Many types of banana (Musa spp.)—one of the most economically important horticultural crops—exist, and their ploidy (diploid, triploid, and tetraploid, usually) and genome types (containing A or/and B genome in most cases) differ. At present, observation and genome type detection are commonly used to identify banana germplasm resources. However, the former is tedious, while the latter cannot distinguish categories below genome types. It is therefore urgent that a simple and effective method for identifying banana germplasm resources is established. We sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm and found that the sequencing peaks, especially the 20 bp region near the 420 bp position (referred to as the “420 bp region”), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the “420 bp region” as a marker, we were able to quickly distinguish bananas belonging to different genome type groups (comprising the AA, AB, AAA, ABB, AAB, ABBB, AAAB, and AAAA groups) or different subgroups in the same genome type group (for example, the Cavendish, Gros Michel, Red, Lakatan, and Ibota Bota subgroups in the AAA group; and the Pisang Raja, Plantain, Pome and Silk subgroups in the AAB group). Moreover, it appeared that Sanger sequencing of ITS could be used for identifying banana hybrid offspring. These results demonstrated that the banana ITS region contains rich genetic information that is useful for genotyping. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement.

This study was designed for the first time to improve phenolic yield and antioxidant activity of ultrasonic-assisted extraction from Acer truncatum leaves (ATL) using response surface methodology, and phenolic composition in ATL extracted under the optimized condition were characterized by UPLC-QTOF-MS/MS. Solvent and extraction time were selected based on preliminary experiments, and a four-factors-three-levels central composite design was conducted to optimize solvent concentration (X₁), material-to-liquid ratio (X₂), ultrasonic temperature (X₃) and power (X₄) for an optimal total phenol yield (Y₁) and DPPH• antioxidant activity (Y₂). The results showed that the optimal combination was ethanol: water (v:v) 66.21%, material-to-liquid ratio 1:15.31 g/mL, ultrasonic temperature 60 °C, power 267.30 W, and time 30 min with three extractions, giving a maximal total phenol yield of 7593.62 mg gallic acid equivalent /100 g d.w. and a maximal DPPH• antioxidant activity of 74241.61 μmol Trolox equivalent/100 g d.w.. Furthermore, 22 phenolics were first identified in ATL extract obtained under the optimized conditions, indicating that gallates, gallotannins, quercetin, myricetin and chlorogenic acid derivatives were the main phenolic composition in ATL. What’s more, a gallotannins pathway existing in ATL from gallic acid to penta-O-galloyl-glucoside was interpreted. All these results provided practical information aiming at full utilization of phenolics in ATL, together with fundamental knowledge for further research.

Understanding morphological and genetic diversity of forest trees is essential to facilitate their conservation, sustainable management and genetic improvement for addressing the economic and environmental demands and challenges. We have examined variation in morphometric seed and pod traits and seed germination of multipurpose and widely distributed forest tree Albizia lebbek (Indian siris) from 12 provenances covering the species’ range in northern India and its relationships with bioclimatic factors. Highly significant inter-provenance variation was observed in seed size (seed length (SL), seed width (SW), SW/SL, SL×SW), seed mass (1000 seed weight), pod size (pod length (PL), pod width (PW), PW/PL), seed germination, number of seeds per pod, and insect infected seeds (IIS). The provenance effect contributed a major portion to the total phenotypic variance. Morphometric variation in all traits except for IIS was not clinal related to longitude, latitude, altitude or rainfall. There was an indication of the presence of ecotypic variation. IIS showed clinal variation with significant negative correlation with latitude. Most seed size and pod size traits showed positive correlations with several temperature bioclimatic factors and negative correlations with several precipitation bioclimatic factors. Our results have significance for genetic improvement, population genetics and genomics studies and conservation and sustainable management of A. lebbek genetic resources.

The increasing demand for higher power in rocket launchers is driving the development of higher power nozzles, achieved essentially by increasing the expansion ratio. However, this can lead to flow separation and resulting unsteady, asymmetrical forces, called side loads, which can limit the life of both the nozzle itself and other engine components. If this problem can be overcome, engine performance can be significantly increased. Therefore, various separation control methods have been proposed, but none have been fully implemented to date due to the uncertainties associated with modeling and predicting the flow phenomena. A numerical study of high area ratio rocket engine is presented to analyze the aeroelastic performance of the structure under the condition of flow separation. The finite volume method, the 2nd order upwind scheme and the extended wall function are used to analyze the flow inside the rocket nozzle and the transition of the Free Shock Separation (FSS) to Restricted Shock Separation (RSS) separation pattern ) to be discussed in detail. Since the location of the flow separation point depends heavily on the flow.

In Tunisia, olive is the most cultivated fruit crop while in the north where rainfall exceeded 400mm.year-1, the olive growing area is in widely extension in marginal soil with high slope gradient. Thus, the inclusion of cover crops is a sustainable solution to increase the ecosystem productivity, improve the soil fertility and oil yields. But, in Tunisia a few study were investigated the effect of legumes cover crop on the olive productivity. Therefore, the aim of this study was to evaluate the short-term (two cropping seasons s 2021 and 2022) effects of different seeded cover crops and soil management practices on the cover crops and soil characteristics, as well as enzymes activities and related microbial diversity. Six intercropping were tested in rainfed olive orchards (cv.Chétoui): Spontaneous vegetation (Spont), Wheat, Vetch, Oat, Fenugreek, mixture Vetch-Oat and compared to control (3 periodic tillage/year without intercropping). During the first cropping season, cover crops were cut as animal feed and only residues were incorporated into the soil. While, during the second year, all cover crops biomass were incorporated into the soil. Results indicate that the dry biomass and carbon uptake were significantly higher in grasses species (Wheat and Oat). But, highest level of nitrogen was found in Fenugreek cover crops. As compared to control, all cover crops including spontaneous vegetation increased soil organic matter and macronutrient level, mainly phosphorus. The most activity of β-glucosidase, phosphatase and arysulphatase was found in the cover crops plot of wheat and oat. In addition, this study improve that the utilization of the carbon sources was dominated by amides, amine and amino-acids in the fenugreek plot; while it was dominated by polymers and carboxylic acids in the case of wheat and oat.

Few studies have examined the dietary protein intake and sources in combination with the longitudinal changes in brain structure markers. Our study aimed to examine the association between dietary protein intake and different sources of dietary protein with the longitudinal rate of change in brain structural markers. A total of 2723 and 2679 participants from the UK Biobank were included in the analysis. The relative and absolute amounts of dietary protein intake were calculated through a 24-hour dietary recall questionnaire. The longitudinal change rates of brain structural biomarkers were computed using two waves of brain imaging data. We utilized multiple linear regression to examine the association between dietary protein and different sources and the longitudinal changes in brain structural biomarkers. Restrictive cubic splines were used to explore nonlinear relationships, and stratified and sensitivity analyses were conducted. Increasing the proportion of animal protein in dietary protein intake is associated with a slower reduction in the total hippocampus volume (THV, β: -0.02524, P<0.05), left hippocampus volume (LHV, β: -0.02435, P<0.01) and right hippocampus volume (RHV, β: -0.02544, P<0.05).Higher intake of animal protein relative to plant protein is linked to a lower atrophy rate in THV (β: -0.01249, P<0.05) and LHV (β: -0.01173, P<0.05) and RHV (β: -0.01193, P<0.05). Individuals with higher intake of seafood exhibit lower longitudinal rate of change in HV compared to those with no consume (THV, β: -0.004514; P<0.05; RHV, β: -0.005527, P<0.05). In subgroup and sensitivity analyses, there was not a significantly alteration. A moderate increase in the intake and proportion of animal protein in the diet, especially from seafood, is associated with a lower longitudinal change rate in hippocampus volume.

Most non-infectious diseases are associated with dysfunction of proteins or protein complexes. Аssociation between sequence and structure is analyzed since a long time, and analysis of sequence organization in domains and motifs is actual research area. A mathematical method is proposed here to identify the hierarchical organization of protein sequences. The method is based on pentapeptide as a unit of protein sequences. This method was applied on a non-homologous dataset of protein sequences. The analysis revealed 11 hierarchical levels of protein sequence organization, showing the relationship of these multiple fragments of sequences. Using different examples, we illustrated how the fragments of the spatial structure of protein correspond to the elements of the hierarchical structure of the protein sequence. A hierarchical structure is observed in the protein sequence. This methodology is an interesting basis for mathematically based classification of elements of spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used for biotechnological and medical problems.

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2115474 SSR, 63588 SNP, and 91547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping.

The theory of water transport in trees, according to which the main driving force of water movement is the suction created by the evaporation of water by the meniscus (the curved surface of the capillary liquid column) on the evaporating elements, supported from below by root pressure, is flawed. The capillary effect in nature is around one meter. In the case of open-air gaps, the leaf cannot suck in the water against gravity because, in this case, the plant would not be sucking in water, but air through the open-air gap. If not, how do trees transport water? When evaporation occurs, there is no suction towards the canopy, but pressure is due to a reduction in the cross-section of the water pipe caused by heat loss through evaporation. At night, when evaporation stops, a thermal equilibration process is triggered, which restores the original cross-section of the pipe. This generates suction and draws water from the soil. As the hydrostatic pressure in the pipe is high for tall trees, the pipe is cut off. To prove my theory, I have given several examples. Water transport is not based on physical mechanical laws alone. There may be complex physiological, biochemical, and biophysical processes behind the operation of the pipe system.

SETMAR is a protein lysine methyltransferase that is involved in several DNA processes, including DNA repair via the non-homologous end joining (NHEJ) pathway, regulation of gene expression, illegitimate DNA integration, and DNA decatenation. However, SETMAR is an atypical protein lysine methyltransferase since in anthropoid primates, the SET domain is fused to an inactive DNA transposase. The presence of the DNA transposase domain confers to SETMAR a DNA binding activity towards the remnants of its transposable element, which has resulted in the emergence of a gene regulatory function. Both the SET and the DNA transposase domains are involved in the different cellular roles of SETMAR, indicating the presence of novel and specific functions in anthropoid primates. In addition, SETMAR is dysregulated in different types of cancer, indicating a potential pathological role. While some light has been shed on SETMAR functions, more research and new tools are needed to better understand the cellular activities of SETMAR and to investigate the therapeutic potential of SETMAR.

Understanding the mechanism, how entirely new (EntNew) gene/protein or the first ancestral gene/protein of a family was created, should be one of the most important issues in the biological sciences. However, the mechanism is totally unknown still now. On the other hand, it is well known that mature protein is generally rigid and one catalytic center exists on the protein. Creation of such a mature EntNew gene/protein should be, of course, carried out through random process, because it cannot be designed in advance. However, the EntNew gene/protein never be created by random polymerization of the respective monomeric units, because of the extraordinary large sequence diversities of ~10¹⁸⁰ and ~10¹³⁰, respectively. Protein 0^th-order structure or a specific amino acid composition, in which immature but water-soluble protein can be produced even through random process, holds the key for solving the difficult problem. As it was fragmentally described in the previous papers how and where EntNew gene/protein was created, I describe in detail in this review three processes generating EntNew gene/protein with some flexibility under three genetic codes, the universal genetic code, SNS primitive code and GNC primeval code, and discuss why the mature gene/protein could be created through the processes.

