Charcot–Marie–Tooth disease (CMT) and associated neuropathies constitute the most predominant genetically transmitted neuromuscular conditions; however, effective pharmacological treatments remain elusive. The extensive genetic heterogeneity of CMT, which impacts the peripheral nerves and results in a lifelong disability, presents a significant barrier to the development of comprehensive treatments. An estimated 100 loci within the human genome are linked to various forms of CMT and its related inherited neuropathies. This review delves into prospective therapeutic strategies used for the most frequently encountered CMT variants, namely CMT1A, CMT1B, CMTX1, and CMT2A. Compounds such as PXT3003, which are currently under clinical and preclinical investigation, and a broad array of therapeutic agents and their corresponding mechanisms have been discussed in this review. Furthermore, the progress in established gene therapy techniques, including gene replacement via viral vectors, exon skipping using antisense oligonucleotides, splicing modification, and gene knockdown, has been appraised. Each of these gene therapies has the potential for substantial advancements in future research.

MicroRNAs (miRNAs) regulate plant growth and development and their responses to biotic and abiotic stresses. Although extensive studies show that miR159 family members regulate leaf and flower development in Arabidopsis thaliana, the roles of miRNAs in soybean (Glycine max) are poorly understood. Here, we identified six MIR159 genes in soybean, MIR159aMIR159f, and investigate their expression patterns in plants under low-phosphorus (low-P), NaCl, or abscisic acid (ABA) treatments. In soybean leaves, MIR159e and MIR159f expression was induced by low-P treatment, while in roots, MIR159b, MIR159c, MIR159e, and MIR159f expression was upregulated. In flowers, low-P led to upregulation of MIR159a, MIR159b, MIR159c, and MIR159f, but downregulation of MIR159d and MIR159e. In soybean nodules, MIR159b was upregulated but MIR159a, MIR159c, and MIR159d was downregulated under P deficiency. NaCl treatment induced MIR159a, MIR159b, MIR159c, and MIR159e expression in leaves, and MIR159aMIR159f expression in roots. ABA treatment upregulated MIR159a, MIR159b, and MIR159c but downregulated MIR159d, MIR159e, and MIR159f in leaves. These results suggest that miR159 family members function in plant abiotic stress responses. Moreover, total P content in leaves was significantly lower in plants overexpressing MIR159e than in the wild type, suggesting that miR159e may regulate P absorption and transport in soybean.

Diabetes is a chronic condition that worsens living conditions and causes significant problems, particularly in the vascular system. Many different treatment options are used to prevent these negative effects of diabetes. The most important of these is changing living conditions and exercising regularly.This study aimed todetermining the impacts of a 6-week anaerobic exercise protocol on the blood glucose levels and Glut4 gene expression in the muscle tissues of streptozocin (STZ)-induced diabetic rats. A total of 45 rats were separate control, sedentary, and exercise groups (n=15 each). The STZ used to induce diabetes in rats was applied once with a single intraperitoneal injection. No diabetes was created in the control group, and no exercise was performed, whereas in the sedentary group, diabetes was induced, and no exercise was applied. It was determined that the Glut4 gene expression in the muscle tissue of the exercise group was importantly increased when compared with the sedentary diabetes group.Glut4 gene is an important gene involved in blood glucose regulation and anaerobic exercise significantly increased the expression level of this gene in our study.

MicroRNAs are tissue-specifically expressed short RNAs that serve post-transcriptional gene reg-ulation. A specific microRNA can bind to mRNAs of different genes and thereby suppress their protein production. In the context of the complex phenotype of fibromyalgia, we used the Axiom miRNA Target Site Genotyping Array to search genome-wide for DNA variations in microRNA genes, their regulatory regions and in the 3'UTR of protein-coding genes. To identify dis-ease-relevant DNA polymorphisms, a cohort of 176 female fibromyalgia patients was studied in comparison to a cohort of 162 healthy women. The association between 48.329 markers and fibromyalgia was investigated using logistic regression adjusted for population stratification. 29 markers had p-values < 1 × 10-3 and the strongest asso-ciation was observed for rs758459 (p-value of 0.0001), located in the Neurogenin 1 gene, targeted by hsa-miR-130a-3p. Furthermore, we identified a gene locus (rs2295963) predicted to disrupt binding of hsa-miR-1-3p. Both microRNAs were previously reported to be differentially expressed in fi-bromyalgia patients. Despite its limited statistical power, this study reports two microRNA-related polymorphisms which may play a functional role in the pathogenesis of fibromyalgia. For a better understanding of the disease pattern, further functional analyses on the biological significance of microRNAs and microRNA-related polymorphisms are required.

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.

Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, gene nomenclature authorities coordinate the assignment of approved gene names that can be readily propagated across species. Theofanopoulou et al. (Theofanopoulou et al. 2021) propose a new nomenclature for the genes encoding oxytocin and arginine vasopressin and their receptors. Rather than changing to a different nomenclature system, we propose minor updates to the current approved nomenclature of these vertebrate genes to better reflect their evolutionary history. We call on authors, journal editors and reviewers to help support communication and indexing of gene-related publications by working with existing gene nomenclature committees and ensuring that standardized gene nomenclature is routinely used.

Background. Mitochondrial dysfunction has been identified as a pathophysiological hallmark of disease onset and progression in patients with Parkinsonian disorders. Besides the overall emergence of gene therapies in treating these patients, this highly relevant molecular concept has not yet been defined as a target for gene therapeutic approaches. Methods. This narrative review will discuss the experimental evidence suggesting mitochondrial dysfunction as a viable treatment target in patients with monogenic and idiopathic Parkinson’s disease. In addition, we will focus on general treatment strategies and crucial challenges which need to be overcome. Results. Our current understanding of mitochondrial biology in parkinsonian disorders opens up the avenue for viable treatment strategies in Parkinsonian disorders. Insights can be obtained from primary mitochondrial diseases. However, substantial knowledge gaps and unique challenges of mitochondria-targeted gene therapies need to be addressed to provide innovative treatments in the future. Conclusions. Mitochondria-targeted gene therapies are a potential strategy to improve an important primary disease mechanism in Parkinsonian disorders. However, further studies are needed to address the unique design challenges for mitochondria-targeted gene therapies.

Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve a SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.

Nuclear protein of testis (NUT), a protein product of the NUTM1 gene (located on the long arm of chromosome 15) with highly restricted physiologic expression in post-meiotic spermatids, is the oncogenic driver of a group of emerging neoplasms when fused with genes involved in transcription regulation. Although initially identified in a group of lethal midline carcinomas in which NUT forms fusion proteins with bromodomain proteins, NUTM1-rearrangement has since been identified in tumors at non-midline locations, with non-bromodomain partners and with varied morphology. The histologic features of these tumors have also expanded to include sarcoma, skin adnexal tumors, and hematologic malignancies that harbor various fusion partners and are associated with markedly different clinical courses varying from benign to malignant. Most of these tumors have nondescript primitive morphology and therefore should be routinely considered in any undifferentiated neoplasm. The diagnosis is facilitated by the immunohistochemical use of the monoclonal C52 antibody, fluorescence in situ hybridization (FISH), and, recently, RNA-Sequencing. The pathogenesis is believed to be altered expression of oncogenes or tumor suppressor genes by NUT-mediated genome-wide histone modification. NUTM1-rearranged neoplasms respond poorly to classical chemotherapy and radiation therapy. Targeted therapies such as bromodomain and extraterminal domain inhibitor (BETi) therapy are being developed. This current review provides an update of NUTM1-rearranged neoplasms, focusing on the correlation between basic sciences and clinical aspects.

