Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol – the RAPIDprep assay – with the aim to provide cause agnostic laboratory diagnosis of infection within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities and extraction kits using a single protocol without input nucleic acid quantification or quality assessment. Furthermore, we demonstrate the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift towards integration of modern genomic techniques to infectious disease investigations.

The deadliest disease in the world, cancer, kills many people every year. The early detection is the only hope for the survival of malignant cancer patients. As a result, in the preliminary stages of , the diagnosis of cancer biomarkers at the cellular level is critical for improving cancer patient survival rates. For decades, scientists have focused their efforts on the invention of biosensors. Biosensors, in addition to being employed in other practical scenarios, can essentially function as cost effective and highly efficient devices for this purpose. Traditional cancer screening procedures are expensive, time-consuming, and inconvenient for repeat screenings. Biomarker-based cancer diagnosis, on the other hand, is rising as one of the most potential tools for early detection, disease progression monitoring, and eventual cancer treatment. As Biosensor is an analytical device, it allows the selected analyte to bind to the biomolecules being studied (– for example RNA, DNA, tissue, proteins, cells). They can be divided based on the kind of biorecognition or transducer elements on the sensor. Most biosensor analyses necessitate the analyte being labeled with a specific marker. In this review article, the application of distinct variants of biosensors against cancer has been described.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50-350 nts in length and smaller RNAs (sncRNA) <50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists and locked nucleic acid sequence specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs summarized.

Despite several decades of research, the physics underlying translation – protein synthesis at the ribosome – remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we have suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome – intersubunit bridges, Fe4S4 cluster and the pivot linking the SSU head to the body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance the molecular biology and medicine.

Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.

Protamine is a natural cationic peptide mixture mostly known as a drug for the neutralization of heparin and as a compound in formulations of slow-release insulin. Protamine is also used for cellular delivery of nucleic acids due to opposite charge-driven coupling. This year marks60 years since the first use of Protamine as a transfection enhancement agent. Since then, Protamine has been broadly used as a stabilization agent for RNA delivery. It has also been involved in several compositions for RNA-based vaccinations in clinical development. Protamine stabilization of RNA shows double functionality: it not only protects RNA from degradation within biological systems, but also enhances penetration into cells. A Protamine-based RNA delivery system is a flexible and versatile platform that can be adjusted according to therapeutic goals: fused with targeting antibodies for precise delivery, digested into a cell penetrating peptide for better transfection efficiency or not-covalently mixed with functional polymers. This manuscript gives an overview of the strategies employed in protamine-based RNA delivery, including the optimization of the nucleic acid’s stability and translational efficiency, as well as the regulation of its immunostimulatory properties from early studies to recent developments.

Kiwifruit vines are generally sensitive to waterlogging stress. So far, molecular responses of different kiwifruit genotypes for waterlogging stress are less well-explored. In this study, using RNA-sequencing, we examined transcriptional regulation in the roots of a waterlogging-tolerant genotype KR5 (Actinidia valvata), and a sensitive genotype ‘Hayward’ (Actinidia deliciosa) subjected to 0, 12, 24, and 72 h of waterlogging. Compared with 0 h, transcriptional adjustments of these two genotypes occurred as early as 12 h and became notably pronounced 72 h after waterlogging. Waterlogging stress for 72 h promoted the expression of genes involved in ethylene biosynthesis, sucrose and hexose transport, anaerobic fermentation, nitrate reduction, alanine accumulation, and reactive oxygen scavenging in both genotypes. The differential regulation of genes encoding 9-cis-epoxycarotenoid dioxygenase, phosphoglucomutase, alanine-glyoxylate transaminase, and other enzymes pointed to their diverse strategies upon waterlogging in these two genotypes. In addition, more sucrose and trehalose contents, as well as a higher activity of alcohol dehydrogenase and manganese superoxide dismutases were stimulated in KR5 roots after 72h of waterlogging than that in ‘Hayward’. Overall, our results provided more insights into the molecular basis of the waterlogging response in kiwifruit.

The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made on complex multicellular organisms, and then modified to fit a DNA-centric view. In this article, I argue that, based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that: i) natural selection plays a dominant role in evolution, and ii) the probability of mutations is independent of the generated phenotype. I will show that the adaptation of a phenotype to an environment does not correspond to organism fitness but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome, and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype, the phenotype ensuring the stability of the genotype in a cellular and environment physicochemical parameter-depending manner.

A model of the early RNA world is proposed. Nearly self-complementary sequences that could adopt double-stranded, smallhairpin-like (shRNA), structures would be selected for due to their greater hydrolytic stability. These would be phosphorylated attheir 5' ends. We suppose that dehydrating conditions arise (perhaps intermittently) in the early environment allowing amino acidsto condense with these RNA molecules. The resulting phosphate-amino acid anhydrides would play the role of early, charged,tRNAs. A crude genetic code could emerge owing to the greater resistance of some amino acid-shRNA pairings to hydrolysisrelative to others. Early on there is no division of labor between mRNAs and tRNAs; the same molecules perform both functions.But the first systems would have encoded little in the way of protein sequence information. Rather they would have served as catalysts for the random polymerization of amino acids. It is speculated that the selective advantage inhering in such systems lay intheir ability to supply raw materials for the formation of coacervates within which the various molecules essential to proto-lifecould be concentrated. This would greatly facilitate the necessary chemistries. The evolution of homochiral protein and RNA populations is discussed. An appealing feature of this model is its ability to explain the transition from phosphorylated amino acids to the 3' ester-linked aminoacyl-tRNAs employed by modern life.

Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs xrRNAs within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3'UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs

Sutherlandia frutescens (S. frutescens) has been traditionally used as an herbal medicine to ameliorate symptoms associated with cancer, infectious diseases, as well as inflammation. The objective of this investigation was to explore the impact of S. frutescens on the expression of genes in a murine macrophage cell line (i.e., RAW 264.7). We found that treatment with an ethanolic-extract of S. frutescens (SFE) 1 h prior to the stimulation with LPS and IFNγ for 24 h significantly affected the expression of 715 genes in RAW 264.7 cells. When the post-stimulation period was shortened to 8 h, the number of genes that were significantly impacted by SFE diminished to 50. Pathway analysis revealed that inflammatory signaling pathways, such as NF-κB, MAPK, and TNF, as well as signaling pathways associated with immune-related responses, were inhibited by SFE treatment. These findings are consistent with previously reported anti-inflammatory activity of SFE and enable better understanding of the immune-modulating properties of this botanical. To our knowledge, this represents the first report on the impact of S. frutescens on global gene expression in an immune cell population.

This study aimed to demonstrate the existence of antiviral RNA silencing mechanisms in Sclerotinia sclerotiorum by probing wild-type and RNA-silencing-deficient strains of the fungus with an RNA virus and a circular DNA virus. Key silencing-related genes, specifically dicers, were disrupted in order to dissect the RNA silencing pathway and provide useful information on fungal control. Dicers Dcl-1, Dcl-2, and both Dcl-1/Dcl-2- genes were displaced by selective marker(s). Disruption mutants were then compared for changes in phenotype, virulence, susceptibility to viral infection, and small RNA accumulation compared to the wild-type strain. Disruption of Dcl-1 or Dcl-2 resulted in no changes in phenotype compared to wild-type S. sclerotiorum; however, the double dicer mutant strain exhibited slower growth. To examine the effect of viral infection on strains containing null-mutations of Dcl-1, Dcl-2 or both genes, mutants were transfected with full-length RNA transcripts of a hypovirus SsHV2L and copies of a single-stranded DNA mycovirus- SsHADV-1 as a synthetic virus. Results indicate that the ΔDcl-1/Dcl-2 double mutant which was slow growing without virus infection exhibited much more severe debilitation following virus infection. Altered colony morphology including: reduced pigmentation, significantly slower growth, and delayed sclerotial formation. Additionally, there is an absence of virus-derived small RNAs in the virus-infected ∆Dcl-1/Dcl-2 mutant compared to the virus-infected wild-type strain which displays a high percentage of virus-derived small RNA. The findings of these studies suggest that if both dicers are silenced, invasive nucleic acids which include mycoviruses ubiquitous in nature- can greatly debilitate the virulence of fungal plant pathogens.

The root extracts of Symphytum officinale (comfrey) are commonly used in traditional medicine to treat muscle, joint, skin and bone disorders. However, little information is available on the biomedical functions of comfrey leaves. In this study, sequencing results of Internal Transcribed Spacer and trnL-trnF genes showed that plants purchased from the local market were comfrey and named as S. officinale WL (WL). The optimal extraction conditions of WL leave with the highest extract yield and contents of total phenols and flavonoids by microwave-assisted extraction were identified. The antioxidative and anti-inflammatory activities and possible molecular mechanism(s) of the WL leaf extract (WLE) were evaluated. Furthermore, the major component of WLE was identified as rosmarinic acid by HPLC. Results showed that the optimal extract condition was obtained with 750W microwave power, 50℃, 75% methanol, the solid-to-solvent ratio of 1:10, and 15 minutes. Results of all DPPH, ABTS and superoxide radical scavenging activities, reducing power, ferrous ion chelating activity, and ferric reducing antioxidant power showed high antioxidative capacities of WLE. Furthermore, WLE showed obvious DNA protecting activity. WLE attenuated lipopolysaccharides-stimulated inflammation by suppressing iNOS, COX-2, IL-1β, IL-6, and TNF-α expressions in RAW264.7 macrophages. These attenuations involved in inactivations of lipopolysaccharides-induced NF-κB and MAPK signaling pathways.

The COVID-19 pandemic affects all parameters, especially health care professionals, drugs and medical supplies. The KERRA is a mixed medicinal plant capsule that is used for the treatment of patients with high fever with food and drug administration approved by FDA Thailand. Recently, KERRA showed quicker recovery for COVID-19 patients. Therefore, it is possible that some ingredients in KERRA could inhibit SARS-CoV-2. In this study, two important replication-related enzymes in SARS-CoV-2, a main protease and an RNA-dependent RNA polymerase (RdRp), were used to study the effect of KERRA. The results showed that KERRA inhibited the SARS-CoV-2 main protease and SARS-CoV-2 RdRp with IC50 values of 49.91 ± 1.75 ng/mL and 36.23 ± 5.23 µg/mL, respectively. KERRA displayed no cytotoxic activity on macrophage cells at concentrations lower than 1 mg/mL and exhibited anti-inflammatory activity. Additionally, KERRA was against a feline coronavirus (feline infectious peritonitis [FIP]) infection with an EC50 value of 134.3 g/mL. This study supports the potential use of KERRA as a candidate drug for COVID-19.

Ribosome assembly is one of the most fundamental processes in gene expression and has served as a playground to investigate the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. The bacterial ribosome is composed of around 50 ribosomal proteins several of which are co-transcriptionally assembled on a ~4,500 nucleotides long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 minutes in vivo and assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades and has resulted in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs. Here we review biochemical, structural and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of this complex and intricate molecular process of assembly. We also discuss emerging cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors and the native cellular environment shape ribosome assembly and RNP assembly at large.

RNA pol II assembly occurs in the cytoplasm before the translocation of the enzyme to the nucleus. Affecting assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination and lead as to proposes that CTD phosphatase Rtr1 could be involved in this process.

The RNA-binding protein Human antigen R (HuR) regulates stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. The protein has been progressively recognized as a relevant therapeutic target for several pathologies like cancer, neurodegeneration, as well as inflammation. Inhibitors of mRNA binding to HuR might thus be beneficial against a variety of diseases. Here we present the rational identification of structurally novel HuR inhibitors. In particular, by combining chemoinformatics approaches, high throughput virtual screening and RNA–protein pull-down assays, we show that the 4-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)benzoate ligand exhibits dose-dependent HuR inhibition in binding experiments. Importantly, the chemical scaffold is new with respect to the so-far known HuR inhibitors, opening up a new avenue for the design of pharmaceutical agents targeting this important protein.

Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3’-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and found to occur with the homologous domains of influenza B and C FluPols. Residues [1-72] of RPB4 were found critical in this interaction. Numerous punctual mutants generated at conserved positions between influenza A, B and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defect. These results suggest that FluPol interacts with several domains/subunits of Pol II, the CTD to bind Pol II initiating host transcription and a second on RPB4 to locate FluPol at the proximity of the 5’-end of nascent host mRNA.

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

This study delves into the extraction and compositional analysis of soybean meal protein isolates (SMPI) compared to soy protein isolates (SPI), focusing on their functional and structural properties, digestibility, amino acid composition, and the impact of various proteases on antinutritional factors. By leveraging alkaline (0.25 % of NH4OH) extraction and isoelectric precipitation, SMPI was efficiently obtained. Compositional characteristics revealed that SMPI has high moisture, protein, and ash, but lower fat, and carbohydrate content compared to SPI. Alcalase, Neutrase and Pepsin hydrolysis indicated lower digestibility of SMPI than SPI. Fourier-transform infrared spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis provided similar molecular structure and protein molecular weight distribution. This comprehensive analysis underscores the valorization of soybean meal, promoting its use beyond conventional animal feed towards nutritional supplements and bio-based products, thereby contributing to environmental sustainability and the enhancement of global food systems.

A hybrid material, consisting of commercially available nitrocellulose (NC) membrane non-covalently modified with amino-polyethylene glycol functionalized reduced graphene oxide (NH2-PEG-rGO) nanoparticles, was successfully synthesized for oligonucleotide extraction. Fourier Transform Infrared Spectroscopy (FTIR) confirmed the modification of the NC membrane, revealing characteristic peaks of both compounds NC and NH2-PEG-rGO. Scanning Electron Microscopy (SEM) exhibited morphological changes in the NC/NH2-PEG-rGO hybrid membrane, marked by the introduction of NH2-PEG-rGO particles, resulting in a distinctly smothered surface compared to the porous surface of the NC control membrane. Wettability assays revealed hydrophobic behavior for the NC/NH2-PEG-rGO hybrid membrane, with a water contact angle exceeding 90°, contrasting with the hydrophilic behavior characterized by a 16.7° contact angle in the NC membrane. The performance of the NC/NH2-PEG-rGO hybrid membrane was evaluated for the extraction of ssDNA with fewer than 50 nucleotides from solutions containing various ionic species (MnCl2, MgCl2, and MnCl2/MgCl2). The NC/NH2-PEG-rGO hybrid membrane exhibited optimal performance when incubated in MgCl2, presenting the highest fluorescence emission at 525 relative fluorescence units (r.f.u.). This corresponds to the extraction of approximately 610 pg (≈13%) of the total oligo-DNA, underscoring the efficacy of the pristine material, which extracts 286 pg (≈6%) of oligo-DNA in complex solutions.

This article utilizes the Canny edge extraction algorithm based on contour curvature and the cross-correlation template matching algorithm to extensively study the impact of high-repetition-rate CO2 pulsed Laser on the target extraction and tracking performance of the infrared imaging detector. It establishes a quantified dazzling pattern for lasers on infrared imaging systems. By conducting laser dazzling and damage experiments, a detailed analysis of the normalized correlation between target and dazzling images is performed to quantitatively describe laser dazzling effects. Simultaneously, an evaluation system, including target distance and laser power evaluation factors, is established to determine the dazzling level and whether the target is recognizable. The research results reveal that laser power and target position are crucial factors affecting the detection performance of infrared imaging-guided weapon systems under laser dazzling. Different laser powers are required to successfully interfere with the recognition algorithm of infrared imaging-guided weapons at different distances. And laser dazzling will produce a lot of false edge information, which seriously affects the performance of pattern recognition algorithm. In laser damage experiments, the detector experienced functional damage, with a quarter of the image displaying as completely black. The energy density threshold required for functional damage to the detector is approximately 3 J/cm2. The dazzling assessment conclusions also apply to evaluating damage results. Finally, the proposed evaluation formula aligns with experimental results, objectively reflecting the actual impact of laser dazzling on the target extraction and tracking performance of infrared imaging systems. This study provides an in-depth and accurate analysis for understanding the influence of lasers on the performance of infrared imaging-guided weapons.

Soil microbiome plays key role in plant health. Native soil microbiome inoculation, metagenomic profiling and high-throughput cultivation require efficient microbe extraction. The sonication and oscillation are most common methods to extract soil microbiome. However, the extraction efficiency of those methods has barely been investigated. Here, we compared the culturable microbe numbers, community structures and alpha diversities among the methods including sonication, oscillation, centrifugation and their processing time. The results showed that, sonication significantly increases culturable colony number compare with oscillation and centrifugation factors. Furthermore, sonication strategy shows a main factor influence extraction efficiency, but increased sonication time can recovery this impact. Finally, processing times of extraction show a significant negative relationship with α diversity among extracted microbiota. In conclusion, sonication is a main factor for enrich in-suit microbiota, and increased extraction time significantly decrease α diversity of extracted microbiota. These results can provide insights into the isolation and utilization of microorganism source.

The removal of harmful arsenic(V) from aqueous solutions using Cyanex 923 (solvation extractant) was investigated under various experimental variables: equilibration time, acidity of the aqueous phase, temperature, extractant and arsenic concentrations, and O/A ratio. Cyanex 923 extracted As(V) (and sulphuric acid) from acidic solutions, thus, its use to remove the metal from slightly acid or neutral solutions it is not possible. Extraction of arsenic is exothermic, and responded to the formation of H3AsO4·nL species in the organic phase (L represented the extractant and the stoichiometric factor n: 1 or 2, depends on the acidity of the aqueous phase). Extraction isotherms are derived from experimental results. Both arsenic and sulphuric acid loaded onto the organic phase can be stripped with water, and stripping isotherms are also derived from the experimental results. The selectivity of the system against the presence of other metals (Cu(II), Ni(II), Bi(III), Sb(III)) are investigated, and also it is investigated the ability of Cyanex 923 to extract As(V) and sulphuric acid against the use of other P=O based solvation reagents, such dibutyl butylphosphonate (DBBP) and tri-butyl phosphate (TBP).

DNA extraction for downstream molecular diagnostic applications can be an expensive, time-consuming process. We devised a method to quickly extract genomic DNA from environmental samples based on sodium hydroxide lysis of cells with or without capture by magnetic beads, for subsequent PCR or quantitative PCR. The final DNA extraction method using NaOH is extremely low-cost and can be completed in 10 minutes at room temperature. NaOH extraction was effective for Gram-negative and Gram-positive bacteria in samples from air, soil, sewage, food, laboratory surfaces, and chicken cloacal swabs. The NaOH extraction method was comparable to commercial kits for extraction of DNA from pig fecal samples for 16S amplicon sequencing analyses. We demonstrate that an impinger and portable pump can efficiently capture bacteria in poultry facilities for rapid DNA extraction for quantification of total bacteria and for detection of specific species using qPCR. The air sampling and NaOH extraction procedures are well-suited for routine, high throughput screening, and for metagenomic analyses for specific pathogens, even in resource-limited situations.

Speciation analysis is a relevant topic since the (eco)toxicity, bioavailability, bio (geo)chemical cycles, and mobility of a given element depend on its chemical forms (oxidation state, organic ligands, etc.). Reliability of analytical results for chemical species of elements depends mostly on the maintaining of their stability during sample pretreatment step and on the selectivity of further separation step. Solid phase extraction (SPE) is a matter of choice as most suitable and widely used procedure for both enrichment of chemical species of elements and their separation. Features of sorbent material are of great importance to ensure extraction efficiency from one side and selectivity from other side of SPE procedure. This review presents an update on the application of polymeric materials in solid-phase extraction used in non-chromatographic methods for speciation analysis.

Currently, with the rapid growth of the population, the demand for metals has increased, especially for the manufacture of electronic devices such as cell phones, computer equipment, among others. Once these devices stop working, most are sent to landfills, which represents a danger since these wastes contain metals and other materials that must be properly managed to prevent them from having a negative effect on the environment and the human being. On the other hand, e-waste contains valuable metals such as copper, gold, and silver, the concentration of which in these materials makes it cost-effective to recover. This paper presents a review of the extraction and recovery of valuable metals from electronic waste by hydrometallurgical methods, as well as patents and industrial processes related to the management and treatment of this waste.

Background: Cataract and Age-related Macular Degeneration are two characteristic diseases of the so-called elderly age (75-90 years and older). Both determine an important visual impairment, so it is often difficult to understand how much of the visual loss is given by the cataract opacities and how much by the degeneration of the macula and this assumes a relevant medico-legal query in clinical practice. Methods: From that pool we randomized in group 735 eyes with wAMD (males 328, females 407) Average age: 76.23±13.87 years, and in Group 819 eyes without clear signs of wAMD (males 361, females 451) Average age: was 75.88±18.21 years to randomize them we used the online randomization program (http://www.graphpad.com/quickcalcs/index.cfm) selecting random numbers and then randomly assign subjects to groups to undergo our observational study. All patients were examined with full ophtalmological visit including Best Corrected Visual Acuity (with Bailey-Lawson Chart), Anterior Segment examination, Fundus Examination, in all cases with wAMD was also performed OCT. ANOVA multifactorial statistical analysis was drawn. Results: number of patients with unsatisfactory surgery is significantly higher in the group of AMD patients, and this is easily understandable from what has been said above, but I would like to underline that in most patients there are very positive results, therefore cataract surgery is also indicated in AMD patients. Conclusions: Cataract surgery has a positive impact on the patient's life in most cases, you shouldn't be afraid to operate. However, it is necessary to find surgical measures capable of minimizing the consequences of the intervention on the retina.

It is crucial to select the right machine learning classifier for image classification and face recog-nition. This study examines the effectiveness of four different face recognition classifiers - Support Vector Machines (SVM), Random Forest, K-Nearest Neighbors (KNN), and Neural Networks. An analysis of the Large Faces in the Wild (LFW) dataset was carried out using Principal Component Analysis (PCA). Classifiers are rigorously trained and evaluated based on the extracted features. Comparison of classifier performance is an insightful way to figure out their strengths and weaknesses. Having a visual representation of the classifier's performance gives a complete understanding of its capabilities. Through the selection of the most appropriate classifier, study results contribute to advancements in image classification, recognition, and biometric identification. The comparison study demonstrated that the Neural Network classifier was exceptionally accurate and proficient in recognizing faces from the LFW dataset when used in conjunction with PCA for feature extraction. According to the comparative analysis, the Neural Network classifier proved exceptionally accurate and proficient at identifying faces from the LFW dataset when combined with PCA for feature extraction.

Recent studies have been able to detect α-synuclein (αSyn) seeding in formaldehyde-fixed paraffin-embedded (FFPE) tissues from patients with synucleinopathies using seed amplification assays (SAAs), but with relatively low sensitivity due to limited protein extraction efficiency. With the aim of introducing an alternative option to frozen tissues, we developed a streamlined protein extraction protocol for evaluating disease-specific seeding in FFPE human brain. We evaluated the protein extraction efficiency of different tissue preparations, deparaffinizations, and protein extraction buffers using formaldehyde-fixed and FFPE tissue of a single Lewy body disease (LBD) subject. Alternatively, we incorporated heat-induced antigen-retrieval and dissociation using a commercially available kit. Our novel protein extraction protocol has been optimized to work with 10 sections of 4.5-µm-thickness or 2-mm-diameter micro-punch of FFPE tissue that can be used to seed SAAs. We demonstrated that extracted proteins from FFPE still preserve seeding potential and further show disease-specific seeding in LBD and multiple system atrophy. To the best of our knowledge, our study is the first to recapitulate disease-specific αSyn seeding behavior in FFPE human brain, with structural validation. Our findings open new perspectives in re-evaluating archived human brain tissue, extending the disease-specific seeding assays to larger cohorts to facilitate molecular subtyping of synucleinopathies.