Proteomics research has become one of the most important topics in the fields of life science and natural science. At present, research on protein–protein interaction networks (PPINs) mainly focuses on detecting protein complexes or function modules. However, existing approaches are either ineffective or incomplete. In this paper, we investigate function module detection mechanisms in PPIN, including open databases, existing detection algorithms and recent solutions. After that, we describe the proposed solution based on simplified swarm optimization (SSO) algorithm and gene ontology knowledge. The proposed solution implements SSO algorithm for clustering proteins with similar function, and imports biological gene ontology knowledge for further identifying function complexes and improving detection accuracy. Furthermore, we use four different categories of species dataset for experiment: Fruitfly, Mouse, Scere, and Human. The testing and analysis result show that the proposed solution is feasible, efficient and could achieve a higher accuracy of prediction than existing approaches.

The ability to detect the presence as well as classify the activities of individuals behind visually obscuring structures is of significant benefit to police, security and emergency services in many situations. This paper presents the analysis from a series of experimental results generated using a through-the-wall (TTW) Frequency Modulated Continuous Wave (FMCW) C-Band radar system named Soprano. The objective of this analysis was to classify whether an individual was carrying an item in both hands or not using micro-Doppler information from a FMCW sensor. The radar was deployed at a standoff distance, of approximately 0.5 m, outside a residential building and used to detect multiple people walking within a room. Through the application of digital filtering, it was shown that significant suppression of the primary wall reflection is possible, significantly enhancing the target signal to clutter ratio. Singular Value Decomposition (SVD) signal processing techniques were then applied to the micro-Doppler signatures from different individuals. Features from the SVD information have been used to classify whether the person was carrying an item or walking free handed. Excellent performance of the classifier was achieved in this challenging scenario with accuracies up to 94%, suggesting that future through wall radar sensors may have the ability to reliably recognize many different types of activities in TTW scenarios using these techniques.

Bicyclic peptides have attracted the interest of pharmaceutical companies because of their remarkable properties putting them on a new path in medicine. Their conformational rigidity that improves proteolytic stability, leads to rapid penetration into tissues via any possible route of administration and elimination, occurring by renal metabolism, is of great importance for people with a history of liver diseases. In addition, each ring can function independently, making them extremely versatile molecules for further optimization. In this paper we compared the potentiometric and spectroscopic properties studied by UV-Vis, MCD, and EPR, of four synthetic analogues of the bi-cyclic peptide c(PKKHP-c(CFWKTC)-PKKH). In particular we correlated the structural and spectral properties of complexes with coordinating abilities toward Cu(II) ions of MCL (Ac-PKKHPc(CFWKTC)PKKH-NH2) that contains the unbinding cycle and N- and C-terminal linear parts, with two histidine residues, one per part; two monocyclic ligands containing one histidine residue, both in the N-terminal position i.e., MCL2 (Ac-PKKHPc(CFWKTC)PKKS-NH2) and in the C-terminal position i.e., MCL3 (Ac-PKKSPc(CFWKTC)PKKH-NH2), respectively, and the linear structure LNL (Ac-PKKHPSFWKTSPKKH-NH2).

The factors that determine the relative rates of amino acid substitution during protein evolution are complex and they are known to vary among taxa. We estimated relative exchangeabilities for pairs of amino acids from clades spread across the tree of life and assessed the historical signal in the distances among these clade-specific models. We trained these models separately on collections of arbitrarily selected protein alignments and on ribosomal protein alignments. In both cases we found a clear separation between the models trained using multiple sequence alignments from bacterial clades and the models trained on archaeal and eukaryotic data. We assessed the predictive power of our novel clade-specific models of sequence evolution by asking whether fit to the models could be used to identify the source of multiple sequence alignments. Model fit was generally able to classify protein alignments correctly at the level of domain (bacterial versus archaeal), but the accuracy of classification at finer scales was much lower. The only exceptions to this were the relatively high classification accuracy for two archaeal lineages: Halobacteriaceae and Thermoprotei. Genomic GC content had a modest impact on relative exchangeabilities despite having a large impact on amino acid frequencies. Relative exchangeabilities involving aromatic residues exhibited the largest differences among models. There were a small number of exchangeabilities that exhibited large differences in comparisons among major clades and between generalized models and ribosomal protein models. Taken as a whole, these results reveal that a small number of relative exchangeabilities are responsible for much of the structure of the “model space” for protein sequence evolution. If we look beyond the information that these clade-specific models reveal about protein evolution the models themselves are likely to be useful tools for phylogenomic inference across the tree of life.

The paper presents a new conception of quasi-distributed sensor for simultaneous measurement of several physical fields and the results of an experimental study of this sensor. A distinctive feature of the sensor defined by the sensitive RC elements connected in the original tree-like structure. The proposed is the structure of the sensor and measurement system as well as corresponding measurement algorithm. The high accuracy demonstrated by the sensor’s prototype gives possibility to effective use the proposed sensors in many technical and scientific applications.

Earthworms and soil microorganisms contribute to soil health, quality and fertility, but their importance in agricultural soils is often underestimated. This study aims at examining whether and to what extent the presence of earthworms [Eisenia fetida (Savigny, 1826)] affected the a) soil bacterial community composition, b) litter decomposition, and c) plant growth (Brassica oleracea L., broccoli; Vicia faba L., faba bean). We performed a mesocosm experiment in which plants were grown outdoors for four months with or without earthworms. Soil bacterial community structure was evaluated by a 16S rRNA-based metabarcoding approach. Litter decomposition rates were determined by using the tea bag index (TBI) and litter bags (olive residues). Earthworm number almost doubled throughout the experimental period. Independently of the plant species, earthworm presence had a significant impact on the structure of soil bacterial communities, in terms of enhanced α- and β-diversity (especially that of Proteobacteria, Bacteroidota, Myxococcota, and Verrucomicrobia) and increased 16S rRNA gene abundance (+89% in broccoli and +223% in faba bean). Microbial decomposition (TBI) was enhanced in the treatments with earthworms, and showed a significantly higher decomposition rate constant (kTBI) and a lower stabilization factor (STBI), whereas decomposition in the litter bags (dlitter) increased by about 6% in broccoli and 5% in faba bean. Earthworms significantly enhanced root growth (in terms of total length and fresh weight) of both the plant species. Our results show the strong influence of earthworms and crop identity in shaping soil bacterial communities, litter decomposition and plant growth. These findings could be used for developing nature-based solutions that ensure the long-term biological sustainability of soil agro- and natural ecosystems.

Structural health monitoring has been studied by a number of researchers as well as various industries to keep up with the increasing demand for preventive maintenance routines. This work presents a novel method for reconstruct prompt, informed strain/stress responses at the hot spots of the structures based on strain measurements at remote locations. The structural responses measured from usage monitoring system at available locations are decomposed into modal responses using empirical mode decomposition. Transformation equations based on finite element modeling are derived to extrapolate the modal responses from the measured locations to critical locations where direct sensor measurements are not available. Then, two numerical examples (a two-span beam and a 19956-degree of freedom simplified airfoil) are used to demonstrate the overall reconstruction method. Finally, the present work investigates the effectiveness and accuracy of the method through a set of experiments conducted on an aluminium alloy cantilever beam commonly used in air vehicle and spacecraft. The experiments collect the vibration strain signals of the beam via optical fiber sensors. Reconstruction results are compared with theoretical solutions and a detailed error analysis is also provided.

Cancer is fundamentally a disease of perturbed genes. Although many mutations can be marked in the genome of a cancer or transformed cell, the initiation and progression were shown to be driven by only a few mutational events viz. driver mutations that progressively govern and execute the functional impacts. The driver mutations are thus believed to dictate and dysregulate the subsequent cellular proliferative function/decisions thereby producing a cancerous state. Therefore, identifying the driver events from the genomic alterations in a patient’s cancer cell gained large attention recently for designing better targeting therapies towards paving way for the precision cancer medicine. With rolling advancements in high-throughput omics technologies, analysis of genetic variations and gene expression profiles for cancer patients has become a routine clinical practice. However, it is anticipated that protein structural alterations resulting from such driver mutations can provide more direct and clinically relevant evidence of disease states than genetic signatures alone. This review comprehensively discusses various aspects and approaches that have been developed for the prediction of cancer drivers using genetic signatures and protein structures, and their potential application in developing precision cancer therapies.Keywords:

Spodoptera frugiperda (J.E. Smith) is a global agricultural pest that poses a threat to crop production, characterized by its refractory polyphagous nature that makes it difficult to control and may lead to damage to woody plants. However, research on its adaptability to woody plants remains limited. This study compares the feeding adaptations (survival rate, pupation time, pupation rate, weight, length, and feeding volume), protective enzyme activities, and feeding preferences of S. frugiperda on leaves of six economically significant tree species (Areca catechu, Aquilaria sinensis, Cocos nucifera, Camellia oleifera, Dalbergia odorifera and Hevea brasiliensis) and maize as a control treatment. The results indicate that A. sinensis as the most vulnerable trees in high risk, H. brasiliensis and C. nucifera presented varying degrees of susceptibility, A. catechu, C. oleifera, and D. odorifera were unsuitability for S. frugiperda. In conclusion, this report extensively explores the feeding effects of S. frugiperda on six economically important tree species, and provides insights into the feeding preferences on these plants, thereby informing the potential threat posed by S. frugiperda to economically vital trees.

A key step in the study of tree pathology is the identification of appropriate method for inoculating pathogens of diseases in branch and trunk. Pathogens of diseases in branch and trunk are commonly inoculated through punching, burning, and toothpick inoculation. However, there is a lack of comparative analysis of the inoculation outcomes of these three methods. In this work, Six‐year‐old P. alba var. pyramidalis were inoculated with V. sordida, using punching, burning, and toothpick techniques, respectively, to investigate the differences in the effectiveness of these inoculation methods. Results reveal that the incidence rate was 93.55% in the toothpick inoculation group, significantly higher than 80.65% in the burning inoculation group (p = 0.007), while punching inoculation exhibited significant pathological responses in the early stages, with spontaneous healing in the later stage. Addi-tionally, toothpick inoculation was more efficient in inducing Valsa canker when inoculating the pathogen at the bottom of the tree, with lower intra‐ and inter‐row spacing (stand density) providing better outcomes than higher intra‐ and inter‐row spacing. The results of this study demonstrate that toothpick inoculation is an optimal option for studying the artificial inoculation of V. sordida in six‐year‐old P. alba var. pyramidalis, providing technical support for research on poplar diseases and offering a theoretical basis for the inoculation of other diseases in branch and trunk.

Recent advancements in artificial intelligence (AI) and deep learning have revolutionized the field of protein engineering, particularly in the area of de novo protein design. This review article explores the impact of AI-driven approaches on protein design, with a specific focus on the role of structure prediction neural networks, such as AlphaFold and RoseTTAFold. The article discusses the paradigm shift brought about by these networks, which have enabled the design of proteins with unique structures and functions that are not found in nature. The review covers various aspects of AI-driven protein design, including the use of protein language models to harness evolutionary information, the development of de novo protein design workflows utilizing deep learning, and the application of generative models like RFdiffusion and RoseTTAFold All-Atom. The article also highlights the successes and applications of AI-driven protein design across diverse domains, such as enzyme engineering, antibody design, and vaccine development. Additionally, the review identifies current challenges and future directions in the field, emphasizing the need to address limitations in modeling conformational dynamics and designing proteins for in vivo functionality. The article concludes by underscoring the potential of AI-driven protein design to transform various aspects of science and technology, while also acknowledging the importance of interdisciplinary collaboration and the development of robust pipelines for the validation and optimization of designed proteins. Overall, this comprehensive review serves as a valuable resource for researchers and practitioners interested in understanding the current state and future prospects of AI-driven protein design.