For developmental processes we know most of the gene networks controlling specific cell responses. We still have to determine how these networks cooperate and how signals become integrated. The JNK pathway is one of the key elements modulating cellular responses during development. Yet, we still know little on how the core components of the pathway interact with additional regulators or how this network modulates cellular responses in the whole organism in homeostasis or during tissue morphogenesis. We have performed a promoter analysis searching for potential regulatory sequences of puc and identified different specific enhancers directing gene expression in different tissues and at different developmental times. Remarkably, some of these domains respond to the JNK activity, but not all. Altogether, these analyses show that puc expression regulation is very complex and that JNK activities participate in non-previously known processes during the development of Drosophila.

Excessive alcohol consumption is one of the significant causes of morbidity and mortality worldwide. Alcohol is oxidized to toxic and carcinogenic acetaldehyde by alcohol dehydrogenase (ADH) and further oxidized to a non-toxic acetate by aldehyde dehydrogenase (ALDH). Emerging evidence shows that Lactobacillus and Bifidobacterium species encode alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH) mediate alcohol and acetaldehyde metabolism, respectively. This study involves supplementation of Lactobacillus and Bifidobacterium probiotic mixture in humans and assessed their effects on alcohol and acetaldehyde metabolism. Here, twenty-seven wild types (ALDH2*1/*1) and the same number ofheterozygotes (ALDH2*2/*1) were recruited for the study. The enrolled participants were randomly divided into either the probiotic (Duolac ProAP4) or the placebo group. Each group received a probiotic or placebo capsule for 15 days with subsequent crossover. Primary outcomes were measurement of alcohol and acetaldehyde in the blood after the alcohol intake. Blood levels of alcohol and acetaldehyde in the ALDH2 heterozygote group were significantly downregulated in the probiotic-supplemented group with no changes in hangover score symptoms than the placebo group. No clinically significant changes were observed in safety parameters. These results suggest that probiotic has a potential to downregulate the alcohol and acetaldehyde concentrations, and their effects depend on the presence or absence of polymorphism on the ALDH2 gene.

Entamoeba histolytica, like other Organismes, is characterized by diversity and heterogeneity in its genetic content, which is one of the most important reasons for survival, and the increase in susceptibility to infection.Non-condensation of chromosomes during the process of cell division and the ambiguity of the chromosomal ploidy makes predicting the exact chromosomal number difficult. Genes distributed across 14 chromosomes as well as many extra-chromosome elements. Most Genes composed of one axon only, with Introns in 25% of Genes. This genome is characterized by the presence of Polymorphic internal repeat regions, and several gene families, one of these large families encoding Transmembrane kinas, Cysteine protease (CP), SREHP protein, and others.

In the present study, fish were exposed to sub-lethal doses of CuONPs (68.92 ± 3.49 nm) (10, 20, and 50 mg/L) for a long exposure period (25 days). Compared to the control group (0.0 mg/L CuONPs), a significant dose-dependent elevation in blood urea and creatinine values, serum alanine transaminase, aspartate transaminase, and alkaline phosphatase enzyme activities were evident in CuONPs-exposed groups (P &lt; 0.05). Fish exposure to 50 mg/L CuONPs significantly upregulated the transcription of pro-inflammatory cytokines (tumor necrosis factor-alpha, interleukin-1beta, interleukin 12, and interleukin 8), heat shock protein 70, apoptosis-related gene (caspase 3), and oxidative stress-related (superoxide dismutase, catalase, and glutathione peroxidase) genes in liver and gills of the exposed fish in comparison with those in the control group (P &lt; 0.05). Moreover, varying histopathological injuries were noticed in the hepatopancreatic tissues, posterior kidneys, and gills of fish groups correlated to the examined exposure dose of CuONPs. In summary, our results provide new insights and helpful information for better understanding the mechanisms of CuONPs toxicity in Nile tilapia at hematological, molecular levels, and tissue levels.

The study presents an updated overview of the 14 non-endemic threatened Crop Wild Relatives (CWR) in Italy: Aegilops biuncialis, Ae. uniaristata, Ae. ventricosa, Asparagus pastorianus, Beta macrocarpa, Brassica insularis, B. montana, Crambe hispanica subsp. hispanica, C. tataria subsp. tataria, Ipomoea sagittata, Lathyrus amphicarpos, L. palustris, Vicia cusnae and V. serinica. Geographical distribution, ecology (with plant communities and habitat 92/43/EEC aspects), genetics (focused on gene pools), property, and in situ and ex situ conservation were analyzed. In addition, with the aim of their protection and valorization, specific actions are recommended.

This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria and to determine the proportion estimates of the important beta-lactamase resistance genes in Nigeria. Sixty-three (63) articles were included in this review based on the eligibility criteria. All the beta-lactamases reported were detected from the Gram-negative bacteria, most especially from Enterobacteriaceae (n=53). Thirty-six different beta-lactamase genes have been reported from Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum, and carbapenemase beta-lactamase resistance genes. Eight (8) genes (bla_DHA, bla_CTXM-1, bla_CTXM-14, bla_GES-1, bla_VEB-1, bla_OXA-1, bla_OXA-2, and bla_TEM-1) were shared between animals and humans, 5 genes (bla_SHV-1, bla_SHV-2, bla_SHV-11, bla_SHV-12, and bla_NDM-1) were common to both humans and environment while none of the genes was unique to both animals and environment. Four genes including bla_CMY, bla_TEM-1, bla_AmpC, and internationally pandemic bla_CTXM-15 gene were unique to animals, humans, and the environment. No carbapenemase gene was reported from animals yet. The pooled proportion estimate of ESBL genes in Nigeria was 31% (95% CI: 26-36%, P<0.0001), while the estimate of bla_CTXM-15 gene in Nigeria was 46% (95% CI: 36-57%, P<0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11-52%, P<0.001), while the estimate for carbapenemases was 8% (95% CI: 5-12%, P<0.001). This study has provided information on the beta-lactamases distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. Given the growing evidence of gut microbiota being involved in psychiatric (including neurodevelopmental) disorders, we aimed to identify differences in gut microbiota composition between participants with ADHD and controls and to investigate the role of the microbiota in inattention and hyperactivity/impulsivity. Fecal samples were collected from 107 participants (NADHD=42; Ncontrols=50; NsubthreholdADHD=15; range age: 13-29 years). The relative quantification of bacterial taxa was done using 16S ribosomal RNA gene amplicon sequencing. Beta-diversity revealed significant differences in bacterial composition between participants with ADHD and healthy controls, which was also significant for inattention, but showing a trend in case of hyperactivity/impulsivity only. Ten genera showed nominal differences (P < 0.05) between both groups, of which seven genera were tested for their association with ADHD symptom scores (adjusting for age, sex, body mass index, time delay between feces collection and symptoms assessment, medication use and family relatedness). Our results show that variation of a genus from the Ruminococcaceae family (Ruminococcaceae_UCG_004) is associated (after multiple testing correction) with inattention symptoms, and suggest a role of gut microbiota in ADHD pathophysiology.

