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.

This article presents multiple novel and compelling arguments to systematically disprove two widely accepted notions: one is that entropy is a measure of disorder, and the other is Schrödinger's notion of negative entropy (negentropy). These two notions have been cited hundreds of times annually in scientific literature for decades. To mathematically describe the second law of thermodynamics, the concept of entropy was created and defined in the 1860s as heat energy divided by thermodynamic temperature, and the entropy of an object increases when it absorbs heat. This is the uncontroversial and fundamental nature of entropy, which is pivotal to current thermodynamics and from which multiple facts are deduced. These facts consistently disprove the above two notions. Some biological facts, such as the one that life orderliness is encoded and provided by inherited genes rather than entropy decline, can also disprove Schrödinger's negentropy notion. Moreover, this article further clarifies the reasoning errors of the two notions. It also shows that the tendency of many natural or social systems to become more disordered over time does not result from the second law of thermodynamics.

Intrinsic subtype of triple-negative breast cancer (TNBC) is based on genomic evaluation. In this study, we report the survival and pathological complete response (pCR) rates of TNBC patients subtyped by IHC and treated with neoadjuvant chemotherapy (NACT). A retrospective cohort of 187 TNBC patients who received NACT between 2008 and 2017 was used, and IHC subtyping was performed on biopsy specimens before chemotherapy. The subtyping revealed predominant basal-like tumors (IHC-BL, 61%), followed by basal-like immune-suppressed (IHC-BLIS, 31%), mesenchymal tumors (12.5%), luminal androgen receptor tumors (IHC-LAR, 12%) and basal-like immune-activated (IHC-BLIA, 10.9%). The pathological complete response (pCR) rate varied among subtypes, with IHC-BLIA showing the highest (30.0%) and IHC-LAR showing the lowest (4.5%). IHC-BLIS led in recurrence sites. Overall and disease-free survival analyses did not show significant differences among subtypes. Although, IHC-BLIA demonstrated a trend toward better survival and IHC-mesenchymal worse. Patients who achieved pCR exhibited significantly better disease-free survival and overall survival than non-responders. This study underscores the potential of IHC-based subtyping in TNBC management, highlighting distinct response patterns to neoadjuvant chemotherapy and potential implications for treatment strategies. Further research is warranted to validate these findings and explore tailored therapeutic approaches for specific TNBC subtypes.

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.

The present study aims to evaluate the antibacterial activity of five commercially available essential oils (EOs): Lavender (LEO), Clove (CEO), Oregano (OEO), Eucalyptus (EEO), and Peppermint (PEO) against the most-known MDR Gram-positive and Gram-negative bacteria - Staphylococcus aureus (ATCC 25923), Escherichia coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 27853) - alone and in various combinations. Gas Chromatography-Mass Spectrometry (GC-MS) analysis established their complex composition. Then, the antibacterial activity was investigated in vitro by diffusimetric antibiogram method, using sterile cellulose discs with Ø 6 mm impregnated with 10 µl of sample and sterile borosilicate glass cylinders loaded with 100 µl of sample; MIC (µg/mL) for each EO was calculated from IZD values (mm) measured after 24 hours. The following EO combinations were evaluated: OEO+CEO, CEO+EEO, CEO+PEO, LEO+EEO, and EEO+PEO. Then, the influence of each dual combination on 3 conventional antibacterial drugs – Neomycin (NEO), Tetracycline (TET), and Bacitracin (BAC) - activity was investigated. The most active EOs against S. aureus and E. coli were LEO and OEO (IZD = 40 mm). They were followed by the CEO and EEO (IZD = 20-27 mm); PEO exhibited the lowest antibacterial activity (IZD = 15-20 mm). EEO alone showed the highest inhibitory activity on P. aeruginosa (IZD = 25-35 mm). It was followed by the CEO, LEO, and EEO (IZD = 7-11 mm), while PEO proved no antibacterial action against it (IZD = 0 mm). Only one synergic action was recorded (OEO+CEO against P. aeruginosa); EEO+PEO revealed partial synergism against S. aureus and CEO+PEO additive behavior against E. coli. Two triple associations with TET showed partial synergism against E. coli, and the other 2 ones (with NEO and TET) evidenced the same behavior against S. aureus; all contained EEO+PEO or CEO+PEO. Most combinations reported indifference. However, numerous cases were of antagonism between constituents included in double and triple combinations, and EOs with the strongest antibacterial activities belong to the highest antagonistic combinations. A consistent statistical analysis supports our results, showing that EOs with moderate antibacterial activities could generate combinations with higher inhibitory effects based on synergistic or additive interactions.

Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gene function prediction.

Build a special identical equation, use its calculation characters to prove and search for solution of any odd converging to 1 equation through (*3+1)/2^k operation, change the operation to (*3+2^m-1)/2^k, and get a solution for this equation, give a specific example to verify. Thus prove the Collatz Conjecture is true. Furthermore, analysis the sequences produced by iteration calculation during the procedure of searching for solution, build a weight function model, prove it decrease progressively to 0, build a complement weight function model, prove it increase to its convergence state. Build a (*3+2^m-1)/2^k odd tree, prove if odd in (*3+2^m-1)/2^k long huge odd sequence can not converge, the sequence must outstep the boundary of the tree after infinite steps of (*3+2^m-1)/2^k operation.

We have now identified two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type A energy processes such as the classical heat engines, apparently well follow the second law of thermodynamics; Type B energy processes, such as the newly discovered thermotrophic function that isothermally utilizes environmental heat energy to do useful work in driving ATP synthesis, which follows the first law of thermodynamics (conservation of mass and energy) but does not have to be constrained by the second law, owing to their special asymmetric functions. Several Type-B energy processes such as asymmetric-function-gated isothermal electricity and epicatalysis have been created through human efforts. The innovative efforts on Type-B processes to enable isothermally utilizing endless environmental heat energy could help to liberate all peoples from their dependence on fossil fuel energy, thus helping to reduce greenhouse gas CO2 emissions and control climate change towards a sustainable future for the humanity on Earth.

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.

We describe a new approach for integrating multiple views of data into a common latent space using non-negative tensor factorization (NTF). This approach, which we refer to as the "Integrated Sources Model" (ISM), consists of two main steps: embedding and analysis. In the embedding step, each view is transformed into a matrix with common non-negative components. In the analysis step, the transformed views are combined into a tensor and decomposed using NTF. Noteworthy, ISM can be extended to process multi-view data sets with missing views. We illustrate the new approach using two examples: the UCI digit dataset and a public cell type gene signatures dataset, to show that multi-view clustering of digits or marker genes by their respective cell type is better achieved with ISM than with other latent space approaches. We also show how the non-negativity and sparsity of the ISM model components enable straightforward interpretations, in contrast to latent factors of mixed signs. Finally, we present potential applications to single-cell multi-omics and spatial mapping, including spatial imaging and spatial transcriptomics, and computational biology, which are currently under evaluation. ISM relies on state-of-the-art algorithms invoked via a simple workflow implemented in a Jupyter Python notebook.

Background: Metastatic triple-negative breast cancer (TNBC) is aggressive with a poor median overall survival (OS), ranging from 8 to 13 months. There exists considerable heterogeneity in the survival at the individual patient level. To better understand the survival heterogeneity and improve risk stratification, our study aims to identify the factors influencing survival utilizing a large patient sample in the National Cancer Database (NCDB). Methods: Women diagnosed with metastatic TNBC from 2010 to 2020 in the NCDB were included. Demographic, clinic-pathological, treatment data, and overall survival (OS) outcomes were collected. Kaplan-Meier curves were used to estimate OS. The log-rank test was used to identify OS differences between groups for each variable in the univariate analysis. For the multivariate analysis, the Cox proportional hazard model with backward elimination was used to identify factors affecting OS. Adjusted hazard ratios and 95% confidence intervals are presented. Results: 2,273 women had a median overall survival of 13.6 months. Factors associated with statistically significantly worse OS included older age, higher comorbidity scores, specific histologies, higher number of metastatic sites, presence of liver or other site metastases in those with only one metastatic site (excluding brain metastases), presence of cranial and extra-cranial metastases, lack of chemotherapy, lack of immunotherapy, lack of surgery to distant sites, lack of radiation to distant sites, and receipt of palliative treatment to alleviate symptoms. In the multivariate analysis, comorbidity score, histology, number of metastatic sites, immunotherapy, and chemotherapy had a statistically significant effect on the OS. Conclusions: Through NCDB analysis, we have identified prognostic factors for metastatic TNBC. These findings will help improve prognostication at diagnosis, optimize treatment strategies, and facilitate patient stratification in future clinical trials.

This study investigates the effects of ambient illumination and negatively polarized text color on visual fatigue, exploring the issue of visual fatigue when using visual display terminals in low-illumination environments. The research methodology utilized an experimental design to collect data on changes in pupil accommodation and blink rate through an eye tracker. Partici-pants completed a reading task while exposed to various text colors and ambient light conditions to evaluate visual fatigue and cognitive performance. The study's findings suggest that text color significantly affects visual fatigue, with red text causing the highest level of visual fatigue and yellow text causing the lowest level of visual fatigue. Improvements in ambient lighting reduce visual fatigue, but the degree of improvement varies depending on the text color. Additionally, cognitive performance is better when using yellow and white text but worse when using red text. Yellow text is the most effective choice for reducing visual fatigue under negative polarity. In-creasing ambient lighting can also improve visual fatigue in low-illumination conditions. These findings will offer valuable guidance for designing visual terminal device interfaces, especially for low-illumination or night environments, to minimize visual fatigue and improve the user ex-perience.

When asked to estimate the carbon footprint of a bundle of relatively low carbon footprint items and relatively high carbon footprint items, people typically report a lower value compared to estimating the high carbon footprint items alone. This finding is called the negative footprint illusion and suggests people report the average rather than sum of the combined items’ carbon footprint. In a recent paper by Gorissen et al. (2024), the authors claimed that people are immune to this illusion if the question is framed differently. Specifically, they found that estimates of the environmental friendliness of a set comprising a burger (high carbon footprint) and an organic apple (low carbon footprint) was higher than for a set comprising the burger alone, whereas no difference was found between the two sets when participants were asked to estimate how environmentally damaging they were. Using larger item categories wherein the degree of the items’ environmental impact is clearly communicated, here we show it does not matter whether participants are required to estimate how friendly or damaging the items are. The roles of attribute substitution, dependent variables, and independent variables (stimulus characteristics) in modulating the negative footprint illusion is discussed.

