Genes Coding Research Articles

Advanced Physical Layer Metasurface‐Empowered Cryptography with Robustness, High Capacity, and Enhanced Security

AbstractPhysical layer metasurface‐empowered cryptography offers a novel approach to secure encryption. This study proposes an encryption method with robustness, high capacity, and enhanced security based on the dual‐band complex‐amplitude metasurface. By leveraging the American Standard Code for Information Interchange (ASCII), both the secret message and the compressed digital signature are encrypted and transmitted together, eliminating codebook transmission and reducing security risks. The modified Visual Secret Sharing (VSS) scheme is employed to strengthen the security, fidelity, and robustness. Additionally, a three‐dimensional wavefront reconstruction algorithm is used to increase the encryption capacity, and a multivariate encryption key provides an extra layer of protection. A prototype metasurface sample is designed, fabricated, and characterized as a proof‐of‐concept demonstration. The measured results closely match the numerical ones and the design objective, confirming the viability and resilience of this high‐capacity, enhanced security encryption method for applications in anti‐counterfeiting and secure data transmission.

Real-time evaluation of an automated computer vision system to monitor pain behavior in older adults.

Regular use of standardized observational tools to assess nonverbal pain behaviors results in improved pain care for older adults with severe dementia. While frequent monitoring of pain behaviors in long-term care (LTC) is constrained by resource limitations, computer vision technology has the potential to mitigate these challenges. A computerized algorithm designed to assess pain behavior in older adults with and without dementia was recently developed and validated using video recordings. This study was the first live, real-time evaluation of the algorithm incorporated in an automated system with community-dwelling older adults in a laboratory. Three safely-administered thermal pain tasks were completed while the system automatically processed facial activity. Receiver Operating Characteristic curves were used to determine the sensitivity and specificity of the system in identifying facial pain expressions using gold standard manual coding. The relationship between scoring methods was analyzed and gender differences were explored. Results supported the potential viability of the system for use with older adults. System performance improved when more intense facial pain expressiveness was considered. While average pain scores remained homogenous between genders, system performance was better for women. Findings will be used to further refine the system prior to future field testing in LTC.

MimIR: An Extensible and Type-Safe Intermediate Representation for the DSL Age

Traditional compilers, designed for optimizing low-level code, fall short when dealing with modern, computation-heavy applications like image processing, machine learning, or numerical simulations. Optimizations should understand the primitive operations of the specific application domain and thus happen on that level. Domain-specific languages (DSLs) fulfill these requirements. However, DSL compilers reinvent the wheel over and over again as standard optimizations, code generators, and general infrastructure & boilerplate code must be reimplemented for each DSL compiler. This paper presents MimIR, an extensible, higher-order intermediate representation. At its core, MimIR is a pure type system and, hence, a form of a typed lambda calculus. Developers can declare the signatures of new (domain-specific) operations, called "axioms". An axiom can be the declaration of a function, a type constructor, or any other entity with a possibly polymorphic, polytypic, and/or dependent type. This way, developers can extend MimIR at any low or high level and bundle them in a "plugin". Plugins extend the compiler and take care of optimizing and lowering the plugins' axioms. We show the expressiveness and effectiveness of MimIR in three case studies: Low-level plugins that operate at the same level of abstraction as LLVM, a regular-expression matching plugin, and plugins for linear algebra and automatic differentiation. We show that in all three studies, MimIR produces code that has state-of-the-art performance.

Ataluren, a 1,2,4‐Oxadiazole‐Containing Drug Candidate for Nonsense Mutations: Major Breakthroughs and an Up‐to‐Date Process Chemistry Review

Ataluren, a 1,2,4‐Oxadiazole‐Containing Drug Candidate for Nonsense Mutations: Major Breakthroughs and an Up‐to‐Date Process Chemistry Review

Functional microbiome assembly in food environments: addressing sustainable development challenges.

