We obtain two generalizations of a known theorem of A. Alam and M. Imdad (Fixed Point Theory Appl. 17 (2015) 693–702) showing that some standard proofs can be obtained involving only Cauchy sequences of the successive approximations instead of the usual successive approximations sequences. Suitable examples prove the effective generalization of our results in metric spaces not necessarily complete.

The smart management of water resources is an increasingly important topic in today's society. In this context, the paradigm of Smart Water Grids (SWGs) aims at a constant monitoring through a network of smart nodes deployed over the water distribution infrastructure. In such a way, a continuous assessment of water quality and state of health of the pipeline infrastructure can be achieved, allowing an early detection of leaks and water contamination. Acoustic wave-based technology has arisen as a viable communication technique among the nodes of the network. Such technology can be suitable to replace traditional wireless networks in SWGs, as the acoustic channel is intrinsically embedded in the water supply network. However, the fluid-filled pipe is one of the most challenging media to be employed for data communication. This paper aims at reviewing those works dealing with acoustic-based communication networks in real large-scale urban water supply networks. An overview on the characteristics, trends and design challenges of existing works is provided as a guideline for future research.

The discovered light modulation capabilities of diatom silicious valves make them an excellent toolkit for photonic devices and applications. In this work, a reproducible surface-enhanced Raman-scattering (SERS) enhancement was achieved with hybrid substrates employing diatom silica valves coated with an ultrathin uniform gold film. Three structurally different hybrid substrates, based on the valves of three dissimilar diatom species, have been compared to elucidate the structural contribution to SERS enhancement. The comparative analysis of obtained results showed that substrates containing cylindrical Aulacoseira sp. valves achieved the highest enhancement up to 14-fold. Numerical analysis based on the frequency domain finite element method was carried out to supplement the experimental results. Our results demonstrate that diatom valves of different shapes can enhance the SERS signal, offering a toolbox for SERS-based sensors, where the magnitude of the enhancement depends on valve geometry and ultrastructure.

Lamb waves occur in thin-walled structures in two wave modes, the symmetric and antisymmetric mode. Their oscillation on the structures‘ surfaces is either in phase (symmetric) or shifted by a phase angle of π (antisymmetric). In this work, a method is developed to compare the surfaces‘ oscillation phase relation. It is based on the evaluation of time signals regarding the instantaneous phase angle using the continuous wavelet transformation and as a comparative method the short-time Fourier transformation. For this purpose, numerical simulations utilizing the finite element method provide time signals from the top and bottom surface of different thin-walled structures. They differ with respect to their material settings and laminate configurations. The numerically obtained time signals are evaluated by the developed methods. The occurring oscillation phase differences on the top and bottom surface are studied and both methods are compared. Subsequently, the oscillation phase is evaluated experimentally for the wave propagation in a fiber metal laminate. It is shown that the method based on the continuous wavelet transformation is suitable for the evaluation of oscillation phase relations in time signals. Additionally, it is proven that fiber metal laminates show only two phase relations which indicates the occurrence of Lamb waves.

This work investigates how integrated polyimide inlays with applied sensor bodies influence the guided ultrasonic wave propagation in narrow glass fiber-reinforced polymer specimens. Preliminary numerical simulations indicate that in a damping-free specimen, the inlays show reflections for the S0-mode propagation. Hence, an air-coupled ultrasonic technique and a 3D laser Doppler vibrometer measurement are used to measure different parts of the propagating waves’ displacement field after burst excitation at different frequencies. No significant reflections on the inlay can be seen in the experiments. However, it is shown that the reflections from the strip specimen’s narrow width cause periodical reflections that superimpose with the excited wave fronts. A continuous wavelet transformation in the time-frequency domain filters discontinuities from the measurement signal and is used for reconstruction of the time signals. The reconstructed signals are used in a spatial continuous wavelet transformation to identify the occurring wavelengths and hence to prove the assumption of reflections from the narrow edges. Since the amplitude of the reflections identified in the numerical data at the polyimide inlays are an order of magnitude smaller than the excited wave packages, it is concluded that material damping of the epoxy resin matrix extincts possible reflections from the inlays.

Structural health monitoring of lightweight constructions made of composite materials can be performed using guided ultrasonic waves. If modern fiber metal laminates are used, this requires integrated sensors that can record the inner displacement oscillations caused by the propagating guided ultrasonic waves. Therefore, we have developed a robust MEMS vibrometer that can be integrated with structural and functional compliance. This vibrometer is directly sensitive to the high-frequency displacements from structure-borne ultrasound when excited between its first and second natural frequency. The vibrometer is mostly realized by processes earlier developed for a pressure sensor but with additional femtosecond laser ablation and wafer bonding. The piezoresistive transducer made from silicon is encapsulated between top and bottom glass lids. The natural frequencies are experimentally determined using an optical micro vibrometer setup. The vibrometer functionality and usability for structural health monitoring are demonstrated on a customized test rig by recording application-relevant guided ultrasonic wave packages with a central frequency of 100 kHz at a distance of 200 mm from the exciting ultrasound transducer.

The aim of this article is to evaluate and compare, retrospectively, the efficacy of two regenerative periodontal procedures in patients suffering from aggressive periodontitis (AgP). Twenty-eight patients were diagnosed with AgP, suffering from multiple intra-bony defects (IBD); that were treated by one of two regenerative modalities of periodontal therapy randomly assigned to each patient: a. guided tissue regeneration (GTR) or b. an application of enamel matrix derivatives (EMD) combined with DBX. The monitoring of the treated sites included recordings of probing depth (PD), clinical attachment level (CAL), and gingival recession. Pre-treatment and follow-up (up to 10 years from the surgery) recordings were analyzed statistically within and between groups. A significant reduction was shown at time on PD and CAL values, however, not between subject groups. CAL values decreased in all sites. At EMD group (44 sites) CAL gain was 1.92 mm (±1.68) from pre-treatment to follow-up (p<0.001) and at the GTR group (12 sites) CAL gain of 2.27 (±1.82) mm. In conclusion, 1-10 years observations have shown that surgical treatment of AgP patients by either GTR or by application of EMD/DBX results in similar successful clinical results.

During last decades multiple therapeutic approaches have been explored for improved management of peritoneally disseminated malignancies – a grim condition known as peritoneal carcinomatosis (PC). Intraperitoneal administration can be used to achieve elevated local concentration and extended half-life of the drugs in the peritoneal cavity to improve their anticancer efficacy. However, IP-administered chemotherapeutics have a short residence time in the IP space, and are not tumor selective. An increasing body of work suggests that functionalization of drugs and nanoparticles with targeting peptides increases their peritoneal retention and provides a robust and specific tumor binding and penetration that translates into improved therapeutic response. Here we review a progress in affinity targeting of intraperitoneal anticancer compounds, imaging agents and nanoparticles with tumor homing peptides. We review classes of tumor homing peptides relevant for PC targeting, payloads for peptide-guided precision delivery, applications for targeted compounds and the effects of nanoformulation of drugs and imaging agents on affinity-based tumor delivery.

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

Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here we apply this technology to assess genetic diversity and taxonomic delimitation in the Encephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Silica dried cycad leaflets were extracted using the Oktopure robot employing Sbeadex chemistry and amplified with fluorescently tagged ISSR primers. Band presence was scored with an ABI 3130 genetic sequencer under three different fluorescence cut-off values. Phenetic analyses were performed in NTSYS software while Bayesian analysis was performed in STRUCTURE, and haplotype network analysis, AMOVA and Tajima’s D statistic was computed with PopART. Our analyses support taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrated the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries.

The current research examines the many characteristics of the $\ell_{p}(\widetilde{F}(\widetilde{r},\widetilde{s}))$ $(1\leq p<\infty)$ and $\ell_{\infty}(\widetilde{F}(\widetilde{r},\widetilde{s}))$ spaces which are the generalized forms of those by Candan in 2024 using Fibonacci numbers and two non-zero real numbers in accordance with a predetermined rule, we have made an effort to go through all the characteristics and features which the author of earlier versions thought are the most valuable. This manuscript contains all the information required to describe the matrix class $(\ell_{1},\ell_{p}(\widetilde{F}(\widetilde{r},\widetilde{s})))$ $(1\leq p<\infty)$ which are going to be given in detail in the following sections of the manuscript. We are going to offer estimates for the norms of the bounded linear operators $L_{A}$ formed by those matrix transformations utilizing the Hausdorff measure of non-compactness and identify prerequisites to derive the relevant subclasses of compact matrix operators. When the findings of the current study are compared to those found in the literature, it can be said that the newly found ones are more inclusive and comprehensive.

Seismic velocity inversion is one of the most critical issues in the field of seismic exploration and has long been the focus of numerous experts and scholars. In recent years, the advancement of machine learning technologies has infused new vitality into the research of seismic velocity inversion and yielded a wealth of research outcomes. Typically, seismic velocity inversion based on machine learning lacks control over physical processes and interpretability. Starting from wave theory and the physical processes of seismic data acquisition, this paper proposes a method for seismic velocity model inversion based on Physical Embedding Recurrent Neural Networks. Firstly, the wave equation is a mathematical representation of the physical process of acoustic waves propagating through a medium, and the finite difference method is an effective approach to solving the wave equation. With this in mind, we introduce the architecture of recurrent neural networks to describe the finite difference solution of the wave equation, realizing the embedding of physical processes into machine learning. Secondly, in seismic data acquisition, the propagation of acoustic waves from multiple sources through the medium represents a high-dimensional causal time series (wavefield snapshots), where the influential variable is the velocity model, and the received signals are the observations of the wavefield. This forms a forward modeling process as the forward simulation of the wavefield equation, and the use of error back-propagation between observations and calculations as the velocity inversion process. Through time-lapse inversion and incorporating the causal information of wavefield propagation, the non-uniqueness issue in velocity inversion is mitigated. Through mathematical derivations and theoretical model analyses, the effectiveness and rationality of the method are demonstrated. In conjunction with simulation results for complex models, the method proposed in this paper can achieve velocity inversion in complex geological structures.

The sharing of genome sequences in online data repositories, allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as development of improved detection methods. Here we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j one Stx2m strain and one Stx2o, all were analyzed for variability from the originally described subtypes [1,2]. Complete genome sequences were assembled from short or long read sequencing and analyzed for serotype, and ST types. The stx2n and Stx2o WGS were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data was used to design OMNI PCR primers for the detection of all known Stx1 (283 bp amplicon), Stx2 (400 bp amplicon), eae (222bp amplicon) and Stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. Analysis of complete genome sequence showed variability in serogroup, virulence genes, ST type, and Stx2 pro-pages showed variability in size, gene composition, and phage insertion sites. The isolates with Stx2n and Stx2o in this study demonstrated toxicity for Vero cells. The Stx2n strain were induced when grown with sub-inhibitory concentrations of Cip, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact in public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in humans in Wuhan City at the end of December 2019. Since then, it has spread to all the countries. Therefore, global interest has been focused on discovering treatments and developing successful vaccines. This study sequenced the complete genome of the SARS-COV-2 Omicron Omicron (BA.1) and sub-variants (BA.1.1, BA.2), which were isolated from 40 individuals in Duhok, Iraq. Ninety-five different mutations were identified when the complete genome of the SARS-COV-2 virus discovered in Wuhan, China (accession number: NC 045512.2) was matched to the virus sequence using sequencing technology (Illumina, USA). Sequence analysis revealed 38 mutations in spike glycoprotein (S), 30 of which were found in ORF1a. Additionally, 11 mutations were found in ORF1b, and 7,3,2,1 mutations were found in Nucleocapsid (N), membrane protein (M), Open Reading Frames 6 (ORF6), Open Reading Frames 9 (ORF9), and Envelope (E) genes, respectively. Phylogenetic analysis and transmission further confirmed that the isolates found in Iraq had distinct infection origins and were closely related to those from other countries and states. According to the findings of this study, a new vaccine can be developed based on identifying new Omicron variant mutations and sub-variants such as BA.2, which were identified for the first time in Iraq.