Deep Neural Network (DNN) inference demands substantial computing power, resulting in significant energy consumption. A large number of negative output activations in convolution layers are rendered zero due to the invocation of the ReLU activation function. This results in a substantial number of unnecessary computations that consume significant amounts of energy. This paper presents ECHO: Energy-efficient Computation Harnessing Onilne Arithmetic - A MSDF-based accelerator for DNN inference, designed for computation pruning, utilizing an unconventional arithmetic paradigm known as online/ most-significant digit first (MSDF) arithmetic which performs computations in a digit-serial manner. The MSDF digital serial computation of online arithmetic enables overlapped computation of successive operations leading to substantial performance improvements. The online arithmetic, coupled with a negative output detection scheme, facilitates early and precise recognition of negative outputs. This, in turn, allows for the timely termination of unnecessary computations, resulting in a reduction of energy consumption. The implemented design has been realized on the Xilinx Virtex-7 VU3P FPGA and subjected to a comprehensive evaluation through a rigorous comparative analysis involving widely used performance metrics. Experimental results demonstrate promising power and throughput improvements compared to contemporary methods. In particular, the proposed design achieved an average improvement in power consumption of up to 81%, 82.9%, and 40.6% for VGG-16, ResNet-18, and ResNet-50 workloads compared to the conventional bit-serial design, respectively. Furthermore, significant average speedups of 2.39×, 2.6×, and 2.42 were observed when comparing the proposed design to conventional bit-serial designs for VGG-16, ResNet-18, and ResNet-50 models respectively.

Triple-negative breast cancer (TNBC) is an aggressive and highly metastatic type of tumor. TNBC is often enriched in tumor-infiltrating neutrophils (TINs), which support cancer growth in part by counteracting tumor-infiltrating lymphocytes (TILs). Prior studies identified the enhancer of zeste homolog 2 (EZH2) as a pro-tumor methyltransferase in primary and metastatic TNBC. We hypothesized that EZH2 inhibition in TNBC cells per se would exert anti-tumor activity by altering the tumor immune microenvironment. To test this hypothesis, we used CRISPR to generate EZH2-knockout (KO) and overexpressing lines from parent (wild-type -WT) 4T1 cells, an established murine TNBC model. In vitro, EZH2 KO and OE cells showed little change in replicative capacity and invasiveness, but marked changes in surface marker profile and cytokine/chemokine secretion compared to WT cells. On in vivo injection, EZH2 KO cells showed significantly reduced primary tumor growth and a 10-fold decrease in lung metastasis compared to WT cells, while EZH2 OE cells were unchanged. Compared to WT tumors, TIN:TIL ratios were greatly reduced in EZH2 KO tumors but unchanged in EZH2 OE tumors. Our findings show a tumor-intrinsic role of EZH2 in the 4T1 TNBC model in regulating TIN/TIL poise, primary tumor progression and lung metastasis in vivo.

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.

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<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<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.

In this study, Silicon Carbide (SiC) nano-particle based serigraphic printing inks were formulated to fabricate highly sensitive and wide temperature range SiC printed thermistors. Initially, commercial silver ink was screen printed to fabricate inter-digitated electrodes (IDE’s) onto flexible Kapton® substrate via screen printing. Thermistor inks with different weight ratios of SiC nano- particles dispersed in polyimide resin matrix were fabricated. The SiC-polyimide temperature sensing inks were screen printed atop the IDE structures to form fully printed thermistors and encapsulated with a adhesive backed polyimide film for humidity inhibition. The high temperature tolerance of the Kapton® allowed the the sensors to be tested over a wide temperature range form 25◦C to 170◦C. The printed SiC thermistors exhibit excellent repeatability and stability over 15 hours of continuous operation. Optimal device performance was achieved with 30 wt.% SiC-polyimide ink. We report highly sensitive devices with a temperature coefficient of Resistance (TCR) of -0.556 %/◦C, a thermal coefficient of 502 K (β-index) and an activation energy of 0.08 eV which are comparable with printed thermistors previous reported. Further, the thermistor demonstrates an accuracy of ±1.35◦C which is well within the range offered by commercially available high sensitivity thermistors. SiC thermistors exhibit a small 6.5% drift due to changes in relative humidity between 10-90 %RH and a 4.2 % drift in baseline resistance after 100 cycles of aggressive bend testing at a 40°angle. The use of commercially available low cost materials, simplicity of design and fabrication techniques coupled with the chemical inertness of the Kapton® substrate and SiC nanoparticles paves the way to use all-printed SiC thermistors towards a wide range of applications where temperature monitoring is vital for optimal system performance.

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.

Public restrooms are often a hub of microbial contamination, and the examination of bacterial contamination in these facilities can serve as an important indicator of the transmission of infectious diseases. This study was conducted to determine the prevalence of bacterial contamination in public restrooms based on the economic class of the building. Samples were collected from various spots in 32 restrooms found in 10 shopping malls, classifying them into two categories: upper-end restrooms and lower-end restrooms. The findings showed that the level of contamination was higher in the lower-end restrooms, with the seat being the most contaminated area. The most dominant Gram-positive bacteria were coagulase-negative staphylococci species, making up 86% of the identified Gram-positive isolates. The most dominant Gram-negative bacteria identified were Klebsiella pneumoniae and Pseudomonas aeruginosa. The antibiotic sensitivity test results revealed the presence of multi-drug resistant bacteria among the Gram-positive and negative isolates, including Staphylococcus haemolyticus, Staphylococcus kloosi, Acinetobacter baumanii, and Pseudomonas aeruginosa. In conclusion, the study underscores the significance of monitoring bacterial contamination in public restrooms and the need for measures to reduce the spread of infectious diseases. Further research is crucial to gain a complete understanding of the bacterial contamination in public restrooms and their resistance patterns, to ensure the safety and health of the public. The implementation of improved cleaning practices and hands-free designs in restrooms can help reduce the risk of cross-contamination and prevent the spread of diseases.

This study explores the perception of a “sense of place” among tourists visiting Hegra, an archaeological site in northern Saudi Arabia, through reviews on TripAdvisor. The 267 reviews reviewed on TripAdvisor between 2020 and 2023 were analyzed with the VADER sentiment po-larity analysis tool and object modeling using the NMF machine learning algorithm. The results highlight positive factors linked to the history and uniqueness of the place while showing some critical issues related to isolation, cost, privatization, and competitiveness. The originality of the research lies in the type of case study chosen, an archaeological site of a country that has recently opened its doors to tourism, and in the pragmatic nature of the investigation, oriented towards the search for possible solutions to be adopted in terms of heritage management based on the feedback received for the development of the tourist destination.

Evolution remains an incessant process in viruses, allowing them to elude host immune response and induce severe diseases, impacting the diagnostic and vaccine effectiveness. Predicting emerging viral genomes is crucial, particularly in diseases like dengue, where viruses disrupt host cells, leading to fatal outcomes. Deep learning has been applied to predict dengue fever cases; there has been relatively less emphasis on its significance in forecasting emerging Dengue Virus (DENV) serotype. While Recurrent Neural Networks (RNN) were originally designed for modeling temporal sequences, our proposed DL-DVE generative and classification model, trained on complete genome data of DENV, transcends traditional approaches by learning semantic relationships between nucleotides in a continuous vector space instead of representing contextual meaning of nucleotide characters. Leveraging 2000 publicly available DENV complete genome sequences, our Long Short-Term Memory (LSTM) based generative and Feedforward Neural Network (FNN) based classification DL-DVE model showcases proficiency in learning intricate patterns and generating sequences for emerging serotype of DENV. The generative model showed accuracy of 93% and the classification model provided insight into the specific serotype label, corroborated by BLAST search verification. Evaluation metrics such as ROC-AUC value 0.818, accuracy, precision, recall and F1 score all to be around 99.00%, demonstrated the classification model’s reliability.  Our model classified the generated sequences as DENV-4, exhibiting 65.99% similarity to DENV-4 and around 63-65% similarity with other serotypes, indicating notable distinction from other serotypes. Moreover, the intra-serotype divergence of sequences with a minimum 90% similarity underscored their uniqueness. We analyzed the conserved motifs in the genome through MEME Suite (version 5.5.5). Our research strives to contribute to the ongoing fight against the Dengue virus by offering predictive insights into its genomic evolution. Looking ahead, proactive predictive modeling before mutations occur holds potential for guiding vaccine design and diagnostic kit development.

This study aims to spatially analyze the distribution characteristics of vacant homes in Asan-si, Chungcheongnam-do, and understand the differences in factors causing vacant homes by type. We use a variety of statistical methods to examine these factors and identify key influencing factors such as the number of vacant stores, changes in overall population, land use complexity, and physical characteristics of land and buildings. The findings reveal that the factors contributing to the occurrence of vacant homes vary significantly by region and property type, highlighting the need for region-specific policies. For instance, in old town areas, small lot ratios and land use complexity are significant, while in rural village, the average number of floors and land use complexity play a major role. This study underscores the diversity of factors influencing vacant homes, suggesting that policies should be tailored to the unique characteristics of different regions to effectively address this issue.

Using assembly theory, we investigate the assembly pathways of fixed-length binary strings formed by joining the individual bits present in the assembly pool and the strings that entered the pool as a result of previous joining operations. We show that the string assembly index is bounded from below and above, and we conjecture about the form of the upper bound. We show that a string having the smallest assembly index can be assembled by an elegant trivial program of length equal to this index, if the length of the string is expressible as a product of Fibonacci numbers. We conjecture that there is no binary program that has a length shorter than the length of the string having the largest assembly index that could assemble this string. We conjecture that a black hole surface is defined by a balanced distinct string that satisfies the upper bound of a distinct string assembly index. The results confirm that four Planck areas provide a minimum information capacity that provides a minimum thermodynamic (Bekenstein-Hawking) entropy. Knowing that the problem of determining the assembly index is at least NP-complete, we conjecture that the problem of determining the assembly index of a given binary string is NP-complete, while the problem of creating the string so that it would have a predetermined maximum assembly index is NP-hard. Therefore, once the new information is assembled by a dissipative structure or by a human, increasing the information entropy according to the second law of infodynamics, it is subject to the second law of thermodynamics, and nature seeks to optimize its assembly pathway.

ABSTRACT Background: To date, the COVID-19 pandemic has been the foremost health concern for humankind in the new millennia. This paper aims to describe the related hospitalizations in Italy during the first two years of the health emergency. Design and methods: This is a retrospective, population-based study of Italian hospitalizations for patients diagnosed with COVID-19 during the 2020-2021 period, extracted from the National Hospital Discharge Registry. The outcome variables considered include hospital admissions, costs, and length of stay, among other hospitalization-level variables. Costs were estimated through the charges associated with the Diagnosis-Related Group and Major Diagnostic Categories coding system, plus an additional cost attributed to COVID-19 admissions. To these charges was added an extra cost defined by the ministry of health. Results: In Italy, there were 357,354 hospitalizations for COVID-19 attributed to 298,856 patients in 2020 and 399,043 hospitalizations for COVID-19 attributed to 333,447 patients in 2021. COVID-19 patients faced a transfer rate thrice that of other patients. Hospitalizations were concentrated predominantly in the northern regions, particularly in the first year. Hospitalization rates varied by age in a sine wave pattern, peaking in the youngest and oldest age groups, with mortality rates escalating with age— tending to remain below 3% for those under 44 but surging to 40% in individuals over 75. The financial impact of COVID-19 hospitalizations was substantial, with total costs reaching €3.97 billion in 2020 and €4.99 billion in 2021. Costs per admission and per day also rose, from €11,112 and €807 in 2020 to €12,503 and €844 in 2021, respectively. Excluding the added financial burden of COVID-19, costs would have been notably lower. Hospitalizations involving continuous invasive mechanical ventilation were particularly costly (about 24.000 euros x admission), reflecting the significant resources required for these treatments. Conclusion: Implementing a protective pad around the entire health system that leverages networks of family doctors and nurses, connected in real time to the entire health system, can be crucial. Such a network, tasked with monitoring the local epidemiological situation, protecting vulnerable individuals also through telehealth visits, and establishing a triage system for infections in the initial phase, may effectively help in managing virus spread and protecting hospitals from unpredictable waves of admission demand. Strengthening primary health care could be a decisive factor for the future and enhance the system's resilience in facing new challenges.