1) Background: CFH and HTRA1 genes are traditional markers of increased risk of AMD across populations. Recent findings suggest that additional genes, for instance, in the dystrophin-associated protein complex might be promising markers for AMD. 2) Methods: Here, we performed a case-control study to assess the effect of SGCD single nucleotide polymorphisms (SNPs), a member of this protein family, on AMD diagnosis and phenotype. We performed a case-control study of 134 cases with 134 unpaired controls. Cases were 60 years or older (CARMS grade 4-5, as assessed by experienced ophthalmologists following the AAO guidelines), without other retinal disease or history of vitreous-retinal surgery. Controls were outpatients aged 60 years or older, with no drusen or RPE changes on fundus exam and negative family history of AMD. We examined SNPs in the SGCD gene: rs931798, rs140617, rs140616, and rs970476 by sequencing and RT-PCR. Genotyping quality check and univariate analyses were performed with PLINK v.1.9. Furthermore, logistic regression models were done in SAS v.9.4 and haplotype configurations in R v.3.3.1. 3) Results: After adjusting for clinical covariates, the G/A genotype of the SGCD gene (rs931798) significantly increases the odds of being diagnosed with AMD in 81% (1.81, 95%CI 1.06-3.14, p=0.031), especially the geographic atrophy phenotype (1.82, 95%CI 1.03-3.21, p=0.038) compared to the G/G homozygous. Moreover, the GATT haplotype in this gene (rs931798, rs140617, rs140616, and rs970476) is associated with lower odds of AMD (Adjusted OR 0.13, 95%CI 0.02-0.91, p=0.041). 4) Conclusions: SGCD is a promising gene for AMD research. Further corroboration in other populations is warranted.

Background: Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer with poor outcomes. The molecular basis of TNBC remains poorly understood. The objective of this study was to explore the relationship between obesity and TNBC in premenopausal and postmenopausal Caucasian women using whole genome transcription profiling. Methods: We compared gene expression levels of tumor samples drawn from normal weight, overweight and obese in pre and postmenopausal women diagnosed with TNBC. We performed hierarchical clustering to assess similarity in patterns of gene expression profiles, and conducted network and pathway analysis to identify molecular networks and biological pathways. Results: We discovered gene signatures distinguishing normal weight from obese, normal weight from overweight and overweight from obese individuals in both premenopausal and postmenopausal women. The analysis revealed molecular networks and biological pathways dysregulated in response to obesity. Among the discovered pathways included the unfolded protein response, endoplasmatic reticulum stress, B cell receptor and the autophagy signaling pathways in obese premenopausal women and the integrin, axonal guidance, ERK/MAPK and Glutathione biosynthesis signaling pathways obese postmenopausal women. Conclusions: The results suggest that both overweight and obesity are associated with TNBC, highlighting the need for conformation of these results in independent studies.

The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to pIgR of multiple teleost species belonging to five perciform sub-orders, including 11 Antarctic and one non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in less cold periantarctic sea. Antarctic pIgR genes displayed particularly long in-trons marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold adapted species pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.

Humans are evolutionary-driven to adult mating and conceive social expectations on the quality of their affiliations. The genetic susceptibility to adverse environments in critical periods can alter close relationships. The current research investigates how the promoter region of the Serotonin Transporter Gene (5-HTTLPR) and perceived caregiving behavior in childhood could influence the social expectations on close adult relationships. For this purpose, 5-HTTLPR data was collected from the buccal mucosa of 65 Italian individuals (33 males). The participants filled a) the Parental Bonding Instrument (PBI) to provide the levels of care and overprotection from mother and father, and b) the Experience in Close Relationships-Revised (ECR-R) to report the social expectations on the intimate relationship assessed in terms of anxiety and avoidance from the partner. An interaction effect between 5-HTTLPR and PBI dimensions on the ECR-R scores was hypothesized. Results confirmed that the interplay between the genetic groups and history of maternal overprotection predicted avoidance experienced in romantic relationships in adulthood. Moreover, both adult anxiety and avoidance felt in an intimate relationship were found to covary as a function of maternal overprotection. The present work proposes further evidence of the genetic and parental mechanisms regulating social expectations involved in close relationships.

Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

In this work, a novel approach is presented for the multivariate prediction of hydrological variables, employing a specialized type of recurrent neural network (RNN) known as the long-term memory network (LSTM).The central objective is to develop a flood prediction model using data collected from two hydrological stations situated along the Atrato River in the Choc´o Department, Colombia. The interconnected variables of water level, water flow, and water precipitation are analyzed in this model to enhance flood prediction accuracy. The LSTM model, integrated into an RNN structure, is designed to capture the complex dynamics and cross-correlations inherent in these hydrological variables. Validation involves a comparison with linear and nonlinear Nonlinear AutoRegressive with eXogenous input (NARX) models, considering factors such as estimation error and computational time. Additionally, the study conducts further analysis for water level prediction under two scenarios: utilizing only outflow and inflow measurements or predicting outflow alongside measuring inflow, with the objective of utilizing the proposed approach as a flood early warning system. † This article is a revised and expanded version of a paper entitled Multivariable NARX based Neural Networks Models for Short-term Water Level Forecasting, which was presented at International Conference on Time Series and Forecasting (ITISE-2023), Gran Canaria, Spain, 12th-14th July, 2023.

In today's context of rising sea levels and subsiding land topography, coastal flooding is a major concern for coastal areas, both nationally, regionally, and internationally. A detailed understanding of these two phenomena is a prerequisite for effective coastal flood management. The main objective of the present study is to contribute to the understanding of the impact of subsidence and sea-level rise on coastal flooding in Saint-Louis, and in particular the Langue de Barbarie, by producing a vulnerability map of submerged surfaces. To this end, the Synthetic Aperture Radar (SAR) interferometry technique is used to process a time series of Sentinel-1 images and estimate land subsidence in the Saint-Louis and Langue de Barbarie area. Interferometric SAR (InSAR) measurements are merged with RCP 2.6 sea-level rise scenarios to identify predicted flooded areas and provide a flood vulnerability map. At the Langue de Barbarie, topographic subsidence is estimated at between -6.4 and -0.4mm/year. In this study, we show that local land subsidence may increase vulnerability to flooding caused by sea-level rise based on 2100 projections. This may represent an increase in the flood zone in the study area. Based on the RCP 2.6 scenario and the subsidence rates obtained, a significant part of the St. Louis coastline and city would be subject to coastal and fluvial flooding for the years 2040 and 2100. For these dates, 29 to and 36 Km2 of the studied area would be occupied by water. Given this situation, research in Saint-Louis needs to focus on adaptation scenarios to coastal risks, to protect coastal communities and safeguard the city's historical heritage.