The global food system faces numerous challenges, creating an urgent need for sustainable reform. Functional microbiome assemblies offer transformative potential by endowing microbial foods with diverse, beneficial characteristics. These assemblies can dynamically influence specific food systems, positioning them as a promising approach for reshaping food production. However, the current applications and types of microbiome assemblies in foods remain limited, with a lack of effective screening and regulatory methods. This review introduces the functions and practical approaches for implementing microbiome assemblies in food systems alongside future directions for enhancing their applications. Several ecological studies evaluated how to regulate functional output and revealed that environmental conditions, which shape the niche for species survival, significantly influenced the functional output of microbiomes. Building on this theoretical foundation, this review presents a model for functional output comprising niche conditions, functional gene codes, and corresponding functional outputs. This model is illustrated with examples to explore sustainable applications and regulatory mechanisms for functional microbiome assemblies. By highlighting the roles of functional outputs in food systems and examining the potential for food environments to induce and modulate microbiome functions, this review provides a roadmap to address emerging challenges in food sustainability.

Automated orthogonal tRNA generation.

The ability to generate orthogonal, active tRNAs-central to genetic code expansion and reprogramming-is still fundamentally limited. In this study, we developed Chi-T, a method for the de novo generation of orthogonal tRNAs. Chi-T segments millions of isoacceptor tRNA sequences into parts and then assembles chimeric tRNAs from these parts. Chi-T fixes the parts, containing identity elements, and combinatorially varies all other parts to generate chimeric sequences. Chi-T also filters the variable parts and chimeric sequences to minimize host identity elements. We show here that experimentally characterized orthogonal tRNAs are more likely to have predicted minimum free energy cloverleaf structures, and Chi-T filters for sequences with a predicted cloverleaf structure. We report RS-ID for the identification of synthetases that may acylate the tRNAs generated by Chi-T. We computationally identified new orthogonal tRNAs and engineered an orthogonal pair generated by Chi-T/RS-ID to direct non-canonical amino acid incorporation, in response to both amber codons and sense codons, with an efficiency similar to benchmark genetic code expansion systems.

Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates.

The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the 'ciliates') are the most prominent exception to this norm, exhibiting the grfeatest diversity of nuclear genetic code variants and evidence of repeated changes in the code. In this study, we report the discovery of multiple independent genetic code changes within the Phyllopharyngea class of ciliates. By mining publicly available ciliate genome datasets, we discovered that three ciliate species from the TARA Oceans eukaryotic metagenome dataset use the UAG codon to putatively encode leucine. We identified novel suppressor tRNA genes in two of these genomes which are predicted to decode the reassigned UAG codon to leucine. Phylogenomics analysis revealed that these three uncultivated taxa form a monophyletic lineage within the Phyllopharyngea class. Expanding our analysis by reassembling published phyllopharyngean genome datasets led to the discovery that the UAG codon had also been reassigned to putatively code for glutamine in Hartmannula sinica and Trochilia petrani. Phylogenomics analysis suggests that this occurred via two independent genetic code change events. These data demonstrate that the reassigned UAG codons have widespread usage as sense codons within the phyllopharyngean ciliates. Furthermore, we show that the function of UAA is firmly fixed as the preferred stop codon. These findings shed light on the evolvability of the genetic code in understudied microbial eukaryotes.

Functional Characterization of FgAsp, a Gene Coding an Aspartic Acid Protease in Fusarium graminearum.