In the present study, piecewise integrated composite (PIC) bumper beam for passenger cars was proposed and design optimisation process for composite bumper beam against IIHS test was carried out with the help of machine learning. Several elements in IIHS bumper FE model have been assigned to be references, in order to collect training data which, allow the machine learning model to study the method of predicting loading types of each finite element. 2-D and 3-D implementations were provided by machine learning models, which determined stacking sequences of each finite element in PIC bumper beam. It was found that the PIC bumper beam, which was designed by machine learning model has direct impact on reducing the possibility of failure as well as increasing bending strength effectively than conventional composite bumper beam. Moreover, 3-D implementation produced better results compared with 2-D implementation since it was preferable to choose loading type information which was achieved from surroundings when the target elements were located either at corner or junction of planes instead of using information came from the same plane of target.

Predictive processes and numerous cognitive, motor, and social skills depend heavily on sequence and statistical learning. The visuomotor Serial Reaction Time Task (SRTT) can measure these fundamental cognitive processes. In this review, we sought to answer whether repetitive transcranial magnetic stimulation (rTMS) is suitable for modulating visuomotor sequence learning and which factors mediate its efficacy. We systematically analyzed the eligible records (n = 17) that attempted to modulate the performance of the SRTT with rTMS. The purpose of the analysis was to determine how the following factors affected SRTT performance: (1) stimulated brain areas, (2) rTMS protocols, (3) stimulated hemisphere, (4) timing of the stimulation, (5) SRTT sequence properties, and (6) other methodological features. The primary motor cortex (M1) and the dorsolateral prefrontal cortex (DLPFC) were found to be the most promising stimulation targets. Low-frequency protocols over the M1 usually weaken performance, but the results are less consistent for the DLPFC. These inconsistencies (at least in part) may be due to the current frequency-based heuristics of rTMS effects developed for explaining local stimulation effects in the motor cortex. Although this review cannot provide an ultimate answer about the optimal stimulation and task parameters, it comprehensively discusses the behavioral effects of six factors that are crucial for designing future studies to modulate sequence learning with rTMS. Moreover, we conclude that synergistically combining functional neuroimaging with rTMS could adequately link the rTMS-induced network effects with the behavioral findings that are crucial to develop a unified cognitive model of visuomotor sequence learning.

This short paper demonstrates that the galactic spiral equations developed from ROTASE model can be used to morphologically simulate the phyllotactic spiral-ring patterns of plants. It is also noticed during this project that although the numbers in the Fibonacci sequence dominate the phyllotactic numbers, there are still significant phyllotactic numbers are not in the Fibonacci sequence, however, most of those numbers are well fit into a Fibonacci sibling sequence starting with numbers 0 and 2. Many plants show the phyllotactic number pairs of 10-16, 16-26 and 26-42 from the Fibonacci sibling sequence, which is the second dominated sequence in the phyllotaxis.

In this paper, we present sums and partial sums of Horadam sequences via generating functions which extends a recent result of Prodinger.

Learning programming is a complex and challenging task for many students. It in-volves both understanding theoretical concepts and acquiring practical skills. Hence, analyzing learners’ data from online learning environments alone fails to capture the full breadth of stu-dents’ actions if part of their learning process takes place elsewhere. Moreover, existing studies on learning analytics applied to programming education have mainly relied on frequency analysis to classify students according to their approach to programming or to predict academic achieve-ment. However, frequency analysis provides limited insights into the individual time-related characteristics of the learning process. The current study examines students’ strategies when learning programming, combining data from the learning management system and from an au-tomated assessment tool. To gain an in-depth understanding of students’ learning process as well as of the types of learners, we used learning analytics methods that account for the temporal order of learning actions. Our results show that students have special preferences for specific learning resources when learning programming, namely slides that support search, and copy and paste. We also found that videos are relatively less consumed by students, especially while working on programming assignments. Lastly, students resort to course forums to seek help only when they struggle.

Here we present 1. a model for amplicon sequencing 2. a definition of the best assignment of a read to a set of reference sequences 3. strategies and structures for indexing reference sequences and computing the best assign- ments of a set of reads efficiently, based on (ultra)metric spaces and their geometry The models, techniques, and ideas are particularly relevant to scenarios akin to 16S taxonomic profiling, where both the number of reference sequences and the read diversity is considerable.

Based on the key molecule of humoral adaptive immunity, the antibody, evolution of the system comprises molecular genetic, cell biologic and immunologic mechanisms, and as a network the system is likely governed and can be characterized by physical rules as well. While deep sequencing can provide vast amounts of data related primarily to clonal relationships, functional interpretation of such data is hampered by the inherent limitations of converting sequence to structure to function. In this paper a novel model of structural interaction space, termed radial adjustment of system resolution, or RADARS, is proposed. The model is based on the radial growth of resolution of structural recognition, corresponding to increasing affinity of immune reactivity, and the virtual infinity of directions of growth, corresponding to the ability to respond to almost any molecular structure. Levels of interaction strength appear as shells of the sphere representing the system. B-cell development and immune responses can be readily interpreted in the model and quantitative properties of the antibody network can be inferred from the physical properties of a quasi-spherical system growing multi-radially. The system is described by double-Pareto distribution, sampling the lognormally distributed equilibrium constants at a rate of phi square. Finally, general strategies for merging antibody sequence space into structural space are outlined.

Relationships between the Farey sequence and the Riemann hypothesis other than the Franel-Landau theorem are discussed. Whether a function similar to Chebyshev’s second function is square-root close to a line having a slope different from 1 is discussed. The nontrivial zeros of the Riemann zeta function can be used to approximate many functions in analytic number theory. For example, it could be said that the nontrival zeta function zeros and the Möbius function generate in essence the same function - the Mertens function. A different approach is to start with a sequence that is analogous to the nontrivial zeros of the zeta function and follow the same procedure with both this sequence and the nontrivial zeros of the zeta function to generate in essence the same function. A procedure for generating such a function is given.

Background: The purpose of this study was to compare the immediate and long-term complications that are associated with the utilized techniques for the insertion of indwelling central venous catheters, that is the open surgical technique, the ultrasound-guided technique and the transcutaneous technique based on external anatomical landmarks in the right internal jugular vein, to a pediatric population. Methods: This was a prospective randomized trial based on a pediatric patient population, under 16 years of age, of a tertiary pediatric-oncological hospital. Procedure was performed by a medical team with varying experience regarding the percutaneous and open insertion methods. We studied the outcome of our procedure, based on the immediate and delayed complication rate, as well as the needed time in order to complete the procedure and mean duration of line use. Results: The patients that were inserted in our protocol were divided into three subgroups, based on the selected technique for the insertion of the central venous catheter. A total number of 88 insertions (25.4%) (out of 346) were based on the technique that was using external anatomical landmarks, 121 insertions were based on the ultrasound-guided transcutaneous technique (34,9%), whereas in 137 cases (39.5%) the open surgical technique was preferred. All cases that were related to catheter re-insertion were excluded from our study. We performed a statistical analysis regarding the catheter dwell time between the three subgroups of patients and no significant difference was recorded. Moreover, the development of thrombosis was investigated, and we mentioned that the higher percentage of this complication was related with the transcutaneous external landmark and open surgical technique. Also, the incidence of infection was taken into consideration, which manifested an increased incidence when the transcutaneous technique based on external landmarks was used. Conclusions: Ultrasound guided percutaneous insertion was considered to be a safe and effective technique for the insertion of central venous catheters. Our study also demonstrated a decrease in operating times, when performed by operators with increasing expertise, increased preservation of the diameter of the venous lumen, and no increase in complication rates when the ultrasound-guided technique was selected.

This paper focuses on parametric model order reduction (PMOR) of guided ultrasonic wave propagation and its interaction with damage in a fiber metal laminate (FML). Structural health monitoring in FML seeks to detect, localize and characterize the damage with high accuracy and minimal use of sensors. This can be achieved by the inverse problem analysis approach which employs the signal measurement data recorded by the embedded sensors in the structure. The inverse analysis requires to solve the forward simulation of the underlying system several thousand times. These simulations are often exorbitantly expensive and triggered the need for improving their computational efficiency. A PMOR approach hinged on the proper orthogonal decomposition method is presented in this paper. An adaptive parameter sampling technique is established with the aid of a surrogate model to efficiently update the reduced-order basis in a greedy fashion. A numerical experiment is conducted to illustrate the parametric training of the reduced-order model. The results show that the reduced-order solution based on the PMOR approach is accurately complying with that of the high fidelity solution.

Probiotics are microorganisms infused in products for health benefits including acceleration of nutrient digestion, however, it is also important to ensure the safety prior to incorporation. Here, we present evidence of the ability of two probiotic isolates,Lacticaseibacillus paracasei BCRC-16100 and Lacticaseibacillus paracasei ZFM54, in the (1) enhancement of carbohydrate digestion, (2) tolerance to stress, and (3) antibiotic resistance. Approaches include whole genome sequence (WGS) analysis and bioactivity assays. WGS revealed genes suggesting the ability of the two isolates to promote carbohydrate digestion, tolerance to stress and antibiotic resistance. Carbohydrate digestive ability was confirmed through a biochemical assay where the two isolates cause glucose release from starch. The two isolates also showed versatility in a range of temperature and alcohol concentration. For antibiotic resistance particularly on vancomycin, there are three mechanisms namely transporter control, transcriptional regulation, and efflux pump. Furthermore, promoter and transposable element analysis showed that some of the active antibiotic resistant (AbR) genes can be laterally transferred. Altogether, we show the potential of two probiotic isolates to be incorporated in products for improved carbohydrate digestion and the need to address the removal of active and mobile antibiotic resistance genes that may compromise safety.

Two strongly curved areas of the Carpathians in Romania are earthquake-prone: Vrancea - in the South-Eastern Carpathians, and Danubian – in the western edge of the Southern Carpathians. By far the highest seismicity episode in 2023 was recorded in the Southern Carpathians, near Targu Jiu city, of more than 4000 earthquakes. A first ML 5.2 mainshock was recorded on 13 February, followed by a second one, ML 5.7, on 14 February. Our purpose is to provide a first analysis of this sequence in order to explain its extent and unusual development, in time. The possible role of fluids in the middle crust, is discussed in connection with the rather unusual character of the space-time distribution of aftershocks. A large and high-quality dataset is provided by the dense array of seismic stations which has been gradually improved by adding new stations in the epicentral area. The thorough revision of the phase picking and location reveals a few interesting and intriguing features of seismicity that still remain worthy to be further investigated. The database built within this paper provides excellent information not only for Targu Jiu area, but for any other investigation in intra-continental regions characterized by diffuse and sporadic seismic activity.

Bacteria belonging to the genus Micromonospora are recognized as microorganisms with potential to be used in biotechnology processes, including their beneficial influence on plant growth and biocontrol of phytopathogens. In this study, nineteen Micromonospora isolates originating from root nodules of white clover plants were taxonomically assigned based on the phylogenetic analysis of the 16S rRNA gene and four housekeeping genes. The antifungal properties of the bacteria against phytopathogenic Botrytis cinerea, Fusarium oxysporum, Fusarium equiseti, Sclerotinia sclerotiorum, and Verticillium albo-atrum were tested with the agar plug test and the dual culture test. The ability to produce various metallophores was determined with the agar plug diffusion test on modified CAS agar medium. ISP2 broth amended with 0.2% L-tryptophan was used to indicate the bacterial ability to produce auxins. Strains belonging to M. tulbaghiae, M. inaquosa, and M. violae showed in vitro potential as antimicrobial agents against the tested fungi. M. inaquosa strain 152, M. violae strain 126, M. violae strain 66 and M. violae strain 45 were recognized as the most efficiency metallophores producers. M. alfalfae strain 55 and M. lupini strain 5052 were identified as the most promising auxin compound producers and, therefore, as potential plant growth promoting bacteria.