Auger electrons (AEs) represent an intriguing topic in the field of radionuclide therapy. They are emitted by several radionuclides commonly used in nuclear medicine (indium-111, iodine-123, iodine-125), allowing for highly localized energy deposition and thus exerting a radiotoxic effect on specific cellular and sub-cellular targets. However, due to their short range in matter, AEs have had limited use in therapeutic applications so far. In recent years, the synthesis of various radiopharmaceuticals capable of binding to the enzyme poly(ADP-ribose) polymerase 1 has reignited interest in this type of therapy, laying the groundwork for a theranostic approach based on radionuclides emitting AEs. The enzyme PARP-1 operates enzymatically in close proximity to DNA that represents the prime target of radionuclide therapies. Following this trend, several PARP-targeted radiopharmaceuticals for AE-based theranostics have been developed. We provide an updated overview of preclinical studies focused on the applications of this new theranostic approach in glioblastoma, breast, prostate and ovarian carcinoma, and pancreatic adenocarcinoma.

Ajuga arabica is an essential medicinal plant found naturally in Saudi Arabia, recognized for its therapeutic characteristics. Nevertheless, research on the genetic diversity and population arrangement of this species in Saudi Arabia is deficient. In this study, we conducted a comparative examination of DNA and gene sequences to evaluate the genetic diversity and population configuration of Ajuga arabica in Saudi Arabia. Our findings demonstrate that there are high levels of genetic diversity within populations, but low levels of genetic differentiation among populations. Moreover, we discovered proof of gene flow among populations, suggesting that there are no significant genetic barriers to gene flow. Our results offer valuable insights into the genetic diversity and population structure of Ajuga arabica in Saudi Arabia, which can support conservation efforts and promote the sustainable use of this valuable medicinal plant.

Count data analysis presents unique challenges due to its discrete nature, often exhibiting excessive zeros and overdispersion. To address these complexities, count models, such as Poisson regression and Negative Binomial regression, have been developed, enabling modeling and prediction of count-based phenomena. Additionally, it’s important to notice that zero inflation, a phenomenon commonly observed in count data, requires specialized techniques for robust analysis. This article provides an overview of count data and count models, explores zero inflation, introduces Likelihood Ratio Tests, and explains how the Vuong Test can be used as a model selection criteria. Furthermore, we created a Vuong Test implementation from scratch using the Python programming language. This implementation enhances the accessibility and applicability of the Vuong Test in real-world scenarios, providing a valuable contribution to the academic community, since Python didn’t have an implementation of this statistical test.

Background: Extracellular Vesicles are pivotal mediators in intercellular communication, facilitating the exchange of biological information among healthy, pathological and tumor cells. Between the diverse subtypes of extracellular vesicles, exosomes have unique properties, clinical and therapeutical applications, even towards cancer. Breast cancer ranks as one of the most prevalent malignancies across the globe. Both the tumor core and its surrounding microenvironment engage in a complex, orchestrated interaction that facilitates the cancer’s growth and spread. Methods: The most valuable and significant PubMed Literature about extracellular vesicles and adipose–derived stem cells exosomes was selected and analyzed in order to report their biological properties and potential applications, in particular on the Triple–Negative Breast Cancer. Results: Adipose–derived stem cells exosomes represent a potential tool to target the tumor core of the Triple–Negative Breast Cancer, its microenvironment and surrounding tissues including metastasis. The authors are developing a supportive Triple–Adipose–derived stem cells Exosomes [T.A.E.] Technology against breast cancer in order to perform a selective preconditioning of the cancer before or while the traditional oncological treatments are running. Conclusion: The possibility to exploit the impact of Adipose–derived stem cells exosomes within the T.A.E. Technology against the Triple–Negative breast cancer is real, highlighting a new era for supportive measures against breast cancer.Keywords: Extracellular vesicles; Exosomes; Adipose–derived stem cells, Tumor microenvironment, Triple–Negative Breast Cancer, T.A.E. Technology.

It has been theorized that black holes are surrounded by firewalls, although there is not universal agreement concerning this. We first review basic concepts pertaining to Schwarzschild black holes and Hawking radiation. Then we discuss the anticipation of Hawking radiation—albeit from non-black holes—initially by R. C. Tolman and shortly thereafter with P. Ehrenfest. We compare evaporation into a vacuum at absolute zero (0 K) of black holes with that of non-black holes, and show that not only black holes but also non-black holes evaporate within a finite time. The times required for evaporation of black holes and non-black holes are compared. Next, we show that (i) if firewalls exist, they can originate via Hawking radiation at the minimum possible ruler distance (the Planck length) beyond the Schwarzschild horizon, where it has not suffered any gravitational redshift, or, alternatively, suffered maximal gravitational blueshift and (ii) the firewall temperature is on the order of the Planck temperature, independently of the mass and hence also of the Schwarzschild radius of a Schwarzschild black hole. We then explain the exponential nature of the gravitational frequency shift as a function of the gravitational potential. Next, we consider the firewall-mass problem, and provide an at least prima facie tentative resolution thereto based on: (i) the mass of a firewall being canceled by the negative gravitational mass = (negative gravitational energy)/c² accompanying its formation, (ii) the unchanged observations of a distant observer upon formation of a firewall, and (iii) Birkhoff's Theorem (actually first discovered by Jørg Tofte Jebsen). We then consider one aspect of thermodynamics in gravitational fields, showing that equilibrium relativistic gravitational temperature gradients cannot be exploited to violate the Second Law of Thermodynamics.

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.

In general, a superconductor has zero resistance, although it requires significant refrigeration or high pressures with high manufacturing costs, which prevents it into practical applications. In other words, solving these issues implies main superconducting researches. To solve these problems, this paper describes a new type of superconductivity, which is independent for temperatures and which operates without pressures. The principles of the presented system are as follows:First a voltage source, a current source and a load are connected in series. Then, the voltage of the voltage source is adjusted to balance the voltage of the load. Under this condition, the balance of the two voltages provides a zero voltage between the taps of the current source and the generated current from the voltage source becomes zero because of the internal infinite resistance of the current source. As a result, the electric powers generated by the two sources are zero, and therefore, the load cannot generate Joule heating because of energy conservation. However, the current from the current source (not the voltage source) is not zero; therefore, we can predict that the resistance of the load must be zero. As a theory, we derived a new electric field and transient attractive force, which result in a very short coherence of an electron pair because there is not the Coulomb repulsive force due to the existence of the above transient attractive force. Note that both the forces are derived by the Poisson equation, which implies that they cannot be compatible. Therefore, the pair combination energy from spins becomes extremely strong, which is not destroyed by the normal heat energy. Moreover, every center-of-mass motion of electron pair results in the Bose-Einstein condensation and the macroscopic wave function, which produces the London equation (i.e., the Meissner effect). Moreover, by introducing the equivalent circuit, this paper conducted numerical calculations. As a result, we could derive numerically zero resistance and responses for additional static magnetic fields as a discharged current, which implies the Meissner effect. Note that this paper has prepared Appendix section, which provides a guide to reproduce actual experiments and preliminary experimental results. These results in the Appendix indicate the zero resistances and Meissner effects.

The antimicrobial quantitative structure–activity relationship of plant flavonoids against Gram-positive bacteria was established in our previous works, and the cell membrane was confirmed as a major site of action. To investigate whether plant flavonoids have similar antibacterial effects and mechanisms against both Gram-negative and Gram-positive bacteria, here, the minimum inhibitory concentrations (MICs) of 37 plant flavonoids against Escherichia coli were determined using the microdilution broth method, and then the correlation between their lipophilic parameter ACD/LogP or LogD_7.40 value and their MIC was analyzed. Simultaneously, the correlation between the ACD/LogP or LogD_7.40 value and the MIC of 46 plant flavonoids reported in literature against E. coli was also analyzed. Both sets of results showed that there is a significant correlation between the LogP value and the MIC of plant flavonoids against Gram-negative bacteria. However, it is difficult to effectively predict the MIC of plant flavonoids against Gram-negative bacteria from their lipophilic parameters. By comparing two regression curves derived from plant flavonoids against Gram-negative and Gram-positive bacteria, it was further discovered that the antibacterial activities of most plant flavonoids against Gram-negative bacteria are stronger than those against Gram-positive bacteria when their LogP values are less than about 3.0, but the opposite is true when their LogP values are more than about 3.6. Moreover, this comparison also suggests that unlike mainly acting on the cell membrane of Gram-positive bacteria, plant flavonoids have multiple mechanisms against Gram-negative species, while the cell membrane is also an important action site among them. Combined with the correlation analyses between the enzyme inhibitory activity and the LogP value of the reported flavonoids, it was further suggested that DNA gyrase is another important target of plant flavonoids against Gram-negative bacteria.

Bioinformatics is a rapidly developing field enabling scientific experiments through computer models and simulations. Considering the vast databases of biological data available, it is ex-tremely important to develop efficient methods and algorithms for their processing. Sequence comparison is the best method for studying the evolutionary interaction between genes. It is based on alignment – the process of arranging two or more sequences to achieve the maximum level of identity and degree of similarity. The paper presents a new version of the algorithm for pairwise DNA sequences alignment, based on a new method called CAT, where a dependency with a previous match and the closes neighbor are taken in consideration to increase uniqueness of the CAT profile and to reduce possible collisions, i.e. two or more sequence having same CAT profiles. This makes proposed algorithm suitable for finding exact match of a concrete DNA se-quence in a big set of DNA data faster. The generation of CAT profiles is made once before data has been uploaded to the database, allowing the profiles to be used as metadata for the sequenc-es. It consists of an algorithm to calculate a CAT profile against the selected reference sequences and an algorithm to compare two sequences based on the calculated CAT profiles. Improve-ments in generation of the CAT profiles, are detailed described in the paper. Block scheme, pseudo code tables and figures were updated according to the proposed new version and ex-perimental results. Experiments have been carried out with the new version of the method and different datasets to align DNA sequences based on the CAT method. New experimental results in terms of collisions, speed, and efficiency of the proposed solutions are presented. Experiments related to the performance comparison with Needleman-Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. An analysis of the per-formance of the proposed CAT based algorithm against Knuth–Morris–Pratt algorithm, which has a complexity of O(n) and is one of the most widely used for searching biological data, was performed. The impact of prior matching dependencies on uniqueness for generated CAT pro-files is investigated. The analysis of the experimental results obtained by sequence alignment shows a small deviation of the proposed algorithm based on the CAT method, which can be ig-nored if this deviation is acceptable at the expense of performance. The time efficiency of the CAT algorithm remains constant, regardless of the length of the sequences. Therefore, the ad-vantage of the proposed method is its fast processing in the alignment of large sequences, for which the execution of the exact algorithms takes a long time. The example code realization of the CAT Method, under the protection of the GNU General Public License v3.0, can be accessed on GitHub at: https://github.com/HristoS/CATSequenceAnalysis.