Measuring and predicting Carbon Emission (CE) is important to enabling the main culprit of various urgent environmental issues including global warming. However, prior studies did not fully incorporate the impact of micro-level urban streetscapes, which might lead to biased prediction of urban CE. To fill the gap, we developed an effective framework to predict residential CE in urban areas from widely existing and publicly available street-view images (SVI) using machine learning. First, we used a semantic segmentation algorithm to classify more than 30 streetscape elements from SVI images to describe the built environment whose features might affect residential and transportation CE. Second, based on the streetscapes quantified, we trained a 10-fold cross-validation method with various machine learning models to predict the CE at the 1KM grid level using CE data from the PlanetData. We found first, built environment features such as sidewalks, roads, fences, buildings, and walls are significantly correlated with the residential CE. Second, the presence of buildings and subtle streetscape features (e.g., walls, fences) indicates higher-density residential areas which are related to more residential CE. Third, vegetation (e.g., trees and grass) are reversely related to residential CE. Our findings shed light on the feasibility of using a single and open data source (i.e., the SVI) to effectively model neighborhood-level CE for regions across diverse urban forms. Our framework is useful for urban planners to inform new town development and urban regeneration towards the low CE goals.

Large-scale crowd phenomena are complex to model because the behaviour of pedestrians needs to be described at both strategic, tactical, and operational levels and is impacted by the density of the crowd. Microscopic models manage to mimic the dynamics at low densities, whereas mesoscopic models achieve better performances in dense situations. This paper proposes and evaluates a novel agent-based architecture to enable agents to dynamically change their operational model based on local density. The ability to combine microscopic and mesoscopic models for multi-scale simulation is studied through a use case of pedestrians at the Festival of Lights, Lyon, France. Pedestrian outflow data is extracted from video recordings of exiting crowds at the festival. The hybrid model is calibrated and validated using a genetic algorithm that optimizes the match between simulated and observed outflow data. Additionally, a local sensitivity analysis is then conducted to identify the most sensitive parameters in the model. Finally, the performance of the hybrid model is compared to different models in terms of density map and computation time. The results demonstrate that the hybrid model has the capacity to effectively simulate pedestrians across varied density scenarios while optimizing computational performance compared to other models.

Infrastructure and urban network operators, city users and industrialists are faced with complex issues to ensure the sustainability of the service, maintain, operate and develop their urban sys-tems, while integrating environmental, economic and societal impacts and being resilient to un-expected geopolitical and climatic upheavals. Urban Digital Twins (UDTs), i.e., digital twins for smart cities and territories are considered as promising tools that can enable all stakeholders to collaborate across disciplinary silos and foster digital transformation in urban and territorial pro-jects to ensure sustainability, resilience and increased inventiveness. However, a widely acknowledged challenge to address in the application of UDTs is the lack of interoperability. One significant barrier is the difficulty that stakeholders have in understanding the level of complexity hidden behind this challenge, and thus the adoption of an adequate interoperability technique. This paper proposes a conceptual framework, which is unique for understanding the various lev-els of interoperability required in deploying and using the full potentials of UDTs. We show how such a high-level modeling approach supports the symbolic manipulation of UDTs interoperabil-ity notions and requirements, and thus eases the design of appropriate solutions for large-scale in-teroperable UDTs.

The Internet of Things (also known as IoT), a revolution, has enhanced the relevance of mobile employees' job efficiency in mobile crowd sensing (MCS). Incentives based on reputation for mobile workers (MW) play an important role in increasing service utilization, motivating mobile employees, and developing confidence in the service. The cell phone is the most exploited entity in mobile crowd-sensing MCS and cloud computing. In the underlying investigation, we observed that they had not evaluated the complexity level of a task, resulting in a strong reputation for executing multiple basic tasks. A person who completes a tough task may have a lower reputation score. Complexity levels of tasks (CLT) were developed for reputation evaluation on a crowd-sensing network, which would be utilized to evaluate the MW reputation. We offered simple and complex levels of challenges to assess reputation scores. Tasks receive incentives based on their reputation. By measuring reputation on (CLT) complexity level of task, this research will help the system to Maintain the reputation of the mobile worker so that entities of the system get the maximum benefit out of it, by hiring well-reputed mobile workers and MW receive an incentive on it. Furthermore, we conduct a comparative analysis between our scheme and various machine learning algorithms to identify the algorithm that best performs in evaluating task complexity. Considering both the simple and complex reputation scores, the comparison suggests that after analyzing the data, it is clear that the CLT (proposed) scheme and the Linear regression scheme not only outperformed the Neural Network scheme in terms of Complex Reputation Scores but also in terms of Simple Reputation Scores. We also apply statistical tests, such as p-tests and t-tests, to determine the significance of the results obtained from different algorithms. Considering MW 308, MW 345, and MW 1045's efforts and abilities, the MCS system may offer incentives and awards to further motivate and consider their continuing contributions. This reputation-based incentivization technique not only encourages strong competition among mobile workers, but also makes sure the delivery of high-quality services inside the MCS system.

A millimeter-wave microstrip leaky-wave antenna array based on the substrate-integrated waveguide (SIW) and the complementary split-ring resonator (CSRR) is proposed in this paper. The slow wave characteristics of the SIW are enhanced by etching two rows of symmetrical CSRR-type slots on the surface of the SIW layer. The magnetic coupling between the CSRR-SIW layer and equally spaced circular patches array on the upper layer realizes the radiation of electromagnetic energy. In the 23~30 GHz (relative bandwidth 26.4%) operating frequency band, the horizontal polarization radiation beam scanning from -62° to -2° is realized, with a peak gain of 9.6~11.7 dBi, and the cross-polarization ratio is more than 43.8 dB.

Sea level rise (SLR) is a critical consequence of climate change, posing significant threats to coastal regions worldwide. Accurate and efficient assessment of potential inundation areas is crucial for effective coastal planning and adaptation strategies. This study aims to explore the utility of free and open source software for geospatial (FOSS4G) tools for mapping SLR inundation, providing cost-effective solutions that are accessible to researchers and policymakers. We employed a combination of geospatial data, including high-resolution elevation models, tidal data, and projected SLR scenarios. Utilizing widely available FOSS4G tools like QGIS, GDAL/OGR and GRASS GIS we developed an integrated workflow to map inundation extents using a passive bathtub approach for various SLR scenarios. Our findings demonstrate that FOSS4G tools offer reliable and accessible means to map SLR inundation, empowering stakeholders to assess coastal vulnerabilities and devise sustainable adaptation measures. The open-source approach facilitates collaboration and reproducibility, fostering a comprehensive understanding of the potential impacts of SLR on coastal ecosystems and communities.