Precise individual tree or sample-based inventories derived from 3D point cloud data of mobile laser scanning can improve our comprehensive understanding of the structure, function, resilience, biodiversity, and ecosystem services of urban forests. This study assessed the performance of a hand-held laser scanning system for the extraction of tree position, diameter at breast height (DBH) and tree height (H) in an urban area. A total of 2083 trees of 13 species from 34 plots were analyzed. The results showed that the registration of tree positions using ground control points (GCPs) demonstrated high accuracy, with errors consistently below 0.4 m, except for a few instances. The extraction accuracy of DBH for all trees and individual species remained consistently high, with a total root mean square error (RMSE) of 2.06 cm (6.89%) and a bias of 0.62 cm (2.07%). Notably, broad-leaved trees outperformed coniferous trees, with RMSE and bias values of 1.86 cm (6%) and 0.76 cm (2.46%) compared to 2.54 cm (9.46%) and 0.23 cm (0.84%). Tree height extraction accuracy varied significantly among different species, with R2 values ranging from 0.65 to 0.92. Generally, both DBH and height were underestimated. Linear mixed effects models (LME) were applied to evaluate factors affecting the performance of HLS with the plot as a random factor. LME analysis revealed that plant type and terrain significantly influenced the accuracy of DBH and H derived from HLS data. Other fixed factors of plot area, tree density and trajectory length didn’t have significance. With a large sample size, we concluded that the HLS demonstrated sufficient accuracy in extracting individual tree parameters in urban forests.

Iberian holm oak meadows are savannah-like ecosystems that result from traditional silvo pastoral practices. However, such traditional uses are declining, driving changes in the typical tree – open grassland structure of these systems. Yet, there are no studies integrating the whole ecosystem — including the arboreal and the herbaceous layer — as drivers of greenhouse gas (GHG: CO2, CH4 and N2O) dynamics. Here we aim at integrating the influence of tree canopies and interactions among plant functional types (PFT: grasses, forbs, and legumes) of the herbaceous layer as GHG exchange drivers. For that purpose, we performed chamber based GHG surveys in plots dominated by representative canopy types of Iberian holm oak meadows, including Quercus species and Pinus pinea stands, the last a common tree plantation replacing traditional stands; and unravelled GHG drivers through a diversity interaction model approach. Our results show that the tree – open grassland structure especially drove CO2 and N2O fluxes, with higher emissions under the canopy than in the open grassland. Emissions under P. pinea canopies being higher than those under Quercus species. In addition, the inclusion of diversity and compositional terms of the herbaceous layer improve the explained variability, legumes enhancing CO2 uptake and N2O emissions. Changes in the tree cover and tree species composition, in combination with changes in the structure and composition of the herbaceous layer, will imply deep changes in the GHG exchange of Iberian holm oak meadows. These results may provide some guidelines to perform better management strategies of this vast but vulnerable ecosystem.

In contemporary construction, the prevalence of vibration serviceability issues in lightweight and slender structures has become increasingly common, owing to advancements in building materials and construction methods. While these structures often meet the criteria for ultimate limit states, they can still elicit complaints due to excessive vibrations induced by human activity. To address this challenge, the Integral Resonant Control (IRC) technique has emerged as a favored approach for actively damping vibrations in various systems. This study introduces a fresh perspective on implementing a multi-input multi-output (MIMO) IRC scheme for active vibration control (AVC) specifically tailored for pedestrian structures utilizing inertial mass actuators. Building upon a common framework and design methodology outlined in previous research, this work presents a novel application of MIMO IRC for AVC. The designed controller is rigorously tested and implemented on a laboratory floor structure to validate its efficacy.

By using the particle swarm optimization algorithm for crystal structure prediction, we reveal a newly orthorhombic Cmcm structure of HfB4, which is more energetically superior to the previously proposed YB4-, ReP4-, FeB4-, CrB4-, and MnB4-type structures in the considered pressure range. The phonon dispersion and elastic constants calculations confirm that the new phase is dynamically and mechanically stable. The calculated large shear modulus (240 GPa) and high hardness (45.7 GPa) imply that the predicted Cmcm-HfB4 is a potential superhard material. Meanwhile, the directional dependences of the Young's modulus, bulk modulus, and shear modulus for HfB4 are systematically investigated. Further analyses of the density of states and electronic localization function indicate that the strong B-B and B-Hf covalent bonds greatly contribute to its high hardness and stability.

Modularity and organizational hierarchy are important concepts in understanding the structure and evolution of interactions in complex biological systems. In this work, we introduce and use a spectral characterization measure (Spectral Entropy) to quantify modularity in protein-to-protein interaction (PPI) networks in species across the tree of life. We evaluated the relation between the size of a PPI network and its (Spectral Entropy-based) modularity, and found a sigmoidal response between the two. We also found significant differences in the distribution of Spectral Entropy values among the three domains of life (Bacteria, Archaea, Eukaryotes). To explore further correlations with biological traits, we focused solely on bacterial PPI networks, which are the most numerous among the three domains and had associated trait metadata, and investigated how modularity impacts or is impacted by growth, aerobicity, selection and location on the tree of life. We found no relation between maximal growth rate and Spectral Entropy, but a strong dependence between G-C content (a proxy for selection) and Spectral Entropy. We also discovered that Spectral Entropy is negatively affected by phylogenetic placement (evolutionary distance from the last universal common ancestor). The general nature of the Spectral Entropy measure of hierarchical modularity in networks suggests that it will be useful in other settings where structural properties of real-world networks are being compared.

We investigate and discuss in detail the structure of the restricted singular value decomposition for a tensor triplet under t-product (T-RSVD). The algorithm is provided with a numerical example illustrating the main result. For applications, we consider color image watermarking processing with T-RSVD.

It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.

To date, Cartesian (x, y, z) coordinate system (CCS) has been the default approach to geometrically specify atomic spatial positions in protein structures since the launch of Protein Data Bank (PDB) in 1971. To this end, this paper proposes a local spherical coordinate system (SCS) approach as an alternative to the default approach and a previously reported global SCS approach. The local SCS approach here requires only two parameters (θ and φ), instead of x, y and z as required by the default CCS approach. Essentially, CCS and SCS are like the two sides of one coin, i.e., geometric coordinate system for three-dimensional position specification. Therefore, this paper furthermore argues that it is time to flip the coin over, and have a look at the other side of the coin, e.g., the local SCS approach, which possesses an intrinsically lower degree of descriptional complexity than that of the default CCS approach, and constitutes a potentially useful alternative perspective for all protein structural research field.

Timely and accurate information on tree species is crucial for the sustainable management of natural resources, forest inventory, biodiversity detection, and carbon stock calculation. The advancement of remote sensing technology and artificial intelligence has facilitated the acquisition and analysis of remote sensing data, resulting in more precise and effective classification of tree species. Multimodal remote sensing data and deep learning seem to be the current tree species classification research mainstream, whether or not. The current review on the remote sensing data and deep learning tree species classification methods perspectives to analyze the unimodal and multimodal remote sensing data and classification methods in this realm is missing. To bridge the gap, we search for major trends in the remote sensing data and tree species classification methods, provide a detailed overview of classic deep learning-based methods for tree species classification, and discuss the limitations.

In this paper, a new axial-type magnetic gear with auxiliary flux-enhancing structure (AFS-AMG) is proposed. Compared to conventional AFS-AMG, it has the higher torque density and higher permanent magnet (PM) utilization factor. Firstly, the design rules and operating principles of proposed AFS-AMG are elaborated. Then, the mapping relation between the radial-type magnetic gears (RMGs) and AMGs are elucidated. Compared to its counterpart in RMGs, AFS-AMGs achieve small size. Then, the geometrical parameters of AFS-AMGs are optimized to obtain the better electromagnetic performances, where the torque density per volume and per PM volume is adopted as the evaluation standard. Finally, three different AMG topologies are constructed in finite element analysis (FEA) software for comparison. It is proven that the AFS-AMG has the largest torque density per volume and per PM volume.

The SK model proposed by Sherrington and Kirkpatrick is an important mean field model for spin glasses. The dependence structure of Hamiltonians of the SK model is considered in this paper. We have investigated the covariance matrix of Hamiltonians of the SK model, and establish a relationship between the rank of the corresponding covariance matrix and the dimension of the space spanned by the Hamiltonians. Finally, we also give an upper bound for the rank of the covariance matrix, which might be the best.

This review deals with the adaptive mechanisms that plants can implement to cope with the challenge of salt stress. Plants tolerant to NaCl implement a series of adaptations to acclimate to salinity, including morphological, physiological and biochemical changes. These changes include increases in the root/canopy ratio and in the chlorophyll content in addition to changes in the leaf anatomy that ultimately lead to preventing leaf ion toxicity, thus maintaining the water status in order to limit water loss and protect the photosynthesis process. Furthermore, we deal with the effect of salt stress on photosynthesis and chlorophyll fluorescence and some of the mechanisms thought to protect the photosynthetic machinery, including the xanthophyll cycle, photorespiration pathway and water-water cycle. Finally, we also provide an updated discussion on salt-induced oxidative stress at the subcellular level and its effect on the antioxidant machinery in both salt-tolerant and salt-sensitive plants. The aim is to extend our understanding of how salinity may affect the physiological characteristics of plants.

This study extends the CGAN-based MODIS cloud vertical-profile (64×64-scene, about 70km width×15km height) retrieval technique developed by Leinonen et al. (2019) [1] to construct seamless 3D cloud fields for the MODIS granules [2]. Firstly, the accuracy and spatial continuity of the Leinonen et al. [1] retrievals are statistically evaluated. Then, according to the characteristics of the retrieval error, a spatially overlapping-scene ensemble generation method and a bi-directional Ensemble Binning Probability Fusion (CGAN-BEBPF) technique are developed, which improves the CGAN retrieval accuracy and support to construct seamless 3D clouds. The CGAN-BEBPF technique involves three steps: cloud masking, intensity scaling, and optimal value selection. It ensures adequate coverage of the low reflectivity areas while preserving the high reflectivity cloud cores. The technique is applied to retrieve the 3D cloud fields of Typhoon Chaba and a multi-cell convective system. The cloud structures of the CGAN-BEBPF results are highly consistent with the ground-based radar observations. It can retrieve weak clouds at the top levels of convective storms and hurricanes that were missed by ground-based radars and fill the gaps of the ground-based radar lower-level PPI scan. Overall, CGAN-BEBPF can be automated to retrieve the rich informative 3D structures of typhoons and severe convective systems over the oceans along the MODIS swath, which certainly presents great value for improving maritime and near-shore typhoons and convection prediction and other cloud-sensitive applications.

Analysis of non-stationary and nonlinear sound signals obtained from dynamical processes is one of the greatest challenges in signal processing. Turning machine operation is a highly dynamic process persuaded by many events such as dynamical responses, chip formations and operational conditions of machining. Traditional and widely used fast Fourier transformation and spectrogram is not suitable for processing sound signals acquired from dynamical systems as its result have significant deficiencies because of stationary assumptions and having priori basis. The relatively new technique, Discrete Wavelet Transform, which uses Wavelet decomposition and the recently developed technique, Hilbert Huang Transform (HHT) which uses Empirical Mode Decomposition have notably better properties in the analysis of nonlinear and non-stationary sound signals. This paper presents a comparative study on the decomposition of multicomponent sound signals using Empirical Mode Decomposition and Wavelet Decomposition to highlight the suitability found in HHT to analyze tool-emitted sound signals received from turning processes. Apart from the short mathematical and theoretical foundations of the transformations, this paper demonstrates their decomposition strength using an experimental case study of tool flank wear monitoring in turning. It also concludes HHT is more suitable than DWT to analyze tool-emitted sound signals received from turning processes.