Recent advances in DNA sequencing technology have shown that the human milk microbiota of healthy women varies substantially. The gDNA extraction method may influence the observed variation, biasing the microbiological reconstruction after all. In this study, a genomic DNA extraction method for DNA isolation from human milk samples was standardized and compared with commercial and standard hose make methods. Spectrophotometric measurements, gel electrophoresis, and PCR amplifications were used as criteria for evaluating the quantity, quality, and functionality of the extracted DNA. Furthermore, the standardized method of extracting gDNA from human milk was evaluated for its ability to isolate functional DNA from gram-positive, and gram-negative bacteria and fungi, to improve the reconstruction of microbiological profiles. The novel DNA extraction method increased the quantity and quality of the gDNA extracted compared with commercial and standard house-make protocols. This method even allowed PCR amplification of the V3-V4 regions of the 16S ribosomal gene in all samples, and the ITS-1 region of the fungal 18S ribosomal gene in 95 % of the samples as well. It is concluded that the proposed method provides better performance for the extraction of gDNA from complex samples such as human milk.

Pedestrian multi-target tracking technology plays an important role in artificial intelligence, driverless, virtual reality and other fields. The pedestrian multi-target tracking algorithm DeepSORT based on detection is widely used in industry. It mainly tracks multiple pedestrian targets continuously and keeps their ID unchanged. In order to improve the applicability and tracking accuracy of DeepSORT algorithm, this paper improved the IOU distance measurement in the matching process. At the same time, ResNet50 is used as the feature extraction backbone network, and combined with FPN (Feature Pyramid Network), the appearance features of multi-layer pedestrians are fused to improve the tracking accuracy of DeepSORT algorithm. The proposed algorithm is verified on the public data set MOT-16 and it’s tracking accuracy is enhanced to 4.1%.

From new understanding of pectin molecular structure and physiological effects on man up to new production methods and new applications, significant new knowledge of pectin has emerged in the last two decades (2010-2020). These developments open the route to new and unexpected applications of this uniquely complex heteropolysaccharide ubiquitous in plants and fruits well beyond its traditional use as food hydrocolloid. This study provides a unified perspective on the new science and technology of pectin. Furthermore, we offer an insight into forthcoming pectin uses from an expanded perspective taking into account selected technology and economic factors that, we argue in this study, will shortly impact the pectin production and uptake in many countries.

Is the production of the “AnchoisFert” organic fertilizer via the circular economy process based on omega-3 lipid extraction of milled anchovy fillet leftovers with citrus limonene followed by mild drying economically and technically viable? This study answers this question and identifies the main obstacles, chiefly of economic and organizational nature, to be overcome prior to commercialization of this new organic fertilizer. Along with non-variable and proven efficacy, successful competition with conventional organic and inorganic fertilizers requires affordable cost and regular supply. This, inter alia, requires to establish new and mutually beneficial relationship between bioeconomy firms and fish processing companies.

Recently, spam emails have become a significant problem with the expanding usage of the Internet. It is to some extend obvious to filter emails. A spam filter is a system that detects undesired and malicious emails and blocks them from getting into the users' inboxes. Spam filters check emails for something "suspicious" in terms of text, email address, header, attachments, and language. However, we have used different features such as word2vec, word n-grams, character n-grams, and a combination of variable length n-grams for comparative analysis in our proposed approach. Different machine learning models such as support vector machine (SVM), decision tree (DT), logistic regression (LR), and multinomial naïve bayes (MNB) are applied to train the extracted features. We use different evaluation metrics such as precision, recall, f1-score, and accuracy to evaluate the experimental results. Among them, SVM provides 97.6 \% of accuracy, 98.8\% of precision, and 94.9\% of f1-score using a combination of n-gram features.

Clove (Syzygium aromaticum L. Myrtaceae) is an aromatic plant widely cultivated in tropical and subtropical countries, rich in volatile compounds and antioxidants such as eugenol, β-caryophyllene, and α-humulene. Clove essential oil has received considerable interest due to its wide application in the perfumery, cosmetic, health, medical, flavoring, and food industries. Clove essential oil has relevant biological activities to human health, including antimicrobial, antioxidant, and insecticide. This review describes the effect of the extraction method (hydrodistillation, steam distillation, ultrasound-assisted extraction, microwave-assisted extraction, cold pressing, and supercritical fluid extraction) on the chemical composition of essential oil and its correlation with their biological activities. Likewise, are summarized the main compounds and their reported biological activities. Furthermore, the main applications in clove essential oil in the food industry are presented. Finally, this review presents the new biological activities such as anti-inflammatory, analgesic, anesthetic, antinociceptive and anticancer, which are beneficial for human health. This review aims to compile the effect of different methods of extracting clove essential oil on chemical composition, food applications, as well as a current description of biological activities of interest to human health. Biological activities have increased interest in research into this essential oil and its future applications in the food or pharmaceutical industry.

Cannabis is a flowering plant that has long been used for medicinal, therapeutic, and recreational purposes. Cannabis contains more than 500 different compounds, including a unique class of terpeno-phenolic compounds known as cannabinoids; Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) are the most prevalent cannabinoids and have been associated with the therapeutic and medicinal properties of the cannabis plant. In this paper, continuous flow microwave assisted extraction (MAE) is presented and compared with other methods for commercial cannabis extraction. The practical issues of each extraction method are discussed. The main advantages of MAE are: continuous-flow method which allows for higher volumes of biomass to be processed in less time than existing extraction methods, improved extraction efficiency leading to increased final product yields, improved extract consistency and quality because the process does not require stopping and restarting material flows, and ease of scale-up to industrial scale without the use of pressurised batch vessels. Moreover, due to the flexibility of changing the operation conditions, MAE eliminates additional steps required in most extraction methods, such as biomass decarboxylation, winterisation, which typically adds at least a half day to the extraction process. Another factor that sets MAE apart is the ability to achieve high extraction efficiency even at the industrial scale. Whereas the typical recovery of active compounds using supercritical CO¬2 remains around 70-80%, via MAE up to 95% of the active compounds from cannabis biomass can be recovered at the industrial scale.

Significant progress has made in pattern recognition technology. However, one obstacle that has not yet overcome is the recognition of words in the Brahmi script, specifically the recognition of characters, compound characters, and word because of complex structure. For this kind of complex pattern recognition problem, it is always difficult to decide which feature extraction and classifier would be the best choice. Moreover, it is also true that different feature extraction and classifiers offer complementary information about the patterns to be classified. Therefore, combining feature extraction and classifiers, in an intelligent way, can be beneficial compared to using any single feature extraction. This study proposed the combination of HOG +zonal density with SVM to recognize the Brahmi words. Keeping these facts in mind, in this paper, information provided by structural and statistical based features are combined using SVM classifier for script recognition (word-level) purpose from the Brahmi words images. Brahmi word dataset contains 6,475 and 536 images of Brahmi words of 170 classes for the training and testing, respectively, and the database is made freely available. The word samples from the mentioned database are classified based on the confidence scores provided by support vector machine (SVM) classifier while HOG and zonal density use to extract the features of Brahmi words. Maximum accuracy suggested by system is 95.17% which is better than previously suggested studies.

A partial extraction procedure was used to study the distribution of uranium in the mineral phases of rocks of an aquifer of sandy-clay deposits of the Vendian in the northwest of Russia. This work is a part of a research project to develop a method for combined radiocarbon and uranium-isotope dating of groundwater. Representative aliquots of each core sample were subjected to five "partial" extractions by treatment with: distilled water, low mineralized fresh natural groundwater, minopolycarboxylic acid chelating agent (0.05M EDTA), 0.5M HCl, 15M HNO₃, and a total digestion, with U isotopes reported in this study for each procedure. The following mineral phases of core samples: adsorbed material, carbonate minerals, amorphous iron oxides, aluminosilicates partial digestion and a crystalline iron oxides, aluminosilicates total digestion and a clay/quartz resistate were characterized. Red-colored siltstones depleted in uranium in relatively readily soluble mineral phases. The concentration of adsorbed uranium was established in the amount of 15.8±2.1 - 30.5±3.9 μg/kg. Carbonate minerals contain even less of this element. In iron hydroxides and the most readily soluble aluminosilicates, its concentrations are in the range 168±24 - 212±28 μg/kg. The most insoluble fraction contains 1.65±0.21 - 4.32±0.45 mg/kg of uranium. In green-colored siltstones, the concentration of adsorbed uranium is much higher: 106±14 - 364±43 μg/kg. Carbonate minerals and amorphous iron oxides contain 1.91±0.21 - 2.34±0.26 mg/kg of uranium. In aluminosilicates and a clay/quartz resistate, uranium concentrations are 5.6±0.5 - 16.8±1.4 mg/kg. Elevated values of ²³⁴U:²³⁸U activity ratio prevail in the adsorbed material and iron hydroxides. In aluminosilicates and clay/quartz resistate, the values decrease. This indicates the replacement of primary sedimentogenic uranium by secondary hydrogenic uranium adsorbed on the surface of minerals and coprecipitated with iron hydroxides. The results obtained made it possible to carry out preliminary quantitative estimates of the retardation factor and recoil loss factor of uranium in the groundwater of siltstones of the studied Vendian aquifer.

Semen Allii Fistulosi is the seed of Allium fistulosum L. of the Liliaceae family. The purpose of this study was to extract, characterize, and evaluate the antioxidant activity in vitro of proteins from Semen Allii Fistulosi (PSAF). Using single factor and orthogonal design, the optimum conditions of extraction were determined to be as follows: extraction time 150 min, pH 8.5, temperature 60℃, and ratio (v/w, mL/g) of extraction solvent to raw material 35. The isoelectric point of the pH was determined to be about 4.4 and 10.2, by measuring the protein content of PSAF solutions at different pH. The amino acid composition of PSAF was determined by high performance liquid chromatography (HPLC), and the results suggested that the species of amino acids contained in the PSAF was complete. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS–PAGE) analysis showed the molecular weight was mainly between 40 and 55 kDa, and Fourier-transform infrared spectroscopy (FTIR) characterized prevalent protein absorption peaks. PSAF exhibited potent scavenging activities against DPPH assays, via targeting of hydroxyl and superoxide radicals, while chelating Fe2+ activity, and demonstrating weak reducing power. This work revealed that PSAF possessed potential antioxidant activity in vitro, suggesting potential for use of PSAF as a natural antioxidant.

A study has been carried out on Ta and Nb recovery by liquid-liquid extraction process using 4-methylacetophenone (4-MAcPh) as organic phase. The 4-MAcPh was compared to methylisobutylketone (MIBK) with respect to extraction efficiencies (kD values) at different concentrations of H2SO4 in the aqueous phase. The results showed a similar extraction of Nb for both solvents. However, for Ta extraction efficiency is increased by a factor of 1.3 for 4-MAcPh. In addition, the MIBK solubilized completely after 6 mol L-1 of H2SO4 against only a loss of 0.14 to 4% for 4-MAcPh between 6 and 9 mol L-1 of H2SO4. The potential of 4-MAcPh has also been studied to selectively recover Ta from a model capacitor waste solution. The results showed a selectivity for Ta in the presence of impurities such as Fe, Ni, Mn. The 4-MAcPh also presents the advantage of having physicochemical properties adapted to its use in liquid-liquid extraction technologies such as mixer-settlers.

Azadirachta indica A. Juss (neem) extracts have been used in pharmaceutical applications as antitumor agents, due to their terpenes and phenolic compounds. To obtain extracts from neem leaves with potential antiproliferative effect, a sequential process of pressurized liquid extraction was carried out in a fixed bed extractor at 25 ºC and 100 bar, using hexane (SH), ethyl acetate (SEA) and then ethanol (SE) as solvents. An extraction using only ethanol (EE) was also conducted to compare the characteristics of the fractionated extracts. The results obtained by liquid chromatography-electrospray ionization mass spectrometry suggested the highest concentration of terpenes for SEA extract in comparison to SH, SE and EE extracts. Therefore, antiproliferative activity showed SEA extracts were the most efficient inhibitors to human tumor cells MCF-7, NCI-H460, HeLa, and HepG2 between all other extracts studied. However, hepatocellular normal cells were more resistant to SH, SEA, SE, and EE compared to malignant cells of breast, lung, hepatocellular, and cervical. Neem fractioned extracts obtained in the present study seem to be more selective for malignant cells compared to the normal cells.