Aspartic proteases (APs), hydrolases with aspartic acid residues as catalytic active sites, are closely associated with processes such as plant growth and development and fungal and bacterial pathogenesis. F. graminearum is the dominant pathogenic fungus that causes Fusarium head blight (FHB) in wheat. However, the relationship of APs to the growth, development, and pathogenesis of F. graminearum is not clear. Therefore, we selected the FGSG_09558 gene, whose function annotation is aspartate protease, for further study. In this study, FGSG_09558 was found to contain a conserved structural domain and signal peptide sequence of aspartic acid protease and was therefore named FgAsp. The function of FgAsp in F. graminearum was investigated by constructing the knockout and complementation mutants of this gene. The results showed that with respect to the wild type (PH-1), the knockout mutant showed a significant reduction in mycelial growth, asexual spore production, and sexual spore formation, highlighting the key role of FgAsp in the growth and development of F. graminearum. In addition, the mutants showed a significant reduction in the virulence and accumulation level of deoxynivalenol (DON) content on maize whiskers, wheat germ sheaths, and wheat ears. DON, as a key factor of virulence, plays an important role in the F. graminearum infection of wheat ears, suggesting that FgAsp is involved in the regulation of F. graminearum pathogenicity by affecting the accumulation of the DON toxin. FgAsp had a significant effect on the ability of F. graminearum to utilize various sugars, especially arabinose. In response to the stress, hydrogen peroxide inhibited the growth of the mutant most significantly, indicating the important function of FgAsp in the strain's response to environmental stress. Finally, FgAsp plays a key role in the regulation of F. graminearum growth and development, pathogenicity, and environmental stress response.

Implementation of a long-wavelength model for parallel magnetic fluctuations in the global GENE code

Abstract A long-wavelength model for the turbulent magnetic fluctuations parallel to the magnetic field (B1,||) has been implemented in the global gyrokinetic code GENE. The model provides a way to include this physical effect with little computational cost, permitting the study of B1,|| on global nonlinear gyrokinetic simulations. The model has been verified through convergence tests and against an arbitrary wavelength solver, resulting in good performance up to moderately high wavelengths (ky ρs ≲ 1). Using this approximation global nonlinear fully electromagnetic simulations were performed with Cyclone Base Case-like parameters to study the impact of B1,|| on different plasma β regimes. A negligible impact for a low beta regime and roughly a doubling of the heat transport when including B1,|| in a high beta KBM regime is found, which is in line with expectations based on linear studies and highlights the impact of B1,|| in KBM driven scenarios.

Assessing the impact of alpha particles on thermal confinement in JET D-T plasmas through global GENE-Tango simulations

Abstract The capability of the global, electromagnetic gyrokinetic GENE code interfaced with the transport Tango solver is exploited to address the impact of fusion alpha particles (in their dual role of fast particles and heating source) on plasma profiles and performance at JET in the discharges with the highest quasi-stationary peak fusion power during the DTE2 experimental campaigns. Employing radially global nonlinear electromagnetic GENE-Tango simulations, we compare results with/without alpha particles and alpha heating. Our findings reveal that alpha particles have a negligible impact on turbulent transport, with GENE-Tango converging to similar plasma profiles regardless of their inclusion as a kinetic species in GENE. On the other hand, alpha heating is found to contribute to the peaking of the electron temperature profiles, leading to a 1 keV drop on the on-axis electron temperature when alpha heating is neglected in Tango. The minimal impact of alpha particles on turbulent transport in this JET discharge–despite this being the shot with the highest fusion output–is attributed to the low content of fusion alpha in this discharge. To assess the potential impact of alpha particles on turbulent transport in regimes with higher alpha particle density, as expected in ITER and fusion reactors, we artificially increased the alpha particle concentration to levels expected for ITER. By performing global nonlinear GENE standalone simulations, we found that increasing the alpha particle density beyond five times the nominal value lead to significant overall turbulence destabilization. These results demonstrate that an increased alpha particle concentration can significantly impact transport properties under simulated JET experimental conditions. However, these findings cannot be directly extrapolated to ITER due to the substantial differences in parameters such as plasma size, magnetic field, plasma current, and thermal pressure.

On the prediction by density functional theory of entropies in solution within implicit solvation models.

Entropies are fundamental contributions to Gibbs energies that carry important chemical information, in particular when investigating reaction mechanisms. However, evaluating them in solution is far from being straightforward. In this paper, we focus on its evaluation within the framework of implicit solvation models. To this aim, successive corrections (with increased complexity) involving only contributions available from any standard quantum chemistry code and macroscopic solvent properties are built and assessed by comparison to more than one hundred experimental entropy values measured in a liquid phase. It turns out that significant improvement with respect to the standard ideal gas approximation can be achieved at an almost negligible computational cost, affording a robust and transferable predictive model. DFT calculations with the ADF software at the PBE or PBE0/TZ2P level of theory with COSMO solvent model. Python scripts for regressions.