China is a traditional agricultural country, and the integration of rural industries has become an essential policy direction for the current strategy of agricultural modernization in China. In recent years, the agricultural industrial chains across various regions of China have consistently expanded and extended. The multifunctionality of agriculture is continuously unearthed, and the principal entities managing agriculture have become increasingly diversified and have grown significantly. New industries and forms in agriculture emerge incessantly. Accurately and profoundly understanding the inherent features of the integration of industries in rural China, establishing a scientific and rational measurement index system in line with the current status and development goals of rural China, and employing appropriate measurement methods to assess its development level and process, is instrumental in comprehending the level of integrated development in various regions. This aids in identifying challenges in the developmental process and proposing targeted developmental strategies. Hence, this paper, rooted in the integration of rural industries, cross-industry, industry extension, industry agglomeration, and industry penetration, sets up an measurement index system. Using provincial panel data from 2011 to 2020, the paper measures the level of integrated development in rural industries across China and its 31 provinces. Based on the measurement results, further techniques such as kernel density estimation and Gini coefficient decomposition have been used to analyze the spatial distribution characteristics and dynamic trends of the integrated development of rural industries in China. Research indicates that during the sample period, the overall level of integrated development in rural industries in various provinces in China has shown an upward trend. Development among the eastern, central, and western regions is highly uneven, but this disparity has been gradually narrowing in recent years. Furthermore, the levels of integrated development in different provinces exhibit significant spatial agglomeration effects. The development level of neighboring regions significantly impacts the province's development status. In the process of integrated development of rural industries in China, there's a trend where "it's easier to downgrade than to upgrade," with very few regions achieving leapfrog development.

Changes in sea level exhibit nonlinearity, nonstationarity, and multivariable characteristics, making traditional time series forecasting methods less effective in producing satisfactory results. To enhance the accuracy of the predictions of changes in sea level, this study introduced an improved VMD–EEMD–LSTM hybrid model. This model decomposes satellite altimetry data from near the Dutch coast using VMD, resulting in components of the Intrinsic Mode Function (IMF) with various frequencies and a residual sequence. EEMD further dissects the residual sequence obtained from VMD into second-order components. These IMFs decomposed by VMD and EEMD are utilized as features in the LSTM model for making predictions, culminating in the final forecasted results. The experimental results demonstrated significant improvements in the predictive performance compared with the VMD–LSTM model. The RMSE (root mean square error) decreased by an average of 58.68%, the MAE (mean absolute error) reduced by an average of 59.96%, and the R2 (coefficient of determination) increased by an average of 49.85% compared with the VMD–LSTM model. In comparison with the EEMD–LSTM model, the RMSE decreased by an average of 26.95%, the MAE decreased by an average of 28.00%, and the R2 increased by an average of 6.53%. The VMD–EEMD–LSTM model exhibited significantly improved predictive performance.

The construction of 22 dams on the Euphrates has reduced the flow of this river, changed the hydrology and destroyed the ecosystem. In order to understand the effect of extreme management on water, 4 coastal points from the Euphrates catchment area were selected to investigate the dynamics of the water level. Using the Cadmium method, the radius of each point was calculated to be 140 meters to study the NDWI index and satellite monitoring. 546 Landsat 8 OLI/TIRS satellite images from 2013 to 2022 were used. The analysis showed that the water level of the Euphrates in the fourth coordinate is directly related to the data of the first and third coordinates and the dynamics of the water level in the fourth coordinate is 3.6 to 4.2 percent of the first coordinate and another 5.2 to 5.9 percent is affected by the third coordinate. Is. Also, the data from August 2013 to 2022 were analyzed. The results showed that the correlation coefficients of the data related to the first coordinates are related to the third and fourth coordinates. It was proved that fluctuations in the first coordinate led to 27% change in the third coordinate in the months of August. Also, the changes in the first point caused 18-19.8% change in the dynamic level of water in the fourth point, and 22.5% of the changes in the water level in the fourth coordinate were affected by the third point.

The goal of this paper is the performance evaluation of a deep learning approach when deployed in fifth-generation (5G) millimeter wave (mmWave) multicellular networks. To this end, the optimum beamforming configuration is defined by two neural networks (NNs) that are properly trained, according to mean square error (MSE) minimization. The first network has as input the requested spectral efficiency (SE) per active sector, while the second network the corresponding energy efficiency (EE). Hence, channel and power variations can now be taken into consideration during adaptive beamforming. The performance of the proposed approach is evaluated with the help of a developed system level simulator via extensive Monte Carlo simulations. According to the presented results, machine learning (ML)-adaptive beamforming can significantly improve EE compared to the standard non-ML framework. Although this improvement comes at the cost of increased blocking probability (BP) and radiating elements (REs) for high data rate services, the corresponding increase ratios are significantly reduced compared to the EE improvement ratio. In particular, considering 21.6 Mbps per active user and ML adaptive beamforming, then EE can reach up to 5.3 Mbps/W, which is significantly improved compared to the non-ML case (0.9 Mbps/W). In this context, BP does not exceed 2.6%, which is slightly worse compared to 1.7% in the standard non-ML case. Moreover, approximately 20% additional REs are required, with respect to the non-ML framework.

In this paper an overview of waste materials in underground coal mines is presented, whereas waste materials can be of anthropogenic or geogenic origin. Complex interactions with mine water and waste materials take place, especially during mine water level rebound. Bearing in mind that under the increasing societal pressure most, if not all underground coal mines are going to be closed rather sooner than later, it is important to understand these interactions and to predict the composition and dynamics of mine water lever rebound in underground coal mines to prevent adverse effects to the environment, especially receiving waters and drinking water resources. The second part of this article focusses on the experiences gained in the Ruhr area, a closed underground coal mining region in Western Germany, where mine water rebound has been ongoing for decades. In this regard, the modelling program DMT-Boxmodel has been developed and applied to predict the hydrodynamics and hydrogeochemical development of the water rebound. As an example, simulation results of water rebound as well as solute and PCB transport in central province of Ruhr mining area are compared to the monitoring data, and predictions over 3 decades are given. The experiences gained in the mine water management in Ruhr area can be applied in mining areas worldwide.

Coastal areas situated at lower elevations are becoming more vulnerable to flooding as a result of the accelerating global sea level rise. As the sea level rises, so does the groundwater. Barriers designed to shield against marine flooding do not provide protection against flooding caused by rising groundwater. Despite the increasing threat of groundwater flooding, there is limited knowledge about the relationship between sea level rise and groundwater fluctuations. This hinders the ability to adequately consider sea level rise induced groundwater flooding in adaptation initiatives. This study aims to investigate how local groundwater in Juelsminde, Denmark, responds to changes in sea level and to evaluate the predictability of these changes using a machine learning model. The influence of the sea on the shallow groundwater level has been investigated using six groundwater loggers located between 45 and 210 m from the coast. An initial manual analysis of the data revealed a systematic delay in the rise of water levels from the coast to inland areas, with a delay of approximately 15–17 hours per 50 m of distance. Subsequently, a support vector regression model was used to predict groundwater levels 24 hours into the future. This study shows how the groundwater level in Juelsminde is affected by sea level fluctuations. Results suggest a need for increased emphasis on this topic.