The electroencephalogram (EEG) is a record of brain activity. Brain Computer Interface (BCI) technology formed by the EEG signal has become one of the hotspots at present. How to extract the feature signal of EEG is the most basic research of BCI technology. In this paper, A new method of recognizing fatigue, conscious, concentrated state of human brain is proposed by the combination of discrete wavelet transform and the neural network based on EEG signal. First of all, the law signal is preprocessed by the wavelet denoising method because the law EEG signal contains a large number of high frequency noise, which is decomposed into multi-layer high frequency signal and low frequency signal. thus, δ wave, θ wave, α wave, β wave are obtained by the wavelet transform. And then, frequency band energy of the different wave is regards as the feature signal of EEG. In the experiment, the feature signal is classified by radial basic function (RBF) and annealed chaotic competitive learning network (ACCLN). RBF and ACCLN networks are trained with 500 sets of sample data and are tested by 100 sets of samples in different mental states. The experimental results show that the average accuracy of RBF network under three conditions are 88.75%, 88.25%, 88.5%, respectively, and the correct rate of ACCLN network is 97%, 98%, 98%, respectively.

Previously, we described a 19-base pair double-stranded RNA with 3'-trinucleotide overhangs, acting as immunostimulatory RNA (isRNA). This molecule demonstrated notable antiproliferative effects on cancer cells, inhibited tumor growth, and elicited immunostimulatory and antiviral responses by inducing cytokine and interferon production. Within this study, we compared the efficiency of lung fibrosis development, initiated in mice by BLM or LPS using different schemes of induction. Then we compared the effect of isRNA used in a preventive or therapeutic regimen on the development of fibrosis in selected BLM- and LPS-induced mouse models and showed that isRNA can be used in pathological conditions accompanied by the development of inflammation and the risk of fibrosis formation, without adverse side effects. Prophylactic regimen of isRNA application is beneficial for prevention of the development of pulmonary fibrosis.

In Virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an “infectious clone”. This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate RNA polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward, since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse transcribed into cDNA before any modification -such as restriction enzyme digestion, gene knock-out or knock-in, site directed mutagenesis, ligation, etc.- can be done. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging, due to the low number of members of this family that propagate in cell cultures. Despite the successful rescue of Feline calicivirus (FCV) from cDNA containing plasmid more than 20 years ago, reverse genetics methods are not routine procedures than can be easily extrapolated to other caliciviruses. Reports of calicivirus reverse genetics systems have been few and far between, in this review, we discuss the main pitfalls, failures, and delays behind several successful calicivirus infectious clones.

The prediction of tertiary RNA structures is significant to the field of medicine (e.g. mRNA vaccines, genome editing), and the exploration of viral transcripts. Though many RNA folding software exist, few studies have condensed their locus of attention solely to viral pseudoknotted RNA. These regulatory pseudoknots play a role in genome replication, gene expression, and protein synthesis. This study explores five RNA folding engines that compute either the minimum free energy (MFE) or the maximum expected accuracy (MEA). These folding engines were tested against 26 experimentally derived short pseudoknotted sequences (20-150nt) using metrics that are commonly applied to software prediction accuracy (e.g. F1 scoring, PPV). This paper reports higher accuracy RNA prediction engines (pKiss) when compared to previous iterations of the software, and when compared to older folding engines. They show that MEA folding software does not always outperform MFE folding software in prediction accuracy when assessed with metrics such as percent error, sensitivity, PPV, and F1 scoring when applied to viral pseudoknotted RNA. Moreover, the results suggest that thermodynamic model parameters will not ensure accuracy if auxiliary parameters such as Mg2+ binding, dangling end options, and H-type penalties are not applied. The observations reported in this paper highlight the quality between different ab initio prediction methods while enforcing the idea that a better understanding of intracellular thermodynamics is necessary for a more efficacious screening of RNAs.

This study explored the effects of pBD114 (porcine β-defensin 114) on inflammatory response. The results in RAW264.7 cells showed that 100 μg/mL of pBD114 significantly increased the concentrations of TNFα and IL-10, and 10 μg/mL of pBD114 significantly decreased the concen-tration of TNFα in LPS-induced RAW264.7 cell cultures at 10 ng/mL. These results suggest that pBD114 can exhibit pro-inflammatory or anti-inflammatory activities under certain conditions. RNA-seq analysis was performed to gain further insight into the effects of pBD114 on the in-flammatory response. Among pBD114 promoting RAW264.7 pro-inflammatory response, pBD114 significantly up-regulated 1170 genes and down-regulated 724 genes. KEGG enrichment found that the DEGs were significantly enriched in immune- and signal-transduction-related signaling pathways. PPI and KDA analyses revealed that Bcl10 and Bcl3 were the key genes. In addition, pBD114 significantly up-regulated 12 genes and down-regulated 38 genes in the an-ti-inflammatory response. KEGG enrichment analysis revealed that the DEGs were mainly en-riched in the "Cytokine-cytokine receptor interaction" signaling pathway, and PPI and KDA analyses showed that Stat1 and Csf2 were the key genes. The results of qRT-PCR verified those of RNA-seq. In vivo mice tests also confirmed the pro- or anti-inflammatory activity of pBD114. Although the inflammatory response is a rapid and complex physiological reaction to noxious stimuli, this study found that pBD114 plays an essential role in the inflammatory response mainly by acting on genes related to immunity, signal transduction, signaling molecules, and interactions.

Cervical cancer presents a significant global health concern with high-risk human papilloma-viruses (HPVs) being identified as the cause of this cancer. Although current treatment methods for cervical cancer can eliminate lesions, preventing metastatic spread and minimizing tissue damage remains a major challenge. Therefore, the development of a safer and innovative thera-peutic approach is of utmost importance. Natural products like Fig latex, derived from the Ficus Carica tree, have demonstrated promising anti-cancer properties when tested on cervical cancer cell lines. However, the specific mechanisms by which Fig latex exerts its effects are still un-known. In this study, we conducted RNA-seq analysis to explore how Fig latex may counteract carcinogenesis in HPV-positive cervical cancer cell lines, namely CaSki (HPV type 16-positive) and HeLa (HPV type 18-positive). Our data from this investigation indicates that Fig latex influ-ences the expression of genes associated with the development and progression of cervical can-cer, including pathways related to " Nonsense-Mediated Decay (NMD) "cell cycle regulation" and Transcriptional Regulation by TP53. This selective impact of Fig latex on cancer-related pathways suggests a potential novel therapeutic approach for HPV-related cervical cancer.

Alternative splicing can produce transcripts that affect cancer development and shows potential for cancer diagnosis and treatment. However, intron retention (IR), a type of alternative splicing, has been less systematically studied in cancer biology research. Here, we generated a pan-cancer IR landscape for more than 10,000 samples across 33 cancer types from The Cancer Genome Atlas (TCGA). We characterized differentially retained introns between tumor and normal samples and identified retained introns associated with survival. We discovered 988 differentially retained introns in 14 cancers, some of which demonstrated diagnostic potential in multiple cancer types. We also inferred a large number of prognosis-related introns in 33 cancer types, and the associated genes included well-known cancer hallmarks such as angiogenesis, metastasis, and DNA mutations. Notably, we discovered a novel intron retention event inside 5′UTR of STN1 that is associated with the survival of lung cancer patients. The retained intron reduces translation efficiency by producing upstream open reading frames (uORFs) and thereby inhibits colony formation and cell migration of lung cancer cells. Besides, the IR-based prognostic model achieved good stratification on certain cancers, as illustrated in acute myeloid leukemia. Taken together, we performed a comprehensive IR survey at a pan-cancer level, and the results implied that IR has the potential to be diagnostic and prognostic cancer biomarkers, as well as new drug targets.

Henipaviruses are single-stranded RNA viruses that have been shown to be virulent in several species including humans, pigs, horses, and rodents. Isolated nearly 30 years ago, these viruses have been shown to be of particular concern to public health, as at least two members (Nipah and Hendra viruses) are highly virulent, as well as zoonotic, and are thus classified as BSL4 pathogens. Although only 5 members of this genus have been isolated and characterized, metagenomics analysis using animal fluids and tissues has demonstrated the existence of other novel henipaviruses, suggesting a far greater degree of phylogenetic diversity than currently known. Using a variety of molecular biology techniques, it has been shown that these viruses exhibit varying degrees of tropism, on a species, organ/tissue, and cellular level. This review will attempt to provide a general overview of our current understanding of henipaviruses, with particular emphasis on viral tropism.

This paper presents ConF, a novel deep learning model designed for accurate and efficient prediction of non-coding RNA families. NcRNAs are essential functional RNA molecules involved in various cellular processes, including replication, transcription, and gene expression. Identifying ncRNA families is crucial for comprehensive RNA research, as ncRNAs within the same family often exhibit similar functionalities. Traditional experimental methods for identifying ncRNA fam-ilies are time-consuming and labor-intensive. Computational approaches relying on annotated secondary structure data face limitations in handling complex structures like pseudoknots and have restricted applicability, resulting in suboptimal prediction performance. To overcome these chal-lenges, ConF integrates mainstream techniques such as residual networks with dilated convolutions and cross multi-head attention mechanisms. By employing a combination of dual-layer convolu-tional networks and BiLSTM, ConF effectively captures intricate features embedded within RNA sequences. This feature extraction process leads to significantly improved prediction accuracy compared to existing methods. Experimental evaluations conducted on a ten-fold publicly available dataset demonstrate the superiority of ConF in terms of accuracy, sensitivity, and other perfor-mance metrics. Overall, ConF represents a promising solution for accurate and efficient ncRNA family prediction, addressing the limitations of traditional experimental and computational methods.

Non-alcoholic steatohepatitis (NASH) is a clinically serious stage of non-alcoholic fatty liver disease (NAFLD). Histologically characterized by hepatocyte ballooning, immune cell infiltration and fibrosis, NASH at a molecular level involves lipid induced hepatocyte death and cytokine production. Currently, there are very few diagnostic biomarkers available to screen NASH, and no pharmacological intervention is available for its treatment. In this study, we show that hepatocyte damage by lipotoxicity results in the release of extracellular RNAs (eRNAs) which serve as damage-associated molecular patterns (DAMPs) that stimulate the expression of pro-apoptotic and pro-inflammatory cytokines, aggravating inflammation, and cell death in HepG2 cells. Furthermore, the inhibition of eRNA activity by RNase 1 significantly increased cellular viability and reduced NF-kB mediated cytokine production. Similarly, RNase 1 administration significantly improved hepatic steatosis, inflammatory and injury markers in a murine NASH model. This study, therefore, for the first time, underscores the therapeutic potential of inhibiting eRNA action as a novel strategy for NASH treatment.

The transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. In this study, we selected Baghlani Nangarhar, an extremely fast dehydration material, and Saturn, a slow dehydration material, based on the results of the previous studies of screening of 165 germplasm materials for dehydration rate phenotypes. Fast dehydration experiment on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified by transcriptome sequencing and quantitative real-time PCR (qRT-PCR). GO and KEGG analyses were carried out. The results showed that in Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. Similarly, in Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 down-regulated. The results of the GO analysis showed that the sites of action of the differentially expressed genes enriched in the fast dehydration modes were concentrated in the cytoplasm, internal components of the membrane and nucleosomes. They play regulatory roles in catalysis, binding, translocation, transcription, protein folding, degradation and replication. They are involved in adaptive responses to adverse external environments such as reactive oxygen species and high temperature. The KEGG analysis showed that the main metabolic pathways enriched are protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation. The key differentially expressed genes and the most important metabolic pathways in the rapidly and slowly dehydrated materials obtained in this study were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism, which are presumed to have important regulatory roles in stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during dehydration and drying of mature seeds. The results of this study could potentially provide a valuable reference for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.

Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated). Infection influenced numerous immunoregulatory interactions between lymphoid and nonlymphoid cells in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T-lymphocyte mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signalling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signalling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of Binding and Uptake of Ligands by Scavenger Receptors in EP and p53 signalling in the EN group was found. In conclusion, this study provides new insights into the disease course and host‒pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.

Brown-marbled grouper is one of the most important mariculture species in China, which is used as an important crossbreeding parent in grouper industry. Enhancing growth rates is a key target in fish breeding, and gaining insight into the underlying mechanisms responsible for growth differences among individuals can aid in the improvement of grouper growth rates. However, the mechanism behind this difference in growth in this fish is unclear. The difference of transcriptome profiles of muscle tissue between fast- and slow-growing brown-marbled grouper was analyzed by RNA-Seq. 77 significantly up-regulated genes and 92 significantly down-regulated genes were identified in the growth extreme groups. The up-regulated of ghr and tnni2 and the down-regulated of stc2 led to the growth advantages of brown-marbled grouper. The differently expressed genes (DEGs) were used for GO and KEGG enrichment analysis. The results of GO enrichments indicated that the significantly upregulated genes in the fast-growing group were involved in protein folding, actin cytoskeleton, myosin complex, etc. The results of KEGG enrichments indicated that the significantly upregulated genes in the fast-growing group were involved in glycolysis/ gluconeogenesis, adipocytokine signaling pathway, MAPK signaling pathway, carbon metabolism, PI3K-Akt signaling pathway, etc. To analysis the difference gene sets between fast- and slow-growing group, the RNA-seq data were used by gene set enrichment analysis (GSEA). The results showed that the PI3K/AKT/mTOR pathway was up-regulated in the fast-growing group. The up-regulated of this pathway could lead to higher nutrient absorption efficiency and lead to muscle growth in the fast-growing group. These results contribute to understanding of the molecular mechanisms of fast growth and regulative pathways regulating growth in brown-marbled grouper.

Adipocytes play a critical role in maintaining a healthy systemic metabolism by storing and releasing energy in the form of fat and helping to regulate glucose and lipid levels in the body. Adipogenesis is the process through which pre-adipocytes are differentiated into mature adipocytes. It is a complex process involving various transcription factors and signaling pathways. Dysregulation of adipogenesis has been implicated in the development of obesity and metabolic disorders. Therefore, understanding the mechanisms that regulate adipogenesis and the factors that contribute to its dysregulation may provide insights into the prevention and treatment of these conditions. RNA Binding Motif Single Stranded Interacting Protein 1 (RBMS1) is a protein that binds to RNA and plays a critical role in various cellular processes such as alternative splicing, mRNA stability, and translation. The RBMS1 polymorphism has been shown to be associated with obesity and Type 2 diabetes, but the role of RBMS1 in adipose metabolism and adipogenesis is not known. We show that RBMS1 is highly expressed during the early phase of differentiation of the murine adipocyte cell line 3T3-L1 and is significantly upregulated in adipose tissue depots and adipocytes of high-fat-fed mice, implying a possible role in adipogenesis and adipose metabolism. Knockdown of RBMS1 in pre-adipocytes impacted the differentiation process and reduced the expression of some of the key adipogenic markers. Transcriptomic and proteomic analysis indicated that RBMS1 depletion affected the expression of several genes involved in major metabolic processes, including carbohydrate and lipid metabolism. Our findings imply that RBMS1 plays an important role in adipocyte metabolism and may offer novel therapeutic opportunity for metabolic disorders such as obesity and type 2 diabetes.

For decades since the central dogma, cancer biology research has been focusing on the involvement of genes encoding proteins. It has been not until more recent times that a new molecular class has been discovered, named non-coding RNA (ncRNA), which has been shown to play crucial roles in shaping the activity of cells. An extraordinary number of studies into shown that ncRNAs represent an extensive and prevalent group of RNAs, including both oncogenic or tumor suppressive molecules. Henceforth, various clinical trials involving ncRNAs as extra ordinary biomarkers or therapies have started to emerge. In this review, we will focus on the prognostic and diagnostic role of ncRNAs for breast cancer.

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during plant growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula. Background and Objectives: The cell cycle factors not only influence cell cycle progression together, but also regulate accretion, division and differentiation of cells, and then regulate growth and development of plant. In this study, we identified the putative cell cycle genes in B. pendula genome, based on the annotated cell cycle genes in A. thaliana. It could serve as a foundation for further functional studies. Materials and Methods: The transcript abundance was determined for all the cell cycle genes in xylem, root, leaf and flower tissues using RNA-seq technology. Results: We identified 59 cell cycle gene models in the genome of B. pendula, 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1 and BpWEE1. Conclusions: We identified 17 core cell cycle genes in the genome of birch by combining phylogenetic analysis and tissue specific expression data.

With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA based approaches i.e. RNAi-mediated gene regulation and site-specific nuclease based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting down-regulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops genome sequence to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.

The physics–biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the physical coupling between the synthesis of nucleic acids and the synthesis of amino acid polymers. Owing to this physical coupling, amino acid polymers (or proto-phenotypes) maintained the physicochemical parameter equilibria (proto-homeostasis) in the immediate environment of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical stresses, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome generating an internal environment whose physicochemical parameters guarantee homeostasis and genome integrity has a higher probability to be reproduced without variation and therefore to reproduce the same phenotype in offspring. Otherwise, the genome is modified by the imbalances of the internal physicochemical parameters it generates, until new emerging biological activities maintain homeostasis. In sum, evolution depends on feedforward and feedback loops between genome and phenotype, since the internal physicochemical conditions that a genome generates in response to environmental fluctuations in turn either guarantee the stability or direct the variation of the genome.

Exogenous RNA comprises the genetic material associated with several diseases which require immediate treatment, and thus mechanisms to hinder intracellular translation and reproduction of RNA viral agents are of great importance. Applying recent developments from this lab in methods relating to the interaction of DNA with steroid hormones, cyclic compounds are presented for intermolecular binding to nucleic acids. The requirements to achieve binding with RNA nucleotide pairs are described, which involve at a minimum functional elements positioned to interact with the lateral phosphate groups for each of the RNA strands through coupling with a positively charged ion, such as Mg2+, Ca2+, or Zn2+ ions; and an intermolecular hydrogen bond with the oxygen element of uracil at the carbon two location. Additional features of the binding molecules are examined for enhancements and differentiation in binding capability and include aromatic groups that have both a structural role of steric hindrance and a functional role to stabilize the binding mechanisms. Several categories of cyclic compounds are associated to have specific binding capabilities, and the interaction of these structures with potential receptor molecules are evaluated for assessment in delivery and binding of the compound to nucleic acids.

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3'UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3'UTR architecture among different CHIKV lineages.

RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA (cDNA) library construction. Here we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance.

Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the "RNA world" hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme, belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the ultraconserved occurrence of HHR in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitously features of life. Those are the versatility and efficiency of small RNAs, viroids and ribozymes, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.

More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m⁷G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m⁷G modification occurs at position 46 in the variable region and is a product of tRNA (m⁷G46) methyltransferase. The m⁷G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. Recently, we have proposed a reaction mechanism for eubacterial tRNA m⁷G methyltransferase (TrmB) based on the results of biochemical studies and previous biochemical, bioinformatic, and structural studies by others. However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. The physiological functions of m⁷G46 in tRNA have started to be determined over the past decade. To be able to better respond to diseases and infections in which the m⁷G modification is considered to be involved, it is still necessary to further understand the catalytic mechanism of AdoMet and/or the tRNA bound form of m⁷G methyltransferases. In this review, information of tRNA m⁷G modifications and tRNA m⁷G methyltransferases are summarized and the differences in reaction mechanism between tRNA m⁷G methyltransferase and rRNA or mRNA m⁷G methylation enzyme are discussed.

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

Viruses continue to provide vital insights into the field of control of gene expression. Viral transactivators, in concert with other viral and cellular proteins, regulate expression of self, other viruses, and host genes with profound effects on infected cells, underlying inflammation, control of immune responses, and pathogenesis. The multifunctional Tat proteins of lentiviruses (HIV-1, HIV-2, and SIV) transactivate gene expression by recruiting host proteins and binding to trans-acting responsive regions (TARs) in viral and host RNAs. SARS-CoV-2 nucleocapsid participates in early viral transcription, recruits similar cellular proteins, and shares intracellular, surface, and extracellular distribution with Tat. SARS-CoV-2 nucleocapsid interacting with the Replication-Transcription complex might, therefore, transactivate viral and cellular RNAs in transcription and reactivation of self and other viruses, acute and chronic pathogenesis, immune evasion, and viral evolution, constituting a potential pan-coronaviral therapeutic target. Here, we show by using primary and secondary structural comparisons that the leaders of SARS-CoV-2 and other coronaviruses contain TAR-like sequences in stem-loops 2 and 3, the coronaviral nucleocapsid C-terminal domains (N-CTDs) harbor a region of similarity to TAR-binding regions of lentiviral Tat proteins, and the coronaviral nonstructural protein 12 has a cysteine-rich metal binding, dimerization domain similar to that in lentiviral Tat proteins.

Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells. It has been demonstrated that the secondary structure of the entire viral genome is often responsible for performing crucial functions in the viral life cycle and also influences virus evolution. To investigate the role of viral RNA secondary structure, alongside experimental techniques, the use of bioinformatics tools is important for analyzing various secondary structure patterns, including hairpin loops, internal loops, multifurcations, external loops, bulges, stems, and pseudoknots. Here, we have introduced a Python package for analyzing RNA secondary structure elements in viral genomes, which includes the recognition of common secondary structure patterns, the generation of descriptive statistics for these structural elements, and the provision of their basic properties. We applied the developed package to analyze the secondary structures of complete viral genomes collected from the literature, aiming to gain insights into viral function and evolution. Both the package and the collection of secondary structures of viral genomes are available at http://github.com/KazanovLab/RNAsselem.

According to the International Agency for Research on Cancer (IARC) of the World Health Organization (data of year 2020), Breast Cancer (BC) is one of the most common cancer types worldwide, with large geographical variations occurring between countries and world regions and highest incidence rates in countries that have undergone economic transition. The risk factors for BC include women ageing, genetic mutations, reproductive history, dense breast tissues, personal history of BC or specific non-cancerous breast diseases, family history of breast or ovarian cancer, previous treatment using radiation therapy, and exposure to hormone-like drugs such as diethylstilbestrol (DES). Additional risk factors include being overweight or having obesity after menopause, and taking hormones. MicroRNAs (miRNAs or miRs) are small non-coding RNA molecules that have an essential role in gene expression and are significantly linked to the tumor development and angiogenesis process in different types of cancer, including BC. In the last years, the knowledge about miRNAs role in BC has significantly improved, and complex interactions among coding and non-coding RNA has been elucidated. In this context, an increasing number of papers had been published regarding the role of miR-125 in BC. In this review, we summarize the state-of-the-art about this research topic in addition to elaborating on the need to set novel ethical and legal standards for the governance of such innovations in healthcare.

The structural transitions RNAs undergo during trafficking are not well-understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and synthesized in vitro, we detected Ty1 gRNA structural alternations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, while the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA:RNA interactions required for retrotransposition.

Under the oxidative stress condition, the small RNA (sRNA) Oxys that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in defection of gene regulation. But, how the Hfq protein interacts with sRNA Oxys and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized Born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result is in excellent correlation with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly comes from the increased van der Waals interactions (vdW). This research explores the binding mechanism between Oxys and chaperone protein Hfq, and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights on the mechanism of gene expression regulation affected by protein mutations.

