The superfamily of Acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the Structural Catalytic Core (SCC), which packs all conserved substructure elements around the catalytic machinery, and which can be found in all enzymes of the Acid proteases superfamily. The SCC is a dimer of several structural blocks, such as the DD-link, the D-loop and the G-loop, around two catalytic aspartates in each protease subunit or within an individual chain. The dimer of two D-loop/DD-link substructures makes a DD-zone, and the dimer of two D-loop/G-loop substructures makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation and protein engineering.

The study of rare diseases is important not only for the individuals affected but also for the advancement of medical knowledge and a deeper understanding of human biology and genetics. The wide repertoire of structural information now available from reliable and accurate prediction methods provides the opportunity to investigate the molecular origins of most of the rare diseases reviewed in the Orpha.net database. Thus, it has been possible to analyze the topology of the missense mutations found in the 2,535 proteins involved in Mendelian rare diseases (MRD), which form the database for our structural bioinformatics study. The amino acid substitutions responsible for MRD show different mutation site distributions at different three-dimensional protein depths. We then predicted the depth-dependent effects of mutations for the 20,248 pathogenic variants that are present in our database. The results of this structural bioinformatics investigation are relevant, as they provide additional clues to mitigate the damage caused by MRD.

The COVID 19 pandemic saw the emergence of various Variants of Concern (VOCs) that took the world by storm, often replacing the ones that preceded them. The characteristic mutant constellations of these VOCs increased viral transmissibility and infectivity. Their origin and evolution remain puzzling. With the help of data mining efforts and the GISAID database, a chronology of 22 haplotypes described viral evolution up until July 23, 2023. Since the 3-dimensional atomic structures of proteins corresponding to the identified haplotypes are not available, ab initio methods were here utilized. Regions of intrinsic disorder proved to be important for viral evolution, as evidenced by the targeted change to the nucleocapsid (N) protein at the sequence, structure, and biochemical levels. The linker region of the N-protein, which binds to the RNA genome and self-oligomerizes for efficient genome packaging, was greatly impacted by mutations throughout the pandemic, followed by changes in structure and intrinsic disorder. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Our strategy of mapping the dynamic evolutionary landscape of genetically linked mutations to the N-protein structure demonstrates the utility of ab initio modeling and deep learning tools for therapeutic intervention.

Visual exploration of complex data helps interpretation, especially in the case of omics data analysis in life sciences and clinical research. Generating and analysing omics data requires bioinformatic skills, while they are interpreted by domain experts, for whom parsing large and complex data structures may be challenging. However, outcomes of visual analytics are often difficult to quantify, which emphasises precision and reproducibility, especially for research on human diseases. Here, we propose a workflow combining a reproducible computational environment with a dedicated visualisation functionality for systems biology diagrams. By linking the Galaxy with the MINERVA Platform, we visualise and explore COVID-19 transcriptomic data to demonstrate the utility of our workflow. Visualised data recapitulate findings of the original publication and offer new insights about the COVID-19 pathology. Our results offer a blueprint for quick prototyping of computational workflows that facilitate communication and exploration of complex data in biomedical research.

All living organisms require some metal ions for their energy production as well as metabolic and biosynthetic processes. Within cells, metal ions are involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been a tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted also by the successful applications of neural networks and deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarize recent DL applications enhancing the functional interpretation of metalloprotein structures.

The intelligent morphing wing structure has the characteristics of flexibility, large deformation and adaptive change, which are different from those of the conventional wing. The motion law of the variable-camber leading edge is analysed by the numerical simulation method based on kinematics theory to solve the problem of verifying the motion function and structural strength of the variable camber wing. The driving deformation and aerodynamic load simulation of the variable camber leading edge are realised by designing a follow-up load test apparatus. Based on the numerical simulation of the mechanical boundary, the motion trajectory of the upper and lower wing loading points was predicted, and a multi-point cooperative control system was developed. Multi-sensor iteration was used to ensure the loading accuracy of the test control. The test results show that the average error of the deflection angle is 4.59% in the variable camber leading edge motion test. In the variable camber leading edge strength test, the average error of applied load magnitude and direction is 0.54% and 0.24%, respectively.

The paper presents the problem of damage detection in steel girders. Static displacements at the selected point of the structure play the role of measured variables. Structural response signal decomposition is performed according to the Mallat pyramid algorithm, which is used to perform the discrete wavelet transform (DWT). This procedure allows us to quite well determine the location of structural damage. The geometry and the placement of any defective part of the structure may have a random character. It can be assumed that the random processes occurring in the broadly understood structure mechanics are Gaussian in nature. The first four probabilistic moments are estimated using three approaches independent: semi-analytical (SAM), perturbative (SPT), and Monte-Carlo simulations (MCS). The semi-analytical random approach seems to be the most optimal due to the necessary computation time. The incorporation of the mathematical stochastic apparatus into the classical (deterministic) analysis of the statics of the structure makes it possible to estimate the reliability measures of the analyzed girder.

The landscape of clinical management for metastatic melanoma (MM) and other solid tumors has been modernized by the advent of immune checkpoint inhibitors (ICI), including programmed cell death-1 (PD-1), programmed cell death-ligand 1 (PD-L1), and cytotoxic T lymphocyte antigen 4 (CTLA-4) inhibitors. While these agents demonstrate efficacy in suppressing tumor growth, they also lead to immune-related adverse events (irAEs), resulting in exacerbation of autoimmune diseases such as Rheumatoid arthritis (RA), Ulcerative colitis (UC), and Crohn’s disease (CD). The immune checkpoint inhibitors offer promising advancements in the treatment of melanoma and other cancers, but they also present significant challenges related to irAEs and autoimmune diseases. Ongoing research is crucial to better understand these challenges and develop strategies for mitigating adverse effects while maximizing therapeutic benefits. In this manuscript, we addressed this challenge using network-based approaches by constructing and analyzing molecular and signaling networks associated with tumor-immune cross-talk.. Our analysis revealed that IL6 is the key regulator responsible for irAEs during ICI therapies. Furthermore, we conducted an integrative network and molecular-level analysis, including virtual screening, of drug libraries, such as the Collection of Open Natural Products (COCONUT) and the Zinc15 FDA-approved library, to identify potential IL-6 inhibitors.. Subsequently, the compound amprenavir was identified as the best molecule that may disrupt essential interactions between IL6 and IL6R responsible for initiating signaling cascades underlying irAEs in ICI therapies.

Dark pigmentation can be observed in various parts of the plant, ranging from foliage to petals to berries. The molecular basis of black pigmentation appears to vary among species, with anthocyanins playing a significant role, although specific anthocyanin types and their mechanisms differ. These findings suggest that the development of phenotypes is species-specific or varies between larger taxonomic groups; this is further supported by the polyphyletic nature of dark pigmentation. Additionally, several different regulatory mechanisms have been described for the occurrence of dark pigmentation. Firstly, the repression or knockout of the competing flavone biosynthesis has been shown to lead to darker pigmentation while another mechanism is based on the activation and upregulation of the anthocyanin biosynthesis genes in the presence of MYB transcription factors. Potential ecological functions of dark pigmentation were identified as the protection of the photosynthesis apparatus, camouflage against herbivores, and the attraction of pollinators. Promising industrial applications include microbial factories for the production of natural food colourants, induction of novel phenotypes for the ornamental plant industry and lastly the increase of anthocyanins within agriculturally relevant crops.

Background: Metabolic flux analysis (MFA) is an indispensable tool in metabolic engineering. The simplest variant of MFA relies on an overdetermined stoichiometric model of the cell’s metabolism under the pseudo-steady state assumption, to evaluate the intracellular flux distribution. Despite its long history, the issue of model error in the overdetermined MFA, particularly misspecifications of the stoichiometric matrix, has not received much attention. Method: We evaluated the performance of statistical tests from linear least square regressions, namely Ramsey RESET test, F-test and Lagrange multiplier test, in detecting model misspecifications in the overdetermined MFA, particularly missing reactions. We further proposed an iterative procedure using the F-test to correct such an issue. Result: Using Chinese hamster ovary and random metabolic networks, we demonstrated that: (1) a statistically significant regression does not guarantee high accuracy of the flux estimates, (2) the removal of a reaction with a low flux magnitude can cause disproportionately large biases in the flux estimates, (3) the F-test could efficiently detect missing reactions, and (4) the proposed iterative procedure could robustly resolve the omission of reactions. Conclusion: Our work demonstrated that statistical analysis and tests could be used to systematically assess, detect and resolve model misspecifications in the overdetermined MFA.

Effects of oxygen content on microstructure and creep property of FGH96 superalloy were investigated. When oxygen content increased from 135ppm to 341ppm, prior particle boundary (PPB) rose from degree 2 to degree 3, and the size of γ′ phase on PPB enlarged from 1.07μm to 1.27μm, and MC carbide size grew from 77.4nm to 104.0nm. Meanwhile, the steady creep rate accelerated form 4.34×10-3 h-1 to 1.87×10-2 h-1, and the creep rupture life shortened from 176h to 94h, and the creep rupture mode transferred from intergranular and transgranular mixed fracture to along PPB fracture. During creep, the micro-twins formation and gliding will be restrained by ∑3 boundaries. FGH96 superalloy with higher oxygen content contains less ∑3 boundaries and its micro-twins cross slipped instead of single direction slip in lower oxygen content superalloy. Consequently, specimen with higher oxygen content creeped faster and raptured earlier.

Structural Maintenance of Chromosomes (SMC) complexes are an evolutionary conserved protein family. In most eukaryotes, three SMC complexes have been characterized: cohesin, condensin, and SMC5-6 complexes. These complexes are involved in a plethora of functions and defects in SMC genes can lead to increased risk of chromosomal abnormalities, infertility, and cancer. To investigate th evolution of SMC complex genes in mammals, we analyzed their selective patterns in an extended phylogeny. Signals of positive selection were identified for condensin NCAPG, for two SMC5/6 complex genes (SMC5 and NSMCE4A) and for all cohesin genes with almost exclusive meiotic expression (RAD21L1, REC8, SMC1B, and STAG3). For the latter, evolutionary rates correlate with expression during female meiosis and most positively selected sites fall in intrinsically disordered regions (IDRs). Our results support growing evidence that IDRs are fast evolving and that most likely contribute to adaptation through modulation of phase separation. We suggest that the natural selection signals identified in SMC complexes may be the result of different selective pressures: a host-pathogen arms race in the condensin and SMC5/6 complexes, and an intragenomic conflict similar to that described for centromeres and telomeres for meiotic cohesin genes.

The increasing prevalence of Metabolic Syndrome (MetS), a serious condition associated with elevated risks of cardiovascular diseases, stroke, and type 2 diabetes, underscores the urgent need for effective diagnostic tools. This research carefully examines the effectiveness of 16 diverse machine learning (ML) models in predicting MetS, a multifaceted health condition linked to increased risks of heart disease and other serious health complications. Utilizing a comprehensive, unpublished dataset of imbalanced blood test results, spanning from 2017 to 2022, from the Laboratory Information System of the General Hospital of Amfissa, Greece, our study embarks on a novel approach to enhance MetS diagnosis. By harnessing the power of advanced ML techniques, we aim to predict MetS with greater accuracy using non-invasive blood test data, thereby reducing the reliance on more invasive diagnostic methods. Central to our methodology is the application of the Borda count method, an innovative technique employed to refine the dataset. This process prioritizes the most relevant variables, as determined by the performance of the leading ML models, ensuring a more focused and effective analysis. Our selection of models, encompassing a wide array of ML techniques, allows for a comprehensive comparison of their individual predictive capabilities in identifying MetS. This study not only illuminates the unique strengths of each ML model in predicting MetS but also reveals the expansive potential of these methods in the broader landscape of health diagnostics. The insights gleaned from our analysis are pivotal in shaping more efficient strategies for the management and prevention of Metabolic Syndrome, thereby addressing a significant concern in public health.

