potential of S. stutzeri NRCB010 culture to resist abiotic stress, promote crop growth, and improve the rhizosphere soil microenvironment; however, its ability to decrease N2O emissions is constrained by soil salinity.

Estimating real-time reproduction number for HPV infection in Xinjiang, China

Objective: This study aimed to investigate the prevalence of human papillomavirus (HPV) infection in Xinjiang, estimate the real-time reproduction number (Rt) of HPV infection, evaluate the effectiveness of local prevention and control policies, and provide a theoretical basis for cervical cancer (CC) control strategies in the region. Methods: Using the R0 package, the R software was employed to estimate the dynamic changes in the real-time reproduction number (Rt) of HPV infection in Xinjiang from January 2015 to December 2019. Four methods—Maximum Likelihood Estimation (ML), Exponential Growth (EG), Sequential Bayesian (SB), and Time-Dependent (TD)—were used to calculate the Rt values. The study compared the results from these methods to determine the most reliable approach for estimating HPV transmission. Results: Among the four methods, the TD method provided the best fit for observed and predicted cases. The estimated overall Rt was 1.1381 (95% CI: 1.0762–1.1972). For the periods 2015–2017 and 2017–2019, the Rt values were 1.2827 and 1.0544, respectively. Notably, the Rt value showed a downward trend after 2017 but remained above 1, indicating continued transmission of HPV. Conclusion: Although HPV infection rates in Xinjiang appear to be decreasing, the persistent Rt values suggest that HPV transmission has not been fully controlled. This highlights the urgent need for strengthened prevention and control measures to reduce HPV-related cervical cancer risk in the region.

Convergent Evolution and Predictability of Gene Copy Numbers Associated with Diets in Mammals.

Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and the capability of organisms to utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether gene copy number changes of particular gene families are linked to diet shifts in mammals and assess whether trophic ecology can be inferred from the copy numbers of a specific set of gene families. Using 86 mammalian genome sequences, we identified 24 gene families with a trend toward higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptors, and xenobiotic metabolism genes, and identify novel gene families whose copy numbers correlate with dietary patterns. For example, omnivores exhibited higher copy numbers of genes encoding regulators of translation. We also established a discriminant function based on the copy numbers of 13 gene families that can help predict trophic ecology to some extent. These findings highlight a possible association between convergent evolution and repeated copy number changes in specific gene families, suggesting the potential to develop a method for predicting animal ecology from genome sequence data.

Impact of Perinatal Death Auditing: Outcomes of An Interventional Study on Perinatal Death Auditing in Two Districts of Karnataka State, India

Background: Perinatal death auditing is useful to identify preventable perinatal deaths and avoidable/preventable factors. Objectives: To know the impact of perinatal death audit like 1). Documentation of Care Provided 2) Changes in Infrastructure and Facilities 3). Number of perinatal deaths 4) Any other impact. Methodology: Perinatal death auditing project implemented in two districts of Karnataka state. As a Part of Intervention, Expert Panel audited the perinatal deaths and provided feedback to the hospitals where these deaths occurred. The feedback included issues identified and suggestion for prevention. Trained Medical-Social Workers conducted evaluation surveys in post-interventional period at 6th monthly intervals. They collected the filled tools from the hospitals and handed over the written feedback of the expert panel to these hospitals. It was anticipated that the process of feedback would initiate some changes in infrastructure, facilities, documentation and number of perinatal deaths. Results: Number of reported perinatal deaths decreased in Koppal District (from 325 to 301) as compared with Dakshina Kannada (from 223 to 221). Improvements in: 1]. Documentation of care provided 2] Assertion of preventability by the doctors 3] Infrastructure &facilities were observed in backward district of Koppal as compared to developed district of Dakshina Kannada. Conclusion: Perinatal Death Auditing reduces the number of perinatal deaths apart from improving documentation, assertion of preventability by doctors, infrastructure & facilities.