Long-term, multi-decade research on planted tree survival in urban settings is sparse. One understudied urban environment is highway rights-of-way (ROW), lands adjacent to high-speed, unsignalized roadways. We conducted a re-inventory of tree planting cohort in northern Illinois, U.S. on a 48 km-long highway near Chicago which were 10-, 21-, and 30-years old to evaluate long-term patterns of survival and diversity. Using each randomly selected planting site along the highway as a unit of observation and analysis, we compared the number of trees documented in record drawing to the number of trees currently alive to determine percent survival. We evaluated 224 planting sites which originally contained 2,944 trees and collected data about the planting site location. For the oldest cohort, 26% of trees were still alive in 2018 (median survival by species = 16%, Q1 = 0%, Q3 = 48%), while 31% of the 21-year-old cohort (med. = 6%, Q1 = 0%, Q3 = 47%) and 86% of the 10-year-old cohort were still alive (med. = 85%, Q1 = 74%, Q3 = 96%). The survival of the 21- and 30-year-old cohort matches urban tree survival estimates by other researchers, while the 10-year-old survival is higher than expected. The only planting location characteristic that significantly affected survival was traffic islands (areas between the highway and entrance/exit ramps). Species with low drought tolerance were less likely to be alive for the 10-year-old cohort. Waterlogging tolerant species were more likely to be alive in the 10-year-old cohort. Since some species in the 21- and 30-year-old cohorts had very low survival, the tree species richness and diversity s in study areas declined between the initial record drawings and reinventory. This study demonstrates the challenges of maintaining long-term survival and diversity in the highway ROW and emphasizes the importance of species selection.

The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made fighting of the COVID-19 pandemic is a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in the lung tissues. Mutations and co-mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, We highlight 128 single mutations and 35 co-mutations in the unique SARS-CoV-2 ORF10 variants in this article. The possible predicted effects of these mutations and co-mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.

The oncogenic potential of high-risk HPVs is focused on producing the E6 and E7 oncoproteins responsible for disrupting the control of the cell cycle. Epidemiological studies propose the presence of the N29S and H51N variants of the HPV16 E7 protein as a significant association with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains unknown. Analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose for the first time a 3D structure of the E7 reference protein and two of its variants (N29S and H51N) and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

The attitude dynamics and orbit dynamics of large rigid space structures are coupled with each other under gravity gradient, which may affect the stability of the large rigid space structures. In this paper, the gravity gradient stability of a large rigid space structure is studied under both small and large disturbances. Based on the rigid body dynamics and orbit dynamics, an accurate dynamic model without any linearization of the large rigid space structure is established via the natural coordinate formulation (NCF), which is able to describe the large overall motions of the structures. By using the generalized-α algorithm, the gravity gradient stability of the large rigid space structure is simulated and analyzed via various examples, including the influence of large disturbance angles, the positions at the stabilization and unstabilization regions. Finally, the relationship between spinning stability and gravity gradient stability is also investigated via a large spinning space structure.

Floral nectar is a key reward in Leguminosae despite the exceptional diversity of flowers in this family. The paper aims to summarize the available data on structure, ontogeny, regulation, and possible evolution of the leguminous floral nectaries. To date, detailed characterization of ultrastructure and mode of secretion is available only for a few representative of the family whereas the majority remains understudied from this perspective. In most cases, regardless of flower symmetry, nectaries are localized between stamens and a carpel. The nectar is usually exuded from modified stomata although the exact mode of secretion by specialized parenchyma may differ between taxa. The leguminous floral nectaries often have certain features of monosymmetry with preferentially abaxial development. Nectaries were independently lost in several lineages, and equally recurrent is the emergence of substitutive, i.e. evolutionary innovative, nectar-producing structures. Floral nectaries possess a certain degree of evolutionary inertia, i.e. they remain stable even in lineages in which flower morphology underwent significant changes compared with an ancestral plan, such as shifts in merism, symmetry, organ number and alike. Due to their evolutionary stability, floral nectaries are rarely used in taxonomy of Leguminosae.

Protein is the proteios building block of life. Evolutionarily, its sequence is not as conserved as its structure, making it more reasonable for protein structure, instead of protein sequence, to be the descriptor of protein function. Yet, in the National Center for Biotechnology Information (NCBI) database, the number of experimentally identified protein sequences is in great excess of that of experimentally determined protein structures inside the almost-half-a-century old Protein Data Bank (PDB). For instance, GPR151 is an proton-sensing G-protein coupled receptor (GPCR) originally identified as homologous to galanin receptors. As of March 19, 2020, GPR151’s structure has not been experimentally determined and deposited in PDB yet. Thus, an ab initio modelling approach was employed here to build a three-dimensional structure of GPR151. Overall, the ab initio GPR151 model presented herein constitutes the first structural hypothesis of GPR151 to be experimentally tested in future with previously published, currently ongoing and future GPR151 studies.

The present work investigates primarily the morphology evolution of the body-centered-cubic (BCC)/B2 phases in AlxNiCoFeCr high-entropy alloys (HEAs) with increasing Al content, which has been neglected so far. There exist two types of microscopic morphologies of BCC and B2 phases in this HEA series: one is the weave-like morphology induced by the spinodal decomposition, and the other is the microstructure of a spherical disordered BCC precipitation on the ordered B2 matrix that appears in HEAs with a much higher Al content. The shape of coherent precipitates is found to be closely related to the lattice misfit between BCC and B2 phases, which is sensitive to Al. The mechanical properties, including the compressive yielding strength and microhardness of the AlxNiCoFeCr HEAs, are also discussed in light of the concept of the valence electron concentration (VEC).

The use of unmanned aerial aircrafts (UAVs) is governed by strict regulatory frameworks that prioritize safety. To guarantee safety, it is necessary to acquire and maintain situational awareness (SA) throughout the operation. Existing Canadian regulations require pilots to operate their aircrafts in visual line-of-sight. Therefore, the task of acquiring and maintaining SA primary falls to the pilots. However, the development of aerial transport is entering a new era with the adoption of a highly dynamic and complex system known as advanced air mobility (AAM), which involves UAV operating autonomously beyond visual line-of-sight. SA must therefore be acquired and maintained primarily by each UAV through specific technologies and procedures. In this paper, we review these technologies and procedures in order to decompose the SA of the UAV in the AAM. We then use the system modeling language to provide a high-level structural and behavioral representation of the AAM as a system having UAV as its main entity. In a case study, we analyze one of the flagships UAVs of our industrial partner. Results show that this UAV doesn’t have all the technologies and methodologies necessary to achieve all the identified SA goals identified for the safety of the AAM. This work is a theoretical framework intended to contribute to the realization of the AAM, and we also expect to impact the future design and utilization of UAVs.

The p53 tumor suppressor protein shows antiviral activity. The replication of viruses is also antagonized by interferons (IFNs) – cytokines, which control immunity genes by the STAT transcription factors. The best studied interferons belong to type I (e.g. IFNα) and type II (IFNγ) groups. IFNα and IFNγ both induce activating phosphorylation of STAT1 on Tyr701. Previously, we noticed that p53 activates SOCS1, which is a negative regulator of STAT1 phosphorylation. Thus, we hypothesized that p53 by activating SOCS1 expression reduces phosphorylation of STAT1 and attenuates activation of genes stimulated either by IFNα or IFNγ. To test this hypothesis, we exposed p53-proficient and p53-deficient cells to strong p53 activators, and either to IFNα or IFNγ. Subsequently, we estimated the phosphorylation status of STAT1 and the expression of genes regulated by either of these cytokines. Strong activation of p53 reduced the phosphorylation of STAT1 on Tyr701, however surprisingly it did not lead to reduced expression of most tested interferon-stimulated genes. On contrary, p53 and IFNγ synergized in the activation of CASP1, IFIT1 and IFIT3 genes. We conclude that the interactions between p53 and interferon-activated pathways are more complicated than initially expected, but the apparent cooperation between p53 and IFNγ deserves further studies.

Lignin is insoluble in water, limiting its use in the synthesis of adhesives. Therefore, in order to increase the amount of lignin raw materials used in the synthesis of adhesives, a kind of aminated lignin compounds was prepared through lignin amination reaction, and conducting structural analysis in this paper. The particle size of the amino lignin is about 100 nm, with the weight average molecular weight of 57,627 g/mol and a water solubility of 0.45g/100ml. The reaction mechanisms were proposed that the phenolic hydroxyl groups of lignin react with ammonia molecules, and thereby successfully introducing amino groups to generate the aminated lignin compounds. Therefore, this article enriches the scientific theory of lignin reactions and provides reference for the widespread application of lignin raw materials in the field of adhesives.

Tree biomass and diversity relationship in mixed forest impacts on forest ecosystem services provisions. Tree biomass yield is driven by several aspects such as species identity, site condition, stand density, tree age as well as tree diversity expressed as species mingling and structural diversity. By comparing diverse degrees of tree mixture in natural forests we can insight on the ecosystem services provision level and dynamic. Two monitoring sites in the Castilian Northern Plateau (Spain) have been analyzed to disentangle the relationships between biodiversity levels and tree biomass yield. Two permanent one ha squared plots were established at Llano de San Marugan and Valdepoza. In each plot all individual trees were measured (diameter and height), georeferenced and its species identity defined. Tree species in the two sites were Pinus sylvestris, Pinus nigra, Pinus pinea, Quercus pyrenaica, Quercus ilex, Quercus faginea and Juniperus thurifera. From these datasets ten diversity indices that fall in three categories (species richness indices, species compositional/mingling indices and vertical structural indices) were used as predictor variables to fit several candidate models. By merging the trees by site (without considering the species identity) selected models include individual tree basal area as explanatory variable combining by addition or interaction with diversity indices. When species are analyzed independently structural diversity impacts on biomass yield in combination (additive or multiplicative) with tree size is negative Pinus nigra and positive for the other species.

The advancement in science and technology has led to luffa sponge (LS) being widely used as a natural material in industrial application as its polyporous structure and light texture. In order to enhance the utility of LS fibers as the reinforcement of lightweight composite materials, this study investigate its water absorption, mechanical properties, anatomical characteristic and thermal performance. Hence, moisture regain, tensile properties of LS fiber bundles were measured in accordance with standards and the structural characteristics were investigated via microscopic observation. Scanning electron microscopy (SEM) was used to observe the surface morphology and fracture surface of fiber bundles. Test results shows that the special structure where the phloem tissues degenerate to cavities had a significant influence on the mechanical properties of LS fiber bundles. Additionally, the transverse sectional area occupied by fibers in a fiber bundle (SF), wall thickness and ratio of wall to lumen of fiber cell, and crystallinity of cellulose had an impact on the mechanical properties of LS fiber bundles. Furthermore, the fiber bundles density of LS varies range of 385.46-468.70 kg/m³, much less than that of jute (1360.40 kg/m³) and Arenga engleri (950.20 kg/m³) while LS fiber bundles has superior specific modulus.

In this study we have investigated the effect of the addition of Nb2O5 (up to 5 mol%) on the structure and luminescent properties of ZnO-B2O3 glass doped with 0.5 mol % Eu2O3 by using of infrared (IR), Raman and photoluminescence (PL) spectroscopy. Physical properties as molar volume, oxygen packing density and glass transition temperature were determined using the results of differential thermal analyisis (DTA) and Archimedes principle for density. IR and Raman spectra revealed that niobium ions incorporate into the base zinc borate glass as NbO4 trtraherda and NbO6 octahedra. A strong red emission from the 5D0 level of Eu3+ ions was registered under near UV (392 nm) excitation using the sharp 7F0 - 5L6 transition of Eu3+. The integrated fluorescence intensity ratio R (5D0 → 7F2/5D0 → 7F1) was calculated to estimate the degree of asymmetry around the active ion, suggesting a location of Eu3+ in non-centrosymmetric sites. The higher Еu3+ luminescence emission observed in zinc borate glasses containing 1÷5 mol% Nb2O5 compared to the Nb2O5-free zinc borate glass evidences that Nb2O5 is suitable component for modification of host glass structure and improving the emission intensity.