Impact of Warm Ischemia Time on HER2 Expression in Breast Cancer Surgical Specimens.

Tissue sample quality control has become increasingly crucial as these samples are integral to basic research and clinical practice, particularly in immunohistochemistry and gene panel testing. Standard PREanalytical Code (SPREC) was developed to standardize pre-analytical processes, including warm ischemia time (WIT), cold ischemia time (CIT), and fixation time (FT), which can influence the surgical specimen quality. This study investigated the impact of WIT, CIT, and FT on estrogen receptor (ER), progesterone receptor (PgR), and human epidermal growth factor receptor 2 (HER2) expression in breast cancer (BC) surgical specimens. We enrolled 277 patients with first-time BC who underwent surgery at Kanagawa Cancer Center between May 2018 and April 2019. WIT, CIT, and FT were recorded using SPREC ver. 3.0, and their effects on ER, PgR, and HER2 expression were analyzed using immunohistochemistry. Surgical specimens were compared with preoperative needle biopsy samples from the same tumors to control for WIT, CIT, and FT variability. The median WIT, CIT, and FT were 23 min, 37 min, and 43 h, respectively. Compliance with the American Society of Clinical Oncology/College of American Pathologists guidelines was 91.7% for CIT and 94.9% for FT. ER and PgR expression in surgical specimens decreased with prolonged CIT and FT, but differences were non-significant. However, HER2 expression increased significantly when WIT exceeded 30 min. WIT could significantly influence HER2 expression in BC surgical specimens, highlighting the need for meticulous WIT control during BC surgery to ensure accurate HER2 assessment, which is critical for guiding therapeutic decisions.

Titrating chimeric antigen receptors on CAR T cells enabled by a microfluidic-based dosage-controlled intracellular mRNA delivery platform.

Chimeric antigen receptor (CAR) T-cell therapy shows unprecedented efficacy for cancer treatment, particularly in treating patients with various blood cancers, most notably B-cell acute lymphoblastic leukemia. In recent years, CAR T-cell therapies have been investigated for treating other hematologic malignancies and solid tumors. Despite the remarkable success of CAR T-cell therapy, cytokine release syndrome (CRS) is an unexpected side effect that is potentially life-threatening. Our aim is to reduce pro-inflammatory cytokine release associated with CRS by controlling CAR surface density on CAR T cells. We show that CAR expression density can be titrated on the surface of primary T cells using an acoustic-electric microfluidic platform. The platform performs dosage-controlled delivery by uniformly mixing and shearing cells, delivering approximately the same amount of CAR gene coding mRNA into each T cell.

The genetic code is not universal.

Recently, a new genetic code with 62 sense codons, coding for 21 amino acids, and only 2 termination codons has been identified in archaea. The authors argue that the appearance of this variant of the genetic code is due to the relatively recent and complete recoding of all UAG stop codons to codons encoding for pyrrolysine. I re-evaluate this discovery by presenting arguments that favour the early, i.e. ancestral, appearance of this variant of the genetic code during the origin of the genetic code itself. These arguments are capable of supporting that during the origin of the organization of the genetic code, at least two versions of the genetic code evolved in the domain of the Archaea. Thus, the genetic code would not be absolutely universal.

Alkaleri Metakaolin Powder Performance Evaluation by Response Surface Method.