Starting from December 2019, coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures and supporting apparatuses. Remdesivir was reported by World Health Organization (WHO) as the most promising drug currently available for the treatment of COVID-19. Here, we use molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). In the absence of a crystal structure of the SARS-CoV-2 RdRp, we first construct the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identify of 95.8%). We then build the putative binding mode by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp. The putative binding structure is further optimized with molecular dynamics simulations and demonstrated to be stable, indicating a reasonable binding mode for remdesivir. The relative binding free energy of remdesivir is calculated to be -8.28 ± 0.65 kcal/mol, much stronger than the natural substrate ATP (-4.14 ± 0.89 kcal/mol) which is needed for the polymerization. The ~800-fold improvement in the K_d from remdesivir over ATP indicates an effective replacement of APT in blocking of the RdRp binding pocket. Key residues D618, S549 and R555 are found to be the contributors to the binding affinity of remdesivir. These findings demonstrate that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA reproduction, with key residues also identified for future lead optimization and/or drug resistance studies.

Rice grassy stunt virus (RGSV) a member of Tenuivirus family, is very potent and destructive which effects rice crop in many countries, particularly China. Non coding RNAs have important functions in development and epigenetic regulation of gene expression in numerous organsisms. There is three type of small non coding RNAs have been found in eukaryotes, which are small interferring RNAs (siRNAs), microRNAs (miRNAs) and piwi interacting RNAs (piRNAs). Small RNAs (sRNAs) origination is from the infecting virus which is known as virus-derived small interfering RNAs (vsiRNAs), has responsibility for RNA silencing in plants. Virus-induced gene silencing (VIGS) is mainly dependent on RNA silencing (RNAi). Interestingly, RNA silencing happens in plants during viral infections. RNAi technique showed significant results in Nephotettix cincticeps. RNAi technique demonstrated the gene silencing of planthopper Nilaparvata lugens. The proteins P5, pcf4, Dnj, psn5, and pn6 act as potential movement proteins and serve as silencing suppressors for RGSV. VsiRNAs originate from dsRNA molecules which require Dicer-like (DCL) proteins, RNA dependent RNA polymerase (RdRP) proteins, and Argonaute (AGO) proteins. RdRP uses ssRNA for perfect RNA amplification process and can also be used for DCL dependent secondary vsiRNA formation. VSRs interfere with the movement of signals during silencing mechanism. Moreover, intercellular movement of viruses is facilitated by virus-encoded movement protein. RNAi is found in many eukaryotes which are related to transcriptional or post-transcriptional regulation by gene suppression. Transcription is bidirectional in ssDNA viruses which are originated from dsRNA molecules. In this review, we highlighted the biology of Rice grassy stunt virus and its insect vector and its silencing suppressors. This work will be helpful for plant virologists to understand the whole biogenesis mechanism for rice viruses especially RGSV.

Evolutionary, sequence and structural analyses of tRNA variable (V) loops provides a new understanding. Type I tRNA V loops have a primordial length of 5 nt, and type II tRNA V loops have a primordial length of 14 nt. Sequence-based alignments of type I and type II V loops gave deceptive results. Type II V loops are characterized by the trajectory of the V arm, the size and sequence of the loop and the first and last V loop nucleotides and their known contacts. Depending on the V arm trajectory, type II V stems and loops can be interaction sites for aminoacyl-tRNA synthetases. So, type II V arms for tRNALeu, tRNASer and tRNATyr (found in Bacteria) were coevolved and selected to distinguish determinants to support cognate tRNA charging. The alignment of type I and type II V loops was adjusted based on tRNA evolution. Results are consistent with Archaea being an older and simpler life form than Bacteria. TRNAome sequences were derived from radiation of an ordered tRNAPri (Pri for primordial) sequence comprised of known RNA repeats and inverted repeats. V loop and tRNA sequences, therefore, convey a history of the primary successful pathway in the origin of life.

Since its initial characterization in 2016, the interferon stimulated gene Shiftless (SHFL) has proven to be a critical piece of the innate immune response to viral infection. SHFL expression stringently restricts the replication of multiple DNA, RNA, and retroviruses with an extraordinary diversity of mechanisms that differ from one virus to the next. These inhibitory strategies include the negative regulation of viral RNA stability, translation, and even the manipulation of RNA granule formation during viral infection. Even more surprisingly, SHFL is the first human protein found to directly inhibit the activity of the -1 programmed ribosomal frameshift, a translation recoding strategy utilized across nearly all domains of life and a several human viruses. Recent literature has shown that SHFL expression also significantly impacts viral pathogenesis in mouse models, highlighting its in-vivo efficacy. To help reconcile the many mechanisms by which SHFL restricts viral replication, we provide here a comprehensive review of this complex ISG, its influence over viral RNA fate, and the implications of its functions on the virus-host arms race for control of the cell.

Despite being a rare disease worldwide, rabies has the highest morbidity and mortality rates, with nearly all symptomatic cases leading to coma and death. Rabies represents an infectious disease caused by the Rabies virus (RABV), which is part of the Lyssavirus group and the Rhabdoviridae family, and it mainly spreads through the bite and scratch of an infected mammal, but particularly of wild animals, such as bats, foxes, wolves and racoons, and of domestic animals, such as dogs and cats, in rabies-prone areas of the world. Airborne transmission has been deemed as extremely rare, and no clinical case as such has been recorded worldwide yet, except in the enclosed environment, such as research laboratories and caves where infected bats are present. Domestic mammals, such as dogs and ferrets, represent other important reservoirs of disease transmission, and the human cases of Asia and Africa amount approximately 95% of all human cases worldwide. Infected animals most commonly start transmitting the virus once the first symptoms have occurred, and if they experience disease aggravation and death within 10 days, a case of rabies is registered, more easily if the incidence occurred in the urban area and then, any person or animal that had been potentially exposed are strongly recommended to receive the inoculation. It is rare for asymptomatic mammals to transmit the illness. Most First-World and several Second-World countries have recently been declared dog rabies-free by the World Health Organization. The disease can only be treated prophylactically, with three doses of a vaccine containing an inactivated form of RABV, or with five doses of the vaccine and two doses of anti-RABV immunoglobulins within 28 days if the patient is believed to have been exposed to the virus beforehand. It has been projected that, once the viral load reaches elements of the central nervous system, prophylactic approaches are no longer effective, even if symptoms have not begun yet, and this highlights the urgent trait of the medical condition, strongly recommending exposed people to receive the prophylactic doses immediately after the potential exposure to the virus. The pathogen first infects the bodily fluids, before reaching the peripheral nervous system, from where it will gradually move toward the spinal cord or the encephalon, at a speed of movement ranging from 1 to 40 cm per day. It was also found, in extremely rare circumstances, to infect the nasopharyngeal cavity and the lungs. The primary cause of a successful, gradual advance of the viral load toward the point of clinical no-return for the patient - the CNS - is a complex mechanism of induced innate immune evasion, with the interferon system being heavily targeted and silenced by RABV proteins. The ‘Milwaukee’ protocol is locally believed to decrease the mortality rate of the clinical illness to approximately 80%, although significantly more research is required in this sense. First-line immune evasion represents the central mechanism developed by viruses during their evolutionary process to gain control over human immunity, so it could be the development and adjustment of a counter-offensive to this evolutionary operating system that could address the core elements of the problem. Human recombinant Type I and Type III Interferons were found to be significant vaccine adjuvants and to considerably delay the clinical onset of the disease. Despite their central role in natural immunity-based prophylaxis, vaccine support and, in often cases, vaccination per se, a local administration of IFNs as such may not be enough to tackle the core problem of the endemic disease, and a specific and systemic treatment of potential host cells with IFN I and III, as well as IFN-stimulating proteins, may constitute a major research requirement in the coming years of disease investigation, as the inoculation efforts with the inactivated virus and immunoglobulin administration continue. The administration of a relatively low dosage of somatic Natural Killer cells, gamma-interferon and perhaps, of somatic helper CD4+ and somatic cytotoxic CD8+ T-lymphocytes treated with alpha-, beta- and lambda-interferon could be merged with the administration of a similar dosage of alpha-, beta- and lambda-interferon during the efforts to develop an effective and less costly prophylactic vaccine against rabies. A combination of a nasal substance containing a low dosage of IFN I and III with a reduced concentration of neutralized RABV copies, and/or with a low dose of anti-RABV IgA antibodies, could also be tested for humans for the purposes of pre- and post-exposure prophylaxis.

The objective of this work was to investigate the deacidification of bio-oils (BOs) from triglyceride-based biomass through the application of liquid-liquid extraction (LLE) in a simple stage, using methanol and water as a binary solvent and feed/solvent ratio of 1/1. For this, the effects of process parameters such as the water content present in the solvent, the content of carboxylic acids present in the bio-oil, and the extraction temperature on the deacidification process through the efficiency and distribution coefficient were evaluated, as well as the effects of such parameters on the quality of deacidified bio-oils through physical-chemical analyzes and GC-MS analysis. The results show that such process parameters significantly affect the quality of deacidified bio-oils. The ideal condition to have the highest acid removal, i.e., the highest deacidification efficiency (72.65%), is the one in which the deacidification process is performed with aqueous methanol (5% water) at 35 °C and for BOs that have a total acid number (TAN) equal to 24.38 mg KOH/g. Therefore, the process of deacidification by LLE using aqueous methanol is a promising alternative for removing carboxylic acids and other oxygenated compounds, contributing significantly to the upgrading or improving biofuels produced by catalytic thermal cracking.

Emerging pollutants (EPs) encompass natural or synthetic substances in the environment that pose potential risks but have only recently been recognized or monitored. EPs consist of various categories including pesticides, pharmaceuticals, hormones, mycotoxins, and endocrine disrupting chemicals (EDCs). Through several pathways, EPs can access food, potentially leading to health impacts when their safe concentrations are exceeded. Milk, being a highly nutritious and a heavily consumed food product by many consumers of different ages, is a crucial food matrix where EPs should be regularly monitored. In literature, large number of studies was dedicated for the determination of different EPs in dairy milk, employing different analytical techniques. Chromatographic based techniques were the most prevalent means for analysis of EPs in milk, which demonstrated significant efficiency, sensitivity and accuracy for this specific purpose. Prior to chromatographic analysis, extraction of EPs from a complex matrix like milk, is essential. This review comprehensively covers relevant research papers on extraction and subsequent detection and determination of EPs in milk by chromatographic methods from 2018 and until 2023.

The solvent extraction of gold(III) by undiluted 2-ethylhexanol or dissolved in toluene from HCl solution has been investigated. The numerical analysis of gold distribution data suggests the formation of HAuCl4·L and HAuCl4·2L (L= 2-ethylhexanol) species in the organic phase with formation constants K11= 38 and K12= 309, respectively. The results derived from gold(III) distribution have been implemented in a solid-supported liquid membrane system. The influence of several variables on gold transport was considered: feed and receiving phases stirring speeds, HCl and gold concentrations in the feed phase and carrier concentration in the membrane phase as well as the presence of base metals (Fe,Cu,Ni) and PGMs in the feed phase. Also, diffusional resistances to mass transfer are estimated. Gold is recovered as zero valent nanoparticles.

This study focuses on the reasoning of symptoms of TCM internal diseases. Taking cough as an example, the BERT-BiLSTM-CRF model is used for entity recognition. Experiments show that the model has the best entity recognition effect on three types of texts, including teaching cases, clinical cases and literature data, and the F1 value is up to 0.967. It can effectively identify symptoms, course of disease, tongue condition and pulse condition in TCM diagnosis and treatment texts, which lays a solid foundation for intelligent assisted syndrome differentiation and treatment of TCM. By constructing four types of entity corpora and using three mainstream entity recognition models for experiments, it is found that the BERT-BiLSTM-CRF model has a good entity recognition effect in three types of data: teaching cases, clinical cases and literature data. Experimental results show that the F1 values of the BERT-bilSTM-CRF model in teaching cases, clinical cases and literature data are 0.967, 0.82 and 0.91, respectively, which provides an effective method for information extraction in the field of TCM syndrome differentiation diagnosis and treatment, and lays a foundation for further research on knowledge reasoning.