Currently, there is a tenacious need to find new ways to purify water by eliminating bacterial biofilms, textile dyes, and toxic water pollutants. These contaminants pose significant risks to both human health and the environment. To address this issue, in this study, we have developed an eco-friendly approach that involves synthesizing Cobalt-doped Cerium Iron Oxide (CCIO) nanocomposite (NC) using an aqueous extract of Gossypium arboreum L. stalks. The resulting nanoparticles can be used to effectively purify water and tackle the challenges associated with these harmful pollutants. Nanoparticles excel in water pollutant removal by providing high surface area for efficient adsorption, versatile design for simultaneous removal of multiple contaminants, catalytic properties for organic pollutant degradation, and magnetic features for easy separation, offering cost-effective and sustainable water treatment solutions. CCIO nanocomposite has been synthesized by green co-precipitation method due to biomolecules and co-enzymes present in the aqueous extract of Gossypium arboreum L. stalk; a single-step procedure completed in 5 h reaction time. Further, the synthesis of nanocomposites was confirmed by various characterization techniques such as Fourier-transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), Field emission scanning electron microscopy (FE-SEM), Transmission electron microscopy (TEM), Thermogravimetric analysis (TGA), Dynamic light scattering (DLS), and Energy Dispersive X-Ray (EDX). CCIO NCs were discovered to have a spherical shape and an average size of 40 nm. Based on DLS zeta potential analysis, CCIO NCs were found to be anionic. Also, CCIO NCs showed significant antimicrobial and antioxidant activity. Overall, considering the physical and chemical properties, the application of CCIO NCs in the adsorption of various dyes (~91 %) and water pollutants (chromium = ~ 60 %) has been considered since they exhibit great adsorption capacity owing to their microporous structure which can be a step forward in water purification.

Gene regulation is vital for cellular function and homeostasis, involving diverse mechanisms controlling specific gene products and contributing to tissue-specific gene expression. Dysregulation leads to diseases, emphasizing the need for understanding these mechanisms. Non-coding regions, notably enhancers and super-enhancers (SEs), act as crucial gene regulators, orchestrating transcriptional activity via transcription factors (TFs). SEs, with high activity, are pivotal in cell identity and disease progression. Current computational approaches focus on individual regulators like TFs and miRNAs, neglecting SE interactions. We emphasize incorporating SEs into models to enhance understanding. Experimental studies have recently linked miRNAs and TFs to SEs. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides valuable SE information. In this review, we categorize computational methods leveraging TF and miRNA data into three areas and explore challenges integrating enhancers/SEs. These include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators, including SEs. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in identifying therapeutic targets and disease biomarkers. We believe that understanding the role of ChIP-Seq data in predicting the effect of miRNA on gene regulation is crucial to construct statistical/computational model that would tackle these challenges.

This literature review provides an in-depth exploration of the research conducted on the investigation and measurement of residual stress (RS) in Wire Arc Additive Manufacturing (WAAM) products, particularly focusing on how process parameters influence the phenomenon. RS plays a crucial role in determining the mechanical behavior and structural integrity of WAAM components. This review article gives an understanding of the relationship between process parameters and RS to optimize the WAAM processes and ensure the durability of the final products. It also summarizes key findings, measurement techniques, challenges, and future directions in this evolving field. The review also analyzes a measurement of RS in the products of WAAM as a function of process parameters depending on examining various research studies, techniques, and methodologies employed in their studies. Experimental measuring techniques and numerical analysis of RS to determine the impacts of RS in mechanical response in products of WAAM were discussed. By offering a comprehensive overview of current research trends and insights, this review serves as a valuable resource to guide future investigations, fostering the advancement of WAAM as a robust and efficient manufacturing technology.

Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated physicochemical variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.

The effectiveness of a hybrid technique for identifying seismic damage in planar, multistory, steel X or V-braced frames is demonstrated here through an example of a six-story frame. This proposed technique, referred to as “M and P”, combines the instrumental Monitoring (M) with Pushover analysis (P). According to the methodology, the diagram of stepping eigenfrequencies of the frame in the inelastic region is initially plotted against seismic roof displacement. The fundamental natural frequency detected via the monitoring process is then utilized in this key diagram to reveal the inelastic roof displacement that corresponds to the damage state of the steel braced frame. This displacement is subsequently used as the target in the pushover analysis, facilitating the identification of seismic damage in the existing steel braced frame. Finally, the damage image is correlated with the damage stiffness matrix of the frame at the same inelastic roof displacement. The investigation results indicate that combining instrumental monitoring with pushover analysis enables accurate identification of seismic damage potential in existing steel braced frames.

The paper delves into the critical issue of damage detection within the guy cable of a truss steel mast, a pivotal component in structural integrity. It introduces a model wherein damage manifests as a localized cross-section reduction in a single element of the cable. Employing Discrete Wavelet Transform (DWT), a pioneering methodology, the study scrutinizes the behavior of the affected elements through static structural analyses. Signal decomposition via the Mallat pyramid algorithm facilitates comprehensive examination. Static displacements at the connection point between the cable and the truss mast serve as the measured variables. Through systematic investigation, the paper evaluates the impact of damage size and location, external loading force, and cable tension force on the efficacy of the proposed approach. Utilizing data derived from Finite Element Method (FEM) computations for wavelet analysis the authors substantiate the findings with numerical examples, thus offering valuable insights into damage detection strategies for structural health monitoring and engineering applications.

This study provides an in-depth review of the available literature on metal composite material machining, focusing on traditional machining operations such as turning, milling, shaping, drilling, and grinding. The motivation for the study is that this composite type has emerged as a vital material in applications requiring functionality, resilience, cost-effective operation, low consumption of energy and lightweight. Despite its superior characteristics, the manufacturing complexity and poor machinability of metal matrix composites have been the primary barriers to its adoption. Nevertheless, there is a reduction of exceptional efficiency, increase in surface roughness, tool wear and so on in metal matrix composites throughout machining. As a result, this review gives a comprehensive investigation of metal matrix composite machining and effect on process parameters and procedures. Furthermore, this study distinguishes metal matrix composites towards sustainable manufacturing and the metals employed by the researchers, as well as the gaps discovered for future recommendations in metal-based composites.

Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms, as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic (P. halocryophilus and E. sibiricum), mesophilic (B. subtilis), and thermophilic (G. stearothermophilus) Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (s4U), 7-methyl-guanosine (m7G), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relation, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacteria at higher temperatures, particularly showing elevated levels of s4U8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies.

The epidemic of obesity has increased worldwide and is associated with comorbidities as diabetes as cardiovascular disease. Strategies that modulate body weight and improves glycemic metabolism has increased, and the bariatric surgeries as Sleeve Gastrectomy (SG) has been highlighted in obesity treatment. However, the mechanism by which SG reduces body weight and improves glycemic control are unknow. C57BL mice were submitted to a 10 weeks high fat-diet protocol and submitted to SG. Food intake, fed/fasted glycemia and hypothalamic anorexigenic and orexigenic gene expression were evaluated. SG reduces body weight, fasting glycemia, insulinemia and leptinemia in obese mice. Moreover, SG reduces food and total calorie intake with no alterations in the expression of anorexigenic and orexigenic gene expression. These data indicates that SG improves obesity associated alterations, at least in part, by reduction on food intake. This effect is not associated with the classic food intake pathway in hypothalamus, indicating the involvement of supplementary pathways in this process.

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed independent organizational, functional and evolutionary units that follow a ‘natural’ historical rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven biological systems. Instead, they are crucial components of holobionts, units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show viruses share protein domain and loop structures with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the ‘is-a-kind-of’ by a ‘is-a-part-of’ logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.

This paper proposes an enhanced Quantum Key Distribution (QKD) protocol by incorporating a Three-Dimensional Angular Momentum Representation (3D AMR) to address vulnerabilities inherent in traditional two-dimensional polarization states-based systems. The 3D AMR method expands the state space, potentially increasing security against sophisticated quantum attacks. We present a theoretical and computational framework that transitions from the conventional two-dimensional polarization to a three-dimensional angular momentum space, which inherently increases the complexity and security of the quantum states used in QKD.

Background: RSV, or respiratory syncytial virus, is a deadly condition that is present all over the world today. The infection is initially contained in the lower respiratory tract without systemic transmission. The objective of the study: Bioinformatics was used in Egypt to create an mRNA vaccine against the Respiratory syncytial virus (RSV). Methodology: In the present screening experimental study, a lipid nanoparticles vaccine of mRNA of the surface fusion protein of Respiratory syncytial virus was manufactured. The present vaccine delivery system was lipid nanoparticles with a particle size of approximately 90 nanometres, manufactured by the hot micro-emulsion method. In stages 1 and 2 of clinical trials, the immunogenicity of the current mRNA RSV vaccine was evaluated. Results: The current vaccine demonstrated 81% immunogenicity in animal testing, but only 69% in stages 1 and 2 of clinical trials. Its side effects were manageable. The results persisted for a while. In the current trial, the vaccination proved effective as a preventative measure against RSV infection. The current vaccination lacked antibody-dependent enhancement, which causes non-protective antibodies to develop. These non-neutralizing antibodies exacerbate infection by activating cytokines and complement cascade through the formation of immune complexes or enhancement of the virus entry and replication in the host cells. On the other hand, the current RSV mRNA vaccine of the surface fusion protein consequent on the production of powerful neutralizing antibodies with prolonged immunity especially to infants and elderly candidates who received the optimal dosage regimen.

Full depth precast deck panel (FDDP) is one element of the prefabricated bridge element and systems (PBES) that allows for quick un-shored assembly of the bridge deck on-site as part of the accelerated bridge construction (ABC) technology. This paper investigates the structural response of full-depth precast deck panels (FDDPs) constructed with new construction materials and connection details. FDDP is cast with normal strength concrete (NSC) and reinforced with high modulus (HM) glass fiber reinforced polymer (GFRP) ribbed bars. The panel-to-girder V-shape connections use the shear pockets to accommodate the clustering of the shear connectors. A novel transverse connection between panels has been developed, featuring three distinct female-to-female joint configurations, each with 175-mm projected GFRP bars extending from the FDDP into the closure strip, complemented by a female vertical shear key and filled with cementitious materials. The ultra-high performance fiber reinforced concrete (UHPFRC) was selectively used to joint-fill the 200-mm transverse joint between adjacent precast panels and the shear pockets connecting the panels to the supporting girders to ensure full shear interaction. Two actual-size FDDP specimens for each type of the three developed joints were erected to perform fatigue tests under the footprint of the Canadian Highway Bridge Design Code (CHBDC) truck wheel loading. The FDDP had a 200-mm thickness, 2500-mm width, and 2400-mm length in traffic direction; the rest was over braced steel twin girders. Two types of fatigue tests were performed; incremental variable amplitude fatigue (VAF) loading and constant amplitude fatigue (CAF) loading, followed by monotonically loading the slab ultimate-to-collapse. It was observed that fatigue test results showed that the ultimate capacity of the slab under VAF loading or after 4 million cycles of CAF exceeds the factored design wheel load specified into the CHBDC. Also, punching shear failure mode was dominant in all the tested FDDP specimens.

Reliable and precise damage localization in mechanical structures is of high importance in the context of structural health monitoring (SHM). The acoustic emission (AE) method has already shown its excellent suitability for damage localization. However, low signal-to-noise ratios (SNRs) are often prevalent in SHM, thus an increase in localization accuracy and robustness is still in demand. The present study faces this task through the integration of various model knowledge for AE source localization. The basis of the presented algorithm is the consideration of the dispersive behavior of elastic waves in thin-walled structures. The continuous wavelet transform (CWT) is used to obtain time-frequency representations of the signals, where frequency-dependent values for time-of-arrival (TOA) are extracted. Furthermore, the algorithm incorporates the knowledge that all sensors receive signals with the same time and location of origin, as well as the slightly different sensitivity of the theoretically equal sensors. The final localization results are achieved by a two-parameter grid search optimization. The algorithm is experimentally tested on a large aluminum plate with four piezoelectric wafer active sensors (PWASs) arranged in an array of 100 mm × 100 mm. The mean localization error of pencil lead breaks at ten different positions within the sensor array is used as an accuracy measure. It is shown that as more of the described model knowledge is incorporated into the localization, the accuracy increases. With the final algorithm, the mean localization error is more than halved compared to AE localization based on classical TOA estimation. Although the experiment described is conducted under laboratory conditions, the remarkable increase in accuracy suggests that AE source localization may be successful even at low SNR as typical for operational conditions.

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

In recent years, there has been an increasing interest in adopting novel sensing technologies for the continuous monitoring of structural systems. In this respect, Micro-Electro-Mechanical System (MEMS) sensors are widely used in several applications, including Structural Health Monitoring (SHM). Thanks to their significantly lower cost, ease of installation on the structure, and lower power consumption, they enable extensive, pervasive, and battery-less monitoring systems. This paper presents an innovative high-performance device for SHM applications, based on a low-noise triaxial MEMS accelerometer, providing a guideline and insightful results about the opportunities and capabilities of these devices. Sensor nodes have been designed, developed, and calibrated to meet structural vibration monitoring and modal identification requirements. These components include a protocol for reliable command dissemination through the network and data collection, and improvements to software components for data pipelining, jitter control, and high-frequency sampling. Devices were tested in the lab using shaker excitation. Results demonstrate that MEMS-based accelerometers are a feasible solution to replace expensive piezo-based accelerometers. Deploying MEMS is promising to minimize sensor node energy consumption. Time and frequency domain analysis show that MEMS can correctly detect modal frequencies, useful parameters for damage detection. The acquired data from the test bed were used to examine the functioning of the network, data transmission, and data quality. The proposed architecture has been successfully deployed in a real case study to monitor the structural health of the Marcus Aurelius Exedra Hall within the Capitoline Museum of Rome. The performance robustness was demonstrated and the results showed that the wired sensor network provides dense and accurate vibration data for structural continuous monitoring.