Robin sequence is a congenital anomaly characterized by a triad of features that include micrognathia, glossoptosis, and airway obstruction. This comprehensive historical review maps the evolution of approaches and appliances for its treatment from the past until current modern possibilities of interdisciplinary combination of modern engineering, medicine, materials, and computer science combined approach with emphasis to design appliances inspired by nature - individual human anatomy. Current biomimetic designs are clinically applied resulting in appliances that are more efficient, comfortable, sustainable, and safer than legacy traditional designs. Review maps the treatment modalities that have been used for patients with Robin sequence over the years. Early management of Robin sequence focused primarily on airway maintenance and feeding support, while current management strategies involve both nonsurgical and surgical interventions and biomimetic biocompatible personalized appliances. The goal of this paper was to provide a review of the evolution of management strategies for patients with Robin sequence that led to the current interdisciplinary biomimetic approaches impacting the future of Robin Sequence treatment with biomimetics at the forefront.

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we present an improved innovative sequence–activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this improved approach, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability than that predicted using the existing data. We successfully improved the determination coefficient (R2) of the model from 0.66 to 0.92. In addition, root mean square deviation (RMSD) and root mean square fluctuation (RMSF) were estimated and conformation analysis based on molecular dynamics simulations was performed to verify the enhanced thermal stability of the screened mutants. The improved innov'SAR algorithm enhanced the predictive accuracy, suggesting a method for modifying the stability of AT-ATA, which may help in directed evolutionary screening and open up new avenues for protein engineering.

Sequence analysis is a robust methodological framework that has gained popularity in various fields, including transportation research. It provides a comprehensive approach to understanding the dynamics and patterns of individual behaviors over time. In the context of the Metropolitan Region of Barcelona, applying sequence analysis to the mobility surveys offers valuable insights into the sequencing and order of travel activities and modes, shedding light on the complex interrelationship between individuals, their travel choices, and the built environment. The Barcelona travel surveys collect detailed data on individuals' travel behavior, such as trip purpose, duration, mode of transportation, and origin-destination pairs. Sequence analysis allows for examining travel behaviors as dynamic processes, unveiling travel patterns' underlying structure and evolution in a day. A data analytics methodological approach is described; it enables the identification of common travel patterns and the exploration of variations across different demographic groups or geographical regions. Sequence analysis reveals insights into the factors influencing mode choice and potential opportunities for sustainable transport interventions. The paper proposes a methodological approach to discover homogeneous travel behavioral segments from diaries included in travel surveys in order to refine transport policies to selected segments by transportation planners and authorities

Bacterial phylogenetics has largely been determined via 16S rRNA gene sequencing and phylogenetic tree reconstruction. Observed utility of this approach has driven the popularity of the 16S rRNA gene amplicon metagenomics method for profiling and identifying diverse microbes from specific habitats. This work sought to develop universal primers for amplifying the 16S rRNA gene from a consortium of disparate microbial species. Using multiple sequence alignment of the 16S rRNA gene of a variety of microbes, the resulting highly conserved region of the consensus sequence was used for design of universal polymerase chain reaction (PCR) primers for 16S rRNA gene. Application of the universal primers in simulated PCR reveals poor amplification efficiency where only 12 species out of 31 generated an amplicon. BLAST analysis of the resulting amplicons reveals a classification error of 50%. More significantly, analysis of the amplicon length indicates variable read length ranging from 81 to 122 base pair compared to the predicted read length of 100 base pairs. This suggests that the 16S rRNA gene harbours significant hitherto underappreciated sequence diversity, and may have unknown alternative splicing and recombination mechanisms. Overall, results from this study suggests that primer design for 16S rRNA amplicon metagenomics may be application and habitat specific, where it is difficult to design universal primers for all bacterial species. Conceptually, this meant that there may be sequence co-evolution in 16S rRNA gene for microbial species in the habitat where environmental and nutritional conditions impact on 16S rRNA gene structure and sequence. In essence, 16S rRNA gene may habour epigenetics signals at the gene level.

Malaria rapid diagnosis test (RDT) is crucial for managing the disease, and the effectiveness of detection depends on parameters such as sensitivity and specificity of the RDT. Several factors can affect the performance of RDT. In this study, we focus on pfhrp2 sequence variation and its impact on RDTs targeted by antigens encoded by pfhrp2. Field samples collected during cross-sectional surveys in Tanzania were sequenced to investigate pfhrp2 sequence diversity and evaluate the impact on HRP2-based RDT performance. We observed significant mean differences in amino acid repeats between current and previous studies. Several new amino acid repeats were found to occur at different frequencies, including types AAY, AHHAHHAAN and AHHAA. Based on the abundance of types 2 and 7 amino acid repeats, the binary predictive model was able to predict RDT insensitivity by about 69 % in the study area. About 85% of the major epitopes targeted by Monoclonal antibodies (MAbs) in RDT were identified. Our study suggests that the extensive sequence variation in the pfhrp2 could contribute to reduced RDT sensitivity. The correlation between the different combinations of amino acid repeats and the performance of RDT in different malaria transmission settings should be investigated further.

In the context of all-digital radar systems, phase-modulated continuous wave (PMCW) based on pseudorandom binary sequences (PRBSs) appears a prominent candidate modulation scheme for applications such as autonomous driving. Among the reasons for that are its simplified transmitter architecture and lower linearity requirements, e.g., compared to orthogonal-frequency division multiplexing radars, as well as its high velocity unambiguity and multiple-input multiple-output operation capability that are characteristic of digital radars. For appropriate operation of a PMCW radar, choosing a PRBS whose periodic autocorrelation function (PACF) has low sidelobes and high robustness to Doppler shifts is paramount. In this sense, this article performs an analysis of Doppler shift tolerance of the PACFs of typically adopted PRBSs in PMCW radar systems supported by simulation and measurement results. To accurately measure the Doppler-shift-induced degradation of PACFs, peak power loss ratio (PPLR), peak sidelobe level ratio (PSLR), and integrated-sidelobe level ratio (ISLR) were used as metrics. Furthermore, to account for effects on targets whose ranges are not multiples of the range resolution, oversampled PACFs are analyzed.

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

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

Analysis of SARS-CoV-2 spike protein sequences of over 19 countries from biological databases submitted around the globe was carried out with help of bioinformatics tools and structure prediction databases. Initial data analysis showed entry of virus into different geographic regions started in the month of January 2020. Meanwhile, alignment of spike protein sequences of SARS-CoV-2 isolates from China and other countries revealed a critical mutation of D614G. Surprisingly, mutation D614G was not seen in early samples submitted in the month of January but gradually it started appearing globally from the month of March 2020. However, the mutations of amino acids in the spike protein other than D614G exhibiting similar pI and altered polarity were found to be specific to geographical regions. Besides, prediction of homology model for interaction of spike protein showed predominant role of chain C of trimeric spike protein in adhering receptor binding domain (RBD) of human ACE2 receptor. Furthermore, the prediction of glycosylation points has revealed that there are about 20 N-glycosylation potential sites on spike protein. We believe that the information present here would not only help in thorough understanding of infectivity but also enhance the knowledge of the scientific community in developing prophylactics and/or therapeutics for SARS-CoV19-2 virus.

Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of overlapping genes likely to encode a functional protein in human parvovirus B19 (genus erythroparvovirus), using an experimentally validated software, Synplot2. Synplot2 detected an open reading frame, X, conserved in all erythroparvoviruses, which overlaps the VP1 capsid gene, and is under highly significant selection pressure. In a related virus, human parvovirus (genus tetraparvovirus), Synplot2 also detected an open reading frame under highly significant selection pressure, ARF1, which overlaps the VP1 gene. X and ARF1 have exactly the same location (both overlap the region of VP1 encoding the phospholipase A2 domain), and encode proteins with similar predicted properties, such as a transmembrane region, strongly suggesting that they are homologous. These findings provide compelling evidence that the X protein must be expressed and functional. It is probably translated either from a polycistronic mRNA by a non-canonical mechanism, or from an unmapped monocistronic mRNA. Finally, we also discovered proteins predicted to be expressed from a frame overlapping VP1 in other species related to parvovirus B19: porcine parvovirus 2 (Z protein) and bovine parvovirus 3 (X-like protein).

This paper presents a comprehensive simulation study of Automated Guided Vehicles (AGVs) in a fabricated production environment for toy car assembly. This paper uses Petri Nets for modeling and the General Petri Net Simulator (GPenSIM) for model implementation on MATLAB and simulation. The primary focus of this research is to analyze the operational efficiency of AGVs under varying conditions, particularly examining the impact of battery charge reduction rates and the strategic placement of charging stations within the production line. By employing Colored Petri Nets (CPN) within GPenSIM, we have developed a detailed and dynamic model that captures the intricate movements and interactions of AGVs in a simulated manufacturing setting. By presenting an approach to simulating AGVs in a production environment, this paper specifically focuses on two critical operational parameters: the battery charge reduction rate of AGVs and the number of charging stations available in the production line. Unlike previous studies that have primarily concentrated on general path planning or bottleneck detection in manufacturing systems, this paper delves into the intricate balance between AGV operational efficiency and the logistical constraints imposed by battery life and charging infrastructure.

We propose a full binary directed tree to represent the set of natural numbers and further divide the set into three sets: pure odd, pure even, and mixed numbers. We utilize a binary string to represent a natural number and demonstrate the composite procedure of odd-number and even-number functions. We analyze the sequence of iteration (or composite) of the Collatz function and reduced Collatz function analog to the inverse function in order to test the Collatz conjecture. We do this by using the parity of a natural number. In order to prove the conjecture, we provide tabular and binary strings to the algebraic formula that states the Collatz sequence. Ultimately, we can convert discrete powers of 2 into continuous powers of 2, ultimately arrive at the smallest natural, 1. If any natural number is the beginning value, the sequence produced by the infinite iterations of the Collatz function becomes the eventually periodic sequence, proving an 87-year-old conjecture.

The early elongation events in transcription or translational control in the N-terminal of genes are assuming critical roles in their heterologous expression. The secretory expression of the alkaline pectin lyase APL in B. subtilis were studied to explore the effects of the N-terminal 5-7 amino acids sequences of different signal peptides on gene transcription and protein secretion in this study. The first 5 amino acid sequences of the N-terminal of the signal peptide LipA were identified to play an important role in promoting the expression of APL for the first time. Meanwhile, it also revealed that the signal peptide LipA could lead to higher secretory expression than other signal peptides not because of its sequence structure associated with secretion is stronger but because the N-terminal sequences showed greater advantages in gene transcription. At this basis, the recombinant strain structed in this work showed a new record for the highest extracellular yields (12 295 U/ml) of APL in B. subtilis which was 1.9 times higher than that expressed in the recombinant Escherichia coli strain we had reported before. The novel theories revealed in this study would assuming significance roles for improving expression of foreign proteins in or out of the cells.

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.

The genus Vigna is penta-tropical having more than 200 species with many desirable economically important traits. The aim of study was to validate the in-silico polymorphism of whole genome sequence developed mungbean specific SSR markers and their transferability among the different Vigna species. The present study utilized a set of 200 SSR markers developed from whole genome sequence of mungbean and validated using a diversity panel of 25 accessions which belongs to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species and the number of alleles amplified varied between 7 to24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Based on allelic data, the 25 Vigna accessions grouped into three clusters based upon the unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree. The principal co-ordinates analysis (PCA) biplot graph and UPGMA based neighbor joining clustering diagram showed similar pattern of Vigna accessions distribution. The population structure assessment has grouped the cultivated and wild species accessions into two sub-population. The estimated marker parameters such as polymorphic information content (0.09 – 0.84), marker index (0.091 – 3.342) and effective multiplex ratio (1.0 – 4.0) suggested their adequacy in several genetic studies such as parental selection, hybrid testing, genetic mapping and marker aided breeding programmes for genetic enhancement of species belonging to the Vigna genus.