Despite UAV multi-target detection exhibits considerable developmental potential worldwide, it suffers distinct challenges compared with traditional tasks in this field. These challenges include insufficient feature extraction capabilities for small targets, limited capabilities for multi-dimensional feature fusion, as well as constraints on hardware computation parameters. Especially in mission scenarios such as disaster detection, these challenges will be further amplified. Consequently, this paper introduces SSE-YOLO, an innovative YOLO framework algorithm specially designed to address these challenges. To enhance the model's feature extraction capability, we employ the SPDConv module to replace the original Conv in the backbone section, utilizing depth-separable convolution instead of traditional convolution pooling. Concurrently, we eliminate the SPPF module at the bottom and address a new Separate Kernel Attention Pyramid Pooling (SKAPP) module, substantially enhancing the feature fusion capability at the model's core. Moreover, to address the challenge of multi-dimensional feature fusion, we replace the Concat module of the neck and head with E-BiFPN, transmitting feature information from the backbone to the lower network through four CBS blocks, which effectively resolves the issue of lost contextual information in the model. Meanwhile, SSE-YOLO undergoes ablation experiments on the VisDrone2019 dataset to evaluate its effectiveness against alternative methods, and experimental results illustrate the model's exceptional precision in detecting UAV targets. In comparison to models with comparable experimental accuracy, SSE-YOLO requires remarkably fewer parameters. On the VisDrone2019-DET-test-dev dataset, SSE-YOLO enhances mAP by 17.3%, with a 42.5% reduction in the parameter amounts. Therefore, the proposed method effectively tackles the challenge of reconciling low parameters and high accuracy, presenting a novel pathway for deep learning-based UAV multi-target detection.

Alginate, a biopolymer promising in food, biomedical, pharmaceutical, and electronic materials industries, is characterized by its biodegradability, biocompatibility, low toxicity, and gel-forming properties. It is most abundantly found in brown algae. However, conventional dilute acid and alkali extraction methods face limitations in commercialization due to their long processing time, low throughput, and high solvent requirements. In this study, a microwave-assisted extraction (MAE) process for sodium alginate was designed to improve extraction efficiency. Solid/liquid ratio, extraction temperature, and extraction solvent concentration were major variables affecting sodium alginate extraction from Undaria pinnatifida(sea mustard). They were then statistically optimized using response surface methodology. Under optimal conditions (13.27 g/L, 91.86 ℃, 2.51 %(w/v), and 15 min), the yield was 38.41 %, which was 93.43 % of the theoretical content of sodium alginate in Undaria pinnatifida. Our work has confirmed the productivity and industrial feasibility of efficient extraction of sodium alginate from marine biomass, and we hope that it will serve as an encouraging case for the application of biopolymers as one of the desirable options for alternative petrochemicals to construct a sustainable society.

Accurate weight measurement is pivotal for monitoring the growth and well-being of cattle. However, the conventional weighing process, which involves physically placing cattle on scales, is labor-intensive and distressing for the animals. Hence, the development of automated cattle weight prediction techniques assumes critical significance. This study proposes a weight prediction approach for Korean cattle using 3D segmentation-based feature extraction and regression machine learning techniques from incomplete 3D shapes acquired from real farm environments. In the initial phase, we generated mesh data of 3D Korean cattle shapes using a multiple-camera system. Subsequently, deep learning-based 3D segmentation with the PointNet network model was employed to segment two dominant parts of the cattle. From these segmented parts, three crucial dimensions of Korean cattle were extracted. Finally, we implemented five regression machine learning models (CatBoost regression, LightGBM, Polynomial regression, Random Forest regression, and XGBoost regression) for weight prediction. To validate our approach, we captured 270 Korean cattle in various poses, totaling 1190 poses of 270 cattle. The best result was achieved with mean absolute error (MAE) of 25.2 kg and mean absolute percent error (MAPE) of 5.81% using the random forest regression model.

Cambodian spices Amomum kravanh, Citrus hystrix and Piper nigrum 'Kampot' have long history of seasoning of food products. In this study, essential oils (EOs) and supercritical CO2 extracts from all three species have been analyzed using GC-MS with two columns of different polarity, whereas EO and CO2 extract from P. nigrum fruits and CO2 extract from the peel of C. hystrix have been isolated and analyzed for the first time. The results showed that A. kravanh EO contained mostly eucalyptol (78.8/ 72.6 %), while CO2 extract was rich in oleic acid (29.26 %) and tricosane (14.74 %). C. hystrix EO was rich in β-pinene (29.95/29.45 %), followed by D-limonene (24.54/23.24 %) and sabinene (9.94/10.23 %). β-pinene (30.2/28.9 %), D-limonene (23.99/23.74 %) and sabinene (13.36/19.55 %) were also predominant in the CO2 extracts. β-Caryophyllene was the main constituent of both EO and CO2 extract from P. nigrum 'Kampot' with contents ranging from 37.84 to 55.84 %, followed by 3-carene (from 7.18 to 18.72 %). Such findings suggest that supercritical CO2 can potentially be used for extraction of all three Cambodian spices. Nevertheless, further research determining the most efficient extraction parameters will be needed before its application in the spice processing practice.

The residue of chestnut processing generates a large amount of waste material, a resource not adequately exploited. The phenolic composition of water extracts from discarded pericarp of four (MURG, LOCG, ILDP and COEV) chestnut accessions and one marron variety belonging to the Sardinian biodiversity was studied. The antioxidant capacity of cold and hot water extracts was determined by DPPH, ABTS and cyclic voltammetry tests. The antiproliferative effect on normal cells (fibroblasts), and colon (RKO and SW48), breast (MCF7) and melanoma (B16F10) cancer cells, was evaluated by biological assays. MTT test demonstrated that temperature and different extraction times significantly influenced the growth of cells, both normal and tumor. The fibroblast viability was significantly reduced by moderate doses of cold extracts, but only by doses greater than 250 µg/ml of hot extracts, regardless of the accession or cultivar. An even more marked effect was observed when RKO and SW48 were treated with cold extracts, while treatments on B16F10 melanoma cells resulted less effective. Differently, the cold extracts of all accessions induced a significant increase in MCF7 cell viability starting from moderate doses (50 µg/ml), whereas hot extracts had a similar, but less evident, effect compared to reference fibroblasts.

Nuts are a staple food consumed throughout the world, and their purity is essential to maintaining human health. However, fungal mycotoxins pose one of the real challenges in keeping nuts clean for human consumption. The high cost of equipment, reagents used, standard samples, as well as increased requirements for personnel qualifications limit the use of chromatographic methods in testing laboratories, both manufacturing enterprises and organizations monitoring food safety. The present study aimed to test a new method for extracting aflatoxin B1 using sodium chloride and citric acid instead of methanol present in imported nuts obtained from local markets in Astana (Kazakhstan). The proposed method for extracting aflatoxin B1 from nuts is chemically safe, since the substances used belong to hazard class 3 of the international classification and do not require separate premises in food safety laboratories of the Astana markets and special training of specialists. The technical objective of the method is to replace the reagent (methanol) during the sample preparation process when conducting cocuret enzyme-linked immunosorbent assay. Aflatoxin B1 levels varied depending on the type of nut. Aflatoxin contamination was observed in 35.8% of samples analyzed. These levels of mycotoxin contamination are alarming and raise serious questions about the purity of imported nuts to ensure food safety.

Context: Despite the effort put into developing standards for structuring construction cost, and the strong interest into the field. Most construction companies still perform the process of data gathering and processing manually. That provokes inconsistencies, different criteria when classifying, misclassifications, and the process becomes very time-consuming, particularly on big projects. Additionally, the lack of standardization makes very difficult the cost estimation and comparison tasks. Objective: To create a method to extract and organize construction cost and quantity data into a consistent format and structure, to enable rapid and reliable digital comparison of the content. Method: The approach consists of a two-step method: Firstly, the system implements data mining to review the input document and determine how it is structured based on the position, format, sequence, and content of descriptive and quantitative data. Secondly, the extracted data is processed and classified with a combination of data science and experts’ knowledge to fit a common format. Results: A big variety of information coming from real historical projects has been successfully extracted and processed into a common format with 97.5% of accuracy, using a subset of 5770 assets located on 18 different files, building a solid base for analysis and comparison. Conclusion: A robust and accurate method was developed for extracting hierarchical project cost data to a common machine-readable format to enable rapid and reliable comparison and benchmarking.

The production of polyurethane films from bark-derived polyols requires the complete solubility of all components in the polyurethane synthesis media. In this study, a comprehensive investigation was conducted to achieve the copolymerization of black alder bark water extract-derived polyol with isocyanate for polyurethane film synthesis in THF solution. A fractionation approach using tetrahydrofuran (THF) as a solvent was employed to dissolve the extract, followed by filtration and removal of the solvent. The resulting THF-soluble fraction comprised 62±1% of the dry weight of the alder bark extract, mainly consisting of the xyloside form of the diarylheptanoid compound oregonin, along with oligomeric flavonoids and carbohydrates. The THF-insoluble fraction was the most enriched with carbohydrate compounds, followed by the crude extract and THF-soluble fraction. Another approach was aimed at obtaining bark extractives based liquid polyols suitable for producing rigid PU foams. For this purpose, oven-dried crude black alder bark water extract was liquefied with polyethylene glycol (PEG 400). The liquefaction of black alder bark and pine bark extractives was studied under different conditions, including varying temperature ranges (130-170⁰C), catalyst concentrations (0-1,5%), and bark extract content in the mixture (15-30%). The results showed that the use of sulphuric acid as a catalyst (1-1.5%) significantly improved the solubility of both extractives, enabling the attainment of extract concentrations up to 25% at 170⁰C. However, increasing the extract content beyond a certain threshold led to incomplete solubility. It was shown that the PEG-insoluble fractions consist mainly of carbohydrate components. To increase the content of biomass in liquid polyols, the effect of glycerol additions into the liquefaction agent is under study. The findings provide insights into tailoring bark-sourced polyols for polyurethane foam production through appropriate liquefaction conditions.

Extracting railway tracks is crucial for creating electronic railway maps. Traditional methods require significant manual labor and resources, while existing neural networks have limitations in efficiency and precision. To address these challenges, a railway track extraction method using an improved DeepLabV3+ model is proposed, which incorporates several key enhancements. Firstly, the encoder part of the method utilizes the lightweight network MobileNetV3 as the backbone extraction network for DeepLabV3+. Secondly, the decoder part adopts the lightweight universal upsampling operator CARAFE for upsampling. Lastly, to address any potential extraction errors, morphological algorithms are applied to optimize the extraction results. Additionally, a dedicated railway track segmentation dataset is created to train and evaluate the proposed method. The experimental results demonstrate that the model achieves impressive performance on the railway track segmentation dataset and DeepGlobe dataset. The MIoU scores are 88.93% and 84.72%, with Recall values of 89.02% and 86.96%. Moreover, the overall accuracy stands at 97.69% and 94.84%. The algorithm's operation time is about 5% lower in comparison to the original network. Furthermore, the morphological algorithm effectively eliminates errors like holes and spots. These findings indicate the model's accuracy, efficiency, and the enhancement brought by the morphological algorithm in error elimination.

In this study, we had investigated the use of high-pressure homogenization (HPH) as a novel pretreatment method for the extraction of sodium alginate (SA) from Laminaria japonica. Our results demonstrated that under optimal condition of 100 MPa HPH pressure, 4 cycles, pH 6.0, and 0.5% ethylene diaminetetra acetic acid tetrasodium salt (EDTA) concentration (w/v) for 3.0 hours, the extraction yield of HPH reached 34%, which was higher than that achieved by previous methods such as complex enzyme hydrolysis (CE), ultrasonic-assisted extraction (UAE), and complex enzyme-ultrasonic combined method (CE-UC). To further characterize the extracted SA, we conducted a comprehensive analysis using SEM, FTIR, MRS, NMR, XRD, TGA, and T-AOC assay. Our findings revealed the following: 1) HPH treatment significantly disrupted the structure of L. japonica cells and reduced their crystallinity to 76.27%, the lowest among all pretreatment samples; 2) the extracted SA had a greater tendency to form elastic gels; and 3) the antioxidant activity of HPH-extracted SA reached 0.02942 mgVceq∙mg-1, which was the highest among all tested methods. Based on these results, we concluded that HPH extraction not only increased the yield of SA but also enhanced its antioxidant activity.