Mitochondrial DNA copy number variations in Epstein-Barr virus-transformed B cells after exposure to radiation: A possible biomarker for dose assessment

Following accidental radiation exposure due to a radiological or nuclear emergency, a dose assessment should be performed based on biological samples from exposed individuals. Although previous biological dose assessment approaches have focused on nuclear DNA damage in peripheral lymphocytes, this study investigated the radiation-induced impact on the mitochondrial genome, particularly the chronological changes in the mitochondrial DNA copy number (mtDNAcn) following exposure to radiation. We used B-lymphoblastoid cell lines transformed by Epstein-Barr virus established from 12 healthy individuals in their 20s (six males, six females) with or without a history of smoking. Using real-time quantitative PCR, we determined the mtDNAcn from the B cells cultured for 6, 24, and 96 h and after exposure to 0, 1, 2, and 4 Gy X-rays. We found a significant relationship between the exposed dose and mtDNAcn in the 96-hour post-irradiation cells for non-smoking males, suggesting the possible role of mtDNAcn as a biomarker for dose assessment.

Single-cell profiling of penta- and tetradactyl mouse limb buds identifies mesenchymal progenitors controlling digit numbers and identities

The cellular interactions controlling digit numbers and identities have remained largely elusive. Here, we leverage the anterior digit and identity loss in Grem1 tetradactyl mouse limb buds to identify early specified limb bud mesenchymal progenitor (LMP) populations whose size and distribution is governed by spatial modulation of BMP activity and SHH signaling. Distal-autopodial LMPs (dLMP) express signature genes required for autopod and digit development, and alterations affecting the dLMP population size prefigure the changes in digit numbers that characterize specific congenital malformations. A second, peripheral LMP (pLMP) population is anteriorly biased and reduction/loss of its asymmetric distribution underlies the loss of middle digit asymmetry and identities in Grem1 tetradactyl and pig limb buds. pLMPs depend on BMP activity, while dLMPs require GREM1-mediated BMP antagonism. Taken together, the spatial alterations in GREM1 antagonism in mouse mutant and evolutionarily diversified pig limb buds tunes BMP activity, which impacts dLMP and pLMP populations in an opposing manner.

Motor modules are largely unaffected by pathological walking biomechanics: a simulation study

BackgroundMotor module (a.k.a. muscle synergy) analysis has frequently been used to provide insight into changes in muscle coordination associated with declines in walking performance, to evaluate the effect of different rehabilitation interventions, and more recently, to control exoskeletons and prosthetic devices. However, it remains unclear whether changes in muscle coordination revealed via motor module analysis stem from abnormal walking biomechanics or neural control. This distinction has important implications for the use of motor module analysis for rehabilitation interventions and device design. Thus, this study aims to elucidate the extent to which motor modules emerge from pathological walking biomechanics, i.e. abnormal walking biomechanics commonly observed in individuals with neurological disease and/or injury.MethodsWe conducted a series of computer simulations using OpenSim Moco to simulate pathological walking biomechanics by manipulating speed, asymmetry, and step width in a three-dimensional musculoskeletal model. We focused on these spatiotemporal metrics because they are commonly altered in individuals with Parkinson’s disease, stroke survivors, etc. and have been associated with changes in motor module number and structure. We extracted motor modules using nonnegative matrix factorization from the muscle activations from each simulation. We then examined how alterations in walking biomechanics influenced the number and structure of extracted motor modules and compared the findings to previous experimental studies.ResultsThe motor modules identified from our simulations were similar to those identified from previously published experiments of non-pathological walking. Moreover, our findings indicate that the same motor modules can be used to generate a range of pathological-like waking biomechanics by modulating their recruitment over the gait cycle. These results contrast with experimental studies in which pathological-like walking biomechanics are accompanied by a reduction in motor module number and alterations in their structure.ConclusionsThis study highlights that pathological walking biomechanics do not necessarily require abnormal motor modules. In other words, changes in number and structure of motor modules can be a valuable indicator of alterations in neuromuscular control and may therefore be useful for guiding rehabilitation interventions and controlling exoskeletons and prosthetic devices in individuals with impaired walking function due to neurological disease or injury.

Responses of skeletal muscle to mechanical stimuli in female rats following and during muscle disuse atrophy.