In recent decades, the requirements for implantable medical devices increased, but the risks of implant rejection still exist. These issues are primarily associated with poor osseointegration, leading to biofilm formation on the implant surface. This study focuses on addressing these issues by developing a biomaterial for implant coatings. 45S5 Bioglass has been widely used in tissue engineering due to its ability to form a hydroxyapatite layer, ensuring a strong bond between the hard tissue and the bioglass. In this context, 45S5 bioglasses, modified by the incorporation of different amounts of copper oxide, from 0 to 8 mol%, were synthesized by the melt-quenching technique. The incorporation of Cu ions does not show a significant change in the glass structure. Since the bioglass exhibited the capacity of being polarized, and therefore promoting the osseointegration effectiveness, the electrical properties of the prepared samples were studied using the impedance spectroscopy method, in the frequency range of 102-106 Hz and temperature range of 200-400 K. The effects of CuO on charge transport mobility were investigated. Additionally, the bioactivity of the modified bioglasses was evaluated through immersion tests in simulated body fluid. The results revealed the initiation of a Ca-P-rich layer formation on the surface within 24 h, indicating the potential of the bioglasses to enhance the bone regeneration process.

Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy lidar (PCL) and ground penetrating radar (GPR) along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence at multiple spatial scales ≤ 10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more evenly distributed by height and depth, respectively, as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5-4 meters, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Our study highlights the potential, and limitations, for fusing lidar and radar technologies to quantitatively couple above- and belowground ecosystem structure.

Calcineurin B-like proteins (CBL)-interacting protein kinases (CIPKs) by interacting with CBLs regulate developmental processes, hormone signalling transduction and mediate stress responses in plants. Although the genome of chickpea is available, information of CIPK gene family has been missing in chickpea. Here, a total of 22 CIPK encoding genes were identified in chickpea and characterized by in silico methods. We found a high structural conservation in chickpea CIPK family. Our analysis showed that chickpea CIPKs have evolved with dicots from common ancestors, and extensive gene duplication events have played an important role in evolution and expansion of CIPK family in chickpea. Most chickpea CIPK proteins localize in cytoplasm and nucleus. Promoter analysis revealed various cis-regulatory elements related to plant development, hormone signaling and abiotic stresses. Expression analysis indicated that CIPKs are significantly expressed in a spectrum of developmental stages, tissue/organs that hinted their important role in plant development. Several CIPK genes had specific and overlapping expressions in different abiotic stresses and seed development stages, suggesting the important role of CIPK family in abiotic stress signaling, and seed development in chickpea. Thus, this study provides the avenue for detailed functional characterization of CIPK family in chickpea and other legume crops.

Knowledge is not merely the characteristic of certain pieces of information being deemed true and justifiable, but rather a process. Within an axiomatic system, the set of information that reaches the status of knowledge forms a universe that provides an interpretation of the reality one aims to describe. Language exchanges information through communication and the process of justification (exchange of information), if it consistently justifies a particular piece of information, it elevates it to knowledge. In this paper, we provide a framework for knowledge within an axiomatic model where we define the fundamental elements of communication and grammar. As a result, the structure dictates that knowledge, to be considered as such, must be investigateable by anyone who utilizes it in its entirety, both in form and content. Ultimately, the development of knowledge processing, referred to as \emph{knowmatics}, represents a clear evolution of the computer science that processes information (subset of knowledge).

The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them appropriately in biomedical research, such as protein-protein interaction studies, protein design, and drug discovery. With the advent of more accurate protein complex (multimer) prediction tools, such as AlphaFold2-Multimer and ESMFold, the estimation of the accuracy of protein complex structures has attracted increasing attention. Many deep learning methods have been developed to tackle this problem; however, there is a noticeable absence of a comprehensive overview of these methods to facilitate future development. Addressing this gap, we present a review of deep learning EMA methods for protein complex structures developed in the past several years, analyzing their methodologies and impacts. We also provide a prospective summary of some potential new developments for further improving the accuracy of the EMA methods.

A picture is worth a thousand words. Many branches of Science have been historically benefited with plots and visual analyses (lately, image processing and deep learning) alongside with traditional number crunching. In Molecular Biophysics, one such problem is the structure validation problem in proteins which stands with a history of plot-tools being effectively serving the complex problem to its complete resolution. Spanning across six decades, validation of protein structures (from experimental to modeled) dates back to the legendary Ramachandran Plot (with its never ending growth and modern-day applications) to the relatively recent innovation of the Complementarity Plot (CP), establishing the dual nature of complementarity as the physical basis of both binding and folding of proteins. Lately, CP has been extended to serve as a trustworthy free energy predictor utilizing supervised learning in the form of a comprehensive web-server (EnCPdock: https://www.scinetmol.in/EnCPdock/) that can be directly used in the design of protein interfaces. The commentary recapitulate the history of structure validation with a special emphasis on plot tools, highlighting key features and important discoveries worth re-visiting.

Background: This study investigated the biological effects on circulating monocytes after challenge with SARS-CoV-2 recombinant spike protein. Methods: Whole blood collected form seven ostensibly healthy healthcare workers was incubated for 15 min with 2 and 20 ng/mL recombinant spike protein of Ancestral, Alpha, Delta and Omicron variants. Samples were analyzed with Sysmex XN and DI-60 analyzers. Results: Cellular complexity (i.e., presence of granules, vacuoles and other cytoplasmic inclusions) increased in all samples challenged with the recombinant spike protein of Ancestral, Alpha and Delta variants, but not in those containing Omicron. The cellular content of nucleic acids was constantly decreased in most samples, achieving statistical significance in those containing 20 ng/mL of Alpha and Delta recombinant spike proteins. The heterogeneity of monocyte volumes significantly increased in all samples, achieving statistical significance in those containing 20 ng/mL of recombinant spike protein of Ancestral, Alpha and Delta variants. The monocyte morphological abnormalities after spike protein challenge included dysmorphia, granulation, intense vacuolization, platelet phagocytosis, development of aberrant nuclei and cytoplasmic extrusions. Conclusions: The SARS-CoV-2 spike protein triggers important monocyte morphological abnormalities, more evident in cells challenged with spike protein of the more clinically severe Alpha and Delta variants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes are at risk of the disease. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include, membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N) and the spike protein (S). The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein. The M protein of SARS-CoV-2 is 98.6% similar to the M protein of bat SARS-CoV, maintains 98.2% homology with pangolin SARS-CoV, and has 90% homology with M protein of SARS-CoV; whereas, the similarity was only 38% with the M protein of MERS-CoV. In silico analyses showed that the M protein of SARS-CoV-2 has a triple helix bundle, form a single 3-transmembrane domain (TM), and are homologous to the prokaryotic sugar transport protein semiSWEET. SemiSWEETs are related to the PQ-loop family that function as cargo receptors in vesicle transport, mediates movement of basic amino acids across lysosomal membranes, and is also involved in phospholipase flippase function. The advantage and role of the M protein having a sugar transport-like structure is not clearly understood. The M protein of SARS-CoV-2 interacts with S, E and N protein. The S protein of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein influences glycosylation of the S protein. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the semiSWEET sugar transporter-like structure of the M protein may be involved in multiple functions that may aid in the rapid proliferation, replication and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the semiSWEET sugar transporter.

On the primitive Earth, both L- and D-amino acids would have been present. However, only L-amino acids are essential blocks to construct proteins in modern life. To study the relative stability of homochiral and heterochiral peptides, a variety of computational methods were employed. 10 prebiotic amino acids (Gly, Ala, Asp, Glu, Ile, Leu, Pro, Ser, Thr, and Val) were previously determined by multiple previous meteorite, spark discharge, and hydrothermal vent studies. We focused on what had been reported as primary early Earth polypeptide analogs: 1ARK, 1PPT, 1ZFI, and 2LZE. Tripeptide composed of only Asp, Ser, and Val exemplified that different positions (i.e., N-terminus, C-terminus, and middle) made a difference in minimal folding energy of peptides, while the classification of amino acid (hydrophobic, acidic, or hydroxylic) did not show significant difference. Hierarchical cluster analysis for dipeptides with all possible combinations of the proposed 10 prebiotic amino acids and their D-amino acid substituted derivatives generated five clusters. Prebiotic polypeptides were built up to test the significance of molecular fluctuations, secondary structure occupancies, and folding energy differences based on these clusters. Most interestingly, among 129 residues, mutation sensitivity profiles presented that the ratio of more stable to less stable to equally stable D-amino acids was about 1:1:1. In conclusion, some combinations of a mixture of L- and D-amino acids can act as essential building blocks of life. Peptides with α-helices, long β-sheets, and long loops are usually less sensitive to D-amino acid replacements in comparison to short β-sheets.

The relationship between the structure characteristics and performances of coal based hydrogenation isomeric base oil (CTL) and metallocene catalyzed coal based polyalphaolefin (mPAO) base oil was clarified here. CTL and mPAO were compared with typical petroleum based and natural gas based commercial API Class III and IV base oils. Pressurized differential scanning calorimetry (PDSC), Rotary Bomb Oxidation Test (RBOT) and four-balls friction tester were used to evaluate the oxidation stability and lubrication performance of base oils under different working conditions. The sensitivity of different base oils to typical antioxidants and extreme pressure antiwear agents was compared. Specially, the composition and structure of CTL base oil are obviously different from GTL and mineral base oil. The coal-based CTL and mPAO base oils exhibit commendable viscosity-temperature properties, characteristics, coupled with low-temperature fluidity, fire safety, and minimal evaporation loss. The lubricating properties, oxidation stability and the sensitivity to extreme pressure antiwear agents of CTL are close to those of similar base oils. But the sensitivity of CTL to typical antioxidants is relatively poor. Besides, compared with commercial PAO base oil, mPAO has lower isomerization degree and fewer isomerization types. The oxidation stability and sensitivity to typical antioxidants of mPAO base oil are comparable with those of commercial PAO base oil, while its lubrication performance and sensitivity to typical extreme pressure antiwear agents are significantly better than those of commercial PAO base oil.

In this paper, the synthesis of two novel luminescent Eu3+ ion complexes [Eu(TFT)3(phen) (1) and Eu(TFT)3(bpy)•Hex (2)] based on the combination of 2-(2,2,2-trifluoroethyl)-1-tetralone (TFT), containing n-donor ligands (1,10-phenanthroline or 2,2'-Bipyridine) and Eu3+ ion is reported herein, and their structural features are discussed on the basis of X-ray crystallographic and thermal analyses. We observed that the ligands transfer energy effectively to the metal center by fluorescence, IR and UV spectrograms studies. The structures and properties of complexes 1-2 were optimized by the DFT theoretical calculation, and the calculation results were consistent with the experimental X-ray structure data and spectral analysis.

The apicomplexan parasite, Sarcocystis neurona causes the degenerative neurological equine protozoal myeloencephalitis (EPM) disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions such as host cell invasion, cell cycle progression and host immune responses evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. Further, three-dimensional (3D) homology models for selected S. neurona putative PKs were constructed and evaluated for inhibitor docking. We identified 92 putative PKs clustering within the AGC, CAMK, CK1, CMGC, STE, TKL, aPK and OPK groups. Although containing the universally conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC, but contained the six apicomplexan conserved CDPKs (CAMK group). The OPK group was represented by ROPKs 19A, 27, 30, 33, 35 and 37, but was devoid of the virulence-associated ROPKs 5, 6, 18 and 38. Two out of the three S. neurona CK1 enzymes had high sequence similarities to T. gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Docking of four inhibitors onto homology models of putative ROP27 and PKA indicated that inhibition of S. neurona PKs is feasible, but needs to be experimentally tested. The essentiality of apicomplexan PKs makes the elucidation of S. neurona kinome a key milestone for development of novel therapeutics for EPM.