Medical data flows in streams as the data related to clinical tests and administered drugs by the doctors flows continuously. The doctors must be immediately alerted if negative associations are found among the drugs they prescribe. Data streams are to be processed in single scans as it is not possible to re-scan the data for any iterative processing. To detect negative drug connections, regular and frequent drug patterns must be processed. Negative correlations between disease-curing medications might create adverse responses that kill patients. This paper proposes an algorithm that finds the negative associations among regular and frequent patterns mined from medical data streams. The negative associations mined are the most effective and reduce the negative associations, which are more critical by 50%.

This review provides an overview of advancements in plant genomics, emphasizing key stages in genomics projects and addressing associated challenges. Long read sequencing enables the cost-effective sequencing of plant DNA and assembly of highly continuous genome sequences - often even separating haplophases. Incorporating external hints, such as cDNA sequences from RNA-seq or full length cDNA sequencing, enhances the identification of gene models. While these steps enable high-throughput exploration of numerous plant genomes, a significant bottleneck lies in elucidating gene functions. The classical approach based on wet lab methods is impractical when dealing with thousands of genes in a new genome sequence. To overcome this challenge, computational tools harnessing existing information for cross species knowledge transfer are essential for expediting the functional annotation process. In support of researchers entering the field of plant genomics, a collection of recommended tools has been curated and is accessible at https://github.com/bpucker/ToolOverview.

Background: As the most invasive breast cancer (BrCa), triple-negative BrCa (TNBC) has the worst survival. The use of dexmedetomidine potentially affected BrCa surgery and dexmedetomidine was reported to have direct effects on TNBC cells. The objective of this study is to explore the mechanisms underlying the effect of dexmedetomidine on TNBC. Methods: Dexmedetomidine targets were predicted using The Cancer Genome Atlas data SwissTargetPrediction. Cell lines MDA-MB-231, MCF7, and MCF10A were used to validate the targets in TNBC with both clinical samples and cell lines. Cancer cell lines and normal breast cell lines were grouped in cancer and normal groups respectively. Both groups were exposed to dexmedetomidine treatment. Cell Counting Kit-8 was used to determine the effect of dexmedetomidine on cells with target silencing. The binding model of the candidate targets was docked and critical amino acids were mutated to validate the binding model. Results: Dexmedetomidine selectively inhibits cancer cells. Catalytic subunit of the DNA-dependent protein kinase (PRKDC), indoleamine 2,3-dioxygenase 1 (IDO1), opioid receptor kappa 1 (OPRK1), glutaminyl-peptide cyclotransferase (QPCT), macrophage migration inhibitory factor (MIF), potassium voltage-gated channel, subfamily H (Eag-related), member 2 (KCNH2), cholinergic receptor, muscarinic 3 (CHRM3), and potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 (KCNN4) were identified as dexmedetomidine targets in TNBC. The expression levels of PRKDC, IDO1, MIF, KCNH2, CHRM3, and KCNN4 were found to be upregulated in TNBC tissues compared to non-TNBC tissues(p<0.05). Silencing of these genes was found to reduce the sensitivity of TNBC cells to dexmedetomidine(p<0.05). This effect was counteracted when the silenced genes were overexpressed, resulting in an increase in the sensitivity of cells to dexmedetomidine (p<0.05). Furthermore, a direct interaction between dexmedetomidine and IDO1 and CHRM3 was observed, which regulated the sensitivity of cells to dexmedetomidine(p<0.05).Conclusion: IDO1 and CHRM3 are direct targets of dexmedetomidine in TNBC.

A significantly reduced stress concentration effect and a stable deformation behavior are exhibited by the arc-like S-shaped auxetic structure. Analytical works beyond the bar and hinge method to capture structural effects, such as bending, shearing, etc., in the S-structure are scarce in the literature. The deformation pattern of the S-structure is dominated by bending and shearing within the linear elastic region. In this work, Timoshenko beam theory is used to derive closed-form expressions for overall elastic modulus and Poisson’s ratio. This agrees well with the results of finite element simulations. An adjusted R-square value of over 0.99 and almost 0.82 is obtained for elastic modulus and Poisson’s ratio, respectively. From parametric studies, it’s established that under quasi-static transverse load, strut thickness and the angle `α’ are the most important parameters for controlling elastic modulus, specific energy absorption, negative Poisson’s ratio (NPR) effect, and relative density of the entire auxetic structure. Also, it’s found that energy absorption and elastic modulus increase together. Interestingly, the elastic modulus of the structure under transverse load lies in the range from 3 MPa to 250 MPa, which means this structure is compliant enough and can be used in cushioning, packaging, soft robotics applications, etc.

Biofilm-associated bacterial infections are the major reason for treatment failure in many diseases including burn trauma infections. Uncontrolled inflammation induced by bacteria leads to materiality, tissue damage and chronic diseases. Specialized proresolving mediators (SPMs), including maresin-like lipid mediators (MarLs), are enzymatically biosynthesized from omega-3 essential long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA) by macrophages and other leukocytes. SPMs exhibit strong inflammation-resolving activities, especially inflammation provoked by bacterial infection. In this study, we explored the potential direct inhibitory activities of three MarLs on gram-positive (Staphylococcus aureus) and gram-negative (Pseudomonas aeruginosa and Escherichia coli) bacteria in their biofilms that are leading bacteria in burn trauma related infections. We also examined the effects of MarLs on the bactericidal activities of a typical broad-spectrum antibiotics carbenicillin on these bacteria in their preformed biofilms. The results revealed that MarLs combined with carbenicillin can inhibit the survival of gram-positive and gram-negative bacteria in their biofilms although MarLs alone did not exhibit bactericidal activity. Thus, our findings suggest that the combination of MarLs and carbenicillin can lower the antibiotic requirements to kill the bacteria in preformed biofilms.

Immune checkpoint receptors play a crucial role in steering tumor progression, prompting a focused investigation into the role of TIM3 in breast cancer. Analysis of TCGA BRCA data unveiled diverse correlations between TIM-3 expression and immune cell infiltration across subtypes. In our in-house cohort studied through IHC, significant changes in TIM3 expression with tumor grades were observed. Higher TIM3 expression correlated with increased disease-free survival in pan breast cancer, marking the first revelation of TIM3's positive role in pan BC prognosis. The study indicates that alluring TIM3 response, rather than suppression, may enhance breast cancer prognosis.

Obesity is one of the most prevalent chronic diseases and has become a global epidemic. Obesity leads to a greater risk of breast cancer (BC), metastases, recurrence, and decreased survival. For sustained weight loss, bariatric surgery is effective as a long-term solution. Bariatric surgery is associated with improved outcomes of several cancers including BC, although the mechanisms mediating this protection are unknown. We hypothesized that elevated bile acid pools detected after bariatric surgery may be factors that contribute to improved BC outcomes. Indeed, patients with greater expression of the bile acid receptor FXR displayed improved survival in specific BC subtypes. Patients with tumors that are estrogen receptor negative (ER-) displayed significantly elevated survival with higher FXR (NR1H4) expression compared to lower expression. FXR is a nuclear hormone receptor activated by bile acids. Therefore, we posited that activating FXR using an established FDA-approved agonist would display anticancer effects. Indeed, FXR agonism by the bile acid mimetic known commercially as OCALIVA (“OCA”), or Obeticholic acid (INT-747), significantly reduced BC progression and overall tumor burden in a pre-clinical model. In human and murine BC analyses in vitro, agonism of FXR significantly and dose-dependently inhibited proliferation, migration, and viability. In contrast, synthetic agonism of another common bile acid receptor, the G protein-coupled bile acid receptor (GPBAR1, TGR5) which is mainly activated by secondary bile acids, failed to significantly alter cancer cell dynamics. In conclusion, agonism of FXR by primary bile acid memetic OCA yields potent anti-tumor effects potentially through inhibition of proliferation and migration and reduced cell viability. Findings suggest that FXR is a tumor suppressor gene with high potential for personalized therapeutic strategies for individuals with BC.

We have successfully synthesized a series of Bi doped BaFe2As2 high quality single crystals for the first time. The x-ray diffraction (XRD) patterns show an expansion of lattice parameter c with Bi doping, indicating a negative pressure effect. By investigating the resistivity, a Fermi liquid (FL) to non-Fermi liquid (NFL) crossover is observed from normal state to antiferromagnetic order state, accompanied by three superconducting transitions labeled as SC I, SC II and SC III which are supposed to be induced from three superconducting realms with various Bi concentration. Thus, the NFL behavior is proposed to be closely related with the presence of superconductivity. The magnetic susceptibility measurements further speculates that the SC I and SC III phases should be filamentary superconductivity while the SC II be a possible bulk superconductivity with TC 7 K.

With the economic recession and the deterioration of the ecological environment becoming more and more prominent in the world, the sustainable operation of enterprises is facing the most difficult choice in history. For each responsible enterprise, it is crucial to choose the market power expansive strategy that can improve the realistic viability or the technological innovation strategy that can improve the future development potential. This is of great significance to reduce the negative external effects of the corporate social environment and ensure their sustainable development. In this paper, we select the data of 18 large listed petrochemical companies from 2003 to 2018 as samples and construct a linear regression model for empirical analysis. Meanwhile, we put forward more practical business management strategies for the sustainable development of petrochemical enterprises in developing countries in further research.

.Background: Negative outcomes associated with medications (NOM) and drug-related problems (DRP) significantly impact individuals with kidney replacement therapy (KRT) given the complexities of managing kidney disease and associated comorbidities. The present study aims to assess the frequency of NOMs/DRPs among KRT patients and identify contributing factors. Methods: A cross-sectional study was conducted at the Virgen de las Nieves University Hospital (Granada, Spain), involving 117 outpatient adults with KRT. Data were collected from February 2021 to July 2023 using electronic records, semi-structured interviews (Dáder Method), and discussions with nephrology specialists. NOMs/DRPs were identified following treatment guidelines. Binary logistic regression determined associated factors (p-value < 0.05). Results: Across 117 patients, 2,436 NOMs and 3,303 DRPs were identified, averaging 20.82 NOMs and 28.23 DRPs per patient. Prevalent NOMs included untreated conditions (58.95%), quantitative ineffectiveness (35.43%), and non-quantitative safety problems (5.13%). Dominant DRPs were undertreated conditions (37.63%), wrong dose/posology/length (33.00%), risk of adverse drug reactions (ADR) (16.14%), and non-adherence (6.87%). Patients with ADR, undertreated condi-tions, and anemia were associated with quantitative ineffectiveness. Risk of ADR and vitamin D deficiency/insufficiency correlated with non-quantitative safety problems. Conclusions: KRT pa-tients exhibited a substantial prevalence of NOMs/DRPs. Further research is needed to deepen our understanding of these complexities for improved patient care.