The purpose of this study was to investigate the ability of mechanotherapy to enhance recovery or prevent loss of muscle size with atrophy, in female rats. Female F344/BN rats were assigned to weight bearing (WB), hindlimb suspended (HS) for 14 days with reambulation for 7 days without (RA) or with (RAM) mechanotherapy (study 1), or to WB, HS for 7 days, with (HSM) or without mechanotherapy (study 2) to gastrocnemius. Muscle fiber cross sectional area (CSA) and type, collagen, satellite cell number, and protein synthesis (Ksyn) and degradation (Kdeg) were assessed. Study 1: muscle weight, but not CSA, was higher in RAM compared to HS, but CSA was higher in RA compared to HS. Myofibrillar Ksyn was higher in RA and RAM compared to WB and HS, but not different between RA and RAM. Myofibrillar Kdeg was lower with mechanotherapy compared to HS. Study 2: muscle weight, CSA, and myofibrillar Ksyn and Kdeg were not different with mechanotherapy. Collagen content was lower with mechanotherapy, but collagen Ksyn was not. Mechanotherapy was not associated with changes in fiber type, satellite cell or myonuclear number in either study. Compared to male, female rats had less muscle loss with HS, which was associated with less loss of myofibrillar Ksyn. Recovery from atrophy was associated with higher Ksyn in female and lower Kdeg in male rats. Conclusion: Female rat muscles do not exhibit a growth response to mechanotherapy with disuse or reambulation. Furthermore, male and female rats show distinct responses to different mechanical stimuli.

Hydroxysilylene (HSi-OH) in the gas phase.

The hydroxysilylene (HSiOH) molecule has been spectroscopically identified in the gas phase for the first time. This highly reactive species was produced in a twin electric discharge jet using separate precursor streams of 16O2/18O2 and Si2H6/Si2D6, both diluted in high pressure argon. The strongest and most stable laser induced fluorescence (LIF) signals were obtained by applying an electric discharge to each of the precursor streams and then merging the discharge products just prior to expansion into vacuum. Bands of the Ã1A-X~1A' electronic transition of HSiOH were found in the 455-420nm region, and single vibronic level emission spectra showed only transitions attributable to the trans-hydroxysilylene ground state isomer. High resolution, rotationally resolved spectra were obtained for the 0-0 bands of HSi16OH and HSi18OH. The rotational constants were used to obtain ground and excited state molecular structures of HSiOH, with some necessary constraints. The derived ground state structure is trans-HSiOH, with geometric parameters similar to theoretical predictions from the literature. In the excited state, a skew-HSiOH structure was obtained with a dihedral angle of 102°. Our own CASSCF/aug-cc-pVTZ calculations predict a similar excited state skew geometry. The lack of odd quantum number changes in the torsional mode in emission and our difficulties in obtaining DSiOD spectra, despite considerable effort, all suggest that further experimental and theoretical efforts will be necessary to thoroughly understand the electronic spectrum of hydroxysilylene.

Li-Ion Mobility and Solvation Structures in Concentrated Poly(ethylene carbonate) Electrolytes: A Molecular Dynamics Simulation Study

With the rapid global increase in the use of digital devices and electric vehicles, solid polymer electrolytes (SPEs) have emerged as promising candidates for all-solid-state batteries. They are expected to resolve safety concerns and overcome the limitations of energy density and charging speed associated with traditional Li-ion batteries with liquid electrolytes. However, a limited understanding of ionic conduction mechanisms remains a significant barrier to their further development and practical application. In this study, we employed molecular dynamics simulations using the COMPASS II force field under NPT/NVT ensembles at 298 K to investigate the static and dynamic properties of poly(ethylene carbonate) (PEC) electrolytes at various salt concentrations. Key analyses included the radial distribution function, solvation free energy, and mean-square displacement (MSD) of individual Li cations. Based on their MSD data, Li cations were categorized into “faster” or “slower” groups, corresponding to conductivity levels above or below the average in each model. Our findings reveal that, at higher concentrations, a smaller fraction of faster Li cations contributes disproportionately more than slower Li cations to the overall mobility, highlighting that targeted manipulation of solvation structures could enhance ion transport efficiency in highly concentrated SPEs. Additionally, changes in coordination number and solvation free energy for both faster and slower Li cations suggest the existence of three different solvation patterns as salt concentration increases. These insights provide a deeper understanding of ionic transport and solvation structures in PEC electrolytes, with potential implications for the design of more efficient all-solid-state batteries.

Comparing the hermaphroditic mating system of a parasitic flatworm between populations with an ancestral, 3-host life cycle and a derived, facultative-precocious life cycle.