This article introduces a novel payload structure, which has been experimentally proven to have smaller impact force while the carried internal electronics remains intact. The study describes in details how materials and geometric structures were chosen based on information analysis. It is clarified how possible geometric structures and materials can be chosen to yield optimal efficiency. Finite element method simulations were carried out to investigate the mechanical properties of several geometric structures, which has led to the dodecahedron form. For the frame, Polylactic Acid were chosen as an optimal material. A low air pressure test for parts of the structure, and also the whole structure were carried out with successful results. Drop tests, with force measuring sensors and high speed videos, were carried out for measuring and comparing the maximal impact force of classical payloads and the novel one. Laboratory and real life tests demonstrated that the developed new structure is safer and it is applicable.

The criteria of “Distinctness, Uniformity and Stability” as well as a high "overall quality index” are used to register the Italian modern varieties to the national register. Differently, local conservation varieties can be certified under different EU Directives having, as overall objective, the preservation of biodiversity and the containment of genetic erosion. In recent years, products derived from an-cient grains are perceived to be healthier and more sustainable by consumer, especially in Italy, with consequent higher market prices. Ancient tetraploid wheat varieties registered in the national reg-ister of conservation varieties are 28, 24 of which are Sicilian. They are supposed to have a wide genetic variability compared to modern ones, making them vulnerable of fraud because they are difficult to trace. It is therefore important to have tools able to discriminate the autochthonous Si-cilian varieties. This can be done by gluten proteins composition, which also gives information on the technological properties of derived products. Fifty-one accessions belonging to 22 ancient va-rieties of Sicilian tetraploid (mostly durum) wheat were analyzed. Although a wide intra-accession and intra-varietal variability was assessed, the gliadin pattern of bulks of seeds belonging to each variety was discriminatory. Moreover, differences in technological attitudes were found between landraces. This paves the way to use gluten protein patterns for traceability allowing local farmers and producers to valorize their products and assure consumers about the transparency of the entire supply chain.

A new generalized definition of Mersenne numbers is proposed of the form (a^n - (a-1)^n), called Global Generalized Mersenne numbers, or simply Generalized Mersenne numbers and noted GM_{a,n} where a is the base and n is the exponent, both being positive integers. The properties are investigated for prime exponents n and several theorems on Mersenne numbers regarding their congruence properties are generalized and demonstrated. In particular, it is found that, for any base a, Generalized Mersenne numbers are in general such that (GM_{a,n} - 1) are even and divisible by n, a and (a-1) for any odd prime exponent n and by (a(a-1)+1) for any prime exponent n > 5. The remaining factor is a function of triangular numbers of (a-1), specific to each prime exponent n. Four theorems on Mersenne numbers are generalized and four new theorems are demonstrated, allowing to show first, that (GM_{a,n} - 1) are divisible by 6, and more precisely GM_{a,n} are congruent to 1(mod 12) or 7(mod 12) depending on the congruence of the base a(mod 4); second, that (GM_{a,n} - 1) are divisible by 10 if n == 1(mod 4) and, if n == 3(mod 4), GM_{a,n} == 1(mod 10), or 7(mod 10) or 9(mod 10) depending on the congruence of the base a(mod 5); third, that all factors c_{i} of GM_{a,n} are of the form (2nf_{i}+1) with f_{i} natural integers such that c_{i} is prime itself or the product of primes of the form (2nj+1) with j natural integer; fourth, that for odd prime exponents n, all GM_{a,n} are periodically congruent to either +/-1\(mod 8) or +/-3(mod 8) depending on the congruence of the base a(mod 8); and fifth, that the factors of a composite GM_{a,n} is of the form (2nf_{i}+1) with f_{i} == u(mod 4) and u being either 0, 1, 2 or 3 depending on the congruence of the exponent n(mod 4) and on the congruence of the base a(mod 8). The potential use of Generalized Mersenne primes in cryptography is shortly addressed.

Polyurethane is used extensively in the furniture industry, primarily in beds and sofas. There is a significant volume of research pertaining to the flammability of polyurethane materials, but very little regarding smoke toxicity. Given toxic fire effluents are a primary cause of injury and fatalities, more work needs to be done to test the toxicity of polyurethane materials and the fire retardants they are coated/bound with. The aim of the review is to provide a comprehensive analysis of the decomposition of polyurethane and discuss the development and application of modern fire retardants and their effect on smoke toxicity. This work then provides discussion on the challenges faced when attempting to quantify the toxicity of the effluent produced during combustion. Future work should aim to reduce the toxicity and flammability of polyurethane simultaneously by; reducing the pyrolysis of the polymer, preventing the escape of volatile products, reducing radicals within the system and lowering the temperature of the system. Before this can be achieved, a better understanding of smoke toxicity and the ability to test materials is needed.

A set of programs for the numerical simulation of the diffusion decomposition processes was developed by using simulation methods, kinetic and particle method. The complex has been validated on the model system Ni-Al by the growth of -phase separations. The results on the evolution of the distribution function and other characteristics of the ensemble, which in the zero volume fraction approximation are asymptotically in good agreement with the theory and the experiment, have been obtained. The peculiarity of the created program complex is the possibility of its adaptation to the description of the decomposition of multicomponent multiphase systems. Fig. 6, list of references - 19 titles.

The thermal decomposition of brominated butyl rubber under air atmosphere was investigated by thermogravimetry (TG) and derivative thermogravimetry (DTG) at various heating rates. The kinetic parameters were evaluated by TG and the isoconversional method developed by Ozawa. One prominent decomposition stage was observed in the DTG curves at high heating rates while an additional small peak was observed at low heating rates. The apparent activation energy determined using the TG method ranged from 219.31–228.13 kJ·mol-1 at various heating rates. The non-isothermal degradation was found to be a first order reaction, and the activation energy, as determined by the isoconversional method, increased with an increase in mass loss. The kinetic data suggested that brominated butyl rubber had excellent thermal stability. This study will indirectly aid in improving rubber pyrolysis methods and in enhancing the heat resistance of materials.

Urban tree classification is pivotal in urban planning and management, facilitating informed decision-making processes. In this study, we introduce a novel data presentation method termed Pseudo Tree Crown, designed to enhance the accuracy and efficiency of urban tree classification. Leveraging the latest advancements in artificial intelligence (AI), we employ a state-of-the-art classification scheme, PyTorch, to maximize the accuracy of tree classification. Our results demonstrate a robust classification accuracy of over 95% from high spatial resolution imagery from Unmanned Aerial Vehicle (UAV), underscoring our proposed approach’s effectiveness. Moreover, the adaptability of our method renders it applicable to various study areas, highlighting its versatility and potential for widespread implementation in urban planning and management initiatives.

As the most active plateau on the Earth, the Qinghai-Tibet Plateau has a complex crust-mantle structure. Knowledge of the distribution of such a structure provides information for understanding the underlying geodynamic processes. We obtains a three-dimensional density model of crustal and upper mantle beneath Qinghai-Tibet plateau and its surrounding areas from the residual geoid anomalies using the Earth Gravitational Model (EGM) 2008. We estimate a refined density model by iterations, using an initial density contrast model. We confirm that the EGM2008 mission products can be used to constrain the crust-mantle density structures. Our major findings are: (1). At 300-400 km depth, high-D anomalies terminate around Jinsha River Suture (JRS) in the central TP, suggesting that the Indian plate has been reached over the Bangong Nujiang Suture (BNS) and almost reach to the JRS. (2). On the eastern TP, low-D anomalies at the depth of 0-300 km together with high-D anomalies at 400-670 km further verified the current eastward subduction of Indian plate. The ongoing subduction provides forces to the occurrences of frequent earthquakes and volcano. (3). At 600 km depth, low-D anomalies inside the TP illustrate the existence of hot weak material beneath there, contributing to the external material inward-thrusting.

Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer’s disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcel-lular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.

Due to the vast conformational space proteins can adopt, accurate and efficient prediction of protein structure remains still a challenging task, coupled with the intricacies of interatomic interactions and the limitations of current computational models in effectively navigating this complex molecular landscape. Additionally, the lack of comprehensive experimental data for all protein structures further exacerbates the difficulty in reliable machine learning-based prediction of the three-dimensional conformations of the proteios building block of life. Geometrically, Cartesian coordinate system (CCS, X, Y and Z) and spherical coordinate system (SCS, ρ, θ and φ) are two interconvertible coordinate systems, and are like two sides of one coin. Since the beginning of Protein Data Bank (PDB) in 1971, CCS has been the default approach to specify atomic positions with X, Y and Z in PDB. In this manuscript, therefore, I present a novel method for the reversible spherical geometric conversion of protein backbone structure coordinate matrices to three independent vectors: ρ, θ and φ. This reversible conversion facilitates lossless extraction of essential structural features from protein backbone structural data, enabling the development of advanced novel algorithms for protein structure prediction in future. In short, this inter-atomic SCS approach offers a comprehensive yet efficient means of representing protein backbone geometry, leveraging spherical coordinates to capture spatial relationships in a compact and intuitive inter-atomic manner, and to provide a robust framework for reversible feature extraction for the ongoing efforts in advancing the field of protein structure prediction, the holy grail of computational structural biology.

Despite the long history of using protein sequences to infer the tree of life the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure; we test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1,500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology (ctenophores sister to other animals) regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments; buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies whereas solvent exposed and helix sites had unequal numbers of sites supporting the minority topologies. Given the plausible trees equal support for minority topologies is consistent with discordance among gene trees, making it possible the relatively slowly evolving buried (and sheet and coil) sites are giving an accurate picture of the true species tree as well as the amount of conflict among gene trees. Alternatively, the apparent support could reflect currently uncharacterized processes of molecular evolution. Regardless, it is clear that analyses of the deepest branches in the animal tree of life using sites in different structural environments are associated with a subtle data type effect that results in distinct phylogenetic signals.

Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that would take into account the particular biological and biophysical properties of MSF complexes. Here we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes, and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.

Chlamydia trachomatis (Ct) infections are the most common sexually-transmitted infection (STI). Despite effective antibiotics for Ct, undetected infections or delayed treatment can lead to infertility, ectopic pregnancies, and chronic pelvic pain. Besides humans, chlamydia poses similar health challenges in animals such as C. suis (Cs) in pigs. Based on the similarities between humans and pigs as well as their chlamydia species, we use pigs as a large biomedical animal model for chlamydia research. In this study, we use the pig model to develop a vaccine candidate against Ct. The vaccine candidate consists of TriAdj-adjuvanted chlamydial protease-like activity factor (CPAF) protein. We tested two weekly administration options – twice intranasal (IN) followed by twice intramuscular (IM), or twice IM followed by twice IN. We assessed the humoral immune response not only in serum by CPAF-specific IgG including antibody avidity determination but also in cervical and rectal swabs by CPAF-specific IgG and IgA ELISAs. The systemic T-cell response was analyzed upon in vitro CPAF-restimulation via IFN-γ and IL-17 ELISpots as well as intracellular cytokine staining flow cytometry. Our data demonstrate that while the IN/IM vaccination mainly led to non-significant systemic immune responses, the vaccine candidate is highly immunogenic if administered IM/IN. This vaccination strategy induced high serum anti-CPAF IgG levels with strong avidity as well as high IgA and IgG levels in vaginal and rectal swabs and in uterine horn flushes. In addition, this vaccination strategy prompted a pronounced cellular immune response: Besides inducing IL-17 production, the vaccine candidate induced a strong IFN-γ response by CD4 T cells. In the IM/IN vaccinated pigs, these cells also significantly downregulated their CCR7 expression – a sign for differentiation into peripheral tissue homing effector/ memory cells. Conclusively, this study demonstrates strong immunogenicity of the IM/IN administered TriAdj-adjuvanted Ct CPAF vaccine candidate. Future studies will test vaccine efficacy of this promising Ct vaccine candidate. In addition, this project demonstrates suitability of the Cs pre-exposed outbred pig model for Ct vaccine development. Thereby, we aim to open the bottleneck of large animal models to facilitate the progression of Ct vaccine candidates into clinical trials.