The market for microfluidic chips is experiencing significant growth; however, their development is hindered by a complex design process and low efficiency. Enhancing microfluidic chips’ design quality and efficiency has emerged as an integral approach to foster their advancement. Currently, the existing structural design schemes lack careful consideration regarding the impact of chip area, microchannel length, and the number of intersections on chip design. This inadequacy leads to redundant chip structures resulting from the separation of layout and wiring design. This study proposes a structural optimization method for microfluidic chips to address these issues utilizing a simulated annealing algorithm. The simulated annealing algorithm generates an initial solution in advance using the fast sequence pair algorithm. Subsequently, an improved simulated annealing algorithm is employed to obtain the optimal solution for the device layout. During the wiring stage, an advanced wiring method is used to designate the high wiring area, thereby increasing the success rate of microfluidic chip wiring. Furthermore, the connection between layout and routing is reinforced through an improved layout adjustment method, which reduces the length of microchannels and the number of intersections. Finally, the effectiveness of the structural optimization approach is validated through six sets of test cases, successfully achieving the objective of enhancing the design quality of microfluidic chips.

Background: To compare the clinical efficacy of Japas osteotomy of the middle foot and first metatarsal sequence osteotomy in treating children with cavovarus foot deformity. Methods: A retrospective analysis was performed on the clinical effect of cavovarus foot surgery from January 2012 to January 2019. Thirty light and medium cavovarus foot cases underwent osteotomy based on soft tissue release. Among them, 16 cases of 22 feet underwent first metatarsal sequence osteotomy, and 14 cases of 21 feet underwent middle foot Japas osteotomy. Ankle-posterior foot (Wicart) scoring system was used to evaluate the good and good rates of the two surgical methods. X-ray films were taken before and after the last follow-up in a standing weight-bearing position, and Meary Angle, Hibb Angle, and Pitch Angle were measured to compare the clinical efficacy of the two surgical methods in correcting the light and medium-cavovarus foot deformity.Results: (1) All patients were followed up for an average of 30 months. There was no significant difference in Meary, Hibb, and Pitch Angle between first metatarsal osteotomy and middle foot Japas osteotomy before surgery, indicating that the severity of malformation was similar between the two groups. (2) The Meary, Hibb, and Pitch Angle of the last follow-up were compared between the two groups (P>0.05), which showed no statistical significance, indicating that the two surgical methods had similar effects on cavovarus deformity correction. (3) At the most recent follow-up, there was no statistically significant difference between the two groups regarding the percentage of patients who achieved an excellent or good Wicart score; for the first metatarsal osteotomy group, the rate was 87%, and for the Japas osteotomy group was 90%; the Fisher test p>0.05 indicates that the postoperative excellent and good rates of the two treatments are comparable.II (4) Comparison of operation time and intraoperative blood loss between the two groups, P<0.05, showed statistically significant differences, indicating that the first metatarsal osteotomy had obvious advantages over Japas osteotomy operation time and intraoperative blood loss. Conclusions: There is no significant difference in postoperative efficacy between first metatarsal osteotomy and Japas osteotomy for light and medium-cavovarus with the apex of the deformity located at the medial cuneus or navicular cuneiform joint. However, the intraoperative blood loss and operative time of first metatarsal osteotomy are superior to Japas osteotomy of the middle foot, and the trauma to children is less. Therefore, the first metatarsal osteotomy can be considered a surgical procedure.

In view of the problem of cracking easily and partial distortion of images after encryption or decryption, a novel image encryption and decryption algorithm based on Arnod Transform and fractional chaotic is proposed. To begin with, the Arnold transform is used to encrypt. So that the spatial confidence of the original image has been comprehensively disturbed. Secondly, the XOR involving the fractional order chaotic sequence is used to encrypt. The key sequence is dynamically generated to ensure the randomness and difference of key generation. When decryption is required, the first decryption is performed using the key and XOR. Then the second decryption is carried out by using the inverse Arnold transform, and finally the decrypted image is obtained. Experimental results show that the improved algorithm has achieved better performance in encryption and decryption.

Cytosine (C) to uracil (U) RNA editing is one of the most important post-transcriptional processes, however exploring C-to-U editing events efficiently within the crop mitochondrial genome remains a challenge. An improving predictive RNA editor for crop mitochondrial genomes, iPReditor-CMG, was proposed, which was based on SVM, three common crop mitochondrial genomes and self-sequenced tobacco mitochondrial ATPase. After multi-combination feature extracting, high-dimension feature screening and multi-test independent predicting, the results showed that the average accuracy of intraspecific prediction was 0.85, and the highest value even up to 0.91, which outperformed the previous reference models. While the prediction accuracies were 0.78 between dicotyledons and no more than 0.56 between dicotyledons and monocotyledons, implying a possible similarity in C-to-U editing mechanisms among close relatives. The best model was finally identified with an independent test accuracy of 0.91 and an area under the curve of 0.88, and further suggested that five unreported feature sequences TGACA, ACAAC, GTAGA, CCGTT and TAACA were closely associated with the editing phenomenon. Multiple evaluation findings supported that the iPReditor-CMG could be effectively applied to predict crop mitochondrial editing sites, which may contribute to insight into their recognition mechanisms and even other post-transcriptional events in crop mitochondria.

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

Background Robotic-assisted thoracic surgery (RATS) has become the standard procedure for treating lung malignancy, offering numerous advantages over traditional methods. However, the minimally invasive nature of RATS presents unique challenges, notably a limited field of view and reduced tactile feedback for the surgeon. These limitations can significantly impact the surgeon's ability to navigate complex anatomical structures during surgery. To address these challenges, we recognized the need for enhanced preoperative familiarization with each patient’s specific anatomy. In response, we developed an innovative virtual reality (VR) surgical navigation system, utilizing head-mounted displays (HMDs), designed to provide surgeons with a more comprehensive and interactive understanding of the patient's anatomy before the actual surgery. This VR system aims to extend the surgeon's capabilities in both preoperative sumilation and intraoperative navigation, potentially mitigating the inherent limitations of RATS. Methods Three-dimensional (3D) volumized data, meticulously extracted from preoperative computed tomography (CT) scans, were seamlessly integrated into the Perspectus VR Education software. These data were then displayed on an HMD, facilitating an interactive 3D reconstruction of pulmonary structures. This reconstruction allowed for each structure to be visualized individually, enabling detailed preoperative resection simulations tailored to each patient's unique anatomy. During RATS, these specific 3D reconstructed images were made accessible within the surgeon's console through the TilePro™ multi-display input, providing real-time, intraoperative guidance. Results During the preoperative simulations, the 3D anatomic structure of the pulmonary vessels, as well as the spatial relationship between the lesion and adjacent tissues, were successfully visualized. This enhanced visualization enabled surgeons to thoroughly evaluate a patient's anatomy, significantly improving the safety and accuracy of the subsequent procedure. The integration of VR software with the HMD provided surgeons with a true 3D interaction with real patient data. This setup not only offered a unique perspective through the surgical console but also allowed for easy manipulation of the data on a mobile laptop, thereby enhancing the overall surgical planning process. Conclusions VR simulation using HMDs offers a viewing experience akin to that of a robotic 3D viewer, potentially providing an innovative avenue for surgeons to develop specific robotic surgical skills without the need for practicing on live patients. This technology, when integrated with routine imaging modalities, can significantly enhance preoperative planning. Such integration not only contributes to the safety but also improves the accuracy of anatomical resections. Our findings suggest that VR simulation with HMDs is particularly effective in assisting surgeons to accurately identify lesion locations in RATS, thereby optimizing surgical outcomes.

Interactions between proteins and ions are essential for various biological functions like structural stability, metabolism, and signal transport. Given that more than half of all proteins bind to ions, it becomes crucial to identify ion-binding sites. Accurate identification of protein-ion binding sites helps us to understand proteins’ biological functions and plays a significant role in drug discovery. While several computational approaches have been proposed, this remains a challenging problem due to the small size and high versatility of metals and acid radicals. In this study, we propose IonPred, a sequence-based approach that employs ELECTRA (Efficiently Learning an Encoder that Classifies Token Replacements Accurately) to predict ion binding sites using only raw protein sequences. We successfully fine-tuned our pretrained model to predict the binding sites for nine metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, and K+) and four acid radical ion ligands (CO32−, SO42−, PO43−, NO2−). IonPred surpassed six current state-of-the-art tools by over 44.65% and 28.46% respectively in F1 score and MCC when compared on an independent test dataset. Our method is more computationally efficient than existing tools producing prediction results for a hundred sequences for a specific ion in under ten minutes.

In this paper, chaos sequence is used to replace the traditional Spread Spectrum sequence. From the perspective of the communication partner, a new method of generating the initial value of chaotic sequence is proposed, which is more suitable for the multi-base Spread Spectrum System and easy to extract. In order to further improve the error performance of the system and ensure the integrity of the system, an improved suboptimal soft information extraction method based on log-likelihood ratio (LLR) is proposed in the channel coding module, which can further improve the error performance of the system. On this basis, we choose the synchronization mode of multiple transmission of one reference signal to solve the problem that chaotic sequence is difficult to obtain synchronization because of its aperiodic characteristics. Finally, the system is simulated in the channel with low SNR. The simulation results show that chaotic sequence as Spread Spectrum code can make the signal transmit accurately in the worse channel environment. The performance gain of applying soft information decoding decision in the M-ary Spread Spectrum System with chaotic sequence as Spread Spectrum code can reach 5.2dB compared with the traditional Direct Spread Spectrum System.

Infectious bursal disease (IBD) is a viral poultry disease known worldwide for impacting the economy and food security. The disease is endemic in Nigeria, with reported outbreaks in vaccinated poultry flocks. To gain insight into the dynamics of infectious bursal disease virus (IBDV) evolution in Nigeria, near-complete genomes of four IBDVs were evaluated. Amino acid sequences in the hypervariable region of the VP2 revealed conserved markers (222A, 242I, 256I, 294I and 299S), associated with very virulent (vv) IBDV, including the serine-rich heptapeptide motif (SWSASGS). Based on the newly proposed classification for segments A and B, the IBDVs clustered in the A3B5 group (where A3 are IBDVs with vvIBDV-like segment A and B5 are from non-vvIBDV-like segment B) forming a monophyletic subcluster. Unique amino acid mutations with yet-to-be-determined biological functions have been observed in both segments. Amino acid sequences of the Nigerian IBDVs showed that they are reassortant viruses. Circulation of reassortant IBDVs may be responsible for the vaccination failures observed in the Nigerian poultry population. Close monitoring of changes in the IBDV genome is recommended to nip deleterious changes in the bud, through the identification and introduction of the most appropriate vaccine candidates and advocacy/extension programs for properly implementing disease control.

In this article, we introduce the concept of soft intervals, soft ordering and sequences of soft real numbers, and some of their structural properties are studied. The notion of soft Lebesgue measure on the soft real numbers has been introduced. Also, a correspondence relationship has been established between the soft Lebesgue measure and the classical Lebesgue measure. Furthermore, we have studied some exciting results and relations between the soft Lebesgue measure and the Lebesgue measure of soft real sets.