Prime period sequences can serve as the fundamental tool to construct arbitrary composite period sequences. This is a review study of prime period perfect Gaussian integer sequence (PGIS). When cyclic group {1,2,…,N−1} can be partitioned into k cosets, where N=kf+1 is an odd prime number, the construction of a degree-(k+1) PGIS can be derived from either matching the flat magnitude spectrum criterion or making the sequence with ideal periodic autocorrelation function (PACF). This is a systematic approach of prime period N=kf+1 PGIS construction, and is applied to construct PGISs with degrees 1, 2, 3 and 5. However, for degrees larger than 3, matching either the flat magnitude spectrum or achieving the ideal PACF encounters a great challenge of solving a system of nonlinear constraint equations. To deal with this problem, the correlation and convolution operations can be applied upon PGIS of lower degrees to generate new PGIS with degree-4 and other higher degrees, e.g., 6, 7, 10, 11, 12, 14, 20 and 21 in this paper. In this convolution based scheme, both degree and pattern of a PGIS vary and can be indeterminant, which is rather nonsystematic compared with the systematic approach. The combination of systematic and nonsystematic schemes contributes the great efficiency for constructing abundant PGISs with various degrees and patterns for the associated applications.

Hypervirulent Klebsiella pneumoniae (hvKp) is a variant that has been increasingly linked to severe, life threatening infections including pyogenic liver abscess and bloodstream infections. HvKp belonging to the capsular serotypes K1 and K2 have been reported worldwide, however very scarce studies are available on the their genomics and virulence. In the current study we report four hypermucoviscous hvKp ESBL clinical strains of capsular serotype K1 and K2 isolated from pus and urine of critically ill patients in tertiary care hospitals in Oman. These strains belong to diverse sequence types (STs) namely ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2). To study their virulence, Galleria Mellonella model and resistance to human serum killing were used. The G. mellonella model revealed that the K1/ST-23 isolate is the most virulent as 50% of the larvae died in the first day, followed by isolate K2/ST-231 for which 75% of the larvae died in the second day and isolate K2/ST-14 for which 50% of the larvae died in the second day. Resistance to human serum killing showed there was complete inhibition of bacterial growth of all four isolates by the end of the first hour and up to the third hour. For ST-23(K1), ST-231(K2), ST-881(K2), and ST-14(K2), there was a gradual decrease in the number of colonies up to the second to third hour, which indicates neutralization of bacterial cells by the serum components. However, this was followed by sudden increase of bacterial growth, indicating possible resistance of bacteria against human serum bactericidal activity. Whole genome sequencing (WGS) revealed that hvKp strains display unique genetic arrangement of k-loci. Whole genome SNP-based phylogenetic analysis revealed that these hvKp isolates are phylogenetically distinct, belonging to diverse clades and belong to different STs in comparison to global isolates. This is the first report from Oman detailing the WGS of hvKp clinical isolates and assessing their resistance and virulence genomics, which reinforce our understanding of their epidemiology and dissemination in clinical settings.

In this communication, we present an innovative approach leveraging advanced Machine Learning (ML) and Artificial Intelligence (AI) techniques, specifically the Non-Negative Matrix Factorization (NMF) method, to analyze downward and upward light spectra collected by Hyperspectral Ocean Color Radiometer (HyperOCR, HOCR) sensors in the water column. Our work focuses on the development of a robust and efficient tool for unraveling the structure and activities of natural microbial assemblages in the ocean. By applying the NMF method to HyperOCR data, we successfully extracted five spectral signatures, representing unique patterns in the data. These signatures were instrumental in predicting the abundances of various microbial components, including bacteria, heterotrophic nanoflagellates, and picoeukaryotes, showcasing the potential of ML and AI in advancing oceanographic studies. To validate the methods, the study area included a shallow coastal area under the influence of freshwater inflow and an open offshore area with a depth of 100 m. The study sites in coastal and offshore waters (Kaštela Bay and Stončica Vis, respectively) had significantly different hydrographic and microbiological characteristics. Kaštela Bay had lower temperatures and salinity than the site on Vis. We have proved by application of different AI and ML methods with specific HOCR sensors prediction of the structure of the microbial community.

Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish (Squalus acanthias) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA that were sequenced. Blast searches with the sequences showed they were not AQP11. An elasmobranch AQP11 nucleotide sequence alignment was produced to identify conserved regions to make further degenerate primers. One primer pair produced a short 148bp fragment showing particularly strong expression in gill and intestine. It was sequenced and represented a piece of the AQP11 gene. However, as the fragment may have resulted from contaminating genomic DNA (in total RNA used to make cDNA), 5’ and 3’ RACE was performed to amplify the two ends of the putative cDNA. 5’ and 3’ RACE amplifications depend on the presence of a 5’ cap nucleotide and a poly A tail respectively on the putative AQP11 mRNA. Hence successful amplification was only possible from cDNA and not genomic DNA. Nested RACE amplifications were performed using gill and intestinal RACE cDNA but none of the DNA fragments were AQP11. Consequently, the spiny dogfish AQP11 gene may represent a pseudogene.

All vaccines exhibit specific and nonspecific effects. Specific effects are shown by the efficacy against the target pathogen, while nonspecific effects can be detected by the change in all-cause mortality. The real-world non-COVID-19 all-cause mortality (NCACM) data for the population of England between January 2021 and May 2023 was assessed. All vaccines administered were based on the original Wuhan antigen. Each gender and age group, along with COVID-19 variant shows its own unique NCACM vaccination benefit/disbenefit time profile. The efficacy of COVID-19 vaccination against COVID-19 disease/death per se is undisputed, however, the nonspecific outcomes of COVID–19 vaccination is far more nuanced than have been widely appreciated. This confirms an earlier study on the unanticipated nonspecific effects of influenza vaccination against all-cause winter mortality. Interestingly, a high proportion of NCACM beneficial effects occurred during the first 21 days following COVID-19 vaccination, while the worst example of increased NCACM occurred during the fourth dose of COVID-19 vaccination in 19–40-year-olds for the interval &gt;21 days post vaccination which led to NCACM 3- to 10-times higher than in the unvaccinated. By the time of the Omicron variant, NCACM outcomes in those aged 90+ are mostly adverse. The beneficial nonspecific effects of COVID-19 vaccination increase with age and reach their maximum effect during the second week post vaccination for age groups below 50 years, rising to during the third week for those aged 70+. Finally, we discuss the mechanisms by which COVID-19 vaccination could induce wider nonspecific effects. Most of these mechanisms seem to depend on gene regulation by noncoding RNAs which also interact with mRNAs. We suggest that further international studies are required to discern the nonspecific NCACM effects of the different COVID-19 variants other than the three variants prevalent in the UK, and different types/manufacturer of COVID-19 vaccines which have been employed around the world. We can only speculate regarding the nonspecific effects of the COVID-19 vaccines administered to persons with an asymptomatic infection, and during vaccine waning. Vaccines not only need to be effective against the target pathogen, as primarily determined by antibody production, but need to minimize any unanticipated adverse nonspecific effects against all-cause mortality.

Breast cancer represents the most common neoplasm worldwide. Viral infections are involved with carcinogenesis, especially those caused by oncogenic Human Papillomavirus (HPV) genotypes. The relationship between HPV and various types of cancer, such as breast and lung, still requires further studies. After infection with HPV, there is a remodeling of the tumor microenvironment, providing a post-infection alteration with immunosuppressive characteristics. This study evaluated the role of HPV in breast adenocarcinoma cell lineage (MDA-MB-231), transfected with the HPV16 E5, E6, and E7 oncogenes and co-cultured with PBMCs. Immunophenotyping was performed. There was an increase in CD4+ T cells number when compared with non-transfected and transfected MDA-MB-231, especially the Treg profile. Moreover, proinflammatory intracellular cytokines, such as IFN-γ, TNF-α, and IL-17 were impaired by transfected cells and a decrease in the cytolytic ac-tivity of the CD8+ and CD56+ lymphocytes was also observed in the presence of HPV oncogenes, mainly with E6 and E7 in NK and TCD8+ cells. In conclusion, MDA-MB-231 breast cell lineage transfected with HPV oncogenes can downregulate the number and function of lymphocytes and monocytes.

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.

Chen, et al., compared two modified polyurethane-based wound dressings (PUE and PUESi), both intended for use in chronic wounds, with a negative control (gauze) and a positive control (PolyMem) via a series of preliminary in vitro and rodent model tests. Future studies may find that one or both of these two new dressings are beneficial. However, the results of this first study cannot be relied upon. Although they exhibited in-depth knowledge of manufacturing techniques, the study designers seem far less familiar with the science of wound healing and with PolyMem wound dressings. This helps explain the flaws in the methods that lead to many of their tests not being translatable to real-world settings. In addition, the interpretation of some of the test results is questionable.

Commercial buildings situated in hot and humid tropical climates rely significantly on cooling systems to maintain optimal occupant comfort. A well-accurate day-ahead load profile prediction plays a pivotal role in planning the energy requirements of cooling systems. Despite the pressing need for effective day-ahead cooling load predictions, current methodologies have not fully harnessed the potential of advanced deep-learning techniques. This research paper aims to address this gap by investigating the application of innovative deep learning models in day-ahead hourly cooling load prediction for commercial buildings situated in tropical climates. A range of deep learning techniques, including Deep Neural Network, Convolutional Neural Networks, Recurrent Neural Networks, and Long Short-Term Memory networks are employed to enhance prediction accuracy. Furthermore, these individual deep learning techniques are synergistically integrated to create hybrid models, such as CNN-LSTM and Sequence-to-Sequence models. An extensive comparative analysis is conducted to identify the most effective hybrid model. Sequence-to-sequence model provided better performance compared to the other single and hybrid models. Experiments are conducted to choose the time horizons from the past that can serve as input to the models. Further, the influence of various categories of input parameters on prediction performance has been assessed. Historical cooling load, calendar features and outdoor weather parameters are found in decreasing order of influence on prediction accuracy. This research focuses on buildings located in Singapore and presents a comprehensive case study to validate the proposed models and methodologies.

An addition sequence is an important operation in many applications of computer science, such as multi-modular exponentiation and outsourcing protocols. Finding an addition sequence for a set of positive integers with the shortest length is challenging due to the high computational time required to find the solution. In this paper, a new metaheuristic algorithm is designed based on the simulated annealing strategy to generate a short addition sequence. The efficiency of the proposed algorithm was proved experimentally by comparing it with the previous exact and heuristic algorithms in terms of running time and the length of the addition sequence.