Evolutionary changes in development and/or host number of parasite life cycles can have subsequent ecological and evolutionary consequences for parasites. One theoretical model based on the mating systems of hermaphroditic parasites assumes a life cycle with fewer hosts will result in more inbreeding, and predicts a truncated life cycle most likely evolves in the absence of inbreeding depression. Many populations of the hermaphroditic trematode Alloglossidium progeneticum maintain an ancestral obligate 3-host life cycle where obligate sexual reproduction occurs among adults in catfish third hosts. However, some populations have evolved a facultative precocious life cycle, where sexual development can occur while encysted within crayfish second hosts, likely leading to high inbreeding as individuals are forced to self-mate while encysted. Whether selfing represents a derived state remains untested. We compared selfing rates of 5 precocious populations to that of 4 populations with an ancestral obligate 3-host life cycle. We also compared demographic estimates to genetic estimates of selfing to test the prediction of no inbreeding depression in precocious populations. Results showed that while the ancestral obligate 3-host life cycle is associated with high outcrossing rates, the facultative precocious populations are highly selfing and show little evidence for inbreeding depression.

Impact of Threonine Supply in Early Ages on Gut Tissue Morphology, Liver Histology, and the Possible Changes in Leukocyte Numbers of Broilers

Delayed feed access post-hatch negatively impacts growth and intestinal development in broilers. Threonine (Thr) is known to support epithelial tissue development. This study evaluated the effects of early feeding strategies, including in ovo Thr administration and hydrogel provision, on broiler performance, gut and liver histomorphology, and leukocyte profiles. Control birds were fed immediately post-hatch, while others experienced a 48 h feed delay. One group received in ovo Thr on day 17 of incubation, while others were given Hydrogel® with or without Thr during the first 48 h post-hatch. Immediate feed birds showed the best performance (p < 0.05), while early Thr supplementation (in ovo or hydrogel) partially mitigated the negative effects of delayed feed access. On day 21, birds treated with in ovo Thr had 4% higher body weight (BW) than untreated birds (p < 0.05). Birds given hydrogel post-hatch showed no significant BW differences compared to other groups (p > 0.05), but 48 h delayed, non-supplemented birds had 34.3% lower BW than immediate-fed birds (p < 0.05). Compensation was linked to improved gut architecture, though no significant effects were observed on leukocyte profiles or liver histology. In ovo Thr feeding is recommended to mitigate the adverse effects of a two-day delay in feed access for broiler chickens.

Fluoride-Mediated Immune Damage Through Cytokine Network Regulation of Tregs

Long-term fluoride exposure can induce inflammatory responses in various tissues of the body, thereby affecting the inflammatory microenvironment. To explore how fluoride induces changes in immune function within this microenvironment, this study collected baseline information and biological samples from participants in areas with the drinking water type of fluorosis, and simultaneously established Wistar rat models with a 12-week and 24-week fluoride exposure, as well as a 12-week fluoride exposure followed by 12-week pure water feeding regimen. Luminex multiplex assays and enzyme-linked immunosorbent assays (ELISAs) were used to measure cytokine expression levels. Subsequently, correlation analysis, multiple linear regression, and mediation analysis were employed to explore the long-term effects induced by the complex cytokine network during fluoride exposure. The population survey results indicated that fluoride suppressed the expression of pro-inflammatory factors such as Interleukin-2 (IL-2), Interleukin-12 (IL-12), Interferon-γ (IFN-γ), Tumor necrosis factor-α (TNF-α), and anti-inflammatory factors such as Interleukin-4 (IL-4), Interleukin-13 (IL-13), and Interleukin-37 (IL-37), while promoting an increase in the proportion of regulatory T cells (Tregs) in peripheral blood. Among these, IL-2 and IFN-γ mediated the fluoride-induced peripheral Tregs expansion. Animal experiments indicate that the proportion of Tregs in peripheral blood and immune organs increases in a time-dependent manner with fluoride exposure. After reducing the fluoride concentration in the drinking water of rats, the number of Tregs remained significantly elevated. The changes in Treg numbers in the 12-week fluoride feeding group, 24-week fluoride feeding group, and 12-week fluoride feeding followed by 12-week water improvement group were related to the cytokine levels. Therefore, the impact of fluoride on the immune homeostasis has cumulative and long-term effects, and may be related to the accumulation and migration of Tregs induced by fluoride in an inflammatory environment, mediated by cytokines.