Purpose To analyse diagnostic and therapeutic impact of molecular imaging TNM (miTNM) stage obtained with 18F-DCFPyL versus 18F-Fluorocholine in head to head comparison in biochemical recurrence (BCR) prostate cancer (PCa). Material and methods Patients with BCR PCa after radical treatment with previous 18F-Fluorocholine-PET/CT (negative or oligometastatic disease) were derived to 18F-DCFPyL-PET/CT. Patients were classified attending to: grade group, EAU classification, PSA, PSA doubling time (PSAdt) and PSA velocity (PSAvel). The overall detection rate (DR) and miTNM stage according to PROMISE criteria were assessed for both radiotracers and also correlation (Kappa). The influence of PSA and kinetics on both PET/CT (DR and miTNM) and predictive value of unfavourable kinetics on miTNM were determined. Cut-off PSA, PSAdt and PSAvel values able to predict PET/CT results were determined. Change in miTNM and treatment derived of 18F-DCFPyL information with respect to 18F-Fluorocholine was also evaluated. Results We studied 138 patients. 18F-DCFPyL showed a higher DR than 18F-Fluorocholine (64.5% vs 33.3%). 18F-DCFPyL and 18F-Fluorocholine detected T in 33.3% versus 19.6%, N in 27.5% versus 13.8%, M in 30.4% versus 8.7%. Both tracers DR showed significant associations with PSA and PSAvel. Significant association was only found between miTNM and PSA on 18F-Fluorocholine-PET/CT (p=0.033). For 18F-Fluorocholine and 18F-DCFPyL PET/CT a PSAdt cut-off of 4.09 and 5.59 months, respectively, were able to predict M stage. 18F-DCFPyL changed therapeutic management in 40/138 patients. Conclusion 18F-DCFPyL provides a higher DR and superior miTNM staging than 18F-Fluorocholine in restaging BCR, especially with high PSA and unfavourable PSA kinetics, showing a fair agreement to 18F-Fluorocholine.

Background: Low-level (LLLT) and high-intensity laser therapy (HILT) can be beneficial additions to knee osteoarthritis (KOA) rehabilitation exercises; however, it is still being determined which modality is more effective. Aim: To compare the effects of LLLT and HILT as adjuncts to rehabilitation exercise (LL+EX and HL+EX) on clinical outcomes in KOA. Methods: Thirty-four adults with mild to moderate KOA were randomly allocated to either LL+EX (n = 17) or HL+EX (n = 17) groups. All participants underwent their designated laser treatment combined with rehabilitation exercises weekly for twelve consecutive weeks. The Knee Injury and Osteoarthritis Outcome Score (KOOS), Numerical Pain Rating Scale (NPRS), active knee flexion, and Timed Up-and-Go test (TUG) were assessed at baseline and immediately post-intervention. Results: Post-intervention, both groups significantly improved their KOOS, NPRS, active knee flexion, and TUG scores compared to baseline (p &lt; 0.01). The mean difference of change in KOOS, NPRS, and active knee flexion scores for the HL+EX group surpassed the minimal clinically important difference threshold. In contrast, the LL+EX group only demonstrated clinical significance in NPRS scores. Conclusions: Incorporating HILT as an adjunct to usual KOA rehabilitation led to significantly higher improvements in pain, physical function, and knee-related disability compared to LLLT.

Continuous water resources monitoring is needed for sustainable urban water supply. Remote sensing techniques have proven useful for monitoring some water qualitative parameters with optical characteristics. The study area was the Marateca reservoir in central inland Portugal. The aims were the following: (1) to explore the water quality parameters at the monitoring points of the Marateca reservoir that may explain the event; (2) to validate optical water quality parameters with the monitoring points data; and (3) to model the reservoir water characteristics regarding its deepness, trophic state, and turbidity. The parameters total phosphorus, total nitrogen, and chlorophyll-a were used to compute a trophic level index. The Sentinel-2 imagery was used to compute spectral indices and bands image ratio; to obtain spectral signatures for the monitoring points, and to model water characteristics. The water parameters were above the recommended values at the reservoir entry point from the Ocreza River. The reservoir trophic level was Hypereutrophic and Eutrophic. The spectral signatures confirmed a Hypereutrophic pattern in the entry point. The Marateca reservoir’s water characteristics modeling forecasted problematic zones by contamination. The methodological approach developed can be easily applied to other reservoirs and is a key support tool for decision-makers.

Since the 1990s, mobile telecommunication networks have gradually become denser around the world. Nowadays, large parts of their backhaul network consist of commercial microwave links (CMLs). Since CML signals are attenuated by rainfall the exploitation of records of this attenua-tion for precipitation monitoring purposes is an innovative and inexpensive solution. Performance data from mobile operators' networks is crucial for the implementation of this technology. And, moreover for near real-time quantification. To meet this requirement, a real-time system for col-lecting and storing CML power levels from the cellular phone operator "Telecel Faso" in Burkina Faso was implemented. This new acquisition system, which uses the Simple Network Manage-ment Protocol (SNMP) can simultaneously record the transmitted and received power levels from all the CML to which it has access, with a time resolution of one minute. Installed at “Laboratoire des Matériaux et Environnement de l’Université Joseph KI-ZERBO (Burkina Faso)”, this acquisi-tion system is dynamic and has gradually grown from eight to more than 1000 radio links Tele-cel Faso CML links between 2019 and 2021. The system covers the capital Ouagadougou and the main cities of Burkina Faso (Bobo Dioulasso, Ouahigouya, Koudougou and Kaya) as well as the axes connecting Ouagadougou to these cities.

State transition in the multiple-levels system has the great potential applications in the quantum technology. In this article we employ a deterministic approach in complex space to analyze the dynamics of the 1s-2p electron transition in the hydrogen atom. The electron’s spin motion is embodied in the framework of quantum Hamilton mechanics that allows us to examine the transition dynamics more precisely. The transition is driven by an oscillating electric field in the z-direction. The electron’s transition process can be visualized by monitoring its motion in the complex space. The quantum potential and the total energy proposed in this paper provide new indices to observe the dynamic changes of electrons in the transition process.

A simple underwater noise model suitable for use with explosive severance of well conductors and piles during the decommissioning of oil and gas subsea structures is introduced and evaluated against data from five projects in the US. This study focuses on a novel model for the determination of sound exposure levels. The model has been developed to enable determination of impact areas for marine mammals and fish. Simulated received underwater sound exposure levels were significantly correlated with measurements for all scenarios. The maximum total error achieved between simulations and measurements was 2.6%, suggesting that predictions are accurate to within 3% of the average measurement. A low relative bias was observed in the simulations when compared to measured values, suggesting only a small systematic underestimate (≤ 0.5% of average measurement) for most severance operations and a small overestimate (0.14%) for open water blasts.