Prompt removal of misfolded membrane proteins and misassembled membrane protein complexes is essential for membrane homeostasis. However, the elimination of these toxic proteins from the hydrophobic membrane environment has high energetic barriers. Transmembrane FtsH is the only known ATP-dependent protease responsible for this task, unlike other well-studied soluble ATP-dependent proteases. The mechanisms by which FtsH recognizes, unfolds, translocates, and proteolyzes its substrates remain unclear. Here, we report the crystal structures of the Thermotoga maritima FtsH periplasmic domain (PD) in an associative trimeric state at a 1.5-1.95 Å resolution. We also describe the pH-dependent oligomerization states of the isolated PD using dynamic light scattering. These observations help us understand how FtsH recognizes membrane-anchored misfolded proteins.

Background: Respiratory syncytial virus[ RSV] is a lethal overwhelming defectiveness that influences people all over the world. The infection gets down in the lower respiratory tract and does not disperse to the remainder of the body. The objective of the study: Bioinformatics was used to create an mRNA vaccine against the Respiratory syncytial virus( RSV). Methodology: Lipid nanoparticle vaccines containing the Respiratory syncytial virus's surface fusion protein's mRNA were created for the current screening experimental investigation. Lipid nanoparticles[ LNP] with a particle size of around 90 nanometres that were created using the hot micro-emulsion process comprise the current vaccine delivery system. In stages 1 and 2 of clinical trials, the immunogenicity of the current mRNA RSV vaccine was evaluated. Results: The current vaccine demonstrated 81% immunogenicity in animal testing, but only 69% in stages 1 and 2 of clinical trials. Its side effects were manageable. The results persisted for a while. In the current trial, the vaccination proved effective as a preventative measure against RSV infection. The current immunization lacks antibody-dependent enhancement, which causes non-protective antibodies to develop. These non-neutralizing antibodies worsen infection by enhancing viral entrance and replication in the host cells, activating cytokines and the complement cascade through the production of immunological complexes, or both. However, the current LPN-RSV mRNA vaccine of the surface fusion protein resulted in the formation of potent neutralizing antibodies with persistent protection, especially for newborns and elderly individuals who get the ideal dose regimen. Conclusion: The invention of the LNP-mRNA RSV vaccine, which might prevent RSV-caused bronchiolitis and fatal pneumonia, made the current study promising

This study presents a detailed computational investigation aimed at identifying and evaluating potential small organic molecular scaffolds as inhibitors targeting the Pks13 protein, a critical enzyme in tuberculosis (TB) drug discovery. Our approach integrates multiple computational techniques, including quantitative structure-activity relationship (QSAR) modelling, compound library generation, molecular docking, biological activity prediction, re-evaluation of screened compounds, molecular dynamics (MD) analysis, and binding free energy estimation using the MM-GBSA approach. We developed a robust QSAR model using multiple linear regression (MLR) techniques, specifically tailored to predict the minimum inhibitory concentration (MIC) values of potential anti-TB agents. This model demonstrated excellent predictive performance, validated through rigorous internal and external validation procedures. Through molecular docking simulations, we identified five promising inhibitors Ethyl (R,Z)-2-(2-((2-chlorobenzyl) oxy)benzylidene)-5-(4-chlorophenyl)-7-methyl-3-oxo-2,3-dihydro-5H-thiazolo [3,2-a] pyrimidine-6-carboxylate (PKD1), (7R,9aR)-7-(2-hydroxyphenyl)-4-(2-methoxyphenyl)-3-methyl-7,8,9,9a-tetrahydroisoxazolo[5,4-b]quinolin-5(6H)-one (PKD2), (7-(4-methoxy phenyl)-2-methyl-3-phenylpyrazolo[1,5-a]pyrimidin-5-yl)(4-(3-(trifluoromethyl)phenyl) piperazin-1-yl)methanone (PKD3), (8S,10S)-10-(((2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl tetrahydro-2H-pyran-2-yl)oxy)-6,8,11-trihydroxy-8-(2-hydroxyacetyl)-1-methoxy-7,8,9,10-tetra-hydrotetracene-5,12-dione (PKD4), 3-(3,4-dimethylphenyl)-5-((2-(4-fluorophenyl)-2-oxoethyl) thio)-6-phenyl-2-thioxo-2,3,5,7a-tetrahydrothiazolo[4,5-d]pyrimidin-7(6H)-one (PKD5)with high binding affinities, prioritizing them based on their binding energies. These selected compounds were further assessed for their biological activity predictions, guiding the selection of candidates for experimental validation. Subsequent re-evaluation using absolute binding free energy estimation and MD simulations provided insights into the stability and dynamics of the protein-ligand complexes over time. Our findings highlighted the potential of identified compounds as stable binders within the Pks13-TE domain binding pocket, underscoring their viability as drug candidates. Additionally, binding free energy analysis using MM-GBSA reaffirmed the strong affinity of the proposed compounds towards Pks13. Our integrated computational approach offers a systematic and detailed framework for the identification and characterization of potential Pks13 inhibitors with specific relevance to TB drug discovery.

Zika virus (ZIKV) is a notable arbovirus with maternal, sexual, and TORCH-related transmission capabilities. After 2015, Brazil had the highest number of ZIVK-infected pregnant women who lost their babies or delivered them with Congenital ZIKV Syndrome (CZS). ZIKV infection has been linked to variations in endogenous retroviruses (ERVs) and interleukins within the placenta. ERVs, remnants of ancient viral infections integrated into the genome, include syncytin receptors crucial for placental development. Interleukins, immune response regulators, aid immune tolerance and support syncytial structure development in the placenta, where syncytin receptors facilitate vital cell-to-cell fusion events. Since ZIKV can infect trophoblast cells, we investigated the relationship between ZIKV infections and ERV and interleukin modulations. Investigating the impact of ZIKV on trophoblast cells, we examined two cell types (BeWo and HTR8) infected with ZIKV-MR766 (African) and ZIKV-IEC-Paraíba (Asia-Brazilian) using Taqman and RT2 Profiler PCR Array assays. While early ZIKV infection (24-48 hours) did not induce differential ERV and interleukin expression, future studies involving additional trophoblastic cell lineages and extended infection timelines will illuminate the dynamic interplay between ZIKV, HERVs, interleukins, and cytokines essential for placental formation and function.

Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle, spreading through direct contact and insect vectors, significantly affecting global cattle farming. Despite available vaccines, their effectiveness is limited by poor bioavailability and adverse effects. Our study aimed to identify potential inhibitors targeting LSD-associated DNA polymerase protein, selecting LSDV039 for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as potent binders among 380 phytocompounds, with respective affinities of -8.965 and -7.195 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.858 and -8.856 kcal/mol) among 718 FDA-approved antiviral drugs. Molecular dynamics simulations of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF but fluctuations in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. The study highlights the promising potential of repurposed drugs and phytocompounds as LSD therapeutics. However, extensive validation through in-vitro, in-vivo, and clinical trials is crucial for their practical application.

The integration of bioinformatics in drug discovery has revolutionized the field of pharmaceutical research. The use of computational tools and techniques has enabled researchers to analyze vast amounts of data, identify potential drug targets, and design new drugs with greater precision and efficiency. The integration of bioinformatics has also facilitated the development of personalized medicine, where drugs can be tailored to individual patients based on their genetic makeup. However, there are still challenges that need to be addressed, such as the need for more accurate predictive models and the ethical considerations surrounding the use of patient data. Overall, the integration of bioinformatics in drug discovery holds great promise for improving human health and advancing our understanding of disease mechanisms. In this mini-review, we discuss how Bioinformatics plays a crucial role in each step of drug discovery by providing tools and techniques to analyze large amounts of data generated from various sources, as well as the challenges and the opportunities offered by bioinformatics.

This paper investigates, experimentally and numerically, the buckling behavior of innovative sustainable Low-Cost Bamboo Composite (LCBC) structural columns under compressive loading. The LCBC columns are manufactured from bamboo culms in combination with bio-based resins to form composite structural columns. Different LCBC cross-sectional configurations are investigated in this study including the Russian doll (RD), Big Russian doll (BRD), Hawser (HAW), and Scrimber (SCR). Extra-large, large, medium, and small sizes of bamboo are employed to form the proposed configurations. Two bio-based resins including one bio-epoxy and one furan-based resin, in addition to a soft bio-based filler and a synthetic epoxy resin are applied. The bamboo species used as the cast-in-place giant bamboo for all configurations include Moso, Guadua, and Tali. In addition to experimental testing of the slender LCBC short columns, finite element analysis (FEA) software ABAQUS is applied to model the composite columns and predict their behavior. A buckling analysis using static Riks method is carried out to determine the LBCB’s response to axial compressive loading. A model is calibrated using test results with various imperfections, accounting for the variable behavior of each bamboo specimen, to accurately predict the behavior of LCBC columns with different resin contents. Slender LCBC columns showed maximum stress at buckling up to 60 MPa, highlighting the potential of bio-based resins for structural applications. The study found that the samples with bio-epoxy resin (BE2) exhibited enhanced material stiffness when compared to with synthetic epoxy (EPX) and furan-based resin (PF1), while PF1 specimens demonstrated increased ductility. The BE2 samples showed strain hardening in their stress-strain behavior, and the PF1 samples exhibited a long plateau phase before reaching the maximum load. Among the specimens with Moso bamboo and BE2 resin, those with SCR and HAW configurations achieved the highest compressive strengths.

The aim of this study was to examine the oxidation of human serum albumin (HSA) caused by oxidative stress after an exhaustive exercise such as ultra-marathon race. Thus, blood samples from 12 adult runners who underwent a 103 km mountain ultra-marathon race were collected pre- and 24, 48 and 72 h post race. HSA was partially purified using affinity chromatography and then was subjected to Western blot analysis for disulfide dimers determination, indicating oxidation. The results were correlated with those from a previous study in which the same samples were analyzed using different oxidative stress markers and a good correlation with protein carbonyls (PC) at all time points was observed. Moreover there was a significant correlation with static oxidation-reduction potential (sORP) at 24 h, and a negative correlation with capacity oxidation-reduction potential (cORP) at 24 and 48 h. In addition, an individual analysis of albumin dimers exhibited great inter-individual differences. This inter-individual variability in the oxidation of HSA may suggest different interventions (e.g. through diet) in order to confront the effects on athletes’ organism after a strenuous exercise. In conclusion, this study supported the importance of the assessment of albumin dimers as a predictive marker for exercise-induced oxidative stress.

The exponential growth of biomedical data in recent years urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research. By enabling automatic feature extraction, selection and generation of predictive models, these methods can be used to efficiently study complex biological systems. Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable features, and enable feature and model investigation. Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology and disease genomics. We outline the challenges posed for machine learning, and in particular, deep learning in biomedicine and suggest unique opportunities for machine learning techniques integrated with established bioinformatics approaches to overcome some of these challenges.

This paper investigates the effect of innovative cross-sectional configurations on Low-Cost Bamboo Composite (LCBC) structural members. The study employs both experimental and numerical methods with different resin matrices and bamboo species. In this study, LCBC short columns are designed with different innovative cross-sectional configurations in an attempt to overcome the costly production processes of engineered bamboo. This approach uses bundles of bamboo, both in culm and strip forms. A compatible, environmentally responsible, and economically justifiable resin matrix is used to fabricate an LCBC member. The production of LCBC members does not necessitate highly advanced technology. This capability enables the production of LCBC members in custom-designed cross-sectional shapes and lengths. This study introduces the Russian doll (RD), Big Russian doll (BRD), Hawser (HAW), and Scrimber (SCR) cross-sectional configurations. Extra-large, large, medium, and small sizes of bamboo are employed. Synthetic Epoxy (EXP), a Bio-based Experimental soft filler (BE1), Bio-Epoxy (BE2), Furan-based (PF1) matrices are applied. Furthermore, Moso, Guadua, Madake, and Tali bamboo species are incorporated. The results of this study reveal that the most efficient cross-sectional configuration for compressive strength is the HAW configuration, closely followed by SCR configuration. LCBC members with bio-resins have shown excellent promise in competing in strength with those made with their synthetic counterparts. The theoretical and numerical modeling of the LCBC members showed excellent correlation with the experimental results which provides the capacity to design LCBC for engineering projects. The LCBC design can be further developed with more bamboo and less resin content.

Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up-to-date as for many cellular genomes. To tackle these problems, we have developed VOGDB, a database of Virus Orthologous Groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote homology. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments and the third layer uses predicted protein structures to find the most remote homology. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGDB uses all virus genomes from RefSeq and partially re-annotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is inclusion of both prokaryotic and eukaryotic viruses in the same clustering process which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at https://vogdb.org under the CC BY 4.0 license.

The application of distributed fiber optic strain and temperature measurement can be utilized to address a multitude of measurement tasks across a diverse range of fields, particularly in the context of structural health monitoring in the domains of building construction, civil engineering, and special foundation engineering. However, a comprehensive understanding of the influences on the measurement method and the sensors is essential to prevent misinterpretations or measurement deviations. In this context, this study investigated the effects of moisture exposure, including various salt solutions and a high pH value, on a distributed strain measurement using Rayleigh backscattering. Three fiber optic sensors with different coating materials and one uncoated fiber were exposed to five different solutions for 24 hours. The study revealed significant discrepancies in deformation between the three coating types depending on the surrounding solution. Furthermore, in contrast to the prevailing literature, which predominantly describes swelling effects, a negative deformation was observed in a magnesium chloride solution. The findings of this study indicate that corresponding effects can impact the precision of measurement, potentially leading to misinterpretations. Conversely, these effects could be used to conduct large-scale monitoring of chemical components using distributed fiber optic sensing.

At the molecular level, aging is often accompanied by dysfunction of stress-induced membrane-less organelles (MLOs) and changes in their material state. In this work, we analyzed the proteins included in the proteome of stress granules (SGs) and P-bodies for their tendency to transform the material state of these MLOs. Particular attention was paid to proteins whose gene expression changes during replicative aging. It was shown that the proteome of the studied MLOs practically does not differ in the analyzed characteristics and consists of completely or partially intrinsically disordered proteins, 30 - 40% of which are potentially capable of liquid-liquid phase separation (LLPS). At the same time, the proportion of proteins capable of spontaneous LLPS is relatively small, which indicates the leading role of nucleic acids in the biogenesis of these membrane-less organelles. Proteins whose gene expression changes during the transition of human cells to a senescent state make up about 20% of the studied proteomes. There is a statistically significant increase in the number of positively charged proteins in both datasets studied compared to the complete proteomes of these organelles. An increase in the relative content of DNA-, but not RNA-binding proteins, was also found in the stress-granules dataset with senescence-related processes. Among SG proteins potentially involved in senescent processes, there is an increase in the abundance of potentially amyloidogenic proteins compared to the whole proteome. The hnRPDL protein has the highest degree of disorder and highest propensity for LLPS among such proteins, which allows us to consider it as “potentially dangerous.” Proteins common to SGs and P bodies, potentially involved in processes associated with senescence, form clusters of interacting proteins. The largest cluster is represented by RNA-binding proteins involved in RNA processing and translation regulation. These data indicate that SG proteins, but not proteins of P-bodies, are more likely to transform the material state of MLOs. Furthermore, these MLOs can participate in processes associated with aging in a coordinated manner.

Eotaxin-3 is a key chemokine with a relevant role in eosinophilic esophagitis, a rare chronic immune/antigen-mediated inflammatory disorder. Eotaxin-3 is a potent activator of eosinophil emergence and migration, which may lead to allergic airway inflammation. We investigated by bioinformatics tools the protein structure and the possible effects of the known variations reported in public databases. Following a procedure already established, we created a 3D model of the whole protein and modelled the structure of 105 protein variants due to known point mutations. The effects of the amino acid substitution at the level of impact on protein structure, stability, and possibly function, were detected by the bioinformatics procedure and described in detail. A web application was implemented to browse the results of the analysis and visualize the 3D models, with the opportunity of downloading the models and analyze by the own software. Among 105 amino acid substitutions investigated, the study evidenced in 44 cases at least one change in any of the investigated structural parameters. Other 6 variations are also relevant, although a structural effect is not detected by our analysis, because they substituted amino acids highly conserved, which suggests a possible function role. All these variations should be the object of particular attention, as they may induce loss of functionality in the protein.

Cancer being a multi-factorial disease, a multi-target approach is needed to treat it with minimal side-effects. Therefore, combined use of a proven herbal formula with chemo-therapy could be the better therapeutic. It may maintain homeostasis by synergistically targeting multiple signaling pathways involved in tumorigenesis, thus circumventing recurrence, resistance, and immunosuppression. Here we aim to determine the effectiveness and safety of an FDA-approved herbal formula, SR033 in combination with 5-fluorouracil (5FU) and paclitaxel (PTX). We report chemo-sensitization and chemo-synergy in HeLa and MCF-7 cell lines, immunomodulation of COX-2, PD-L1, VEGF and TGFβ and overall survival in-vitro and in-vivo via oral and topical delivery of SR033. In-vitro, SR033/5FU significantly reverses 5FU and PTX-resistance, lower COX-2, and PD-L1, resulting in TGFβ/ VEGF axis modulation. Furthermore, the study suggests that due to anti-oxidative potential of SR033, oral administration exerts chemo-preventive activity and restores cellular compartment in solid tumor and ascites-bearing mice models. Furthermore, the topical application, SR033L with low-dose 5FU increases survival rate, reduces tumor growth, and completely restores local and peripheral neutrophil-lymphocyte ratio in solid tumor mice model. The study indicates that SR033 could be a strong candidate in combination with low-dose 5FU and PTX for a holistic approach to cancer management.

Caveolin-1 (Cav-1) is 22 kDa caveolae protein, acts as a scaffold within caveolar membranes. It interacts with alpha subunits of G-protein and thereby regulates their activity. Earlier studies reported elevated or up-regulated levels of caveolin-1 in the serum of prostate cancer patients. Secreted Cav-1 promotes angiogenesis, cell proliferation and anti-apoptotic activities in prostate cancer patients. Cav-1 upregulation is mainly related to prostate cancer metastasis. Keeping above facts in view, the present study was designed to explore Cav-1 as a target for prostate cancer therapy using computational approach. Molecular docking, structural base molecular modelling and molecular dynamics simulations were performed to investigate Cav-1 inhibitors. A predictive model was generated and validated to establish a stable structure. ZINC database of biogenic compounds was used for induced fit docking (IFD) and high throughput virtual screening. The H-bond interactions of the compounds with active site residues of Cav-1 were estimated by IFD and 100 ns long molecular dynamic simulations. The reported compounds showed significant binding and thus can be considered as potent therapeutic inhibitors of Cav-1. This study provides a valuable insight into biochemical interactions of Cav-1 for therapeutic applications and warrants for experimental validation of the predicted ‘active(s)’.

Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell’s response to environmental stress. Experiments have proven that the amounts of free σB (SigB) are controlled by a system of anti- (RsbW) and anti-anti-sigma (RsbV) factors expressed from the same operon as SigB. Moreover, the phosphorylation state of RsbV is controlled by phosphatases RsbP and RsbU, which directly dephosphorylates RsbV. A set of chemical equations describing the network controlling the levels of free SigB was converted to a set of differential equations quantifying the dynamics of the network. The solution of these equations allowed the simulation of the kinetic behavior of the network and its components under real conditions. In this study, the time series of protein expression measured by mass spectrometry were utilized to investigate the role of the phosphatases RsbU/RsbP in transmitting the environmental signal. Additionally, the influence of kinetic constants and the amounts of other network components on the functioning of the network was investigated. A comparison with the same simulation performed using transcriptomic dataset showed that while the time series between the proteomic and transcriptomic datasets) are not correlated, the results are the same. This indicates that when modeling is done within one dataset, it does not matter whether the data come from the mRNA or protein level. In summary, the computational results based on experimental data provide quantitative insight into the functioning of the SigB-dependent circuit and offer a template for the quantitative study of similar systems.

This paper introduces innovative sensitivity indices based on Cliff's Delta for global sensitivity analysis of structural reliability. These indices build on Sobol's method, using binary outcomes (success or failure), but avoid the need to calculate failure probability Pf and the associated distributional assumptions of resistance R and load F. Cliff's Delta, originally for ordinal data, evaluates the dominance of resistance over load without specific assumptions. The mathematical formulations for computing Cliff's Delta between R and F quantify structural reliability by assessing the random realizations of R > F using a double-nested-loop approach. The derived sensitivity indices, based on the squared value of Cliff's Delta​, exhibit properties analogous to those in Sobol's sensitivity analysis, including first-order, second-order, and higher-order indices. This provides a comprehensive framework for evaluating the contributions of input variables and their interactions on structural reliability. This method is particularly significant for FEM applications, where repeated simulations of R or F are computationally intensive. The double-nested-loop algorithm of Cliff's Delta maximizes the extraction of information about structural reliability from these simulations. However, the high computational demand of Cliff's Delta is a disadvantage. Future research should optimize computational demands, especially for small Pf​, where the inner loop may often be unnecessary.

The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at https://bacspad.altrabio.com.

Research into lightweight structural concrete using volcanic tuff is of great importance to the construction industry. These materials have excellent thermal insulation properties, which helps improve the energy efficiency of buildings. A three-factor experimental design was used to build the statistical model. The test methods used were methods for determining the crushability of volcanic tuff, determining the average density, compressive strength and thermal conductivity of lightweight structural concrete. The influence of basalt fiber on the properties of lightweight structural concrete has been determined. The optimal compositions of lightweight structural concrete using tuff have been selected. The compressive strength of lightweight structural concrete reached 32.0 MPa. The average density range is 1754.6-2114.0 kg/m³. Good thermal conductivity values ​​were obtained in the range of 0.653-0.818 W/m·K. The article obtained the optimal compositions of lightweight structural concrete using volcanic tuff as a filler.

With the exponential growth of machine learning and development of Artificial Neural Network (ANNs) in recent years, there is great opportunity to leverage this approach and accelarate bio-logical discoveries through applications on the analysis of bioinformatics data. Various types of datasets including for example protein or gene interaction networks, molecular structures and cellular signalling pathways, have already been used for machine learning by training ANNs for inference and pattern classification. However, unlike regular data structures that are commonly used in the computer science and engineering fields, bioinformatics datasets present challenges that require unique algorithmic approaches. The recent development of the geometric and deep learning approach within the machine learning field, is very promising towards accelerating analysis complex bioinformatics datasets. The principles of ANNs and their importance for bio-informatics machine learning is demonstrated herein, through presentation of the undelying mathematical and statistical foundations from group theory, symmetry, linear algebra. Further-more, the structure and functions of ANN algorithms that form the core principles of artificial intelligence are explained, in relation to the bioinformatics data domain. Overall, the manuscript provides guidance for researchers to understand the principles required for practicing machine learning and artificial intelligence, with the special considerations towards bioinformatics applications.

This study unveils verapamil's compelling cytoprotective and proliferative effects on pancreatic β-cells amidst diabetic stressors, spotlighting its unforeseen role in augmenting cholecystokinin (CCK) expression. Through rigorous investigations employing MIN6 β-cells and zebrafish models under type 1 and type 2 diabetic conditions, we demonstrate verapamil's capacity to significantly boost β-cell proliferation, enhance glucose-stimulated insulin secretion, and fortify cellular resil-ience. A pivotal revelation of our research is verapamil's induction of CCK, a peptide hormone known for its role in nutrient digestion and insulin secretion, which signifies a novel pathway through which verapamil exerts its therapeutic effects. Furthermore, our mechanistic insights reveal that verapamil orchestrates a broad spectrum of gene and protein expressions pivotal for β-cell survival and adaptation to immune-metabolic challenges. In vivo validation in a zebrafish larvae model confirms verapamil's efficacy in fostering β-cell recovery post-metronidazole inflic-tion. Collectively, our findings advocate for verapamil's reevaluation as a multifaceted agent in diabetes therapy, highlighting its novel function in CCK upregulation alongside enhancing β-cell proliferation, glucose sensing, and oxidative respiration. This research enriches the therapeutic landscape, proposing verapamil not only as a cytoprotector but also as a promoter of β-cell re-generation, thereby offering fresh avenues for diabetes management strategies aimed at pre-serving and augmenting β-cell functionality.

Longitudinal cutting is a most common process in steel structure manufacturing, and the man-hours of the process provide an important basis for enterprises to generate production schedules.However, currently the man-hours in factories are mainly estimated by experts, and the accuracy of this method is relatively low.In this study,we propose a system that predicts man-hours with history data in the manufacturing process and that can be applied in practical structural steel fabrication.The system addresses the data inconsistency problem by one-hot encoding and data normalization techniques,Pearson correlation coefficient for feature selection,and the Random Forest Regression(RFR) for prediction.Compared with the other three Machine Learning(ML) algorithms, the Random Forest algorithm has the best performance.The results demonstrate that the proposed system outperforms the conventional approach and has better forecast accuracy, so that it is suitable for man-hours prediction.