Effects of Bans on Prostitution on Prevalence of Induced Abortions

Background: Prostitutes are at high risk of unintended pregnancy, and induced abortions are widely practised among this cohort.Aims: This study examined the effects of prostitution bans on the prevalence of induced abortions. We focused particularly on the bans on juvenile prostitution, which were introduced by 32 states of Japan between 1975 and 1998.Methods: This was a cross-sectional study employing event-study analyses and a difference-in-difference-in-differences methodology. We compared the changes in numbers of induced abortions before and after the bans were introduced, among women under 20 years of age and among those aged 20―24 years, over states.Results: The number of induced abortions among women under 20 years of age increased after the juvenile prostitution bans were implemented. In the fifth year of implementation, the number increased by 56.79 percentage points (p < 0.001) compared with the previous year.Conclusion: The number of induced abortions among adolescents increased after juvenile prostitution was banned. As to its mechanism, the outcomes of our additional identification suggest that former juvenile prostitutes who retired due to the bans contributed to the increase.

Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes.

DNA copy number changes via chromosomal rearrangements or the production of extrachromosomal circular DNA. Here, we demonstrate that the histone deacetylase Sir2 maintains the copy number of budding yeast ribosomal RNA gene [ribosomal DNA (rDNA)] by suppressing end resection of DNA double-strand breaks (DSBs) formed upon DNA replication fork arrest in the rDNA and their subsequent homologous recombination (HR)-mediated rDNA copy number changes during DSB repair. Sir2 represses transcription from the regulatory promoter E-pro located near the fork arresting site. When Sir2 is absent, this transcription is stimulated but terminated by arrested replication forks. This transcription-replication collision induces DSB formation, DSB end resection and the Mre11-Rad50-Xrs2 complex-dependent DSB repair that is prone to chromosomal rDNA copy number changes and the production of extrachromosomal rDNA circles. Therefore, repression of transcription near arrested replication forks is critical for the maintenance of rDNA stability by directing DSB repair into the HR-independent, rearrangement-free pathway.

A chaotic digital signature algorithm based on a dynamic substitution box

Given the large volumes of sensitive information transmitted over the Internet, digital signatures are essential for verifying message authenticity and integrity. A key challenge is minimizing computationally intensive operations, such as modular inverses, without compromising security. In this research, we propose the DSADH algorithm, which introduces a confusion step directly into the signature itself, rather than only applying it to the message, using a dynamic substitution box. It is generated with the number pi and changes with each signing. In addition, to enhance security, this work uses a 2048-bit prime, double the length frequently used. This proposal induces chaotic behavior in the signature, making it highly sensitive to any changes in the signer’s private key or message content, thereby enhancing authentication and integrity verification. Moreover, the proposed algorithm computes a single multiplicative modular inverse during verification and none during signing, unlike other approaches that require inverse computation in both stages. Since the required inverse is for the Diffie-Hellman session key, it always exists and can be precomputed per communication rather than per message. Consequently, DSADH is on average 45 times faster than DSA. Additionally, we introduce a method to assess signature security by constructing images from signature bytes generated by slight changes to the signer’s private key and message. Then, their chaotic behavior is evaluated with cryptographic metrics.

Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures.

Common wheat is allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3' RNA-seq, is a technology efficient at obtaining homoeolog-distinguished transcriptomes. Here we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia. Roots and seedlings were similar to each other in transcriptome profiles, but they were different from the leaves. We then asked how three homoeologous genes from different subgenomes (i.e., triads) show different levels of expression. Specifically, we examined the effects of subgenomes, lines and their interaction on the expression levels of each homoeolog triad, separately in each tissue. Of the 19,805 homoeolog triads, 51-55% showed significant effect of subgenome, suggesting cis-regulation, whereas 24-30% showed significant effect line, suggesting trans-regulation. We also found that 7.7-9.0% triads showed significant effects of the interaction. Hierarchical clustering and co-trans regulation network analysis of homoeolog triads revealed that the patterns of expression polymorphisms among the lines were shared in different genes. Our results also implied that expression variation between lines is caused by changes in a smaller number of common trans-factors. We performed GO term enrichment analysis using newly annotated and substantially improved GO annotations, which revealed that GO terms related to each tissue type function were enriched in genes expressed in the leaves and roots. Our information provides fundamental knowledge for the future breeding of plants possessing complex gene regulatory networks such as common wheat.