The incorporation of renewable energy into power systems poses serious challenges to the transmission and distribution power system operators (TSOs and DSOs). To fully leverage these resources there is a need for a new market design with improved coordination between TSOs and DSOs. In this paper we propose two coordination schemes between TSOs and DSOs: one centralised and another decentralised that facilitate the integration of distributed based generation; minimise operational cost; relieve congestion; and promote a sustainable system. To this end, we approximate the power equations with linearised equations so that the resulting optimal power flows (OPFs) in both the TSO and DSO become convex optimisation problems. In the resulting decentralised scheme, the TSO and DSO collaborate to optimally allocate all resources in the system. In particular, we propose an iterative bi-level optimisation technique where the upper level is the TSO that solves its own OPF and determines the locational marginal prices at substations. We demonstrate numerically that the algorithm converges to a near optimal solution. We study the interaction of TSOs and DSOs and the existence of any conflicting objectives with the centralised scheme. More specifically, we approximate the Pareto front of the multi-objective optimal power flow problem where the entire system, i.e., transmission and distribution systems, is modelled. The proposed ideas are illustrated through a five bus transmission system connected with distribution systems, represented by the IEEE 33 and 69 bus feeders.

Timely diagnosis of Alzheimer's diseases(AD) is crucial to obtain more practical treatments. In this paper, a novel approach Based on Multi-Level Fuzzy Neural Networks (MLFNN) for early detection of AD is proposed. The focus of study was on the problem of diagnosing AD and MCI patients from healthy people using MLFNN and selecting the best feature(s) and most compatible classification algorithm. In this way, we achieve an excellent performance using only a single feature i.e. MMSE score, by fitting the optimum algorithm to the best area using optimum possible feature(s) namely one feature for a real life problem. It can be said, the proposed method is a discovery that help patients and healthy people get rid of painful and time consuming experiments. Experiments shows the effectiveness of proposed method in current research for diagnosis of AD with one of the highest performance (accuracy rates of 96.6%), ever reported in the literature.

Green Infrastructures (GI) are considered key to reconcile ecological and social benefits by providing multiple functions. The concept is increasingly promoted and guidelines for its implementation have been developed in many countries and regions of the Western Hemisphere. However, for other parts of the world, especially for countries with less developed infrastructures, promotion, guidance for decision-making and manuals for GI are often lacking. But the state of infrastructure development and often unplanned character of settlements in the Global South differ and result in specific constraints as well as demands to GI that need to be addressed explicitly. This study presents a methodological approach to explicitly address the specific conditions and physical limitations to GI development in urban areas of the Global South. A four step methodology was developed to assess the implementation potential for retrofitted and multifunctional urban green infrastructure in public areas. An initial site analysis (1) and the definition of design criteria as well as general strategies (2) to achieve the different dimensions of multi-functionality are the basis to derive spatial typologies (3) for GI elements and finally the spatial suitability assessment for potential placements (4). An application of the methodology to a study area in the metropolitan region of San José, Costa Rica, shows exemplarily that the potential to improve the hydrological conditions (up to 34% of surface runoff reduction), ecological conditions (increase of green space by 2,2 %, creation of 1500 m length of roadside greenery and two new habitat types), and social conditions (2.200 m of road type upgrading) of multi-functionality of the site through Green Infrastructures. These assessment results of different multi-functionality dimension can serve as a guidance for GI promotion and implementation in urban areas of the Global South.

Many clustering approaches succeed in pattern segmentation in many applications. This unsupervised segmentation should be effective to reduce an expert labelling time: i.e, they must be able to detect the number of patterns and identify them in a sequence or map with the right cuts. Several direct and hierarchical clustering approaches are compared for this task. A divisive spectral clustering architecture with a no-cut criteria is also proposed. This new algorithm achieves promise segmentation of spatial UCI databases and marine time series compared to other approaches.

This article presents a method of segmenting images with gray levels that uses Onicescu's information energy calculated in the context of the neutrosophic theory. Starting from the information energy calculation for complete neutrosophic information, it is shown how to extend its calculation for incomplete and inconsistent neutrosophic information. The segmentation method is based on calculation of thresholds for separating the gray levels using the local maximum points of the Onicescu information energy.

High-Rise buildings with their particular features can affects on surrounding environment and makes new microclimates. In the windy conditions, the spaces that are between building blocks changes to passages and affects on the wind velocity, intensity and it’s other parameters.The importance of this effect is different in each level of building height. The Pedestrian-Level is the lowest and one of important areas. Markets, playgrounds and pedestrian access had located in this area and any unwanted microclimate changes like high velocity and turbulence in this level can makes discomfort and dangerous condition for residents. So this research tries to consider the pedestrian- level wind comfort in some High-Rise building complexes arrangement that had located in Tehran district 22 with Computational Fluid Dynamics (CFD) modeling and reaching to a suitable arrangement pattern. It had collected the required data through field study and librarian databases and then compared them with standard guidelines and analyzed them by comparative comparison method. As a result a linear arrangement that placed crossover to wind direction for providing wind comfort and preventing wind danger is been suggested in this region.

Sea level rise is one of the main factor of risk for the preservation of cultural heritage sites located along the coasts of the Mediterranean basin. Coastal retreat, erosion and storm surges are yet posing serious threats to archaeological and historical structures built along the coastal zones of this region. In order to assess the coastal changes by the end of 2100 under an expected sea level rise of about 1 m, a detailed determination of the current coastline position and the availability of high resolution DSM, is needed. This paper focuses on the use of very high-resolution UAV imagery for the generation of ultra-high resolution mapping of the coastal archaeological area of Pyrgi, near Rome (Italy). The processing of the UAV imagery resulted in the generation of a DSM and an orthophoto, with an accuracy of 1.94 cm/pixel. The integration of topographic data with two sea level rise projections in the IPCC AR5 2.6 and 8.5 climatic scenarios for this area of the Mediterranean, were used to map sea level rise scenarios for 2050 and 2100. The effects of the Vertical Land Motion (VLM) as estimated from two nearby continuous GPS stations located as much as close to the coastline, were included in the analysis. Relative sea level rise projections provide values at 0.30±0.15 cm by 2050 and 0.56±0.22 by 2100, for the IPCC AR5 8.5 scenarios and at 0.13±0.05 cm by 2050 and 0.17±0.22 by 2100, for the IPCC AR5 2.6 scenario. These values of rise will correspond to a potential beach loss between 12.6% and 23.5% in 2100 for RCP 2.6 and 8.5 scenarios, respectively, while during the highest tides the beach will be reduced up to 46.4%. With these sea level rise scenarios, Pyrgi with its nearby Etruscan temples and the medieval castle of Santa Severa will be soon exposed to high risk of marine flooding, especially during storm surges, thus requiring suitable adaptation strategies.