The method of doublet frequency distance (DFD-) maps was applied, here, for visualization of DNA sequence structures of yeast chromosomes. The colour scale “rainbow” of the Octave programming tool is well suited for such visualization. The DFD-maps are generated by comparison of the differences in the number of all base doublets in a shifting frame with all other positions of this frame in a regarded DNA sequence section. This procedure can be applied from DNA-sections of between a few hundred bases (bps) up to a complete chromosome with a million or more bps. An orthogonal DFD-map pattern dominates all chromosomes and its parts. It can be interpreted by a large number of successive mutation events during evolution. In contrast, diagonal patterns indicate duplications of sequence sections and multiple tandem repeats. These periodic structures are found in several chromosomes and are more or less regular or noised. The larger tandem repeat in the subtelomeric region of chromosome 12 presents a characteristic example of a nested multiple-repeat structure. Its pattern in the DFD-map illustrates obviously a temporal order of duplication and mutation events leading to a hierarchical sequence architecture.

The investigation of membrane proteins, key constituents of cells, is hampered by the difficulty and complexity of their in vitro synthesis, of unpredictable yield. Cell-free synthesis is herein employed to unravel the impact of the expression construct on gene transcription and translation, without the complex regulatory mechanisms of cellular systems. Through the systematic design of plasmids in the immediacy of the start of the target gene, it was possible to identify translation initiation and the conformation of mRNA as the main factors governing the cell-free expression efficiency of the human voltage dependent anion channel (VDAC), a relevant membrane protein in drug-based therapy. A simple translation initiation model was developed to quantitatively assess the expression potential for the designed constructs. A scoring function is proposed that quantifies the feasibility of formation of the translation initiation complex through the ribosome-mRNA hybridization energy and the accessibility of the mRNA segment binding to the ribosome. The scoring function enables to optimize plasmid sequences and semi-quantitatively predict protein expression efficiencies. This scoring function is publicly available as webservice XenoExpressO at rna.tbi.univie.ac.at.

Heavy metals are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P1B-1-ATPase, 5 putative P1B-3-ATPase and 4 putative Zn(II)/Cd(II) P1B-4 type ATPase, and 16 putative RND-type metal transporter systems. Moreover, the four genomes carry a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci include genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system) respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

Background: Glioblastoma remains a challenging brain tumor to treat due to its infiltrative nature. Accurately identifying tumor boundaries during surgery is crucial for successful tumor resection. This study introduces an innovative intraoperative visualization method utilizing a surgical fluorescence microscope to precisely locate tumor cells. The focus of the study is on IR-Glint, a novel preparation comprising Cy7.5-labeled aptamers Gli-233nt and Gli-55_3L specific to human glioblastoma. Methods: The aptamers were modified using molecular modeling and quantum chemical techniques. The effectiveness of the preparation was assessed using flow cytometry and microscopy on primary cultures of human glioblastoma. In vivo studies were conducted on mouse and rabbit models, employing orthotopic xenotransplantation of human brain glioblastoma with various imaging techniques, including PET/CT, in vivo fluorescence visualization, confocal laser scanning, and surgical microscopy. Results: The experiments validated the potential of IR-Glint for intraoperative visualization of glioblastoma using infrared imaging. Surface application of the aptamer-based formulation on the brain allowed clear visualization of the tumor, aiding surgeons in tumor resection. This approach also reduces the dosage required and mitigates potential toxic effects on the patient. Conclusions: This study demonstrates the promising potential of using in-frared dye-labeled aptamers for intraoperative visualization of glioblastoma. By improving surgical treatment outcomes in neurosurgery, this novel approach may pave the way for future advancements in the field.

This article aims to assess, discuss and analyze the disturbances caused by electromagnetic field (EMF) noise of medical devices used nearby living tissues, as well as the corresponding functional control via the electromagnetic compatibility (EMC) of these devices. These are minimally invasive and non-ionizing devices allowing various healthcare actions involving monitoring, assistance, diagnosis and image-guided medical interventions. Following to an introduction of the main items of the paper, the different imaging methodologies are conferred, accounting for their nature, functioning, employment condition and patient comfort and safety. Then the magnetic resonance imaging (MRI) components and their fields, the consequential MRI-compatibility concept and possible image artifacts are detailed and analyzed. Next, the MRI-assisted robotic treatments, the possible robotic external matter introductions in the imager, the features of MRI-compatible materials and the conformity control of MRI-compatibility, are analyzed and conferred. Afterward, the embedded, wearable and detachable medical devices, their EMF perturbation control and their necessary shielding protection technologies are presented and analyzed. Then, the EMC control procedure, the EMF governing equations, the body numerical virtual models, are conferred and reviewed. A qualitative methodology, case study, simple example illustrating the mentioned methodology is presented. The last Section of the paper discussed potential details and expansions of the different notions conferred in the paper, in the perspective of monitoring the disturbances due to EMF noise of medical devices working near living tissues.

Spinal metastatic tumors are common and often cause debilitating symptoms. Image-guided percutaneous thermal ablation (IPTA) has gained significant recognition in managing spinal column tumors due to its exceptional precision and effectiveness. Conventional guidance modalities, including computed tomography, fluoroscopy, and ultrasound, have been important in targeting spinal column tumors while minimizing harm to adjacent critical structures. This study presents a novel approach utilizing a fusion of Cone Beam Computed Tomography with Magnetic Resonance Imaging to guide percutaneous thermal ablation for four patients with secondary spinal column tumors. The visual analog scale (VAS) evaluated procedure effectiveness during an 18-month follow-up. Percutaneous vertebroplasty was performed in two cases, and a thermostat was used during all procedures. Imaging was performed using the Stealth Station navigation system Spine 8 (SSS8) and a 1.5T MRI machine. The fusion of CBCT with MRI allowed precise tumor localization and guidance for thermal ablation. Initial results indicate successful tumor ablation and symptom reduction, emphasizing the potential of CBCT-MRI fusion in spinal column tumor management. This innovative approach is promising in optimizing therapy for secondary spinal column tumors. Further studies are necessary to validate its efficacy and applicability.

Classifying spinal tumors can be challenging due to nonspecific clinical and radiological qualities, and a precise biopsy is crucial for an accurate diagnosis and treatment planning. This study aimed to enhance the accuracy and efficiency of spinal biopsies integrating Cone Beam Computed Tomography (CBCT) and magnetic resonance imaging (MRI) modalities using an O-arm CT navigation system. Eighteen patients with diverse spinal lesions underwent 18 biopsies following the Stealth Station navigation system Spine 8 protocol. Preoperative MRI scans were merged with intraoperative CT navigation systems for continuous monitoring during the biopsy process. The combined imaging technique accurately identified the diseased lesion type in all biopsies, demonstrating 100% sensitivity and specificity. In conclusion, combining MRI and CT imaging modalities significantly improved spinal biopsy accuracy and efficiency, differentiating between pathological entities. However, large-scale studies are desired to validate these findings and investigate potential benefits in different clinical scenarios. Although this method requires general anesthesia, its potential profits in avoiding misdiagnosed lesions and decreasing the need for further invasive procedures make it a promising approach for improving spinal biopsy accuracy and efficiency.

СrAss-like phages play an important role in maintaining ecological balance in the human intestine microbiome. However, their lifestyle and genetic diversity are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon сrAss-like phage genomes was found. Detailed analysis indicated that CrAssE-Sib encodes unusual proteins – DNA primase, virion RNA polymerase, prophage antirepressor, and transcriptional repressor, as well as reverse transcriptase (RT) and receptor binding protein (RBP) that are part of diversity-generating retroelement (DGR). Comparative analysis showed that all epsilon сrAss-like phages are divided into two putative genera, which were proposed to name Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the first of them. RT from CrAssE-Sib and several Epsilonunoviruses contains a specific motif in its fourth domain that was not previously found in RTs from phage and bacterial DGRs. In addition, RBP from CrAssE-Sib and all Epsilonunoviruses has a unique structure. The presence of the conservative prophage repressor and anti–repressors that belong to the lysogenic-to-lytic cycle switches indicate that CrAssE-Sib and other Epsilonunoviruses could be temperate. Epsilon сrAss-like phage substantially differ from other crAss-like phages, including zeta сrAss-like phages. This fact indicates the need to isolate these phages into a separate family.

Drug-target affinity (DTA) prediction is crucial for understanding molecular interactions and aiding drug discovery and development. While various computational methods have been proposed for DTA prediction, their predictive accuracy remains limited, failing to delve into the structural nuances of interactions. With increasingly accurate and accessible structure prediction of targets, we developed a novel deep learning model, named S2DTA, to accurately predict DTA by fusing sequence and structural knowledge of drugs, targets, and pockets using heterogeneous models based on graph and semantic networks. Experimental findings underscored that complex feature representations imparted negligible enhancements to the model’s performance. However, the integration of heterogeneous models demonstrably bolstered predictive accuracy. In comparison to three state-of-the-art methodologies, the supremacy of S2DTA became strikingly apparent. It showcased a noteworthy 25.2% reduction in Mean Absolute Error (MAE) and an impressive 20.1% decrease in Root Mean Square Error (RMSE). Furthermore, S2DTA exhibited substantial advancements in other pivotal metrics, including Pearson Correlation Coefficient (PCC), Spearman, Concordance Index (CI), and R2. These metrics experienced remarkable increments of at least 19.6%, 17.5%, 8.1%, and a remarkable 49.4%, respectively. Finally, we conducted interpretability analysis on the effectiveness of S2DTA by bidirectional self-attention mechanism, fully proving that S2DTA is a valuable and accurate tool for predicting DTA. For further exploration, the source data and code repository can be accessed at https://github.com/dldxzx/S2DTA.

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in people in the city of Wuhan at the end of December 2019, and it has since spread to all continents. Global interest has been focused on discovering a treatment and developing a successful coronavirus vaccine as a result of the emergence of this new coronavirus. In this research, we sequenced the whole genome of the SARS-COV-2 virus that were isolated from 40 patients in Duhok, Iraq. 95 different mutations were identified in our isolation when such the whole genome sequence of the SARS-COV-2 isolated from the city of Wuhan, China (Accession number: NC 045512.2) was matched to the virus's sequence using Sequencing technology (Illumina , USA ) and Assembly method (iVar 1.3.1). Sequence analysis revealed that 38 mutations were found at spike glycoprotein (S), 30 of which were found in the ORF1b , 11 mutations were found in ORF1b ,7,3,2,1 mutations were found in ( N,M,ORF6 ,ORF9 /E ) genes which had been linked to structural changes at various places. The conclusion that the cases in Iraq were of different origins of infections and had a close relationship with the isolates from different country and state were further confirmed by phylogenetic analysis and transmission. The whole genome sequence of the SARS-CoV-2 , which were identified from the Iraqi Kurdistan region, and reported as a first study in Kurdistan region.

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 chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

Bacterial cellulose (BC) is receiving great attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of high cost and low productivity. In this light, the isolation of new BC producing bacteria and selection of high productive strains became a promising issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly by strains belonging to the genus Komagataeibacter. In this study Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability in producing BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30 used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods, which are the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using two different approaches revealed the suitability of the fingerprints techniques, showing a discrimination power, calculated as D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model from the two genotyping experiments was performed, allowing to discriminate among strains.

The determination of crack propagation velocities can provide valuable information for a better understanding of damage processes of concrete. The spatio-temporal analysis of crack patterns developing at a speed of several hundred meters per second is a rather challenging task. In the paper, a photogrammetric procedure for the determination of crack propagation velocities in concrete specimens using high-speed camera image sequences is presented. A cascaded image sequence processing which starts with the computation of displacement vector fields for a dense pattern of points on the specimen’s surface between consecutive time steps of the image sequence chain has been developed. These surface points are triangulated into a mesh, and as representations of cracks, discontinuities in the displacement vector fields are found by a deformation analysis applied to all triangles of the mesh. Connected components of the deformed triangles are computed using region-growing techniques. Then, the crack tips are determined using principal component analysis. The tips are tracked in the image sequence and the velocities between the time stamps of the images are derived. A major advantage of this method as compared to established techniques is in the fact of its allowing for spatio-temporally resolved, full-field measurements rather than point-wise measurements and that information on crack width can be obtained simultaneously. To validate the experimentation, the authors processed image sequences of tests on four compact-tension specimens performed on a split-Hopkinson tension bar. The images were taken by a high-speed camera at a frame rate of 160,000 images per second. By applying to these datasets the image sequence processing procedure as developed, crack propagation velocities of about 800 m/s were determined with a precision in the order of 50 m/s.