Alkaleri metakaolin (AMK) based geopolymer binder has been identified as one of the alternatives to the Ordinary Portland Cement (OPC), which qualifies the criteria for green construction material. In this work, 20No of experimental mix proportions (RUNs) were designed by Central Composite Design (CDD) of Response Surface Method (RSM). Mixture of AMK and Alkaline Solution was heated for 45mins at 60oc with stirring interval of 15mins, after which aggregates were added to the hot mix. 60No of 100X100X100mm cubes were cast. Samples were tested at the 28th day of ambient curing. The reported Compressive Strengths are the average of the 60 sample tested with 38.6N/mm2 as the maximum, hence established the experimental optimum mix proportion (EOMP). The ANOVA model developed statistically validated by having F-value of 15.54 and P-value of less than 0.0001 indicating that the model is statistically significant. Also, the adequate precision of 10.7850 which is greater than 4.00 indicates adequate signal and desirable. Furthermore, the difference between predicted R2 and adjusted R2 is less than 0.2 testifying that they are rationally in good agreement. Effects of three principal variables namely: molarity of sodium hydroxide, sodium silicate to sodium hydroxide ratio, and fineness (particle size) on the properties of the fresh and hardened AMK geopolymer concrete (normal consistency, soundness, setting times, slump, dry density, water absorption, compressive strength, flexural strength, split tensile strength, sorptivity and acid attack) were investigated. All the results for the properties investigated were found to have fallen within the ranges of the international standard codes such as ASTM and British Standard, hence AMK is qualify to be used as Metakaolin based geopolymer binder.

Analysis and Design of a Multistorey Building on Sloped and Flat Grounds (Stilt + Ground + 4)

This project focuses on the planning, static analysis, and structural design of a (Stilt + Ground + 4) residential building, located on both sloping and flat ground, using ETABS software. The primary goal is to study the impact of ground conditions on the structural behavior and design considerations of the building. The project incorporates planning principles to create a functional and efficient layout, ensuring compliance with Indian Standard codes for beams, columns, slabs, and other structural elements. Key aspects such as load distribution, stability, reinforcement detailing, and member sizing are thoroughly examined to ensure the building's safety and adherence to IS guidelines. A comparative analysis between sloping and flat ground conditions highlights the differences in design parameters, such as member forces, moments, and reinforcement requirements, with particular attention to the unique challenges posed by sloping ground. The findings of the study aim to offer insights into cost- effective and optimized design strategies that cater to different site conditions. By exploring these variations, the study contributes to the development of advanced modeling techniques for structural analysis and design. It also emphasizes the importance of adaptable strategies to ensure safe, resilient, and efficient residential buildings, regardless of topography. This research enhances the understanding of how varying ground conditions influence the design process and promotes the development of residential structures that are both safe and cost-efficient across diverse terrains. Keywords: Residential Building Design, Sloping Ground, Flat Ground, ETABS, Static Analysis, Structural Components, Indian Standards, Comparative Study, Planning Principles, Reinforcement Detailing.

Joint Probability Distribution of Extreme Wind Speed and Air Density Based on the Copula Function to Evaluate Basic Wind Pressure

To investigate an appropriate wind load design for buildings considering dynamic air density changes, classical extreme value and copula theories were utilized. Using wind speed, air temperature, and air pressure data from 123 meteorological stations in Shandong Province from 2004 to 2017, a joint probability distribution model was established for extreme wind speed and air density. The basic wind pressure was calculated for various conditional return periods. The results indicated that the Gumbel and Gaussian mixture model distributions performed well in extreme wind speed and air density fitting, respectively. The joint extreme wind speed and air density distribution exhibited a distinct bimodal pattern. The higher the wind speed was, the greater the air density for the same return conditional period. For the 10-year return period, the air density surpassed the standard air density, exceeding 1.30 kg/m3. The basic wind pressures under the different conditional return periods were more than 10% greater than those calculated from standard codes. Applying the air density based on the conditional return period in engineering design could enhance structural safety regionally.