Two desirable functions of healthy soil are nutrient cycling and pest suppression. We review recent literature on the contributions of soil microarthropods to soil health through their intersecting roles in decomposition and nutrient cycling and direct and indirect suppression of plant pests. Microarthropods can impact soil and plant health directly by feeding on pest organisms or serving as alternate prey for larger predatory arthropods, and indirectly, by mediating the ability of crop plants to resist or tolerate insect pests and diseases through interactions with the decomposition food web in support of plant nutrition. Soil fauna, including microarthropods, are key regulators of decomposition at local scales but their role at larger scales is unresolved. Future research priorities include the incorporation of multi-channel omnivory into food web modeling and understanding the vulnerability of our soil carbon to increased global temperatures.

We explored the dynamics of the two interacting information systems. We show that for the Markovian marginal systems the driving force for information dynamics is determined by both the information landscape and information flux. While the information landscape can be used to construct the driving force to describe the equilibrium time reversible information system dynamics, the information flux can be used to describe the nonequilibrium time-irreversible behaviours of the information system dynamics. The information flux explicitly breaks the detailed balance and is a direct measure of the degree of the nonequilibriumness or time irreversibility. We further demonstrate that the mutual information rate between the two subsystems can be decomposed into the equilibrium time-reversible and nonequilibrium time-irreversible parts respectively. This decomposition of the mutual information rate (MIR) corresponds to the information landscape-flux decomposition explicitly when the two subsystems behave as Markov chains. Finally, we uncover the intimate relationship between the nonequilibrium thermodynamics in terms of the entropy production rates and the time-irreversible part of the mutual information rate. We found that this relationship and MIR decomposition still hold for the more general stationary and ergodic cases. We demonstrate the above features with two examples of the bivariate Markov chains.

Growth and yield of boreal tree species are discussed. A growth model is applied, along with verified yield models of sawlogs and veneer logs. Using the normal forest-principle, thinning schedules and rotation ages maximizing the estate-level capital return rate are clarified. Regeneration expenses are amortized at the end of any rotation. Consequently, capitalizations are greater and rotations longer than in recent studies. The capital return rate is a weak function of initial stem count but differs by tree species. The initial stem count strongly contributes to biomass stored in trees. The most promising way of increasing the capital return rate is the reduction of regeneration expenses. Thinnings are triggered by stand volumes of at least 200 m3/ha. The average commercial trunk volume of trees removed in thinnings always exceeds 200 liters. Risk aversion theory proposes short rotations and low stem count in seedling planting unless carbon storage compensation exists.

Clock Network Design (CDN) is a critical step while designing any Integrated-Circuits (ICs). It holds vital importance in the performance of entire circuit. Due to continuous scaling, 3D ICs stacked with TSV are gaining importance, with an objective to continue with the Moore's law. Through-Silicon-Via (TSV) provides the vertical interconnection between two die, which allows the electrical signal to flow through it. 3D ICs has many advantages over conventional 2D planar ICs like reduced power, area, cost, wire-length etc. The proposed work is mainly focused on power reduction and obstacle avoidance for 3D ICs. Various techniques have already been introduced for minimizing clock power within specified clock constraints of the 3D CND network. Proposed 3D Clock Tree Synthesis (CTS) is a combination of various algorithms with an objective to meet reduction in power as well as avoidance of obstacle or blockages while routing the clock signal from one sink to other sink. These blockages like RAM, ROM, PLL etc. are fixed during the placement process. The work is carried out mainly in three steps- first is Generation of 3D Clock tree avoiding the blockages, then Buffering and Embedding and finally validating the results by SPICE simulation. The experimental result shows that our CTS approach results in significant 9% reduction in power as compare to the existing work.

The partial information decomposition (PID) framework is concerned with decomposing the information that a set of random variables has with respect to a target variable into three types of components: redundant, synergistic, and unique. Classical information theory alone does not provide a unique way to decompose information in this manner and additional assumptions have to be made. Inspired by Kolchinsky's recent proposal for measures of intersection information, we introduce three new measures based on well-known partial orders between communication channels and study some of their properties.

In this study, 12 organic waste materials were subjected to TG/DTG thermogravimetric analysis and DSC calorimetric analysis. These analyses provided basic information about thermochemical transformations and degradation rates during organic waste pyrolysis. Waste materials were chosen to cover the most abundant waste that can be found in the municipal solid waste stream. Based on TG results, kinetic parameters according to Coats–Redfern method were determined. The pyrolysis activation energy was the highest for cotton 134.5 kJ∙(mol∙K)-1 and the lowest for leather 25.2 kJ∙(mol∙K)-1. The DSC analysis showed number of transformations occurred during pyrolysis for each material. For each transformation, normalized energy required for transformation, or released during transformation were determined and then summarized to present energy balance. The study found that only for three waste materials: PET (-220.1 J⸱g-1), leather (-66.9 J⸱g-1), and chicken meat (-130.3 J⸱g-1) energy balance was negative, while the highest positive balance value was found for potato peelings (367.8 J⸱g-1). The obtained results may be applied for the modelling of energy and mass balance of municipal solid waste pyrolysis.

This research delves into a detailed exploration of the thermal decomposition behavior of bio-based polymers, specifically Thermoplastic Starch (TPS) and Poly(lactic acid) (PLA). The study focuses on the impact of three different heating rates under a nitrogen atmosphere, providing comprehensive insights into the thermal stability of these eco-friendly polymers. In particular, the TPS kinetic model is examined, encompassing the decomposition of three distinct fractions. In contrast, PLA exhibits a simplified kinetic behavior requiring only a fraction described by a zero-order model. The kinetic study involves a systematic investigation into the individual contributions of key components within TPS, including starch, glycerin, and polyvinyl alcohol (PVA). This nuanced analysis contributes to a comprehensive understanding of the thermal degradation process of TPS and PLA, enabling the optimization of processing conditions and the prediction of material behavior across varying thermal environments. Furthermore, the incorporation of different starch sources and calcium carbonate additives in TPS enhances our understanding of the polymer's thermal stability, offering insights into potential applications in diverse industries.

Spatio-Temporal Dynamic Mode Decomposition (STDMD) is an extension of Dynamic Mode Decomposition (DMD) designed to handle spatio-temporal datasets. It extends the framework so that it can analyze data that has both spatial and temporal variations, allowing for the extraction of spatial structures and their temporal evolution. The STDMD method extracts temporal and spatial development information simultaneously, including wavenumber, frequencies and growth rates, which is essential in complex dynamic systems. We provide a comprehensive mathematical framework for sequential and parallel STDMD approaches. We also introduce delay coordinates generalization to the presented algorithms to extend the scope of their application. The extension, labeled delay embedding STDMD allows the use of delayed data, which can be both time-delayed and space-delayed. An explicit expression of the presented algorithms in matrix form is also provided, which facilitates theoretical analysis and provides a solid foundation for further research and development. The novel approach is demonstrated using some illustrative model dynamics.

As a fast and nondestructive spectroscopic analysis technique, Raman spectroscopy has been widely applied in chemistry. However, noise is usually unavoidable in Raman spectra. Hence, denoising is an important step before Raman spectral analysis. A novel spectral denoising method based on variational mode decomposition (VMD) was introduced to solve the above problem. The spectrum is decomposed into a series of modes (uk) by VMD. Then, the high frequency noise modes are removed and the remaining modes are reconstructed to obtain the denoised spectrum. The proposed method was verified by two artificial noised signals and two actual Raman spectra. As comparison, empirical mode decomposition (EMD), Savitzky-Golay (SG) smoothing and discrete wavelet transformation (DWT) are also investigated. At the same time, signal-to-noise ratio (SNR) was introduced as evaluation indicators to verify the performance of the proposed method. The results show that compared with EMD, VMD can significantly improve mode mixing and endpoint effect. Some information of the small sharp peak is lost after VMD denoising. However, VMD lost fewer information than that of EMD, SG smoothing and DWT. Moreover, the Raman spectrum by VMD denoising is more excellent than that of EMD, SG smoothing and DWT in terms of visualization and SNR. Therefore, VMD provides superior denoising capabilities for Raman spectra.

The solution of structural problems with nonlinear material behaviour in a model order reduction framework is investigated in this paper. In such a framework, greedy algorithms or adaptive strategies are interesting as they adjust the reduced order basis (ROB) to the problem of interest. However, these greedy strategies may lead to an excessive increase in the size of the reduced basis, i.e. the solution is no more represented in its optimal low-dimensional expansion. Here, an optimised strategy is proposed to maintain, at each step of the greedy algorithm, the lowest dimension of the PGD basis using a randomised SVD algorithm. Comparing to conventional approaches such as Gram-Schmidt orthonormalisation or deterministic SVD, it is shown to be very efficient both in terms of numerical cost and optimality of the reduced basis. Examples with different mesh densities are investigated to demonstrate the numerical efficiency of the presented method.

We propose an electrocardiogram (ECG) signal-based algorithm to estimate the respiratory rate is a significant informative indicator of physiological state of a patient. The consecutive ECG signals reflect the information about the respiration because inhalation and exhalation make transthoracic impedance vary. The proposed algorithm extracts the respiration-related signal by finding out the commonality between the frequency and amplitude features in the ECG pulse train. The respiration rate can be calculated from the principle components after the procedure of the singular spectrum analysis. We achieved 1.7569 breaths per min of root-mean-squared error and 1.7517 of standard deviation with a 32-seconds signal window of the Capnobase dataset, which gives notable improvement compared with the conventional Autoregressive model based estimation methods.

Multi-level direct networks fueled by the evolving technology of active optical cables and increasing pin-bandwidth achieve reduced diameters and cost, with high-radix switches. These networks, like Dragonfly, are becoming the preferred aspirants for extreme high-performance parallel machines such as exa-scale computing. In this paper, we introduce a Hyper Z-Tree topology, which deploys the Z-Tree, a variant of fat-tree, as a computing node of a Generalized Hypercube (GHC) configuration. The resulting configuration provides higher bisection bandwidth, lower latency for some applications and higher throughput. Furthermore, the levels of the fat tree offer several path diversities across the GHC dimensions, hence conceding a more fault tolerant architecture. To profit from these path diversities, we propose two adaptive routing algorithms, which are extensions to the routing algorithm suggested in HyperX topology. These two algorithms exhibit better latencies and throughput than the HyperX.

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

Capital structure decision plays an imperative role in firm’s performance. Recognizing the importance, there has been many studies inspected the rapport of capital structure with performance of firms and findings of those studies are inconclusive. In addition, there is relative deficiency of empirical studies examining the link of capital structure with performance of banks in Bangladesh. This paper attempted to fill this gap. Using panel data of 22 banks for the period of 2005-2014, this study empirically examined the impacts of capital structure on the performance of Bangladeshi banks assessed by return on equity, return on assets and earnings per share. Results from pooled ordinary least square analysis show that there are inverse impacts of capital structure on bank’s performance. Empirical findings of this study is of greater significance for the developing countries like Bangladesh because it will call upon concentration of the bank management and policy makers to pursue such policies to reduce reliance on debt and to accomplish optimal level capital structure. This research also contributes to empirical literatures by reconfirming (or otherwise) findings of previous studies.