The shortage of physicians in rural communities contributes to increased mortality rates among Medicare beneficiaries. This increase in mortality risk is commonly due to diseases such as heart disease and cancer, including melanoma and non-melanoma skin cancer (NMSC). Mohs micrographic surgery (MMS) is considered the gold-standard treatment for NMSC tumors, however, due to a shortage of dermatologists and Mohs surgeons in rural areas, access to MMS is limited. In these areas, image guided superficial radiation therapy (IGSRT) serves as a viable option for the treatment of NMSC lesions, with fewer recurrences and 99% cure rates, which are comparable to MMS cure rates. IGSRT is performed in dermatology clinics with support from a multidisciplinary team, including radiation therapists, medical physicists, radiation oncologists, and dermatologists. As IGSRT is able to be performed by general dermatologists, Medicare beneficiaries in rural communities will have an increase in access to treatment options and a decrease in delayed skin cancer treatment.

Introduction – Molecular tests can contribute to improve the preoperative diagnosis of thyroid nodules. Tests available are expensive and not adapted to different population. Aim – This study aimed to compare the cyto-histological genetic profile, and to evaluate the reliability of molecular tests on Ultrasound-guided Fine Needle Aspiration Cytology (US-FNAC) in accurately diagnosing differentiated thyroid carcinomas (DTCs) and predicting biologic behavior of papillary thyroid carcinomas (PTCs). Material and methods – The series included 259 patients with paired cyto-histological samples totalizing 518 samples. The genetic alterations were analyzed by PCR/Sanger sequencing. The association with clinicopathologic features was evaluated in PTCs. Results/Discussion – From the 259 patients included, histologies were 50 (19.3%) benign controls and 209 (80.7%) DTCs cases, from which 182 were PTCs; cytologies were 5.8% non-diagnostic, 18.2% benign, 39% indeterminate and 37.1% malignant. In histology, indeterminate nodules (n=101) were 22.8% benign and 77.2% malignant. Mutation frequencies in cytology and histology specimens were, respectively, TERTp: 3.7% vs. 7.9%; BRAF: 19.5% vs. 25.1%; RAS: 11% vs. 17.5%. The overall cyto-histological agreement of the genetic mutations was 94.9%, Cohen’s k=0.67, and in indeterminate nodules 95.7%, k=0.64. The identified mutations exhibited a discriminative ability in diagnosing DTC with a specificity of 100% for TERTp and BRAF, and of 94% for RAS, albeit with low sensitivity. TERTp and BRAF mutations were associated with aggressive clinicopathological features and tumor progression in PTCs (p<0.001). The obtained good cyto-histological agreement suggests that molecular analysis in US-FNAC may anticipate the genetic profile and the behavior of thyroid tumors, confirming malignancy and contributing to refer patients towards surgery.

Neisseria meningitidis (N. meningitidis) serogroup B (MenB) is the leading cause of invasive meningococcal disease worldwide. The pathogen has a wide range of virulence factors, which are potential vaccine components. Studying the genetic variability of antigens within a population, especially their long-term persistence, is necessary to develop new vaccines and predict the effectiveness of existing ones. The multicomponent 4CMenB vaccine (Bexsero), used since 2014, contains three major genome-derived recombinant proteins: factor H-binding protein (fHbp), Neisserial Heparin-Binding Antigen (NHBA) and Neisserial adhesin A (NadA). Here, we assessed the prevalence and sequence variations of these vaccine antigens in a panel of 5667 meningococcal isolates collected worldwide over the past 10 years and deposited in the PubMLST database. Using multiple amino acid sequence alignments and machine learning methods, we estimated the potential strain coverage by fHbp and NHBA vaccine variants (51 and about 30%, respectively); the NadA antigen sequence was found in only 17.8% of MenB genomes analyzed, but cross-reactive variants were present in less than 1% of isolates. Based on our findings, we proposed various strategies to improve the 4CMenB vaccine and broaden coverage of N. meningitidis strains.

The genus Fusarium includes several agronomically important and toxin-producing species, that are worldwide distributed and can cause a wide range of diseases. Crown and stalk rots and grain infections are among the most severe symptoms that Fusarium spp. can cause on maize. The disease development usually occurs during germination, but it may also affect the later phases of plant growth. The purpose of this study was to investigate the diversity and the patho-genicity of 41 isolates recovered from symptomatic seedlings collected in Northern Italy, and from seeds with five different geographical origins during 2019 and 2020. The pathogenicity was tested and confirmed on 23 isolates causing rotting on maize seedlings. A multi-locus phylogeny analysis, based on four genomic loci (tef1-α, rpb2, calm and tub2), was performed for 23 repre-sentative isolates. Representative isolates were identified as species belonging to three species complexes (SC). Fusarium verticillioides and F. annulatum in the F. fujikuroi SC. Fusarium commune was identified in the F. nisikadoi SC, and three different lineages were found in the Fusarium ox-ysporum SC. This study reports F. annulatum, and two lineages of the Fusarium oxysporum SC as maize pathogens for the first time in Italy.

Adult stem cells (ASCs) can be cultured with difficulty from most tissues, often requiring chemical or transgenic modification to achieve adequate quantities. We show here that mouse primary fibroblasts grown in suspension change from the elongated and flattened morphology observed under standard adherent culture conditions generating rounded cells with large nuclei and scant cytoplasm expressing the mesenchymal stem cell (MSC) marker (Sca1; Ly6A) within 24hrs. Based on this initial observation, we describe here a suspension culture method that, irrespective of the lineage used, mouse fibroblast, primary human somatic cells (fibroblasts, hepatocytes and keratinocytes), is capable of generating a high yield of cells in spheroid form which display expression of ASCs surface markers, circumventing the anoikis which often occurs at this stage. Moreover, mouse fibroblasts-derived spheroids can be differentiated into adipogenic and osteogenic lineages. Analysis of single cell RNA sequence data identified 8 distinct cell clusters with one in particular comprising approximately 10% of the cells showing high levels of proliferative capacity expressing high levels of genes related to MSCs and self-renewal as well as extracellular matrix (ECM). We believe the rapid, high-yield generation of proliferative, multi-potent ASC-like cells by the process we term suspension-induced stem cell transition (SIST) could have significant implications for regenerative medicine.

Patients receiving hemodialysis are at risk of vascular access infections (VAIs) and particularly vulnerable to the opportunistic pathogen Staphylococcus aureus. Hemodialysis patients were also at increased risk of infection during the COVID-19 pandemic. Therefore, this study determined the change in the molecular and antibiotic resistance profiles of S. aureus isolates from VAIs during the pandemic compared with before. 102 S. aureus isolates were collected from VAIs between November 2013 and December 2021. Before the pandemic, 69 isolates were collected, 58%, 39.1%, and 2.9% from arteriovenous grafts (AVGs), tunneled cuffed catheters (TCCs), and arteriovenous fistulas (AVFs), respectively. The prevalence of AVG and TCC isolates changed to 39.4% and 60.6%, respectively, of 33 isolates during the pandemic. Sequence type (ST)59 was the predominant clone in TCC-methicillin-resistant S. aureus (MRSA) and AVG-MRSA before the pandemic, whereas the predominant clone was ST8 in AVG-MRSA during the pandemic. ST59 carrying the ermB gene was resistant to clindamycin and erythromycin. By contrast, ST8 carrying the msrA gene was exclusively resistant to erythromycin. The ST distribution for different VAIs changed from before to during the pandemic. The change in antibiotic resistance rate for different VAIs was closely related to the distribution of specific STs.

The bacterial composition of oral samples has traditionally been determined by PCR amplicon sequencing of 16S rRNA genes. Recent amplicon sequence variant (ASV)-based analyses of 16S rRNA genes differ from that based on operational taxonomic unit (OTU) clustering in the way it deals with sequences having potential errors. However, little information is available on its application in oral microbiome studies. Here, we conducted ASV-based analysis of oral microbiome samples using QIIME 2. We investigated the optimal parameters for sequence denoising, using DADA2, and found the trimming of the first 20 nucleotides from 5′-end of both paired reads avoided excessive sequence loss during chimera removal. Truncating reads at positions 240–245 allowed the removal of low-quality sequences while maintaining sufficient length to merge matching paired ends. Taxonomic assignment, using the naïve Bayes classifier trained with the V3-V4 region of reference 16S rRNA sequences in the extended human oral microbiome database (eHOMD), resulted in bacterial compositions similar to those of OTU-based analyses. Contrary to OTU-based clustering, ASV-based analysis showed taxonomic abundance at the genus or species level to not differ significantly in tongue microbiomes, regardless of brushing. QIIME 2 can, therefore, be a standard pipeline for ASV-based analysis of oral microbiomes.

Today massive amounts of sequenced metagenomic and -transcriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the various flavours of biological sequence data, and how this information can be interpreted to increase our scientific knowledge and understanding. We argue that a mechanistic understanding is required to consistently interpret experimental observations, and that this understanding is greatly facilitated by the generation and analysis of dynamic mathematical models. We conclude that, in order to construct mathematical models and to test mechanistic hypotheses, time-series data is of critical importance. We review diverse techniques to analyse time-series data and discuss various approaches by which time-series of biological sequence data was successfully used to derive and test mechanistic hypotheses. Analysing the bottlenecks of current strategies in the extraction of knowledge and understanding from data, we conclude that combined experimental and theoretical efforts should be implemented as early as possible during the planning phase of individual experiments and scientific research projects.

For any odd positive integer $x$, define $(x_n)_{n\geqslant 0} $ and $(a_n )_{n\geqslant 1} $ by setting $x_{0}=x, \,\, x_n =\cfrac{3x_{n-1} +1}{2^{a_n }}$ such that all $x_n $ are odd. The 3x+1 problem asserts that there is an $x_n =1$ for all $x$. Usually, $(x_n )_{n\geqslant 0} $ is called the trajectory of $x$. In this paper, we concentrate on $(a_n )_{n\geqslant 1} $ and call it the E-sequence of $x$. The idea is that, we consider any infinite sequence $(a_n )_{n\geqslant 1} $ of positive integers and call it an E-sequence. We then define $(a_n )_{n\geqslant 1} $ to be $\Omega-$convergent to $x$ if it is the E-sequence of $x$ and to be $\Omega-$divergent if it is not the E-sequence of any odd positive integer. We prove a remarkable fact that the $\Omega-$divergence of all non-periodic E-sequences implies the periodicity of $(x_n )_{n\geqslant 0} $ for all $x_0$. The principal results of this paper are to prove the $\Omega-$divergence of several classes of non-periodic E-sequences. Especially, we prove that all non-periodic E-sequences $(a_n )_{n\geqslant 1} $ with $\mathop {\overline {\lim } }\limits_{n\to \infty } \cfrac{b_n }{n}>\log _23$ are $\Omega-$divergent by using the Wendel's inequality and the Matthews and Watts's formula $x_n =\cfrac{3^n x_0 }{2^{b_n }}\prod\limits_{k=0}^{n-1} {(1+\cfrac{1}{3x_k })} $, where $b_n =\sum\limits_{k=1}^n {a_k } $. These results present a possible way to prove the periodicity of trajectories of all positive integers in the 3x + 1 problem and we call it the E-sequence approach.