STAAD Based G+2 Single-Column Residential Analysis

The principle cause of this study is to layout a whole building relaxation on a single column. The rapid increase in population and scarcity of land tends to the development of construction technology and high- rise commercial structures. The building plays a vital role in improving various activities in the late world. The Aim of present study “Analysis and design of high rise building by staad pro is to define proper technique for creating Geometry, cross sections for column and beam etc, developing specification and supports conditions, types of Loads and load combinations. In this study a 30- storey high rise structure is analyzed for seismic and wind load combination using staad pro and comparison is drawn. Currently, there are four mosques on Java Island recognized as Saka Tunggal Mosques, which employ a single wooden column as the main column, placed at the center of the prayer hall to support the roof. This unique structural system, when compared to the traditional four-column system, is remarkable even if its style is exceptional for mosques on Java Island. This study aims to provide scientific data and promote the local government's understanding about the importance of the Saka Tunggal Mosques by focusing on the one in Banyumas, which is placed at a cultural heritage site, founded in 1871. The rapid increase in population and scarcity of land tends to the development of construction technology and high-rise commercial structures. Building plays a vital role for improving the various activities. In the late world, prompt to action of peoples from one place to another is of great extent mainly for earnings. In building more facilities like financing section, computer section, administration section, design section and drawing section are provided. The aim of the project is to analyse and design of multi-storey building resting on the single column by using different code provisions. A lay out plan of the proposed building is drawn by using AUTO CADD. The structure consists of ground floor plus five floors, each floor having the one house. Staircase must be provided separately. The planning is done as per Indian standard code provisions. The building frames are analyzed using the various text books. Using this so many standard books analysis of bending moment, shear force, deflection, end moments and foundation reactions are calculated. Detailed structural drawings for critical and typical R.C.C. members are also drawn. Recent studies regarding progressive collapse resistance of buildings considered only single critical column removal scenario. However, limited investigations have been conducted so far to assess multi-column removal scenarios. Hence this study is made to compare progressive collapse resistance of a multi-story building under both single and multi-column removal scenarios. An eight-storey reinforced concrete building was analyzed by using linear static analysis procedure and DCR values of the members are calculated to investigate the potential of progressive collapse as per GSA guideline.

Association of multiple sclerosis with psychiatric disorders and homelessness among veterans in the United States Department of Veterans Affairs healthcare system.

To describe and compare the prevalence of psychosocial and psychiatric disorders among veterans with multiple sclerosis (MS) and a propensity-score-matched group of veterans without MS, and to identify sociodemographic and clinical characteristics associated with comorbid psychosocial and psychiatric problems among veterans with MS. Data were linked and extracted from the Veterans Affairs (VA) Homeless Operations Management and Evaluation System and the Corporate Data Warehouse. The total sample comprised 27,342 veterans in the VA healthcare system between January 1, 2022, and June 30, 2023, who met eligibility criteria for an MS diagnosis (n=13,671) and 1:1 propensity-score-matched sample of veterans who did not have MS (n=13,671). MS diagnosis, substance use disorder (SUD), mental illness, and homelessness were defined using standard ICD-10 codes. Covariates included sex, age, Charlson Comorbidity Index (CCI), and VA service-connected disability rating. A higher prevalence of mental illness among veterans with MS (33%) was found compared with those without MS (31%). Multivariable logistic regression models indicated MS was negatively associated with diagnoses of alcohol use disorder, stimulant use disorders, posttraumatic stress disorder, and schizophrenia/schizoaffective disorder but positively associated with diagnoses of cannabis use disorder and major depressive disorder. MS was not significantly related to homelessness. Disparities in psychosocial and psychiatric disorders among veterans with MS are described. This study provides novel insights regarding rates of homelessness, SUD, and mental illnesses among veterans with MS. Interdisciplinary approaches to identification and management of mental illness, SUD, and homelessness among veterans with MS are critically needed.

Color-coding real-time detection for the health of lithium-ion batteries

Lithium-ion batteries (LIBs) are pivotal energy devices in our daily lives, yet ensuring the quality and health of LIBs throughout their manufacturing and application processes remains a significant challenge. Here we propose a universal “color-coding” technique to indicate the health of LIBs, by which specific property characteristic and evolution inside LIBs can be unfolded. By defining the standard color coding for the entire manufacturing and application processes of LIBs, we show the change in material characteristics during various processes can be described by variations in standard color coding. Therefore, by establishing a universal color-property database, the proposed “color-coding” method has potential to be used as a practical tool to ensure the quality of materials and healthy operation of batteries.