PIEZO1 plays a crucial role in the human body as a mechanosensory ion channel. It has been demonstrated that PIEZO1 is important in tissue development and regulating many essential physiological processes. Studies have suggested that the PIEZO1 ion channel plays a role in invasion and progression in cancer; elevated levels of PIEZO1 have been correlated with increased migration in breast cancer cells, chemo-resistance and invasion in gastric cancer cells, and increased invasion of osteosarcoma cells. In addition, high PIEZO1 expression levels were correlated with a worse prognosis in glioma patients. On the other hand, studies in lung cancer have attributed high PIEZO1 levels to better patient outcomes. However, the clinical impact of PIEZO1 in breast cancer is not well characterized. Therefore, our goal was to determine the clinical relevance of PIEZO1 in breast cancer. Analysis of breast cancer data from The Cancer Genome Atlas (TCGA) was conducted to investigate PIEZO1 expression levels and correlation to survival, followed by validation in an independent dataset, GSE3494. We also performed gene set enrichment analysis (GSEA) and analyzed immune cell levels in breast tumors from TCGA through a CIBERSORT algorithm. Our results demonstrated that PIEZO1 expression levels are higher in hormone receptor (HR) negative than HR positive cohorts. High PIEZO1 expression is correlated with a significant decrease in survival in HR negative cohorts, suggesting that PIEZO1 could be utilized as a prognostic biomarker in HR negative breast cancer. GSEA showed that various signaling pathways associated with more invasive phenotypes and resistance to treatments, including epithelial-mesenchymal transition (EMT), hypoxia, and multiple signaling pathways, are enriched in high PIEZO1 HR negative tumors. Our results also demonstrated a decrease in CD8+ and CD4+ T cell infiltration in high PIEZO1 HR negative tumors. Further investigations are necessary to elucidate the mechanistic roles of PIEZO1 in HR negative breast cancer.

Coagulase-Negative Staphylococci (CoNS) are commensal on human body surfaces and for years, they were not considered a cause of bloodstream infection and were often regardered as contamination. However, the association of CoNS with nosocomial infection is increasingly recognized. The insertion of cannulas and intravascular catheters represents the first source of CoNS entry into the bloodstream, causing bacteremia and sepsis. They owe their pathogenic power to their ability to produce biofilms on surfaces, such as medical devices. In this study, we evaluate the adhesive capacity of CoNS isolated from blood cultures by comparing spectrophotometric phenotypic assay with genotypic analysis based on the evidence of the ica operon. We retrospectively reviewed the database of CoNS isolated from blood cultures, that were considered to be responsible for 361 bloodstream infections. Among them, we selected 89 ones who had full records. Our data show that S. epidermidis was the predominant species isolated, and with greater adhesive capacities, especially those with the complete operon. Knowing the adhesive capabilities of a microorganism responsible for sepsis can be useful in implementing appropriate corrective and preventive measures, as conventional antibiotic therapy cannot effectively eradicate biofilms.

In some applications of microgrid and distributed generation, it is required to feed islanded or stand-alone loads with high-quality voltage to provide low total harmonic distortion (THD). To fulfil these demands, an LC filter is connected to the output terminals of power electronics converters. A cascaded voltage and current control loop with pulse-width modulation schemes are used to regulate the voltage and current in these systems. However, these strategies have some drawbacks, particularly when multiple-input multiple-output plants (MIMO) are controlled using single-input single-output (SISO) design methods. This methodology usually produces a sluggish transient response and cross-coupling between different control loops. In this paper, a model predictive control (MPC) strategy based on the concept of optimal switching sequences (OSS) is designed to control voltage and current in an LC filter connected to a three-level neutral-point clamped converter. The strategy solves two well-formulated optimisation problems to achieve control of the LC filter variables and the voltages of the DC-link capacitors. Hardware-in-the-Loop (HIL) results are obtained to validate the feasibility of the proposed strategy, using a PLECS-RT HIL platform and a DSP Microlab Box controller. In addition to the good dynamic performance of the proposed OSS-MPC, it is demonstrated by the HIL results that the control algorithm is capable of obtaining low total harmonic distortion (THD) in the output voltage for different conditions.

Negative thermal quenching (NTQ) denotes that the integral emission spectral intensity of a given phosphor increases continuously with increasing temperature up to a certain elevated temperature. NTQ has been a subject of intensive investigation in recent years and a large number of phosphors were reportedly to have exhibited NTQ. In this paper, a collection of results in the archival literature about NTQ of specific phosphors are discussed from a macroscopic viewpoint in the following three aspects:1) Could NTQ of a given phosphor be reproducible?2) Could the associated data for a given phosphor exhibited NTQ be in line with the law of conservation of energy?3) Could NTQ of a given phosphor be demonstrated in a prototype WLED device? By analyzing typical cases based on common sense, it is hoped to increase the awareness for the issues with the papers reporting NTQ of the specific phosphors based on spectral intensity along with for the importance of keeping stability and consistency of the measurement conditions in temperature-dependent spectral intensity measurement which is a prerequisite for the validity of the measurement results.

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.

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.

Hidradenitis suppurativa and Langerhans cell histiocytosis are rare disorders that can reveal similar clinical manifestations, making differential diagnosis difficult. A definitive diagnosis requires biopsy and histological confirmation in suspicious cases. The complex pathophysiology of these diseases has still not been understood, therefore the treatment is still a challenge for physicians. It is seen with predilection in the intertriginous areas of the body, predominantly in the axillary region, rarely requiring a surgical procedure. However perineal, perianal, and gluteal HS usually necessitates some form of surgical treatment. Langerhans cell histiocytosis (histiocytosis X) is a very rare systemic disease manifested by clonal cell proliferation of histiocytic-dendritic nature, with pseudonodular manifestation that deeply infiltrates the hypodermis and ulcerates the epidermis on the surface. Langerhans cells are dendritic, antigen-presenting cells localized in the suprabasal regions of the squamous epithelium of the skin and mucous membranes, which help regulate the immune system. In this report, we present our experience with extensive gluteal, perineal, and perianal hidradenitis suppurativa and Langerhans cell histiocytosis cases, including our treatment methods and outcomes.

The study aimed to investigate the effect of climate change exposure on affect and pro-environmental behavioural intentions in a randomised controlled trial. An online survey was completed by 100 adult participants and included measures of affect and pro-environmental behavioural intentions pre- and post-exposure. Participants were randomly allocated to a group that saw a climate change video (n=55) or a group that saw a non-climate change video (n=45). The findings showed were that participants in the climate change group showed a significant increase in negative affect and pro-environmental behavioural intention scores post-video exposure compared to the non-climate change video group. This suggests that climate change video exposure negatively influences affect but also potentially increases the intention to act pro-environmentally. These findings have the potential to support policies and societal change, however further investigation into the type of contents, actual behaviour change, and impacts on diverse populations (e.g., minority groups) is needed that influences pro-environmental behaviours is required. Furthermore, to achieve a greater impact, future research should be conducted measuring actual pro-environmental behaviour change, including with those from diverse populations.

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.

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.

We discuss two queueing-inventory systems with catastrophes in the warehouse. Catastrophes occur according to Poisson process and upon arrival of a catastrophe all inventory in the system is instantly destroyed. But consumer customers in the system (in the server or in the buffer) continue still waiting for the replenishment of the stock. The arrivals of the consumer customers follow a Markovian Arrival Process (MAP) and they can be queued in an infinite buffer. Service time of a consumer customer follows a phase-type distribution. The system receives negative customers whose have Poisson flows to service facility and upon arrival of a negative customer one consumer customer is pushed out from the system, if any. One of two replenishment policies can be used in the system: either (s,S) or (s,Q). If upon arrival of the consumer customer, the inventory level is zero, then according to the Bernoulli scheme, this customer is either lost (lost sale scheme) or join the queue (backorder sale scheme). The system is formulated by a four-dimensional continuous-time Markov chain. Steady state distribution is obtained using the matrix-geometric method. A comprehensive numerical study is performed on the performance measures under various replenishment policies. Finally, an optimization study is presented.

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.

Most of the research in data mining concentrated on finding the positive associations that exist in frequent patterns. Frequent patterns have no bearing on the time duration and, therefore, lose interestingness. The Regularity of an itemset is related to the time at which the transaction occurred and the time distance between the transactions. Frequent Regular item sets can be generated considering the Frequency and the Regularity of the occurrence of the Item Sets. The frequent and regular Item sets will be so huge that they cannot be handled in real time. The count of Frequent and regular item sets gets reduced drastically when the properties “closed” and “Maximality” are applied. Finding negative associations among such patterns are important in the field of medicine. Many drugs administered to cure some diseases have counter reactions leading to many other diseases. Negative associations among the mined patterns are important as they reveal significant contradictions frequently among medical drugs administered by medical practitioners to cure some diseases. This paper proposes a method that mines medical databases to find regular, frequent patterns applied with closed and maximal properties and find negative associations among those patterns. The proposed algorithm is accurate to 98% and performs 9% more efficiently than the other algorithms presented in the literature.

Shared micromobility has gained significant attention in the field of transportation engineering in recent years as an environmentally friendly, convenient, and easily accessible transportation mode. Like other medium-sized cities, Birmingham, Alabama implemented a shared micromobility pilot program in 2021 that captured the attention of local travelers. This study examined shared e-scooter usage and associated travel patterns in Birmingham using 2021-2022 field data. From these data, ArcGIS maps were used to showcase trip origins and destinations. To gain a further understanding of e-scooter travel patterns in the study area, zip code and block group densities were calculated. Additionally, a negative binomial regression model was constructed to identify determinants of shared e-scooter trips. The analysis results showed that the usage of shared e-scooters was the highest during the nighttime, on weekends, and in the fall season. Furthermore, the research findings indicated that shared e-scooters experienced their highest utilization rates in areas with a higher proportion of educated and higher-income individuals. These findings suggest that travelers’ mode choice related to the use of micromobility modes is influenced by environmental and demographic factors. Overall, this case study offers valuable contributions to the understanding of the role of shared e-scooters in Birmingham's transportation landscape and can guide transportation authorities in other medium-sized cities in their efforts to plan for micromobility options.

We present a differential-calculus-based method which allows one to derive more identities from {\it any} given Fibonacci-Lucas identity containing a finite number of terms and having at least one free index. The strength of our method is that no additional information is required about the given original identity. The method readily extends to a generalized Fibonacci sequence.