Living systems are intricate repositories of biomolecules, where the interactions between these molecules play an important role in maintaining homeostasis. Interruptions in these interactions can lead to diseases, underscoring the significance of biomolecular interactions and their molecular basis. HUGENICS (Human Genetic Database) is a comprehensive biological database that focuses on molecular interactions between human and microbial proteins, particularly emphasizing protein-protein interactions (PPIs). This database offers insights into disease pathways by elucidating the interplay between microbial surface/secretory proteins and human disease-related proteins. This white paper highlights the significance, scope, and potential applications of HUGENICS in advancing biomedical research and improving human health.

The synthesis of enantiomeric forms of D-amino acids can be achieved by a two-step "hydantoinase process" based on the sequential catalysis of substrates by specific enzymes, D-carbamoylase and D-hydantoinase. In addition to our previously studied D-hydantoinase, we describe here the structural features of D-carbamoylase from Pseudomonas, the encoded gene of which was chemically synthesized and cloned into Escherichia coli. A significant fraction of the overexpressed recombinant protein forms insoluble inclusion bodies, which are partially converted to a soluble state upon treatment with N-lauroylsarcosine or upon incubation of the cells at low temperatures. Analysis of the substrate specificity of the purified His-tag protein showed that D-carbamoylase exhibits the highest activity toward N-carbamoyl-D-alanine and N-carbamoyl-D-tryptophan. Molecular docking analysis revealed the location of the substrate binding site in the three-dimensional structure of D-carbamoylase. Molecular dynamics simulations showed that the binding pocket of the enzyme in complex with N-carbamoyl-D-tryptophan is stabilized within 100 ns. The free energy of binding indicated a possible role of residues Arg176 and Asn173 in the formation of hydrogen bonds between the enzyme and N-carbamoyl-D-tryptophan. The properties of the studied D-carbamoylase and D-hydantoinase support further development of a combined biotechnological process for the production of new drugs and peptide hormones.

Algorithmic systems used in healthcare contexts are primarily developed for the benefit of the public. It is therefore essential that these systems are trusted by the individuals for whose benefit they are deployed. Drawing inspiration from the principles embedded in the testing of the safety, efficacy and effectiveness of new medicinal products, concurrent design engineering and pro-fessional certification requirements, the authors propose, for the first time, a preliminary com-petency-based ‘Algorithmic Ethics’ Effectiveness Impact Assessment’ framework for developers of AI systems used in healthcare contexts. They concluded that this set of principles should en-compass the algorithmic systems ‘production lifecycle’, to guarantee the optimized use of the AI technologies, avoiding biases and discrimination while ensuring the best possible outcomes, simultaneously increasing decision-making capacity and the accuracy of the results. As AI is as good as those who program it and the system in which it operates, the robustness and trustworthiness of their ‘creators’ and ‘deployers’, should be fostered by a certification system guaranteeing the latter’s knowledge and understanding of ethical aspects as well as their com-petencies in integrating these aspects in trustworthy AI systems when used in healthcare con-texts.

By introducing environmental mediator, for avoiding randomness in selecting indicators and subjectivity in deciding interaction path coefficients to reveal interaction mechanism among forest industry, ecology and environmental capacity, structural Pressure–State–Impact–Response (PSIR) and quantitative Structural Equation Modeling (SEM) are utilized with data on thirty–one provinces of China. We can find that: (i) forest industry has a negative influence on ecology, whereas ecology has a positive influence on industry; (ii) the destructive influence that industry has on ecology is much greater than the positive effect ecology has on industry; and (iii) environmental capacity plays a partial mediating role between industry and ecology. According to these results we can conclude that: (i) forest industry and ecology are not in a symbiotic relationship and have not reached a level of ecological security; (ii) the interaction between industry and ecology is in a period of transition from antagonistic to beneficial; and (iii) industry dominates ecology. However, we prospect the following advice: (i) methods of forest industry should be changed; (ii) new modes of industrial integration and circular economy should be developed; and (iii) the ability of the environment to sustain itself should be enhanced. The level of forest ecological security to discuss the symbiotic mechanism of industry and ecology will propose to be measured in future.

Background: Studies have tried to identify predictors of functional markers of keratoconus progression, whereas structural outcomes of collagen cross-linking have not been properly investigated. Objective: find and set up a combination of diagnostic modalities and measurements to reliably reflect CXL efficiency. Material and methods: We retrospectively reviewed the medical histories of 107 KC patients (131 eyes) who underwent CXL in a medical center from January 2018 to December 2022. The dataset included preoperative examinations and follow-up results, which provided a total of 796 observations. The cases of other corneal diseases, repeated CXL, pregnancy, and observations without follow-up examinations were excluded. Results: The study findings revealed a significant drop in the central and corneal thickness during 14.01±9.98 months of observations. Linear and polynomial equations suggested different trends in pachymetry change after CXL. The linear model showed corneal thinning, and according to the polynomials, pachymetry findings return to baseline values two years after CXL. Conclusion: The most reliable prognosis of postoperative corneal thickness is achieved with the models trained on keratometry readings and topography indices. BAD indices are also reliable predictors of the corneal thickness after CXL. A combination of the aforementioned structural parameters and their derivatives can reliably predict CXL efficiency.

Leishmaniasis are neglected diseases that affect regions such as South Asia, South Africa and Latin America, less developed regions. Current treatment, for cutaneous, mucocutaneous and visceral leishmaniosis, which are the main forms of the disease, is based on the administration of pentavalent antimonial and amphotericin B. However, these drugs have low efficacy and high toxicity. For this reason, the search for new treatments for this disease is necessary, based on studies of new molecules and their conformations. The research proposed the conformational study of brominated guanidine compounds with potential antileishmanial activity using Nuclear Magnetic Resonance (NMR) and X-ray diffraction (XRD) techniques. The present study involves the bro-minated molecules, LQOF-G2, LQOF-G30, LQOF-G35 and LQOF-G35-Br. The later was synthesized by the reaction of LQOF-G35 with NBS under IR irradiation at 120 Watts of potency and dichloro-methane as solvent by 12-h of exposition. The obtained results demonstrated the efficiency of the bromination method, since two bromines atoms entered the molecule. Furthermore, NMR analysis showed the occurrence of a conformational change from Z to E when compound LQOF-G35 was brominated to LQOF-G35-Br. This feature was well confirmed by comparative DRX study of the LQOF-G35 and LQOF-G35-Br compounds. The antileishmanial activity of LQOF-G2 e LQOF-G35 motivated the synthesis of new brominated compounds LQOF-G30 e LQOF-G35-Br.

This paper details the comprehensive activities conducted in a laboratory setting to assess the Structural Health Monitoring (SHM) of prefabricated building envelopes. Aimed at enhancing the structural evaluation of buildings, the focus of this research lies in employing nondestructive sensors for SHM with the objective to advance in the understanding and assessment of facade conditions. The paper outlines the methodologies employed, starting with a modal analysis to define the structural vibration's modal frequency. Subsequently, tests were defined and executed to validate building envelope compliance in case of stress typical of high-rise building. Throughout these tests, continuous monitoring of the façade was conducted using both conventional (accelerometers, extensimeter washers) and non-conventional sensors (Fiber Optic Sensing) The gathered data underwent thorough processing and analysis to provide an overall perspective on the structure's behavior during the stress test. The investigation aimed to identify whether specific physical phenomena correlate with distinct signals and to evaluate if continuous façade monitoring over the building's lifespan aids in preventing potential structural damage. Moreover, two modal analyses were conducted to compare final data and frequencies with earlier data, enabling the detection of any structural alterations. The results from compliance testing and structural analysis yielded noteworthy insights contributing to the evolving field of structural health monitoring, offering valuable findings that advance our ability to proactively manage and maintain the integrity of building structures.

Artificial intelligence AI or machine learning has proven to be a potential activity in the health and biomedical sciences. Previous research it has found that AI can learn new data and transform it into the useful knowledge. In the field of pharmacology, the aim is to design more efficient and novel vaccines using this method which are also cost effective. The underlying fact is to predict the molecular mechanism and structure for increased likelihood of developing new drugs. Clinical, electronic and high resolution imaging datasets can be used as inputs to aid the drug development niche. Moreover, the use of comprehensive target activity has been performed for repurposing a drug molecule by extending target profiles of drugs which also include off targets with therapeutic potential providing a new indication.

The study of the tribological behavior of the braking system in auto vehicles requires knowing the characteristics of the material in contact and, in the work process, for the friction pair, brake disc-pads. Materials structural analysis is necessary because the wear process depends on the friction pair chemical composition, and brake disk-pads, respectively on the work process parameters (pressing force, rotational speed, traffic conditions, etc.). The material of the brake discs is generally the same gray cast iron, but the brake pads can be semi-metallic (particles of steel, copper, brass, and graphite, all united with a special resin), organic materials (particles of rubber, glass, and kevlar all joined with the help of a resin), composite materials that contain different constituents and ceramic materials (rarely have small copper particles). Therefore, the purpose of the paper is to know the crystalline structure and the mechanical properties of the brake pad materials, through specific studies and analyses, with important implications on the friction and wear behavior.

Related studies have shown that mitophagy plays a role in the progression of Atherosclerosis (AS). Utilizing GSE43292, GSE100927, and GSE159677 datasets, WGCNA and differential expression analysis identified mitophagy-related module genes and DEGs1, while single-cell analysis screened DEGs2. MR analysis revealed causal AS-linked genes in DEGs1. LASSO and expression validation identified biomarkers, evaluated via ROC curves. Further analyses included GSEA, immune infiltration, ANN, regulatory networks, and drug prediction. Four candidate genes were identified through WGCNA, differential expression analysis and MR analysis. The LASSO analysis identified CD36, IL1RN, and MME as biomarkers, while the MR analysis showed that IL1RN and MME are protective factors and CD36 is a risk factor in AS. The ROC curves disclosed that the ANN model had greater diagnostic power for AS than any other biomarker. The GSEA revealed that the biomarkers were enriched in lysosomes and hematopoietic cell lineage and were significantly positively correlated with monocytes. The regulatory network construct showed that small nucleolar RNA host gene 16 regulates MME via the micro RNAs. This study identified CD36, IL1RN, and MME as biomarkers of mitophagy in AS and indicated that they could be applied in the diagnosis and treatment of this condition.

Medicinal plants have been a cornerstone of traditional medicine systems for centuries, offering a vast array of bioactive compounds with therapeutic potential. However, the identification, characterization, and elucidation of the pharmacological properties of these plants have often been challenging due to their complex chemical composition and diverse biological activities. Bioinformatics, with its interdisciplinary approach combining biology, computer science, and information technology, presents a powerful toolkit for the systematic study of medicinal plants. This review provides an overview of bioinformatics methodologies and resources that can facilitate the identification, phytochemical analysis, pharmacological investigation, and conservation of medicinal plants. It highlights the integration of omics technologies, computational algorithms, database resources, and molecular modeling techniques in advancing our understanding of medicinal plants' therapeutic potential and their applications in drug discovery and development.

Recent studies suggest that PEBP1/RKIP and YY1, despite having distinct molecular functions, may interact and mutually influence one another's activity. They exhibit reciprocal control over each other's expression through regulatory loops, prompting the hypothesis that their interplay could be pivotal in cancer advancement and resistance to drugs. To delve into this interplay's functional characteristics, we conducted a comprehensive analysis using bioinformatics tools across a range of cancers. Our results confirm the association between elevated YY1 mRNA levels and varying survival outcomes in diverse tumors. Furthermore, we observed differing degrees of inhibitory or stimulatory effects of these two genes in various cancer pathways, along with correlations between their mRNA expression and immune infiltration. Additionally, YY1/PEBP1 expression (or methylation) displayed connections with genomic alterations across cancer types. Notably, we uncovered links between YY1/PEBP1 and different indicators of immunosuppression, such as immune checkpoint blockade response, and T-cell dysfunction/exclusion levels, across different patient groups. Overall, our findings underscore the significant role of the interplay between YY1 and PEBP1 in cancer progression, influencing genomic changes, tumor immunity or the tumor microenvironment. Additionally, these two gene products appear to impact the sensitivity of anticancer drugs, opening new avenues for cancer therapy.