The focus of this study was to evaluate the effectiveness of incorporation of phenolic compounds from blueberry juice into pear slices using a combination of ohmic heating (OH) and vacuum impregnation (VI), followed by air- or freeze-drying. The results showed that OH is a valuable technique to increase the content of bioactive compounds and antioxidant capacity of blueberry juice. The optimal OH treatment is heating the juice at 50 °C for 20 min under an electric field of 13 V/cm. Furthermore, the combination of VI and OH showed the efficiency of enriching pear slices with bioactive compounds from blueberry juice. The best treatment is to immerse the slices for 90 min at 50 °C and an electric field of 7.8 V/cm. The presence of anthocyanin pigments from blueberry juice affects the color parameters of pear slices by increasing the a* parameter and decreasing the b* and L* parameters. However, both freeze-drying and air-drying (at temperatures of 40, 50, and 60 °C) negatively affected the phenolic content and antioxidant capacity. Notably, air-drying at 60 °C highest levels of phenolic compounds and antioxidant potential for both impregnated and non-impregnated pear slices among the drying processes applied.

With the proliferation and development of social media platforms, social media data has become an important source for acquiring spatio-temporal information on various urban events. Providing accurate spatio-temporal information for events contributes to enhancing the capabilities of urban management and emergency response. However, existing research on mining spatio-temporal information of events often focuses solely on textual content, neglecting data from other modalities such as images and videos. Therefore, this study proposes an innovative spatio-temporal information extraction method for multi-modal social media data (MIST-SMMD), which extracts the spatio-temporal information of events from multi-modal data on Weibo at coarse and fine-grained hierarchical levels, serving as a beneficial supplement to existing urban event monitoring methods. This paper takes the "July 20th Zhengzhou Heavy Rainfall" incident as an example, to evaluate and analyze the effectiveness of the proposed method. The results indicate that in the coarse-grained spatial information extraction using only textual data, our method achieves a Spatial Precision of 87.54% within a 60m range, and reaches 100% Spatial Precision for ranges beyond 200m. For fine-grained spatial information extraction, the introduction of other modal data such as images and videos results in a significant improvement in Spatial Error. These results demonstrate the ability of the MIST-SMMD method to extract spatio-temporal information from urban events at both coarse and fine levels, and confirms the significant advantages of multi-modal data in enhancing the precision of spatial information extraction.

Covid-19 is a lung disease caused by a Coronavirus family virus. Due to its extraordinary prevalence and death rates, it has spread quickly to every country in the world. Thus, achieving peaks and outlines and curing different types of relapses is extremely important. Given the worldwide prevalence of Coronavirus and the participation of physicians in all countries, Information has been gathered regarding the properties of the virus, its diverse types, and the means of analyzing it. Numerous approaches have been used to identify this evolving virus. It is generally considered the most accurate and acceptable method of examining the patient's lungs and chest through a CT scan. As part of the feature extraction process, a method known as fractional Fourier transform (FrFT) has been applied as one of the time-frequency domain transformations. The proposed method was applied to a database consisting of 2481 CT images. Following the transformation of all images into equal sizes and the removal of non-lung areas, multiple combination windows are used to reduce the number of features extracted from the images. In this paper, the results obtained for KNN and SVM classification have been obtained with accuracy values of 99.84% and 99.90%, respectively.

Phytochemicals are gaining popularity due to their antioxidant effects and potential protection against inflammation, cardiovascular disease, and certain types of cancer. The retention of these phytochemicals during extraction must be maximized. This research focused on extracting bioactive compounds from Psidium guajava Linn leaves using solvent extraction (SE), microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE) with distilled water (DW) or 60% (v/v) ethanol/water (ET). Phytochemical screening demonstrated that all of the screening showed positive results in all extraction methods, except glycoside. There were no significant (p&gt;0.05) differences in total phenolic (TPC) and flavonoid content (TFC) during MAE, SE, and UAE in case of ET. However, SE shows better (p&lt;0.05) extraction of TPC and TFC than UAE and MAE in case of DW. ET shows better (p&lt;0.05) extraction of TPC and TFC than DW. Antioxidant analysis shows the same trend though both DPPH and FRAP values were higher in MAE and SE for ET and DW, respectively. MAE/ET showed the highest inhibitory activity and dose-dependent response using SW480 cell via MTT assay. HPLC and TLC analysis reveal the fingerprint of morin, might function as an anticancer agent. In conclusion, MAE/ET is the most efficient among the extraction techniques in terms of anticancer activity.

The wheat aleurone layer is, according to millers, the main bran fraction. It is a source of nutritionally valuable compounds, such as dietary fibres, proteins, minerals and vitamins, that may exhibit health benefits. Despite these advantages, the aleurone layer is scarce on the market, probably due to issues related to its extraction. Many processes exist with some patents, but a choice must be made between the quality and quantity of the resulting product. Nonetheless, its potential has been studied mainly in bread and pasta. While the nutritional benefits of aleurone-rich flour addition to bread agree, opposite results have been obtained concerning its effects on end-product characteristics (namely loaf volume and sensory characteristics), thus ensuing different acceptability responses from consumers. However, the observed negative effects of aleurone-rich flour on bread dough could be reduced by subjecting it to pre- or post-extracting treatments meant to either reduce the particle size of the aleurone’s fibres or to change the conformation of its components.

Hexane is a solvent used extensively in the food industry for the extraction of various products such as vegetable oils, fats, flavours, fragrances, colour additives or other bioactive ingredients. As it is classified as a "processing aid", it does not have to be declared on the label under current legislation. Therefore, although traces of hexane may be found in final products, especially in processed products, its presence is not known to consumers. However, hexane, and in particular the n-hexane isomer, has been shown to be neurotoxic to humans and has even been listed as a cause of occupational diseases in several European countries since the 1970s. In order to support the European strategy for a toxic-free environment (and toxic-free food), it seemed important to collect scientific information on this substance by reviewing the available literature. This review contains valuable information on the nature and origin of the solvent hexane, its applications in the food industry, its toxicological evaluation and possible alternatives for the extraction of natural products. Numerous publications have investigated the toxicity of hexane, and several studies have demonstrated the presence of its toxic metabolite 2,5-hexanedione (2,5-HD) in the urine of the general, non-occupationally exposed population. Surprisingly, a tolerable daily intake (TDI) has apparently never been established by any food safety authority. Since hexane residues are undoubtedly found in various foods, it seems more than necessary to clearly assess the risks associated with this hidden exposure. A clear indication on food packaging and better information on the toxicity of hexane could encourage industry to switch towards one of the numerous other alternative extraction methods already developed.

Biorefining by enzymatic hydrolysis (EH) of lignocellulosic waste material due to low costs and affordability has received enormous interest amongst scientists as a potential strategy suitable for the production of bioactive ingredients and chemicals. In the present study, a sustainable and eco-friendly approach to the extraction of bound ferulic acid (FA) has been demonstrated using a single-step EH by a mixture of lignocellulose-degrading enzymes. For comparative purposes of the efficiency of EH, an online SFE-SFC-MS extraction and analysis approach was applied. The experimental results demonstrated up to 369.3 mg 100 g−1 FA released from rye bran after 48 h EH with Viscozyme L. The EH of wheat and oat bran with Viscoferm for 48 h resulted in 255.1 and 33.5 mg 100 g−1 of FA, respectively. The extraction of FA from bran matrix using the SFE-CO2-EtOH delivered up to 464.3 mg 100 g−1 of FA, though the extractability varied depending on the parameters used. The 10-fold and 30-fold scale-up experiments confirmed the applicability of EH as a bioprocessing method valid for industrial-scale. The highest yield of FA in both scale-up experiments was obtained from rye bran after 48 h of EH with Viscozyme L. In purified extracts, the absence of xylose, arabinose, and glucose as final degradation products of lignocellulose was proven by a HPLC-RID system. Up to 94.0% purity of FA was achieved by SPE using the polymeric reversed-phase Strata X column and 50% EtOH as eluent.

A major problem in the post-inversion geophysical interpretation is the extraction of geological information from inverted physical property models, which do not necessarily represent all underlying geological features. No matter how accurate the inversions are, each inverted physical property model is sensitive to limited aspects of subsurface geology and is insensitive to other geological features that are otherwise detectable with complementary physical property models. Therefore, specific parts of the geological model can be reconstructed from different physical property models. To show how this reconstruction works, we simulated a complex geological system that comprises an original layered earth model that has passed several geological deformations and alteration overprints. Linear combination of complex geological features comprised three physical property distributions: Electrical resistivity, induced polarization chargeability, and magnetic susceptibility models. This study proposes a multivariate feature extraction approach to extract information about the underlying geological features comprising the bulk physical properties. We evaluated our method in numerical simulations and compared three feature extraction algorithms to see the tolerance of each method to the geological artifacts and noises. We show that the fast-independent component analysis (fast-ICA) algorithm by negentropy maximization is a robust method in the geological feature extraction that can handle the added unknown geological noises. The post-inversion physical properties are also used to reconstruct the underlying geological sources. We show that the sharpness of the inverted images is an important constraint on the feature extraction process. Our method successfully separates geological features in multiple 3D physical property models. This methodology is reproducible for any number of lithologies and physical property combinations and can recover the latent geological features, including the background geological patterns from overprints of chemical alteration.

Existing methods for building extraction from remotely sensed images strongly rely on aerial or satellite-based images with very high resolution, which are usually limited by spatiotemporally accessibility and cost. In contrast, relatively low-resolution images have better spatial and temporal availability but cannot directly contribute to fine- and/or high-resolution building extraction. In this paper, based on image super-resolution and segmentation techniques, we propose a two-stage framework (SRBuildingSeg) for achieving super-resolution (SR) building extraction using relatively low-resolution remotely sensed images. SRBuildingSeg can fully utilize inherent information from the given low-resolution images to achieve high-resolution building extraction. In contrast to the existing building extraction methods, we first utilize an internal pairs generation module (IPG) to obtain SR training datasets from the given low-resolution images and an edge-aware super-resolution module (EASR) to improve the perceptional features, following the dual-encoder building segmentation module (DES). Both qualitative and quantitative experimental results demonstrate that our proposed approach is capable of achieving high-resolution (e.g. 0.5 m) building extraction results at 2×, 4× and 8× SR. Our approach outperforms 8 other methods with respect to the extraction result of mean Intersection over Union (mIoU) values by a ratio of 9.38%, 8.20% and 7.89% with SR ratio factors of 2, 4, and 8, respectively. The results indicate that the edges and borders reconstructed in super-resolved images serve a pivotal role in subsequent building extraction and reveal the potential of the proposed approach to achieve super-resolution building extraction. Our code is available at https://github.com/xian1234/SRBuildSeg.

Atlantic salmon (Salmo Salar) is one of the fish species that rich in omega-3 fatty acids. Consumption of omega-3 fatty acids can lower down the risk of cardiovascular disease and coronary heart disease. The extraction of omega-3 fish oil from Atlantic salmon by using hexane and isopropanol was conducted in this research. Response Surface Methodology (RSM) was used to study the impact of parameters which were temperature (50-90°C), centrifuge speed (1000-3000rpm) and solvent ratio of hexane to isopropanol (0.5-1.5) to the percentage of oil yield. The results obtained shows that 15.23%± 0.61 of oil yield from Atlantic salmon under an optimum condition of 70°C, 3000 rpm and solvent ratio of hexane to isopropanol of 1.5. The acid value, peroxide value and p-anisidine value of the fish oil obtained were 7.48 mg KOH/g, 1.94 meq/kg and 5.56 respectively which were all within the acceptable limit which stipulated by Global Organization for EPA and DHA (GOED) and Food and Agricultural Organization of the United Nations (FAO). The FTIR analysis proved the presence of alkane and carboxylic acid in the fish oil. Furthermore, GC-MS analysis showed that the fish oil contains higher monounsaturated fatty acids (MUFA) contents followed by polyunsaturated fatty acids (PUFA) and 4.5525% of total omega-3 fatty acids.