Attack investigation is an important research field in forensics analysis. Many existing supervised attack investigation methods rely on well-labeled data for effective training. While the unsupervised approach based on BERT can mitigate the issues, the high degree of similarity between certain real-world attack and normal behaviors makes it challenging to accurately identify disguised attacks. This paper proposes ConLBS, an attack investigation approach that combines the contrastive learning framework and multi-layer Transformer network to realize the classification of behavior sequences. Specifically, ConLBS constructs behavior sequences describing behavior patterns from audit logs, and a novel lemmatization strategy is proposed to map the semantics to the attack pattern layer. Four different augmentation strategies are explored to enhance the differentiation between attack and normal behavior sequences. Moreover, ConLBS can perform unsupervised representation learning on unlabeled sequences, and can be trained either supervised or unsupervised depending on the availability of labeled data. The performance of ConLBS is evaluated in two public datasets. The results show that ConLBS can effectively identify at-tack behavior sequences in the cases of unlabeled data or less labeled data to realize attack investigation, and achieve the superior effectiveness compared to existing methods and models.

Background: Cervical cancer prevention in regions with limited access to screening and HPV vaccination necessitates innovative approaches. This study explored the potential of a test-and-treat strategy using mRNA HPV tests to impact cervical cancer prevention in a high-prevalence HIV population. Methods: A cervical screening study was conducted at three South African hospitals involving 710 under-screened, non-pregnant women (25 to 65 years) without known cervical diseases. Cytology, HPV testing, colposcopy, and biopsies were performed concurrently. Histopathologists determined final histological diagnoses based on biopsy and LLETZ histology. mRNA-HPV-genotyping for 3 (16, 18, 45) to 8 (16, 18, 31, 33, 35, 45, 52, 58) high-risk types was performed on leftover liquid-based cytology material. The preventive potential of the test-and-treat approach was estimated based on published data, reporting the causative HPV types in cervical cancer tissue from South African women. Treatment was provided as needed. Results: HPV positivity rate more than doubled from 3-type (15.2%; 95% CI: 12.6-17.8) to 8-type mRNA (31.5%; 95% CI: 28.8-34.9) combinations, significantly higher among HIV-positive women. CIN3+ prevalence among HIV-positive women (26.4%) was double that of HIV-negative women (12.9%) (p&lt;0.01). The 6-type combination showed the best balance of sensitivity, specificity and treatment group size, and effectiveness to prevent cervical cancer. A 4-type combination (16, 18, 35, 45) could potentially prevent 77.6% (95% CI: 71.2-84.0) of cervical cancer burden by treating 20% and detecting 41.1% of CIN3 cases in the study group. Similarly, a 6-type combination (16, 18, 31, 33, 35, 45), treating 25% and including 62% of CIN3 cases, might prevent 85% of cervical cancer cases (95% CI: 79.6-90.6) among HIV-positive and negative women. Conclusion: Employing mRNA HPV tests within a test-and-treat approach holds huge promise for targeted cervical cancer prevention in under-screened populations. Testing for mRNA of the 6 highest-risk HPV types in this population and treating them all is projected to effectively prevent progression from CIN3 to invasive cervical cancer while reducing overtreatment in resource-constrained settings.

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.

We describe the development and validation of a HPLC-MS/MS method to assess the pharmacokinetics and tumour distribution of ZST316, an arginine analogue with inhibitory activity towards dimethylarginine dimethylaminohydrolase 1 (DDAH1) and vasculogenic mimicry, and its active metabolite L-257 in a xenograft model of triple negative breast cancer (TNBC). The method proved to be reproducible, precise, and highly accurate for the measurement of both compounds in plasma and tumour tissue following acute and chronic (five days) intraperitoneal administration of ZST316 (30mg/Kg daily) in six-week-old SCID mice inoculated with MDA-MB-231 TNBC cells. ZST316 was detected in tumour tissue and plasma after 1 hour (6.47 and 9.01M, respectively) and 24 hours (0.13 and 0.16M, respectively) following acute administration, without accumulation during chronic treatment. Similarly, the metabolite L-257 was found in tumour tissue and plasma after 1 hour (15.06 and 8.72M, respectively) and 24 hours (0.17 and 0.17M, respectively) following acute administration of ZST316, without accumulation during chronic treatment. The half-live after acute and chronic treatment ranged between 4.4-7.1hrs (plasma) and 4.5-5.0hrs (tumour) for ZST316, and 4.2-5.3hrs (plasma) and 3.6-4.9hrs (tumour) for L-257. The results of our study demonstrate the a) capacity to accurately measure ZST316 and L-257 concentrations in plasma and tumour tissue in mice using the newly developed HPLC-MS/MS method, b) rapid conversion of ZST316 into L-257, c) good intra-tumour penetration of both compounds, and d) lack of accumulation of both ZST316 and L-257 in plasma and tumour tissue during chronic administration. The new HPLC-MS/MS method is useful to investigate the in vivo effects of ZST316 and L-257 on vasculogenic mimicry, tumour mass, and metastatic burden in xenograft models of TNBC.

The precise molecular basis of anti-tumor immunity is not yet fully understood, although commensal Bifidobacterium (c-BIF) is expected to be one of the key players in cancer control via antigenic mimicry. We investigated the sequence similarity between c-BIF and cytotoxic T lymphocyte (CTL) epitope peptides against human tumor-associated antigens to better understand the molecular basis of antigenic mimicry. We used two different similarity analyses for this purpose, a linear sequence analysis and a similarity analysis of T cell receptor (TCR)-mediated recognition of CTL epitope peptides on antigen-presenting cells. The linear sequence analysis revealed 3,900 positive numbers of similarity sites between them with 126 mean per peptide and 107 median per peptide, while the TCR-mediated recognition analysis revealed 5,018 positive numbers with a mean of 162 and median of 132 per peptide. These results demonstrated the existence of durable and abundant sequence similarities between c-BIF and CTL epitope peptides, suggesting that the former play a pivotal in inducing cellular and humoral immunity against the latter in the absence of cancer cells via antigenic mimicry.

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.

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.

This research work deals with the formulation of numerical scheme with algorithm to compute singularly perturbed partial differential equations(SP-PDEs) involving a significant negative shift. The problem involves small parameter which causes a rapidly changing boundary layers in the vicinity of a body, and the negative shift term causes interior layer. Such appearance of an abruptly varying layers causes difficulties to find the exact solution and it is not adequate to employ classical numerical methods. The technique presented in this research work simplifies these challenges and yields accurate numerical solution.The stability and convergence analyses of the methods are examined and proven. To test the developed technique, numerical experiments are carried out and confirmed with theoretical analysis.

The paper provides a comprehensive review of the recent advancements and methodologies in Human-Robot Collaboration (HRC) applied to the manufacturing assembly process. In modern manufacturing, the assembly process involves intricate and time-consuming operations, often necessitating flexible manual interventions. However, the cost and stability issues associated with manual labor highlight the need for collaborative solutions integrating humans and robots. HRC, as a viable solution, involves the joint effort of humans and robots in manufacturing tasks, presenting advantages in terms of precision, reproducibility, and cycle time. This review categorizes and discusses methodologies such as task allocation, reinforcement learning, and Cyber-Physical Systems (CPS)-based planning approaches that facilitate HRC in the assembly process. It also explores experiments and future trends to address challenges and enhance efficiency in manufacturing assembly through intelligent collaboration between humans and robots. The objective of this research is to provide insights and directions for further research in HRC to optimize manufacturing processes. By analyzing the existing state-of-the-art and presenting future prospects, this paper aims to guide researchers and practitioners toward more effective implementations of HRC in manufacturing assembly, ultimately leading to improved operational efficiency and productivity.

Sepsis is a life-threatening complication of an infectious process that results from excessive and uncontrolled activation of the host's pro-inflammatory immune response to a pathogen. Lipopolysaccharide (LPS), also known as endotoxin, which is a major component of the Gram-negative bacteria outer membrane, plays a key role in the development of Gram-negative sepsis and septic shock in humans. To date, no specific and effective drug against sepsis has been developed. This review summarizes data on LPS-binding proteins from marine invertebrates (ILBPs), that inhibit LPS toxic effects, and are of interest as potential drugs for the sepsis treatment. The structure, physicochemical properties, antimicrobial and LPS-binding/neutralizing activity of these proteins and their synthetic analogues are considered in details. Problems that arise during clinical trials of potential anti-endotoxic drugs are discussed.

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.

Breast cancer stands as the prevailing malignancy across all six Gulf Cooperation Council (GCC) nations. In this literature review, we highlighted the incidence and trend of BC in the GCC. Most of the studies reported a consistent increase in BC incidence over the past decades, which was particularly attributed to the adoption of a westernized lifestyle in the region and the implications of emerging risk factors and other environmental and societal factors, the increase in screening uptake, as well as the improvement in data collection and reporting in the GCC. The data about BC risk factors in GCC was limited. In this geographic region, breast cancer frequently manifests with distinctive characteristics, including an early onset, typically occurring before the age of 50, an advanced stage at presentation, and a higher pathological grade. Additionally, it often exhibits more aggressive features such as human epidermal growth factor receptor 2 (HER2) positivity or the presence of triple-negative (TN) attributes, particularly among younger patients. Despite the growing body of literature on breast cancer in the GCC, data pertaining to survival rates are, regrettably, meager. Reports on breast cancer survival rates emanating from the GCC region are largely confined to Saudi Arabia and the United Arab Emirates (UAE). In the UAE, predictive modeling reveals 2-year and 5-year survival rates of 97% and 89%, respectively, for the same period under scrutiny. These rates, when compared to Western counterparts such as Australia (89.5%) and Canada (88.2%), fall within the expected range. Conversely, Saudi Arabia reports a notably lower 5-year survival rate, standing at 72%. This disparity in survival rates underscores the need for further research directed towards elucidating risk factors and barriers that hinder early detection and screening. Additionally, there is a pressing need for expanded data reporting on survival outcomes within the GCC. In sum, a more comprehensive and nuanced understanding of breast cancer dynamics in this region is imperative to inform effective strategies for prevention, early detection, and improved patient outcomes.

The two main strategies used in this study are the binary representation and the decomposition of a natural number into many compound functions of odd function and even function. The Collatz conjecture regarding odd even numbers in number theory can be examined and discussed using them in this way: The sequence created by the finite iterations of the Collatz function becomes the ultimately periodic sequence if any natural number is the beginning value, proving the conjecture that has been held for 85 years.

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.

The present studies were undertaken to address the role of fetuin-A in the growth and invasion potential in a triple negative breast cancer (TNBC) cell line, MDA-MB-468. Basal like TNBC that express high levels of ectopic fetuin-A have poorer prognosis for the patients compared to those that express low levels of the protein. We overexpressed fetuin-A in MDA-MB-468 and then determined the invasive potential of fetuin-A overexpressing cells vs controls transfected with empty vector. We also determined the adhesion and growth potential of the cells in the presence of only fetuin-A in serum free medium and also in complete medium. Our data suggest that fetuin-A overexpression significantly enhances the invasive potential of the cells and also the expression of Toll like receptor 4 (TLR4) on these cells. More importantly, the cells rely on fetuin-A-TLR4 signaling network for growth and invasion because the specific TLR4 inhibitor CLI-095 (resatorvid) abrogates fetuin-A mediated growth and invasion. Taken together, the data suggest that fetuin-A-TLR4 signaling network plays a significant role in the growth and invasion potential of TNBC.