Methylenetetrahydrofolate reductase (MTHFR), an enzyme expressed in mammalian testes exerts direct effect on spermatogenesis; however, its protein characteristics in bovine testes remain unknown. Here, we analysed bovine testicular structure, MTHFR bioinformatics profile, mRNA, and protein expression characteristics in yellow-cattle (y-c) and yak testis using histological procedures, bioinformatics analysis, qRT-PCR, and western blot. Testes from 13 bovines, ≤ 2 years juvenile (y-c, n = 3; yak, n=3) and ≥ 3 years adult (y-c, n = 3; yak, n = 4) were collected and analysed. Anatomical characteristics of testis in y-c and yak were similar except the weight or size for which that of y-c was significantly higher or greater than yak. In y-c, an open reading frame (ORF) for 2600 nucleotides sequence, encoding 655 amino acids showed high homology with zebu cattle (99.51%) and wild yak (98.68%). Secondary and 3D protein structures were similar to that of humans with differences in number of nucleotides, amino acids, and some physico-chemical characteristics. MTHFR mRNA expression in y-c and yak were significantly higher in adult testes compared with juvenile ones. However, its protein expression was higher but not statistically significant in adult y-c and yak compared to the juvenile ones. The highlights and inferences of these and other findings are discussed.

Myocardial infarction, more commonly known as heart attack, is a huge health problem around the world. It is a result of inadequate blood supply to certain parts of the heart and death of heart muscle cells in that region. Although it has been around for a long time, newer and newer ways of probing myocardial infarction is being followed. Bioinformatics and Systems Biology are relatively recent fields to try to give new insights into myocardial infarction. Following the footsteps of others, this in silico study has tried to chime in on the investigation into myocardial infarction. The study began with the gene expression omnibus dataset uploaded to the NCBI from a whole-genome gene expression analysis carried out at Mayo Clinic in Rochester, Minnesota. From the dataset, differentially expressed genes following first-time myocardial infarction were identified and classified into up-regulated and down-regulated ones. Gene Set Enrichment Analysis (GSEA) was carried out on the up-regulated genes which were statistically significant and corresponded with the NCBI generated annotations. Protein-Protein Interaction Network for these genes was constructed. GSEA revealed 5 transcription factors, 5 microRNAs and 3 pathways significantly associated with them. From the Protein-Protein Interaction Network, 6 key proteins (hub nodes) have been identified. These 6 proteins may open a new window of opportunity for the discovery/design of new drugs for mitigating the damage caused by myocardial infarction.

The identification of biomarkers is crucial for cancer diagnosis, understanding the underlying biological mechanisms, and developing targeted therapies. In this study we propose a machine learning approach to predict the outcome and platinum resistance status of ovarian cancer patients using public available gene expression data. Six classical machine learning algorithms are compared on their predictive performance. Those with the highest score are analyzed by their feature importance using the SHAP algorithm. We were able to select multiple genes that were correlating with the outcome and platinum resistance status of the patients and validated those using Kaplan-Meier plots. In comparison to similar approaches the performance of the models were higher and different genes using feature importance analysis were identified. The most promising identified genes that could be used as biomarkers are: TMEFF2, ACSM3, SLC4A1 and ALDH4A1.

Selectins are responsible for the early stages of cell migration as they control cell adhesion. They make the microenvironment permissive for metastatic events by promoting the activation of other cell adhesion molecules (CAMs). We employed several robust bioinformatics tools to evaluate gene sequence; single nucleotide polymorphisms (SNPs) in intronic and UTR regions; and missense SNPs with amino acid change in L-selectin (SELL), E-selectin (SELE), P-selectin (SELP) and PSGL-1 (SELPLG). We demonstrated that gene polymorphisms rs2229569, rs1131498, rs4987360, rs4987301 and rs2205849; polymorphisms rs3917777, rs2205894 and rs2205893 of SELP gene; rs7138370, rs7300972 and rs2228315 variants of SELPLG gene; and rs1534904 and rs5368 polymorphisms of SELE gene may produce important alterations in the DNA structure and consequent alterations in the morphology and function of the corresponding proteins. These Selectin polymorphic variants deserve further investigation in cancer patients, as they may become useful clinical markers for risk determination, diagnostic and prognostic biomarkers or even targets for targeted therapies.

Drug design is used for different applications of bioinformatics tools analyze DNA, genome, and sequence target region of a small organic molecule in order to understand the molecules of disease. Bioinformatics tools are identified a newly wide research field and minimize future risks through web servers and data mining. Clinical sample test performed with the bioinformatics tools as the biomedical detective. A particular structure and configuration of protein obliging in Drug design concluded Bioinformatics. This review bioinformatics tools and webserver will discuss functions of small organic molecules according to clinical pharmacology.

In recent years, cerium dioxide (CeO2) has attracted considerable attention owing to its remarkable performance in various applications, including photocatalysis, fuel cells, and catalysis. This study explores the effect of nickel (Ni) doping on the structural, thermal, and chemical properties of CeO2 nanorods, particularly focusing on oxygen vacancy-related phenomena. Utilizing X-ray powder diffraction (XRD), alterations in crystal structure and peak shifts were observed, indicating successful Ni doping and the formation of Ni2O3 at higher doping levels, likely due to non-equilibrium reactions. Thermal gravimetric analysis (TGA) revealed changes in oxygen release mechanisms, with increasing Ni doping resulting in the release of lattice oxygen at lower temperatures. Raman spectroscopy corroborated these findings by identifying characteristic peaks associated with oxygen vacancies, facilitating the assessment of Ni doping levels. Overall, this study underscores the substantial impact of Ni doping on CeO2 nanorods, shedding light on tailored catalytic applications through modulation of oxygen vacancies while preserving the nanorod morphology.

It is of great academic significance to understand how the atomic structure of interfaces and boundaries in materials impacts the magnetic coupling nature across the boundaries and encourage development of state-of-the-art magnetic devices. Here, we carry out a systematic investigation of the atomic and electronic structures of twin boundaries (TBs) in LiFe5O8 thin films and determine their concurrent magnetic couplings using atomic-resolution transmission electron microscopy and atomistic first-principles calculations. The results show ferromagnetic or antiferromagnetic coupling can exist across the different TBs in LiFe5O8 (LFO) thin films and electrical structures within a few atomic layers directly rely on the TB atomic core structures. Uncovering one-to-one relationship between the magnetic properties of individual TB and the local atomic structures will clarify a thorough comprehension of numerous fascinating magnetic properties of commonly utilized magnetic materials, which will undoubtedly encourage the progress of sophisticated magnetic materials and devices.

The resilience of towns and cities refers to their ability to adapt and recover when confronted with pressures or challenges. This study employs ten variables as indicators to assess the resilience of urban areas by analyzing official data and constructing a multilevel mixed-effects structural equation model. The empirical findings demonstrate that enhancing resilience significantly influ-ences urban service functions, such as strengthening healthcare systems, stabilizing the real estate market, and addressing socio-economic challenges. Specifically, factors such as healthcare re-sources, housing demand, population structure, and social security exhibit varying levels of resil-ience, which profoundly impact the spatial distribution of these factors and socio-economic de-velopment. Disparities in healthcare resource allocation, demographic aging trends, and shifts in the housing market closely correlate with resilience levels in different regions. Additionally, the study emphasizes that improving resilience not only boosts the reliability and security of urban services but also ensures that communities receive necessary support and protection during times of adversity. Consequently, policymakers should recognize the pivotal role of urban resilience in resource allocation and social equity, devising corresponding strategies to enhance the resilience of these areas.

With challenged early detection came the collapse of a school roof, initiating a storm of public mistrust and hundreds of schools under investigation in the United Kingdom. The culprit is a poorly understood material heavily used in the 1950s to mid-1990s, reinforced autoclaved aerated concrete (RAAC). As a lightweight material with excellent insulation, RAAC was mainly used in roof and floor panels in many parts of the world. However, RAAC has a comparatively weak compressive strength, poor reinforcement anchorage, and high permeability and susceptibility to creep. The uniqueness of RAAC properties is exacerbated by poor manufacturing, negligent construction and maintenance as well as structural deviations from original design intent. Current guidance lacks in specifying RAAC management strategies beyond recommendations for periodic surveying. This paper delivers a state-of-the-art review of the material properties and structural performance of RAAC to recommend improved measures characterised by non-destructive testing methods and digital asset management. The reviewed literature targets understanding the influence of variable environmental exposure conditions, reinforcement condition, operational loading variations, structural deficiencies, and ageing, to predict their effect on the mechanism of RAAC failure. The established risk factors of RAAC are examined to inform of feasible response strategies against specific issues encountered in affected RAAC structures such as inadequate bearings, compromised transverse reinforcement, and environmental conditions.

The exploration and identification of targets and pathways for Atopic dermatitis (AD) treatment and diagnosis are critical for AD control. The conventional target exploration approach such as the literature review is not satisfying in terms of efficiency and accuracy. Recently, the bioinformatic approach is drawing attention for its unique advantage of high-volume data analysis for target and pathway exploration; Open Targets Platform is the targets source for this study to extract top 200 high-rank proteins from 3122 AD associated proteins. STRING, Cytoscape, CytoHubba, ClueGo, and CluePedia function had been applied for data analysis. The KEGG Mapper search & colour pathway was the pathway map resource for identified pathways; 23 key hub genes (VDR, KIT, BCL2L11, NFKBIA, KRAS, IL13, JAK2, STAT3, IL21, IL4R, REL, PDGFRB, FOXP3, RARA, RELB, EGFR, IL21R, MYC, CREBBP, NR3C1, IL2, JAK1, and KITLG). Additionally, 8 correlated pathways and the biological process had been identified; Through this study, a viable approach for target and pathway exploration had been presented. The identified AD targets and pathways will be tested for upcoming research for traditional Chinese medicinal herb interactions

Frontal Temporal Dementia (FTD) is a neurological disorder known to have less therapeutic options. So far only a few biomarkers are available for FTD that can be used as potential comorbidity targets. To this end, in the present study we aim to identify potential biomarkers or susceptible genes for FTD that show comorbidities with diseases such as COVID-19 and Breast Cancer. Gene expression Omnibus datasets containing FTD expression profiles from African American and white ethnicity background were included in our study. In FTD samples of GSE193391 dataset, we identified 305 DEGs with 168 genes being up-regulated and 137 genes being down-regulated. We conducted comorbidity analysis for COVID-19 and Breast cancer followed by analysis of potential drug interactions, pathogenicity, analysis of genetic variants and functional enrichment analysis. Resulting genes AKT3, GFAP, ADCYAP1R1, VDAC1, and C4A showed significant transcriptomic alterations in FTD and significant comorbidity status with COVID-19 and Breast cancer. Functional pathway analysis revealed that these comorbid genes were significantly enriched in the pathways such as glioma, JAK/STAT signaling, systematic lupus erythematosus, neurodegeneration-multiple diseases and neuroactive ligand-receptor interaction. Overall, from these results, we concluded that these genes could be recommended as potential therapeutic targets for the treatment of comorbidities in FTD.

Sequence analysis program is outlined that analyzes and investigates homology between various nucleic acid or protein sequence. The dot matrix technique compares the sequences and the consensus sequence is obtained by superimposing on each other all the dot matrices. Local Alignment and Global Alignment both sequence from start to end is the best possible alignment over the entire duration between the two sequences. This method is more important to align with two closely related sequences roughly the same length. This method may not able to generate optimal results for divergent sequences and variable length sequence because between the two sequences it does not recognize very similar local region.

The COVID-19 outbreaks have caused universities all across the globe to close their campuses and forced them to initiate online teaching. This article reviews the pedagogical foundations for developing effective distance education practices, starting from the assumption that promoting autonomous thinking is an essential element to guarantee full citizenship in a democracy and for moral decision making in situations of rapid change, which has become a pressing need in the context of a pandemic. In addition, the main obstacles related to this new context are identified, and solutions are proposed according to the existing bibliography in learning sciences.

The COVID-2019 disease caused by the SARS-CoV-2 virus (aka 2019-nCoV) has raised significant health concerns in China and worldwide. While novel drug discovery and vaccine studies are long, repurposing old drugs against the COVID-2019 epidemic can help identify treatments, with known preclinical, pharmacokinetic, pharmacodynamic, and toxicity profiles, which can rapidly enter Phase 3 or 4 or can be used directly in clinical settings. In this study, we presented a novel network based drug repurposing platform to identify potential drugs for the treatment of COVID-2019. We first analysed the genome sequence of SARS-CoV-2 and identified SARS as the closest disease, based on genome similarity between both causal viruses, followed by MERS and other human coronavirus diseases. Using our AutoSeed pipeline (text mining and database searches), we obtained 34 COVID-2019-related genes. Taking those genes as seeds, we automatically built a molecular network for which our module detection and drug prioritization algorithms identified 24 disease-related human pathways, five modules and finally suggested 78 drugs to repurpose. Following manual filtering based on clinical knowledge, we re-prioritized 30 potential repurposable drugs against COVID-2019 (including pseudoephedrine, andrographolide, chloroquine, abacavir, and thalidomide) . We hope that this data can provide critical insights into SARS-CoV-2 biology and help design rapid clinical trials of treatments against COVID-2019.