Diversity-generating retroelements (DGRs) are prokaryotic systems providing rapid modification and adaptation of target proteins. In phages, the main targets of DGRs are receptor-binding proteins that are usually parts of tail structures and the variability of such host-recognizing structures enables phage adaptation to changes on the bacterial host surface. Sometimes, more than one target gene containing a hypermutated variable repeat (VR) can be found in phage DGRs. The role of mutagenesis of two functionally different genes is unclear. In this study, several phage genomes that contain DGRs with two target genes were found in the gut virome of healthy volunteer. Bioinformatics analysis of these genes indicated that they encode proteins with different topology; however, both proteins contain the C-type lectin (C-lec) domain with a hypermutated beta-hairpin on its surface. One of the target proteins belongs to a new family of proteins with a specific topology: N-terminal C-lec domain followed by one or more immunoglobulin domains. Proteins from the new family were named tentaclins after TENTACLe+proteIN. The genes encoding such proteins were found in the genomes of prophages and phages from the gut metagenomes. We hypothesized that tentaclins are involved in binding either to bacterial receptors or intestinal/immune cells.

Conjugative transposons in Gram-negative bacteria have a significant role in the dissemination of antibiotic-resistance-conferring genes between bacteria. This study aims to genomically characterize plasmids and conjugative transposons carrying integrons in clinical isolates of Klebsiella pneumoniae. Genetic composition of conjugative transposons and phenotypic assessment of 50 multidrug-resistant K. pneumoniae isolates from Tertiary-care Hospital (SQUH), Muscat, Oman was investigated. Horizontal transferability was investigated by filter- mating conjugation experiments. Whole genome sequencing (WGS) was performed to determine the sequence type (ST), acquired resistome and plasmidome of integron-carrying strains. Class 1 integron was detected in 96% of isolates and among integron-positive isolates, 18 stains contained variable regions. Horizontal transferability by conjugation confirmed the successful transfer of integrons between cells and WGS confirmed their presence in conjugative plasmids. Dihydrofolate reductase (dfrA14) was the most prevalent (34.8%) gene cassettes in class 1 integrons. MLST analysis detected predominantly ST-231 and ST-395. BlaOXA-232 and blaCTX-M-15 were the most frequently detected carbapenems and beta-lactamases in sequenced isolates. This study highlighted the high transmissibility of MDR-conferring conjugative plasmids in clinical isolates of K. pneumoniae. Therefore, the wise use of antibiotics and the adherence to effective infection control measures are necessary to limit further dissemination of multidrug-resistant organisms.

Reptilians or reptoids are staple characters of Hollywood cinema, science fiction literature, ufology and conspiracy theories. Despite its popularity, the reptoid has been dismissed by the scientific community as a figment of the imagination; born out of a speculation, paranoia and wanton anthropocentricism. In this paper, however, the Life Sequence Conjecture is advanced as a supportive framework for the notion of reptilian extraterrestrials. This paper is not an argument in support of the existence of extraterrestrials. Rather, it proposes that if extraterrestrials do exist, then a reptilian morphology is not untenable.

The article is devoted to biological models using recurrence sequences, which are connected with the harmonic progression 1, 1/2, …, 1/n, and some cooperative properties of genomes. The harmonic progression is itself one of the recurrence sequences based on the harmonic mean. This progression appears in the hyperbolic rules of oligomer cooperative organization in eukaryotic and prokaryotic genomes. This allows thinking that the harmonic progression is also related to inherited physiological systems, which must be structurally consistent with the genetic coding system for their transmission to descendants and survival in evolution. The harmonic progression is one of historically known mathematical series, whose features were studied by Pythagoras, Leibniz, Newton, Euler, Fourier, Dirichlet, Riemann. It is widely used in many known algorithms and is closely related to some other important mathematical objects, for example, the function of the natural logarithm and harmonic numbers. Accordingly, the article describes the possibilities of using these interrelated mathematical objects to model biological structures, including logarithmic spirals and some other. Modeling inherited spiral configurations seems to be a particularly urgent task, since they are extremely common at all levels of organization of living bodies and, according to Goethe, are lines of life. The principle of a recurrence similarity, that is a special similarity of parts and transformations presented in recurrence sequences of numbers and matrix operators (the scale similarity and scale transformations are only particular cases of such similarity), is considered as one of the key principles of structural organization of living bodies.

This paper describes a proposed fractional filter-based multi-scale underwater and hazy image enhancement algorithm. The proposed system combines a modified global contrast operator with fractional order-based multi-scale filters used to generate several images, which are fused based on entropy and standard deviation. The multi-scale-global enhancement technique enables fully adaptive and controlled colour correction and contrast enhancement without over exposure of highlights when processing hazy and underwater images. This in addition to illumination/reflectance estimation coupled with global and local contrast enhancement. The proposed algorithm is also compared with the most recent available state-of-the-art multi-scale fusion de-hazing algorithm. Experimental comparisons indicate that the proposed approach yields better edge and contrast enhancement results without halo effect, colour degradation and is faster and more adaptive than all other algorithms from the literature.

Hungary's first national park was created in 1973 in the Hortobágy area to protect Europe's largest contiguous steppe area with its flora and fauna. The Hortobágy National Park - the Puszta was inscribed on the UNESCO World Heritage List as a cultural landscape in 1999. The park's outstanding importance is due to the predominantly non-arboreal steppe vegetation, home to a unique bird fauna, and the alkaline and chernozem soils with a complex, mosaic-like spatial structure. In addition, the landscape of the Hortobágy has a pastoral history stretching back thousands of years. Several hypotheses have been put forward, which suggest that the alkaline soils and the habitats that cover them were formed as a result of human activities related to river regulation that began in the second half of the 19th century. However, palaeoecological and palaeobiological studies over the last 30-40 years have pointed to the natural origin of the alkaline steppes, dating back to the end of the Ice Age. For thousands of years human activities, in particular grazing by domestic animals, hardly influenced the natural evolution of the area. Drainage of marshy and flooded areas began in the 19th century, and the introduction of more and more intensive agriculture, had a significant impact on the landscape. This paper aims to describe the past natural development of this special alkaline steppe ecosystem, with particular reference to the impacts of past and present human activities, including conservation measures.

Ribotoxin-like proteins (RL-Ps) are specific ribonucleases found in mushrooms that are able to cleave a single phosphodiester bond located in the Sarcin-Ricin Loop (SRL) of the large rRNA. The cleaved SRL interacts differently with some ribosomal proteins (P-stalk). This action blocks protein synthesis because the damaged ribosomes are unable to interact with elongation factors. Here, the amino acid sequence of eryngitin 3 and 4, RL-Ps isolated from Pleurotus eryngii fruiting bodies, was determined to: i) obtain structural information on this specific ribonuclease family from edible mushrooms; and ii) explore the structural determinants which justify their different biological and antipathogenic activities. Indeed, eryngitin 3 (exhibited higher toxicity with respect to eryngitin 4 against tumoral cell lines and model fungi. Structurally, eryngitin 3 and 4 consist of 132 amino acids, most of them identical and exhibit a single free cysteinyl residue. The amino acidic differences between the two toxins are: i) an additional phenylalanyl residue at the N-terminus of eryngitin 3, not retrieved in eryngitin 4; and ii) an additional arginyl residue at C-terminus of eryngitin 4, not retrieved in eryngitin 3. The 3D-models of eryngitins show slight differences at the N- and C-terminal regions. In particular, the positive electrostatic surface at C-terminal of eryngitin 4 is due to the additional arginyl residue not retrieved in eryngitin 3. This additional positive charge could interfere with the binding to the SRL (substrate) or with some ribosomal proteins (P-stalk structure), during substrate recognition.

Whole-genome sequencing (WGS) was used for genomic characterization of 110 strains of Listeria innocua isolated from 23 cattle farms, 8 beef abattoirs, and 48 retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (sources and types of samples) of the L. innocua isolates. The study detected 12 STs, 13 resistance genes, and 23 virulence genes. Of the 12 STs de-tected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (P<0.05). All 110 isolates of L. innocua were car-riers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (P<0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1.svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels (farm, abattoir, and retail outlets) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications..

Quantitative polymerase chain reaction (qPCR) has emerged as an important bioanalytical method for assessing the pharmacokinetics of human cell-based medicinal products after xenotransplantation into immunodeficient mice. A particular challenge in bioanalytical qPCR studies is that the different tissues of the host organism can affect amplification efficiency and amplicon detection to varying degrees, and ignoring these matrix effects can easily cause a significant underestimation of the true number of target cells in a sample. Here we describe the development and drug regulatory-compliant validation of a TaqMan® qPCR assay for quantification of mesenchymal stromal cells in the range of 125 to 20,000 cells/200 µl lysate by amplification of a human-specific, highly repetitive αsatellite DNA sequence of the chromosome 17 centromere region HSSATA17. Assessment of matrix effects in 14 different mouse tissues and blood revealed a wide range of spike recovery rates across the different tissue types from 11 to 174%. Based on these observations, we propose to perform systematic spike-and-recovery experiments during assay validation and to correct for the effects of the different tissue matrices on cell quantification in subsequent bioanalytical studies by multiplying the back-calculated cell number by tissue-specific factors derived from the inverse of the validated percent recovery rate.

We introduce the Open Research Knowledge Graph Agriculture Named Entity Recognition (the ORKG Agri-NER) corpus and service for contribution-centric scientific entity extraction and classification. The ORKG Agri-NER corpus is a seminal benchmark for the evaluation of contribution-centric scientific entity extraction and classification in the agricultural domain. It comprises titles of scholarly papers that are available as Open Access articles on a major publishing platform. We describe the creation of this corpus and highlight the obtained findings in terms of the following features: 1) a generic conceptual formalism focused on capturing scientific entities in agriculture that reflect the direct contribution of a work; 2) a performance benchmark for named entity recognition of scientific entities in the agricultural domain by empirically evaluating various state-of-the-art sequence labeling neural architectures and transformer models; and 3) a delineated 3-step automatic entity resolution procedure for the resolution of the scientific entities to an authoritative ontology, specifically AGROVOC that is released in the Linked Open Vocabularies cloud. With this work we aim to provide a strong foundation for future work on the automatic discovery of scientific entities in the scholarly literature of the agricultural domain.

The Golden ratio is an irrational number that has a tendency to appear in many different scientific and artistic fields. It may be found in natural phenomena across a vast range of length scales; from galactic to atomic. In this review, the mathematical properties of the Golden ratio are discussed before exploring where in nature it has been found; beginning at astronomical scales and progressing to smaller lengths, until reaching those of atomic and quantum physics. In making such a tour across length scales, it is illustrated just how prevalent this single number is within the natural universe.

Facing unprecedented global declines in the extent and integrity of ecosystems, the 15^th UN Biodiversity Conference (COP-15) in Kunming, China, presents an opportunity for transformative change. However, a lack of consensus on two key issues – resource mobilization and Access and Benefit Sharing (ABS) associated with Digital Sequence Information (DSI) – risks stalling negotiations for an ambitious ‘Post-2020 Global Biodiversity Framework’ as the next 10-year strategic plan under the Convention on Biological Diversity. We highlight systemic misconceptions concerning the financing of biodiversity and the burden this places on the ABS system. In the context of DSI, we caution that conflating ABS with resource mobilization risks disrupting modern science policy built on open access, with potentially severe ramifications for scientific research and innovation. To resolve these tensions, we call for a recalibration of discussions on ABS in order to maximize the value delivered by biodiversity for all of society, including indigenous peoples and local communities.