Balsam fir trees are a specialty agricultural species that are largely used as Christmas trees. Soil or tissue sampling is seldom performed to assess balsam fir nutrition needs, which can contribute to over or under fertilization and subsequent environmental challenges. Remote sensing to determine the normalized difference vegetation index (NDVI) has had strong relationships with nutrition in other plants. This research aimed to determine whether there is a relationship between NDVI and nutrition in balsam fir. A random sample of 45 trees was selected in autumn of 2021 and then another 70 trees selected in spring of 2022. Soil and needle tissue samples were analyzed for N, P, K, Ca, Mg, S, Fe, Zn, Mn, B, and Cu. An uncrewed aerial vehicle equipped with a multispectral camera was flown over the orchard to determine the NDVI for each tree. Nutrition and NDVI were analyzed for correlations through all sampled trees. Separate correlation analyses were repeated for mature trees (greater than 5 years old) and young trees (less than 5 years old). Soil nutrients N, P, K had a significant relationship with NDVI in autumn sampling. Only N was correlated consistently in both autumn and spring, with R2 of 37% and 33% respectively. Relationships were much stronger when only mature trees were considered, increasing to 60% and 51% respectively. NDVI was found to offer predictive power for tissue N that can be useful to producers to help optimize fertilizer input. However, further work is needed to refine these relationships.

Protein tyrosine phosphatase receptor type E (PTPRE) is a member of the “classical” protein tyrosine phosphatase subfamily and regulates a variety of cellular processes in a tissue-specific manner by antagonizing the function of protein tyrosine kinases. PTPRE plays a tumorigenic role in different human cancer cells, but its role in retinoblastoma (RB), the most common malignant eye cancer in children, remains to be elucidated. Etoposide resistant RB cell lines and RB patients display significant higher PTPRE expression levels compared to chemosensitive counterparts and the healthy human retina, respectively. PTPRE promotor methylation analyses revealed that PTPRE expression in RB is not regulated via this mechanism. Lentiviral PTPRE knockdown (KD) induced a significant decrease in growth kinetics, cell viability, and anchorage independent growth of etoposide resistant Y79 and WERI RB cells. Caspase-dependent apoptosis rates were significantly increased and a re-sensitization for etoposide could be observed after PTPRE depletion. In vivo chicken chorioallantoic membrane (CAM) assays revealed decreased tumor formation capacity as well as reduced tumor size and weight following PTPRE KD. Expression levels of miR631 were significantly downregulated in etoposide resistant RB cells and patients. Transient miR631 overexpression resulted in significantly decreased PTPRE levels and concomitantly decreased proliferation and increased apoptosis levels in etoposide resistant RB cells, impacts mirroring PTPRE KD effects and indicating PTPRE regulation via this miR. Additionally, PTPRE KD led to altered phosphorylation of protein kinase SGK3 and - dependent on the cell line - also AKT and ERK1/2, suggesting potential PTPRE downstream signaling pathways. In summary, these results indicate an oncogenic role of PTPRE in chemoresistant retinoblastoma.

Structure–function relationships in proteins have been one of the crucial scientific topics. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure–function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure–function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB–OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with very different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure–function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.

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 p53 tumor suppressor protein is an activator of transcription. Diverse stress factors lead to various sets of posttranslational modifications of p53 what results in different sets of upregulat-ed genes. We noticed that actinomycin D and nutlin-3a (A+N) synergize in inducing activating phosphorylations of p53 and upregulation of selected p53-target genes. Here we found that one of these genes is DUSP13, which codes for poorly-studied, dual-specificity phosphatase having at least two isoforms, one expressed in testis and the other in skeletal muscles. In cancer cells ex-posed to A+N, DUSP13 is expressed from an alternative promoter in intron, what results in ex-pression of isoform named TMDP-L1. The luciferase reporter tests demonstrated that this pro-moter is activated by both endogenous and ectopically expressed p53. We showed for the first time that mRNA expressed from this promoter actually produces the protein, which can be de-tected by Western blotting in all examined cancer cell lines with wild-type p53 exposed to A+N. In some cell lines it is also induced by clinically relevant camptothecin or by nutlin-3a acting alone. This isoform, fused with green fluorescent protein localizes in perinuclear region of cells. Thus, TMDP-L1 isoform may be an important element of p53-regulated stress response system.

The COVID-19 pandemic over the past years has shown a great need for rapid, low-cost and on-site detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, an aptamer-based colloidal gold nanoparticle lateral flow test strip was well developed to realize the visual detection of wild type SARS-CoV-2 spike protein (SP) and multiple variants. Under the optimal reaction conditions, a low detection limit of SARS-CoV-2 S protein of 0.68 nM was acquired, and the actual detection recovery was 83.3% to 108.8% for real world samples. This suggests a potential tool for the prompt detection of SARS-CoV-2 with good sensitivity and accuracy, and a new method for the development of alternative antibody test strips for the detection of other viral targets.

Empirical models help us understand the process of plant residue decomposition and nutrient release into the soil. The objective of this study was to determine an appropriate model to describe the decomposition of hairy vetch (Vicia villosa Roth) and cereal rye (Secale cereale L.) cover crop (CC) residue and nitrogen (N) release. Data pertaining to above and belowground CC residue mass loss and N release for up to 2633 cumulative decomposition degree days (112 d) after litterbag installation were obtained from two cropping system experiments, one conducted in 2015 and the other in 2017 and 2018 at the humid subtropical environment of southern IL, USA. Six exponential and two hyperbolic models were fit to percent mass and N remaining data to find the one with minimum Akaike Information Criterion (AIC) and residual sum of squares. Modified three-parameter single exponential and two- or three-parameter hyperbolic models best met the assumed criteria of selection for above and belowground CC residue, respectively. Fitting a double exponential model to a combined data for percent mass and N remaining, which identified two mass and N pools, a fast and a slow pool with different rate constants. A five-parameter double exponential with an asymptote met the preset criteria and passed all tests for normally distributed population, constant variance, and independence of residuals at α = 0.05 when fit to combined data of hairy vetch shoot mass and N remaining. However, a two-parameter hyperbolic and three-parameter asymptotic hyperbolic model provided the best fit to a combined data of cereal rye shoot mass and N remaining, respectively. Both hyperbolic decay models showed a good fit for belowground mass decomposition and N release for both CCs. Cereal rye had poorer fit than hairy vetch for mass and N remaining of both above and belowground mass. The best-selected decay models can be used to estimate the decomposition and N release rates of hairy vetch and cereal rye above and belowground residue in a similar environment.

More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae, which turn out to be an effective barcode gene for these corals. However, its function remains unknown. Recently, this gene revealed the existence of a hybrid Stylophora lineage (RS_LinA) inhabiting in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C) with its parental species (RS_LinB). Furthermore, in RS_LinB, the mtORF uncovered phylogeographic patterns that were strongly correlated with environmental variations. This was similar to the patterns unraveled by hsp70, suggesting that mtORF too might be involved in thermal adaptation. Here we used computational approaches to characterize the mtORF and to identify its potential role. Results showed that this gene encodes a transmembrane protein (0.97<P< 1.00) involved in transport (0.80<P< 0.87), regulation of metabolic processes (0.70<P<0.85), and likely in the cell-surface receptor signaling pathway (0.56<P<0.80). Predicted protein functions differed among Stylophora lineages and interestingly, in RS_LinB only, the protein was intrinsically disordered and displayed domains involved in cellular complexes and stress response (0.0001< P <0.001). These characteristics, exclusive of an endemic lineage adapted to extreme environmental fluctuations, support a role of the mtORF in stress response, speciation and adaptation.

The paper investigates new robust code constructions based on bent functions and spline–wavelet transformation. Implementation of bent functions in codes construction increases the probability of error detection in the data channel and cryptographic devices. Meanwhile, use of spline–wavelets theory for constructing the codes gives the possibility to increase system security from the actions of an attacker. Presented constructions combines spline–wavelets functions and bent functions. Developed robust codes, compared to existing ones, have a higher parameter of maximum error masking probability. Illustrated codes are ensuring the security of transmitted information. Some of the granted constructions were implemented on FPGA.

Dysfunction of the WW domain-containing adaptor with coiled-coil, WAC, gene underlies a rare autosomal dominant disorder, DeSanto-Shinawi syndrome (DESSH). DESSH is associated with facial dysmorphia, hypotonia, and cognitive alterations, including attention deficit hyperactivity disorder and autism. How the WAC protein localizes and functions in neural cells is critical to understanding its role during development. To understand the genotype-phenotype role of WAC, we developed a knowledgebase of WAC expression, evolution, human genomics, and structural/motif analysis combined with human protein domain deletions to assess how conserved domains guide cellular distribution. Then assessed in a cell type implicated in DESSH, cortical GABAergic neurons. WAC contains conserved charged amino acids, phosphorylation signals, and enriched nuclear motifs, suggesting a role in cellular signaling and gene transcription. Human DESSH variants are found within these regions. We also discovered and tested a nuclear localaization domain that impacts the cellular distribution of the protein. These data provide new insights into the potential roles of this critical developmental gene, establishing a platform to assess further translational studies, including the screening of missense genetic variants in WAC. Moreover, these studies are essential for understanding the role of human WAC variants in more diverse neurological phenotypes, including autism spectrum disorder.

The extracellular matrix (ECM) plays a key role as both structural scaffold and regulator of cell signal transduction in tissues. In times of ECM assembly and turnover, cells upregulate assembly of the ECM protein, fibronectin (FN). FN is assembled by cells into viscoelastic fibrils that can bind upward of 40 distinct growth factors and cytokines. These fibrils play a key role in assembling a provisional ECM during embryonic development and wound healing. Fibril assembly is also often upregulated during disease states, including cancer and fibrotic diseases. FN fibrils have unique mechanical properties, which allow them to alter mechanotransduction signals sensed and relayed by cells. Binding of soluble growth factors to FN fibrils alters signal transduction from these proteins, while binding of other ECM proteins, including collagens, elastins, and proteoglycans, to FN fibrils facilitates the maturation and tissue specificity of the ECM. In this review, we will discuss the assembly of FN fibrils from individual FN molecules; the composition, structure, and mechanics of FN fibrils; the interaction of FN fibrils with other ECM proteins and growth factors; the role of FN in transmitting mechanobiology signaling events; and approaches for studying the mechanics of FN fibrils.

This study aimed to evaluate the impact of Candida albicans on subgingival biofilm formation on dental implant surfaces. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to compare biofilm structure and microbial biomass in the presence and absence of the fungus after periods of 24, 48, and 72 h. Quantitative polymerase chain reaction (qPCR) was used to quantify the number of viable and total micro-organisms for each of the biofilm-forming strains. A general linear model was applied to compare CLSM and qPCR results between control and test conditions. The biofilm developed with C. albicans at 72 h had a higher bacterial biomass, with a significantly higher cell viability (p &lt; 0.05). After both 48 and 72 h of incubation, in the presence of C. albicans, there was a significant increase in counts of Fusobacterium nucleatum and Porphyromonas gingivalis and in the cell viability of Streptococcus oralis, Aggregatibacter actinomycetemcomitans, F. nucleatum, and P. gingivalis. Using a dynamic in vitro multispecies biofilm model, C. albicans exacerbated the development of the biofilm grown on dental implant surfaces, significantly increasing the number and cell viability of periodontal bacteria.