The thymus, a central lymphoid organ in animals serves as the site for T cell development, differentiation and maturation, vital to adaptive immunity. Thymus is critical for maintaining tissue homeostasis to protect against tumors and tissue damage. Overactive or prolonged immune response can lead to oxidative stress from increased production of reactive oxygen species. Heat stress induces oxidative stress and overwhelms the natural antioxidant defense mechanisms. The study objectives were to investigate the protective properties of astaxanthin against heat-induced oxidative stress and apoptosis in the chicken thymus, by comparing the growth performance and gene signaling pathways among three groups- thermal neutral, heat stress and heat stress with astaxanthin. The thermal neutral temperature conditions were 21-22°C and heat stress temperature was 32-35°C. Both heat stress groups experienced reduced growth performance, while the astaxanthin treated group showed a slightly lesser decline. The inflammatory response and antioxidant defense system were activated by the upregulation of the NF-kB, NFE2L2, PPARα, cytoprotective capacity and apoptotic gene pathways in the heat stress compared to the thermal neutral group. Conversely, expression levels were without significance between the thermal neutral and heat stress with antioxidant groups, suggesting astaxanthin antioxidant effectiveness to mitigate inflammation and oxidative stress damage.

The increased cultivation of Cannabis sativa L. in North America, represented by high Δ9-tetrahydrocannabinol-containing (high-THC) cannabis genotypes and low THC-containing hemp genotypes, has been impacted by an increasing number of plant pathogens. These include fungi which destroy roots, stems and leaves, in some cases causing a build-up of populations and mycotoxins in the inflorescences that can negatively impact quality. Viroids and viruses have also increased in prevalence and severity and can reduce plant growth and product quality. Rapid diagnosis of the occurrence and spread of these pathogens is critical. Techniques in the area of molecular diagnostics have been applied to study these pathogens in both cannabis and hemp. These include polymerase chain reaction (PCR)-based technologies, including RT-PCR, multiplex RT-PCR, RT-qPCR, and ddPCR, as well as whole genome sequencing (NGS) and bioinformatics. In this study, examples of how these technologies have enhanced the rapidity and sensitivity of pathogen diagnosis on cannabis and hemp will be illustrated. These molecular tools have also enabled studies on the diversity and origins of specific pathogens, specifically viruses and viroids, and these will be illustrated. Comparative studies on the genomics and metabolomics of healthy and diseased plants are urgently needed to provide insight into their impact on quality and composition of cannabis and hemp-derived products. Management of these pathogens will require monitoring of their spread and survival using the appropriate technologies to allow accurate detection, followed by appropriate implementation of disease control measures.

Conventional data visualization software have greatly improved the efficiency of the mining and visualization of biomedical data. However, when one applies a grid computing approach the efficiency and complexity of such visualization allows for a hypothetical increase in research opportunities. This paper will present data visualization examples presented in conventional networks, then go into higher details about more complex techniques related to leveraging parallel processing architecture. Part of these complex techniques include the attempt to build a basic general adversarial network (GAN) in order to increase the statistical pool of biomedical data for analysis as well as an introduction to the project utilizing the decentralized-internet SDK. This paper is meant to show you said conventional examples then go into details about the deeper experimentation and self contained results.

Expansion tube is ideal energy absorber which dissipates kinetic energy through plastic deformation and friction. There is an urgent need to understand the influence of key parameter, e.g. semi angle, tube material, and friction coefficient, on the mechanical response and energy absorption characteristics of expansion tube. In the present work, the material properties of the tubes were tested under quasi-static loading condition, and the numerical simulations were carried out by using commercial software ABAQUS. Based on the validated finite element simulation, all the semi angle, tube material, and friction have significant effects on the energy absorption capacity of expansion tube. The expansion tube with high tensile stress of parent material have high energy absorption capacity, while the specific energy absorption is linear with the tensile stress/density of tube material. This work would give a guidance to the structural design and parent materials selection for expansion tubes.

The optimal structural design is imperative to minimize material consumption and reduce the environmental impact of construction. Given the complexity in the formulation of structural design problems, the process of optimization is commonly performed using artificial intelligence (AI) global optimization, such as Genetic Algorithm (GA). However, the integration of AI-based optimization together with visual programming (VP) in building information modeling (BIM) projects warrants further investigation. This study proposes a workflow by combining structure analysis, VP, BIM, and GA to optimize trusses. The methodology encompasses several steps including: (i) generation of parametric trusses in Dynamo VP; (ii) performing the finite element modeling (FEM) using Robot Structural Analysis (RSA); (iii) retrieving and evaluating the FEM results interchangeably between Dynamo and RSA; (iv) finding the best solution using GA; and (v) importing the optimized model into Revit, enabling the user to perform simulations and engineering analysis, such as life cycle assessment (LCA) and quantity surveying. The feasibility of the proposed workflow was tested on benchmark problems and compared with open literature. The outcomes of this study offer insight into the opportunities and limitations of combining VP, GA, FEA, and BIM for structural optimization applications, particularly to enhance structural efficiency and sustainability in construction.

Variable flow emitters are a new type of emitter for underground drip irrigation that are used in locations where soil moisture is difficult to transport to the surface, which leads to crop emer-gence difficulties. The flow channel structure parameters of emitters affect the hydraulic per-formance of the emitter and its anticlogging ability. In this study, the variable flow emitter at the conventional low–flow water supply stage is taken as the research object. A combination of CFD numerical simulation of a two–phase flow of water and sand and clear water testing of test samples is applied to study the influence laws of 10 groups of variable flow emitter structural combinations on the effluent flow rate (q), flow index (x), particle passage rate and flow field inside the flow channel. The results show that the Realizable k–ε turbulence model can be used to simulate the flow field inside the variable flow emitter flow channel. The nRMSE between the measured and simulated values of q is 11.23%, and the relative error between the measured and simulated values of x is 4.66%, which gives a high simulation accuracy. The polar analysis shows that the tooth angle A has the smallest effect on the effluent flow rate q0.1 under 0.1 MPa, x, and particle passage rate of the variable flow emitter. The depth of the flow channel D, the spacing of the teeth B, and the height of the teeth E have a different order of precedence in the influence of the three indices, which are D > B > E > A, B > E > D > A, and E > B > D > A, respectively. The value of particle passage rate is positively correlated with the mean flow velocity (v) and the mean turbulent kinetic energy (k) in the flow channel, and particle passage rate tends to increase and then decrease with the increase of x. The retention time (t) of the particles in the flow channel is closely related to the magnitude of v and k. Three multivariate linear regression equations (R2 = 0.883 ~ 0.995) were constructed for q0.1, x, and particle passage rate versus the flow channel structural parameters. Using the scipy.optimize.minimize function in Python, we de-termined the three optimal combinations of flow channel structural parameters corresponding to better hydraulic performance: q0.1 is 1.5 or 2 L/h (objective function y = min x), better clogging resistance (y = max particle passage rate), and both (y = min (0.5 x - 0.5 particle passage rate)). The research results can provide a ref-erence for the optimal design of variable flow emitters.

In the conservation of monumental heritage, the collection and utilization of information are of primary importance. The Heritage Building Information Modeling (HBIM) procedure harnesses the potential of three-dimensional models, offering significant advantages in accessing documentation, interoperability, multidimensionality of intervention design, cost evaluation and maintenance management. Attention here is focused on the Certosa di Pisa, a large historical complex built in the 14th century as a monastery of the Carthusian order, currently in a state of deterioration and in need of restoration and re-functionalization. The multifaceted nature of this monumental complex, with its intricate interplay of architectural elements spanning different historical periods and featuring diverse techniques, poses a significant challenge for structural safety assessment. This case study presents an opportunity to explore an HBIM approach to streamline the diagnostic process and facilitate the intervention design phase. The goal is achieved by utilizing an accurate 3D model enriched with data from multiple sources and automating certain operations for structural assessment. The usefulness of the HBIM methodology is highlighted as a valuable tool in the realm of Cultural Heritage structures for both technicians and scholars alike.

Chitosan (CS) nanoparticles are under investigation for a wide range of applications in nanomedicine. The structural, molecular and physicochemical properties of chitosan nanoparticles have a direct bearing on their efficacy in drug conjugation and delivery, gene delivery, and tissue engineering. Herein we report on the structural, morphological and molecular properties of chitosan nanoparticles synthesized using the ionic gelation method with the intended purpose of being used for drug delivery. The chitosan nanoparticles (CS-NPs) were prepared in the 0.25 to 1.0% w/v concentration range, whereas separate samples of the 1.0% w/v CS-NPs were also functionalized with polyethylene oxide (PEO) alone and with a diblock copolymer of PEO and polypropylene glycol (PPG). The average size of the CS-NPs was determined from TEM imaging to be in the range of 11.3 to 14.8 nm. The XRD and TEM analyses show that the CS-NPs have semi-crystalline structure with the degree of crystallinity depending upon the nature of synthesis. Our results show that functionalizing the 1.0% w/v CS-NPs with PEO increases the degree of crystallinity whereas functionalizing with the diblock copolymer PEO - PPG results in a significant increase in their degree crystallinity. The CS/TPP concentration (CS:TPP fixed at 1:1 ratio) had no apparent effect on the degree of crystallinity of the CS-NPs. The results from the FTIR analysis confirm incorporation of TPP with CS in the CS-NPs. Additionally, FTIR analysis shows an enhancement of hydrogen bonding that is consistent with the increase in the degree of crystallinity of the CS-NPs.

Aging-related disorders pose significant challenges due to their complex interplay of physiological and metabolic factors, including inflammation, oxidative stress, and mitochondrial dysfunction. Curcumin, a natural compound with potent antioxidant and anti-inflammatory properties, has emerged as a promising candidate for mitigating these age-related processes. However, gaps in understanding the precise mechanisms of curcumin's effects and the optimal dosages for different conditions necessitate further investigation. This systematic review synthesizes current evidence on curcumin's potential in addressing age-related disorders, emphasizing its impact on cognitive function, neurodegeneration, and muscle health in older adults. By evaluating the safety, efficacy, and mechanisms of action of curcumin supplementation, this review aims to provide insights into its therapeutic potential for promoting healthy aging. A systematic search across three databases using specific keywords yielded 2,256 documents, leading to the selection of 15 clinical trials for synthesis. Here we highlight the promising potential of curcumin as a multifaceted therapeutic agent in combating age-related disorders. The findings of this review suggest that curcumin could offer a natural and effective approach to enhancing the quality of life of aging individuals. Further research and well-designed clinical trials are essential to validate these findings and optimize the use of curcumin in personalized medicine approaches for age-related conditions.

New dimers of selected dipyridothiazines with an m-xylene linker have been designed, synthesized and characterized. Their structure was identified using 1H and 13C NMR as well as 2D NMR techniques (COSY, ROESY, HSQC and HMBC experiments) and HR MS spectrometry. The compounds were subjected to preliminary in silico biological profile tests using the Way2Drug server and analysis of the probable cytotoxic effect on various cancer cell lines. Preliminary in vitro cytotoxicity tests were performed against normal cell lines (HaCaT) and five cancer cell lines (SW480, SW620, MDA-MB-231, A-549, LN-229) showing moderate activity. An analysis of the structure-activity relationship was performed.

Innovative tissue engineering biomimetic hydrogels based on hydrophilic polymers have been investigated for their physical and mechanical properties. 5% to 25% by volume loading PHEMA-nanosilica glassy hybrid samples were equilibrated at 37°C in aqueous physiological isotonic and hypotonic saline solutions (0.15 and 0.05 M NaCl) simulating two limiting possible compositions of physiological extracellular fluids. The glassy and hydrated hybrid materials were characterized both for dynamo-mechanical properties and equilibrium absorptions in the two physiological-like aqueous solutions. Mechanical and the morphological modifications occurring in the samples have been described. The 5% volume nanosilica loading hybrid nanocomposite composition showed mechanical characteristics in the dry and hydrated states that were comparable to those of cortical bone and articular cartilage, respectively, and then chosen for further sorption kinetics characterization. Sorption and swelling kinetics were monitored up to equilibrium. Changes in water activities and osmotic pressures in the water-hybrid systems equilibrated at the two limiting solute molarities of the physiological solutions have been related to the observed anomalous sorption modes using the Flory-Huggins interaction parameter approach. The bulk modulus of the dry and glassy PHEMA-5% nanosilica hybrid at 37°C has been observed to be comparable with the values of the osmotic pressures generated from the sorption of isotonic and hypotonic solutions. The anomalous sorption modes and swelling rates are coherent with the difference between osmotic swelling pressures and hybrid glassy nano-composite bulk modulus: the lower the differences the higher the swelling rate and equilibrium solution uptakes. Bone tissue engineering benefits of use of tuneable biomimetic scaffold biomaterials that can be “designed” to act as biocompatible and biomechanically active hybrid interfaces are discussed.