Mitochondrial carriers facilitate the transfer of small molecules across the inner mitochondrial membrane (IMM) to support mitochondrial function and core cellular processes. In addition to the classical mitochondrial carrier family SLC25, the past decade led to the discovery of additional protein families that exhibit IMM localization and transporter-like properties. These include mitochondrial pyruvate carriers, sideroflexins and mitochondrial cation/H+ exchangers that have been linked to vital physiological functions and disease. Their structures and transport mechanisms are still largely unknown and understudied. Protein sequence analysis per se can often pinpoint hotspots that are of functional or structural importance. In this review, we summarize current knowledge about sequence features of mitochondrial transporters with a special focus on the newly included SLC54, SLC55 and SLC56 families of the SLC solute carrier superfamily. Taking a step further, we combined sequence conservation analysis with transmembrane segment and secondary structure prediction methods to extract residue positions and sequence motifs that likely play a role in substrate binding, binding site gating or structural stability. We hope that our review will help guide future experimental efforts by the scientific community to unravel the transport mechanism and structure of these novel mitochondrial carriers.

We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.

Surgical navigation has evolved as a vital tool in maxillofacial surgery, offering precise and patient-specific data. This study explores the clinical applications and accuracy of intraoperative tool tracking in maxillofacial surgery. The research includes 37 patients with various pathologies who underwent surgery assisted by a surgical navigation system using tracked instruments. The study showcases two representative cases: one involving coronoid hyperplasia with mouth opening deficit and another addressing nose-orbital-ethmoidal-frontal ossifying fibroma resection. The results indicate that surgical navigation with tracked instruments provides high precision (<1.5 mm error), reduced surgical time, and less invasive approaches. The study highlights the potential for reproducible outcomes and increased safety, especially in complex cases. Despite some limitations, the synergy between surgical navigation and tracked instruments offers a promising approach in maxillofacial surgery, expanding its applications beyond current practices.

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

This study investigates the interpretability of machine learning (ML) models applied to cumulative damage prediction during a sequence of earthquakes, emphasizing the use of techniques such as SHapley Additive exPlanations (SHAP), Partial Dependence Plots (PDPs), Local Interpretable Model-agnostic Explanations (LIME), Accumulated Local Effects (ALE), Permutation and Impurity-based technique. The research explores the cumulative damage during seismic sequences, aiming to identify critical predictors and assess their influence on the cumulative damage. Moreover, the predictors contribution in respect with the range of final damage is evaluated. Nonlinear time history analyses are applied to extract the seismic response of an eight-story Reinforced Concrete (RC) frame. The regression problem’s input variables are divided into two distinct physical classes: pre-existing damage from the initial seismic event and seismic parameters representing the intensity of the subsequent earthquake, expressed by Park and Ang damage index (DIPA) and Intensity Measures (IMs), respectively. The study offers a comprehensive review of cutting-edge ML methods, hyperparameter tuning, and ML method comparisons. A LightGBM model emerges as the most efficient, among 15 different ML methods examined, with critical predictors for final damage being the initial damage caused by the first shock and the IMs of the subsequent shock: IFVF and SIH. The importance of these predictors is supported by feature importance analysis and local/global explanation methods, enhancing the interpretability and practical utility of the developed model.

In this paper, we investigate the effects of mean stress, multiaxial loading, and residual stresses on the fatigue life of springs. We study the fatigue life of a homogeneously stressed material subjected to cyclic loading with nonzero mean stress. Traditional methods for estimating fatigue life are based on Goodman and HAIGH diagrams. The formal analytical descriptions, namely "stress-life" and "strain-life" approaches, are found to be more suitable for the numerical methods. The fatigue analysis method described above, which describes crack growth per cycle, is extended. The extensions allow consideration of the mean stress of a load cycle. Closed-form expressions for crack length versus number of cycles are derived. The complementary effects on the fatigue life of springs, which ultimately have a significant influence on the fatigue life of springs, are summarized. For the proposed unified fatigue life functions, the ranges for the stress loading factor are extended by introducing the effective stress intensity. The solution leads to the factor range for the effective stress intensity, the effective mean value of the stress intensity factor and the effective stress ratio. The developed method assumes the homogeneous stress state in the whole spring element. For the non-homogeneously loaded structural elements, the weak-link concept is applied to account for fatigue.

Advanced machine learning algorithms, have the potential to be successfully applied to many areas of system modelling. In the present study the capability of ten machine learning algorithms in predicting the structural damage of an 8-storey reinforced concrete frame building subjected to single and successive ground motions is examined. From this point of view, the initial damage state of the structural system, as well as 16 well known ground motion intensity measures are adopted as the features of the machine-learning algorithms that aim to predict the structural damage after each seismic event. The structural analyses are performed considering both real and artificial mainshock–aftershock sequences, while the structural damage is expressed in terms of two overall damage indices. The comparative study results in the most efficient damage index, as well as the most promising machine learning algorithm in predicting the structural response of a reinforced concrete building under single or multiple seismic events. Finally, the configured methodology deployed in a user-friendly web-application.

With the automotive industry moving towards automated driving, sensing is increasingly important in enabling technology. The virtual sensors allow data fusion from various vehicle sensors and provide a prediction for measurement that is hard or too expensive to measure in another way or in the case of demand on continuous detection. In this paper, virtual sensing is discussed for the case of vehicle suspension control, where information about the relative velocity of the unsprung mass for each vehicle corner is required. The corresponding goal can be identified as a regression task with multi-input sequence input. The hypothesis is that the state-of-art method of Bidirectional Long-Short Term Memory (BiLSMT) can solve it. In this paper, a virtual sensor has been proposed and developed by training a neural network model. The simulations have been performed using an experimentally validated full vehicle model in IPG Carmaker. Simulations provided the reference data which was used for Neural Network (NN) training. The extensive dataset covering 26 scenarios has been used to obtain training, validation and testing data. The Bayesian Search was used to select the best neural network structure using root mean square error as a metric. The best network is made of 167 BiLSTM, 256 fully connected hidden units and 4 output units. Error histograms and spectral analysis of the predicted signal compared to the reference signal are presented. The results demonstrate the good applicability of neural network-based virtual sensors to estimate vehicle unsprung mass relative velocity.

Automated lying-posture tracking is important in preventing bed-related disorders such as pressure injuries, sleep apnea, and lower-back pain. Prior research studied in-bed lying posture tracking using sensors of different modalities (e.g., accelerometer and pressure sensors). However, there remain significant gaps in research about how to design efficient in-bed lying posture tracking systems. These gaps can be articulated through several research questions as follows. First, can we design a single-sensor, pervasive, and inexpensive system that can accurately detect lying postures? Second, what computational models are most effective in the accurate detection of lying postures? Finally, what physical configuration of the sensor system is most effective for lying posture tracking? To answer these important research questions, in this article, we propose a comprehensive approach to design a sensor system that uses a single accelerometer along with machine learning algorithms for in-bed lying posture classification. We design two categories of machine learning algorithms based on deep learning and traditional classification with handcrafted features to detect lying postures. We also investigate what wearing sites are most effective in accurate detection of lying postures. We extensively evaluate the performance of the proposed algorithms on nine different body locations and four human lying postures using two datasets. Our results show that a system with a single accelerometer can be used with either deep learning or traditional classifiers to accurately detect lying postures. The best models in our approach achieve an F-Score that ranges from 95.2% to 97.8% with a coefficient of variation from 0.03 to 0.05. The results also identify the thighs and chest as the most salient body sites for lying posture tracking. Our findings in this article suggest that because accelerometers are ubiquitous and inexpensive sensors, they can be a viable source of information for pervasive monitoring of in-bed postures.

Due to the rapid developments in aquaculture industry, Artemia franciscana, originally an American species, has been intentionally introduced to the Eurasia, Africa and Australia. In the present study, we used a partial sequence of the mitochondrial DNA Cytochrome Oxidase subunit I (mt-DNA COI) gene and genomic fingerprinting by Inter-Simple Sequence Repeats (ISSRs) to determine the genetic variability and population structure of Artemia populations (indigenous and introduced) from 14 different geographical locations in Western Asia. Based on the haplotype spanning network, Artemia urmiana has exhibited higher genetic variation than native parthenogenetic populations. Although A. urmiana represented a completely private haplotype distribution, no apparent genetic structure was recognized among the native parthenogenetic and invasive A. franciscana populations. Our ISSR findings have documented that despite invasive populations have lower variation than source population in Great Salt Lake (Utah, USA), they have significantly revealed higher genetic variability compare to the native populations in Western Asia. According to the ISSR results, the native populations were not fully differentiated by the PCoA analysis, but the exotic A. franciscana populations were geographically divided in four genetic groups. We believe that during the colonization, invasive populations have experienced substantial genetic divergences, under new ecological conditions in the non-indigenous regions.

Abstract: A recent approach to radiotherapy for prostate cancer is the administration of high doses of radiation to the prostate while minimizing the risk of side effects. Thus, image-guided radiotherapy utilizes advanced imaging techniques and is a feasible strategy for increasing the radiation dose. New radioactive particles are another approach to achieving high doses and safe procedures. Prostate brachytherapy is currently considered as a combination therapy. Spacers are useful to protect adjacent organs, specifically the rectum, from excessive radiation exposure.

A method for generating fluoroscopic (time-varying) volumetric images using patient-specific motion models derived from 4-dimensional cone-beam CT (4D-CBCT) images is developed. 4D-CBCT images acquired immediately prior to treatment have the potential to accurately represent patient anatomy and respiration during treatment. Fluoroscopic 3D image estimation is done in two steps: 1) deriving motion models and 2) optimization. To derive motion models, every phase in a 4D-CBCT set is registered to a reference phase chosen from the same set using deformable image registration (DIR). Principal components analysis (PCA) is used to reduce the dimensionality of the displacement vector fields (DVFs) resulting from DIR into a few vectors representing organ motion found in the DVFs. The PCA motion models are optimized iteratively by comparing a cone-beam CT (CBCT) projection to a simulated projection computed from both the motion model and a reference 4D-CBCT phase, resulting in a sequence of fluoroscopic 3D images. Patient datasets were used to evaluate the method by estimating the tumor location in the generated images compared to manually defined ground truth positions. Experimental results showed that the average tumor mean absolute error (MAE) along the superior-inferior (SI) direction and the 95th percentile in two patient datasets were (2.29 mm and 5.79 mm) for patient 1 and (1.89 mm and 4.82 mm) for patient 2. This study has demonstrated the feasibility of deriving 4D-CBCT-based PCA motion models that have the potential to account for the 3D non-rigid patient motion and localize tumors and other patient anatomical structures on the day of treatment.

Newcastle disease virus (NDV) genotype VII is a highly pathogenic Orthoavulavirus that has caused multiple outbreaks among poultry in Egypt since 2011. This study aimed to investigate the genetic diversity of NDV prevailing in domestic and wild birds in Egyptian governorates. A total of 37 oropharyngeal swabs from wild birds and 101 swabs from domestic bird flocks including chickens, ducks, turkeys, and swans were collected from different geographic regions within 13 governorates during 2019-2020. Virus isolation and propagation via embryonated eggs revealed 91 swab samples produced allantoic fluid containing hemagglutination activity, suggestive of virus presence. The use of RT-PCR targeted to F gene successfully detected NDV in 85 samples. The geographical prevalence of NDV spread to 12 governorates in domestic birds, migratory and non-migratory wild birds. Following whole genome sequencing, we assembled six NDV genome sequences (70 - 99% of genome coverage), including five full F gene sequences. All NDV strains carried high virulence, based on the presence of polybasic amino acids (RRQRF) at the F gene cleavage site. Phylogenetic analysis revealed that the NDV strains belonged to class II within genotype VII.1.1. The presence of genetically similar virulent NDV in wild birds further highlights their role in the dissemination of NDV in poultry populations across Egypt. Continued genomic surveillance in both wild birds and poultry would be necessary for monitoring NDV incursions and genetic diversification.