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).

Phospholipases are among the important elements involved in lipid-dependent cell signaling that lead to the induction of downstream pathways. In the current study, phospholipases D (PLDs) gene family was characterized and compared in two important oilseeds crops, Brassica napus and Camelina sativa. The results revealed that PLD has 33 members in Camelina sativa (CsPLD) and 41 members in Brassica napus (BnPLD). All studied PLDs showed a negative GRAVY value, indicating that PLDs are probably hydrophilic proteins. Phylogenetic analysis separated PLDs into five subfamilies; gamma, delta, beta, alpha, and zeta. According to evolution analysis, a different evolution process was observed between CsPLD and BnPLD. In addition, the results disclosed that the most of the PLD genes have been segmentally duplicated under purifying selection. Cis-regulatory elements related to ABA and auxin responsiveness were more found in upstream region of CsPLDs, while elements linked with MeJA responsiveness were more dis-tributed in promoter region of BnPLDs. Analysis of the expression data showed that PLD alpha genes have a wide expression and are expressed in most tissues. Quantitative expression analysis (qPCR) of CsPLD genes under salt stress, 200 mM of NaCl, was done in different time series. The results revealed that the CsPLD genes are involved in the response to salinity stress and their expression levels enhance with the increase of salinity stress time. The outcomes of this research will be useful for future molecular work related to lipid signaling in oilseed plants.

We tested the possibility of using “adverse events count” (AEC) as a drug-risk indicator and side-effect severity indicator. Data from 3938 adverse event (AE) reports for COVID-19 vaccines (Comirnaty, Moderna, Vaxzevria, and Janssen) and 6869 AE reports for other medicines were collected from the Bulgarian Drug Agency database (01.01.2018–31.03.2022). AEC was modeled with zero-adjusted negative binomial (ZANBI) and zero-adjusted Poisson inverse Gaussian (ZAPIG) regression models, which account for zero absence and overdispersion. The models’ fit was checked with residual diagnostic plots and parametric correspondence to normality. Explanatory variables were: age, sex, sequence number (order of submission), severity of AE, and vaccine type. Average AEC was higher in severe vs. non-severe AE, and in females vs. males; it decreased with age and was lower in Comirnaty than other vaccines. Variability of AEC for COVID-19 data decreased with sequence number in severe AE and increased in non-severe AE. Full ZANBI models had greater sensitivity than parametric ZANBI or ZAPIG models. Results showed correlation between AEC and AE severity, suggesting AEC as a simple and reliable measure of drug-risk and side-effect severity for clinicians and regulators, especially for COVID-19 vaccines.

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.

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.

Bacterial resistance to antibiotics is a public health menace that needs urgent efforts to mitigate and forestall their transmission in the general environment. Plasmid-mediated metallo beta-lactamase (MBL) gives bacteria an exceptional ability to transmit resistance genes. This study investigated plasmid-mediated resistance in MBL P. aeruginosa isolates from poultry food chain settings. Cloacal swab samples (n=120) were bacteriologically analyzed for the isolation of P. aeruginosa isolates. Susceptibility studies were performed by the CLSI guideline using selected antibiotics. MBL was phenotypically detected using modified Hodges test, and confirmed using PCR technique. Plasmid curing studies detected the presence of plasmids in the isolates. P. aeruginosa isolates (n=48) showed high levels of reduced susceptibility to cefoxitin (93.8%), imipenem (81.3%), gentamicin (85.4%), amikacin (85.4%), nitrofurantoin (83.3%), ofloxacin (72.9%) and cefotaxime (77.1%). MBL was phenotypically detected in 7 (14%) isolates of P. aeruginosa. The presence of blaIMP-1 and blaIMP-2 MBL genes in P. aeruginosa (n=5) isolates was confirmed by PCR. The PCR did not detect blaVIM-1 and blaVIM-2 MBL genes. The P. aeruginosa isolates were multidrug resistant, with about 50% of the isolates showing multidrug resistance (MDR) to the antibiotics. The genes for MDR in the P. aeruginosa isolates were borne on plasmids, indicating a high possibility of community transmission of MBL resistance genes. Finally, the P. aeruginosa isolates from poultry food chain milieus are multidrug resistant, produce MBL, and harbour their resistance genes on plasmids. Since many antibiotic resistance genes in bacteria are associated with mobile genetic elements (MGEs) like plasmids, it is important to step up actions to mitigate incessant use of antibiotics in poultry and other agricultural practices in Nigeria in order to diminish the evolution and spread of plasmid-mediated resistance which is capable of initiating community acquired infections that may prove difficult to treat in our hospitals with the available antibiotics.

Sepsis is a life-threatening condition caused by the body's overwhelming response to an infection, such as pneumonia or urinary tract infection. It occurs when the immune system releases cytokines into the bloodstream, triggering widespread inflammation. If not treated, it can lead to organ failure and death. Unfortunately, sepsis has a high mortality rate, with studies reporting rates ranging from 20% to over 50%, depending on the severity and promptness of treatment. According to the World Health Organization (WHO), the annual death toll in the world is about 11 million. One of the main toxins responsible for inflammation induction are lipopolysaccharides (LPS, endotoxin) from Gram-negative bacteria, which ranks among the most potent immunostimulants found in nature. Antibiotics are consistently prescribed as a part of anti-sepsis-therapy. However, antibiotic therapy (i) is increasingly ineffective due to resistance development and (ii) most antibiotics are unable to bind and neutralize LPS, a prerequisite to inhibit the interaction of endotoxin with its cellular receptor complex, namely Toll-like receptor 4 (TLR4)/MD-2, responsible for the intracellular cascade leading to pro-inflammatory cytokine secretion. The pandemic virus SARS-CoV-2 has infected hundreds of millions of humans worldwide since its emergence in 2019. The COVID-19 (Coronavirus disease-19) caused by this virus is associated with high lethality, particularly for elderly and immunocompromised people. As of August 2023, nearly 7 million deaths were reported worldwide due to this disease. According to some reported studies, upregulation of TLR4 and the subsequent inflammatory signaling detected in COVID-19 patients “mimics bacterial sepsis”. Furthermore, the immune response to SARS-CoV-2 was described by others as “mirror image of sepsis”. Similarly, the cytokine profile in sera from severe COVID-19 patients was very similar to those suffering from the acute respiratory distress syndrome (ARDS) and sepsis. Finally, the severe COVID-19 infection was frequently accompanied by bacterial co-infections, as well as by the presence of significant LPS concentrations. These data indicate similarity and interdependences of both syndromes, but also significant differences which will be discussed in the present review.

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.

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.

Abstract: A prevalence boundary (PB) marks the point in prevalence where the false omission rate, RFO=FN/(TN+FN), exceeds the tolerance limit for missed diagnoses. Objectives were to mathematically analyze rapid antigen test (RAgT) performance, determine why PBs are breeched, and evaluate the merits of testing three times over five days, now required by the US Food and Drug Administration for asymptomatic persons. Equations were derived to compare test performance patterns, calculate PBs, and perform recursive computations. An independent July 2023 FDA-university-commercial evaluation of RAgTs provided performance data used in theoretical calculations. Tiered sensitivity/specificity comprise: Tier-1) 90%, 95%; Tier-2) 95%, 97.5%; and Tier-3) 100%, ≥99%, respectively. Repeating a T2 test improves the PB from 44.6% to 95.2% (RFO 5%). In the FDA-university-commercial evaluation, RAgTs generated sensitivity of 34.4%, which improved to 55.3% when repeated, then 68.5% with the third test. With RFO=5%, PBs were 7.37/10.46/14.22%, respectively. PB analysis suggests RAgTs should achieve clinically proven sensitivity of 91.0-91.4%. When prevalence exceeds PBs, missed diagnoses can perpetuate virus transmission. Repeating low-sensitivity RAgTs delays diagnosis. In homes, high-risk settings, and hotspots, PB breaches may prolong contagion, defeat mitigation, facilitate new variants, and transform outbreaks into endemic disease. Molecular diagnostics can help avoid these potential vicious cycles

Transportation authorities aim to boost road safety by identifying risky locations and applying suitable safety measures. The Highway Safety Manual (HSM) is a vital resource for US transportation professionals, aiding in the creation of Safety Performance Functions (SPFs), which are predictive models for crashes. These models rely on Negative Binomial distribution-based regression and misinterpreting them due to unmet statistical assumptions can lead to erroneous conclusions, including inaccurately assessing crash rates or missing high-risk sites. The Florida Department of Transportation (FDOT) has introduced context classifications to HSM SPFs, complicating assumption violation identification. This study, part of an FDOT-sponsored project, investigates established statistical diagnostic tests to identify model violations and proposes a novel approach to determine optimal spatial regions for Empirical Bayes adjustment. This adjustment aligns HSM-SPFs with regression assumptions. The study employs a case study involving Florida roads. Results indicate that a 20-mile radius offers an optimal spatial sample size for modeling crashes of all injury levels, ensuring accurate assumptions. For severe injury crashes, which are less frequent and harder to predict, a 60-mile radius is suggested to fulfill statistical modeling assumptions. This methodology guides FDOT practitioners in assessing the conformity of HSM-SPFs with intended assumptions and determining appropriate region sizes.

Diffusion-controlled cyclic voltammograms at fast scan rates show peak shifts as well as decreases in the peak currents from the predicted diffusion-controlled currents especially when currents are large in low concentration of supporting electrolyte. This has been conventionally recognized as an IR-drop effect by solution resistance on the peaks as well as heterogeneous kinetics. It is also brought about by negatively capacitive currents associated with charge transfer reactions. The reaction product generates dipoles with counterions to yield a capacitance, of which current flows oppositely to that of the double layer capacitance. The three effects are specified here in the oxidation of a ferrocenyl derivative by fast scan voltammetry. The expression for voltammograms complicated with IR-drop is derived analytically, and yields deformed voltammograms. The peak shift is approximately linear with the IR-term, but exhibits a convex variation. Dependence of some parameters on the peaks by the IR-drop is compared with those by the negative capacitance. The latter is more conspicuous than the former under conventional conditions. The two effects cannot be distinguished specifically except for variations of conductance of the solution.

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.

Alfalfa is an important forage crop around the world. LncRNAs are considered to be a class of functional biomacromolecules, while little is known about lncRNAs in alfalfa. In this study, RNAs from different tissues of alfalfa were sequenced and anlyzed with full-length transcriptome sequencing technology, yielding the full-length transcripts dataset of alfalfa. Based on sequencing and public RNA-seq data, lncRNAs of alfalfa were predicted genome-wide by CPC2 and PLEK. The results showed most lncRNAs shared low sequence conservation with those in other plant species, part of which seems originate from plastid genome. We also identified 88563 lncRNAs, approximately 99.8% of total lncRNAs, with possibility of coding small ORFs using two prediction tools. Our research generated the biggest sequence set of alfalfa lncRNAs, and revealed some plastid originated lncRNAs with high sequence conservation.

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