Triazole derivatives of fluorescein containing N,N-dimethylaminopropyl fragments and their ammonium salts were synthesized with yields of 74 - 85%. The resulting compounds exhibit fluorescent properties in the green region of the visible spectrum. The critical aggregation concentration (CAC) was estimated using a py-rene fluorescent probe corresponding to a range of 0.28 - 1.43 mM, and at concentrations above the CAC the compounds form stable aggregates ranging from 165 to 202 nm. A relative quantum yield of 5-24% has been calculated based on fluorescence and UV spectra. The best value is shown by a derivative containing a tetradecyl substituent. When studying the photocatalytic properties of synthesized compounds through the reaction between N-substituted 1,2,3,4-tetrahydroisoquinoline and malonic ester, the mono-tetradecyl deriva-tive demonstrated the best results. According to gas chromatography-mass spectrometry (GC-MS) data, the conversion of the initial heterocycle reached 95%. Therefore, these resulting compounds have the potential to act as an effective photocatalysts.

In 2018, Iran witnessed approximately 21,000 fatalities resulting from road accidents, ranking it as the fifth leading cause of death across all age groups. These incidents carry substantial economic and social burden for the nation, claiming more than 5% of its GDP. Human behavior emerges as a significant contributing factor to high-risk driving offenses. It has been proposed that by influencing general deterrence, a rigorous defense can be established against such violations. Various theories posit that by reinforcing or diminishing influential factors, general deterrence perception can be molded, presenting a potential avenue for an effective deterrent against traffic infractions. This study examines deterrence perceptions prevailing among the public in Iran regarding the enforcement of traffic laws. Employing Structural Equation Modeling (SEM), we delve into the intricate relationships between variables, allowing for a comprehensive exploration of the factors influencing general deterrence. The study draws on the data derived from a survey comprising 548 questionnaires for modeling purposes. An innovative concept, private sector enforcement, is introduced and incorporated into the questioning and modeling process. The findings reveal that socioeconomic status (p-value<0.01), police enforcement (p-value<0.05), private sector enforcement (p-value<0.05), specific deterrence (p-value<0.01), and the use of technology (p-value<0.01) have direct and indirect impacts on the general deterrence perception of drivers.

The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for calibration and quality assurance of inactivated SARS-COV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. Heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)- C-terminal domain (CTD) across all SARS-COV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprising of UV-inactivated SARS CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (Limit of Detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a twenty amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust ‘pan-variant’ antigen-based assays for viruses prone to high mutational rates.

Hashimoto’s thyroiditis (HT) is a common autoimmune disease, with its prevalence rapidly increasing. Both genetic and environmental risk factors contribute to the development of HT. Recently, viral infection has been suggested to act as a trigger of HT by eliciting the host immune response and subsequent autoreactivity. We analyzed features of HT through bioinformatics analysis so as to identify markers of HT development. We accessed public microarray data of HT patients from the Gene Expression Omnibus (GEO) and obtained differentially expressed genes (DEGs) under HT. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed for functional clustering of our protein-protein interaction (PPI) network. Utilizing ranked gene lists, we performed Gene Set Enrichment Analysis (GSEA) using the clusterprofiler R package. By comparing the expression signatures of the huge perturbation database with the queried rank-ordered gene list, connectivity map (CMap) analysis was performed to screen potential therapeutic targets and agents. The gene expression profile of the HT group was in line with general characteristics of HT. Biological processes related to the immune response and viral infection pathways were obtained for the upregulated DEGs. GSEA results revealed activation of autoimmune disease-related pathways and several viral infection pathways. Autoimmune disease and viral infection pathways were highly interconnected by common genes, while the HLA genes which are shared by both were significantly upregulated. CMap analysis suggested that perturbagens, including SRRM1, NLK, and CCDC92, have the potential to reverse the HT expression profile. Several lines of evidence suggested that viral infection and the host immune response are activated during HT. Viral infection is suspected to act as a key trigger of HT by causing autoimmunity. SRRM1, an alternative splicing factor, which responds to viral activity, might serve as potential marker of HT.

The seismic events of 2015 in Nepal exposed the challenges associated with constructing earthquake-resistant 2-story self-built stone masonry structures in high-elevation rural regions, especially post-disaster. The Department of Urban Development and Building Construction (DUDBC) provided designs that failed to preserve the local architectural landscape and craftsmanship while adding unfamiliar knowledge and technology. To address the challenges related to architecture, structure, and socio-economic concerns in designing and implementing post-earthquake houses, a need-based building development framework is required for standardized practice. This study presents a novel framework to assess, design, and implement a self-built house after a disaster, consisting of five stages: 1) post-disaster problem assessment, 2) need identification, 3) material selection, 4) design development, and 5) validation and implementation. Based on this framework, we proposed a novel gabions building construction technology for two-story stone masonry structures that effectively mitigate post-disaster challenges such as logistic, resilience, and socioeconomic aspects while improving disaster resiliency specifically in the high-elevation rural areas of Nepal. The proposed two-story gabion building preserves architectural values, enhances structural integrity, and provides cost-effectiveness when compared with its DUDBC peer models while providing much-needed relief to the vulnerable community. The proposed resilient house, G- 2.1, utilizes locally sourced materials and craftsmanship, and innovative gabion technology that ensures affordability and facilitates knowledge transfer. The contribution of this study includes a development framework and a two-story gabions house that is most suitable for self-built post-disaster reconstruction and resilient to local architecture and socio-economic conditions while providing structural integrity and safety.

Abstract Octreotide is the first synthetic peptide hormone, consisted of eight amino acids, that mimics the activity of somatostatin, a natural hormone in the body. During the past decades, advanced instrumentation and crystallographic software established X-ray Powder Diffraction (XRPD) as a valuable tool for extracting structural information of biological macromolecules. The latter was demonstrated by the successful structural determination of octreotide at a remarkably high d-spacing resolution (1.87 Å) (PDB code: 6vc1). This study focuses on the response of octreotide to different humidity levels and temperatures, with a particular focus on the stability of the polycrystalline sample. XRPD measurements were accomplished employing an Anton Paar MHC-trans humidity-temperature chamber installed within a laboratory X’Pert Pro diffractometer (Malvern Panalytical). The chamber is employed to control and maintain precise humidity and temperature levels of samples during XRPD data collection. Pawley analysis of the collected data sets revealed that the octreotide polycrystalline sample is remarkably stable and no structural transitions were observed. The compound retains its orthorhombic symmetry (space group: P212121, a = 18.57744(4) Å, b = 30.17338(6) Å, c = 39.70590(9) Å, d~ 2.35 Å). However, a characteristic structural evolution in terms of lattice parameters and volume of the unit-cell is reported mainly upon controlled relative humidity variation. In addition, an improvement of signal-to-noise ratio in the XRPD data under a cycle of dehydration/rehydration is reported. These results underline the importance of considering the impact of environmental factors, as humidity and temperature, in the context of structure-based drug design, thereby contributing to the development of more effective and stable pharmaceutical products.

A new class of nano-cube core-shell heterostructures containing Ag coating on the top of WO₃ was fabricated. Physical vapor deposition was used to produce WO₃ based nano-heterostructures. All kind of wet toxic chemical process was avoided to make the process simple and contaminant free. Sputtering of WO₃ and a subsequent thermal annealing process was done to create nano-cubes of WO₃. After that, sputtering of Ag was performed to form the Ag-WO₃ core-shell nano-heterostructures (CSNH). The CSNHs were characterized using field emission scanning electron microscopy (FESEM), energy dispersive spectroscopy (EDS), X-ray diffraction analysis (XRD) and UV-vis spectroscopy. The morphologies, elemental analysis, interfaces, crystallinity, phases, and chemical compositions were analyzed. The bottom-up growth of WO₃ nanocubes was studied using different time periods at 900°C. Ag coating was also studied before and after annealing. Finally, an optical property (band gap) was also analyzed using Tauc plot derive from absorption spectra. The tailoring the band gap of WO₃ from ~2.9eV to ~ 2.45 eV was observed while Ag-WO₃ CSNH formed.

Prostate cancer (PCa) is characterised by androgen-dependency. Unfortunately, under anti-androgen treatment pressure, castration-resistant prostate cancer (CRPC) emerges, characterised by heterogeneous cell populations that, over time, lead to the development of different androgen-dependent or -independent phenotypes. Despite important advances in therapeutic strategies, CRPC remains incurable. Context-specific essential genes represent valuable candidates for targeted anti-cancer therapies. Through the investigation of gene and protein annotations and the integration of several published transcriptomic data, we identified two consensus lists to stratify PCa patients' risk and discriminate CRPC phenotypes based on androgen receptor activity. ROC and Kaplan-Meier survival analyses were used for gene set validation in independent datasets. We further evaluated these genes for their association with cancer dependency. The deregulated expression of the PCa-related genes was associated with overall and disease-specific survival, metastasis and/or high recurrence risk, while the CRPC-related genes clearly discriminated between adeno and neuroendocrine phenotypes. Some of the genes showed context-specific essentiality. We further identified candidate drugs through a computational repositioning approach for targeting these genes and treating lethal variants of PCa. This work provides a proof-of-concept for the use of an integrative approach to identify candidate biomarkers involved in PCa progression and CRPC pathogenesis within the goal of precision medicine.

Recently, the outbreak of coronavirus disease 2019 (COVID-19) is threatening human health globally. There is a dire need to find potential therapeutic agents. Angiotensin converting enzyme 2 (ACE2), as an entry receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is considered as potential therapeutic target in COVID-19 pandemic. Here, our bioinformatics analysis revealed that the biological function of ACE2 was correlated with regulation of blood pressure and mediation of SARS-CoV-2 entry into host cells. Ten ACE2 cooperative proteins were identified by using STRING with a high score. ACE2 expressed highly in the small intestine, testis, and kidney. The level of ACE2 expression in tumor tissues varies in different types of cancers compared with that in normal tissues. It was worth noting that the expression level of ACE2 in the tumor has no effect on patient survival. MiRNA hsa-miR-942-5p, and three transcription factors (TFs) including Signal transducer and activator of transcription 4 (STAT4), Estrogen related receptor α (ESRRA), and Signal transducer and activator of transcription 3 (STAT3) were selected as novel ACE2 regulators. Moreover, nine potential therapeutic drugs were predicted by two online databases. Thus, our research may expand the overall view of ACE2 in COVID-19 treatment.

Structural deformations are one of the most significant factor that affects machine tool (MT) positioning accuracy. These induced errors are complex to be represented by a model, nevertheless they need to be evaluated and predicted in order to increase the machining performance. This paper presents a novel approach to calibrate a machine tool in real-time, analyzing the thermo-mechanical errors through Fibre Bragg Grating (FBG) sensors embedded in the MT frame. The proposed configuration consists of an adaptronic structure of passive materials, Carbon Fibre Reinforced Polymers (CFRP), equipped by FBG sensors that are able to measure in real-time the deformed conditions of the frame. By using a proper thermo-mechanical kinematic model, the displacement of the end effector may be predicted and corrected when it is subjected to external undesired factors. By starting from a set of FE simulations to develop a model able to describe the MT structure stresses, a prototype has been fabricated and tested. The scope was to compare the numerical model with the experimental tests using FBG sensors. The experimental campaign has been performed varying the structure temperature over time and measuring the tool tip point (TTP) positions. The obtained results showed a substantial matching between the real and the predicted position of TTP confirming the effectiveness of the proposed calibration system.

Retinoic acid receptor-related orphan receptor γ (RORγ) is a transcription factor regulating the expression of the pro-inflammatory cytokine IL-17 in human T helper 17 (Th17) cells. Activating RORγ can induce multiple IL-17-mediated autoimmune diseases but may also be useful for anticancer therapy. Its deep immunological functions make RORɣ an attractive drug target. Over 100 crystal structures have been published describing atomic interactions between RORɣ and agonists and inverse agonists. In this review, we focus on the role of dynamic properties and plasticity of the RORɣ orthosteric and allosteric binding sites by examining structural information from crystal structures and simulated models. We discuss the possible influences of allosteric ligands on the orthosteric binding site. We find that high structural plasticity favors the druggability of RORɣ, especially for allosteric ligands.