Along with density and mass variations of the oceans driven by global warming, Glacial Isostatic Adjustment (GIA) in response to the last deglaciation still contributes significantly to present-day sea-level change. Indeed, in order to reveal the impacts of climate change, long term observations at tide gauges and recent absolute altimetry data need to be decontaminated from the effects of GIA. This is now realized by means of global models constrained by the observed evolution of the paleo-shorelines since the Last Glacial Maximum, which account for the complex interactions between the solid Earth, the cryosphere and the oceans. In the recent literature, past and present-day effects of GIA are often expressed in terms of fingerprints describing the spatial variations of several geodetic quantities like crustal deformation, the harmonic components of the Earth's gravity field, relative and absolute sea level. However, since it is driven by the sluggish readjustment occurring within the viscous mantle, GIA shall taint the pattern of sea-level variability also during the forthcoming centuries. The shapes of the GIA fingerprints reflect inextricable deformational, gravitational, and rotational interactions occurring within the Earth system. Using up-to-date numerical modeling tools, our purpose is to revisit and to explore some of the physical and geometrical features of the fingerprints, their symmetries and intercorrelations, also illustrating how they stem from the fundamental equation that governs GIA, i.e., the Sea Level Equation.

Noise pollution is an environmental problem due to its effect on hearing and other related health issues. The elevated noise levels above standard limits cause hearing loss and other attendant problems. In Nigeria, viewing centers where football matches are watched via satellite are known as ‘Mini Stadium’. In this study, the noise pollution of a viewing center was assessed. To do this, five top teams each from the English Premier League (EPL), La Liga, Bundesliga, League 1, and Serie A were selected for the assessment. A sound level meter (GB: 2266204, made in China) was used for the monitoring. The range of noise levels in dBA showed as follow: EPL (56-108); La Liga (46-106); Bundesliga (54-102); Serie A (49-101); and Ligue 1 (54-101). The results when compared with the standard limits, it was observed that part of the results exceeded the limits, this means that the viewers and others within the viewing center may be prone to the hearing problem. It is recommended that acoustic insulators and hearing aids should be used to reduce the attendant problems associated with noise.

Fibrin rich of platelets (PRF^®) of Choukroun represents a new step in the therapeutic concept of platelet gel with a simplified processing and biochemical changes little artificial. A valid method of preparation of the PRF must effectively separate the plates by erythrocytes and concentrate without damaging or lysing the plates themselves. In this study the experimental design is to standardize the production of L-PRF in horse directing it to human production. Our hypothesis is that the L-PRF is easy to produce in the horse, without modifications of the human protocol, thus allowing a better standardization of the human protocol. A new device for the preparation and the standardization of L-PRF clots and membranes is the L-PRF Wound Box^®. The optical microscopy, most cell bodies were highlighted concentrated in the proximal portion of each membrane, the last 1/4 was observed at the center; the distal part had only residual traces of cell bodies. The L-PRF will form constantly when the phases described above are strictly adhered to. The success of the art L-PRF depends entirely on the speed of blood collection and transfer in centrifuge within a minute and by a temperature of centrifugation and compression is higher than 21°C (between 21 and 30°C). Our experiments on the horse will no doubt be able to improve our understanding on wound healing, in particularly in chronic skin lesions therapy.

Age-related macular degeneration (AMD) is an eye disease and the most common cause of vision loss in the Western World. In its advanced stage, AMD occurs in two clinically distinguished forms: dry and wet, but only wet AMD is treatable. However, the treatment based on repeated injections with vascular endothelial growth factor A (VEGFA) antagonists may at best stop the disease progression and prevent or delay vision loss but without an improvement of visual dysfunction. Moreover, it is a serious mental and financial burden for patients and may be linked with some complications. The recent first success of intravitreal gene therapy with ADVM-022, which transformed retinal cells to continuous production of aflibercept, a VEGF antagonist, after a single injection, has opened a revolutionary perspective in wet AMD treatment. Promising results obtained so far in other ongoing clinical trials support this perspective. In this narrative/hypothesis review, we present basic information on wet AMD pathogenesis and treatment, the idea of gene therapy in retinal diseases, update evidence on completed and ongoing clinical trials with gene therapy for wet AMD, and perspectives on the road to the clinic of “one and done” therapy for wet AMD to replace a lifetime of injections. Gene editing targeting the VEGFA gene is also presented as another gene therapy strategy to improve wet AMD management.

Modules composed of a resistance gene flanked by Xer site-specific recombination sites, the vast majority of which were found in Acinetobacter baumannii, are thought to behave as elements that facilitate horizontal dissemination. The A. baumannii xerC and xerD genes were cloned, and the recombinant clones used to complement the cognate Escherichia coli mutants. The complemented strains supported resolution of plasmid dimers, and, as is the case with E. coli and Klebsiella pneumoniae plasmids, the activity was enhanced when cells were growing in low osmolarity growth medium. Binding experiments showed that partially purified A. baumannii XerC and XerD proteins (XerC_Ab and XerD_Ab) bound synthetic Xer site-specific recombination sites, some of them with a nucleotide sequence deduced from existing A. baumannii plasmids. Incubation with suicide substrates resulted in covalent attachment of DNA to a recombinase, probably XerC_Ab, indicating that the first step in the recombination reaction took place. The results described show that XerC_Ab and XerD_Ab are functional proteins and support the hypothesis that they participate in horizontal dissemination of resistant genes among bacteria.

Sea level rise due to global warming is a continuing and, disappointingly, accelerating process, which has already affected and will further impact coastal lowlands and the social and economic activities in these areas. Delos Island, situated in the middle of the Cyclades in the Aegean Sea, was considered the most sacred of all islands in ancient Greek culture and a trading hub for the entire eastern Mediterranean. Uninhabited since the 7th century AD, and consistently the focus of research and touristic attention, the island is designated as an archaeological site and inscribed on the Unesco World Heritage List. Previous studies on the relative sea level (rsl) changes suggest a steadily rsl rise during the last 6,300 years, starting from a sea level at -4.80±0.20m in the Late Neolithic. The seafront of the ancient city of Delos is subject to the effects of the rsl rise, which have caused significant coastline retreat and exposure to the northerly winds and waves, whereas parts of the coastal lowland where the remains of the ancient city lie are inundated, forming extended wetlands. The future impacts of rsl rise on the seafront of ancient Delos are illustrated on very high-resolution digital surface models, evaluating both the flooding risk under different climatic projections, as provided by the IPCC AR6 report, and the ongoing land subsidence, as recorded by GNSS data. An rsl rise ranging from 87cm (SSP1-2.6 scenario) to 148cm (SSP5-8.5 scenario) is anticipated by 2150, requiring both resilience strategies and adaptation solutions as well as mitigation policies to cope with the effects of climate change.

The superconductivity of CaC6 as a function of pressure and of abundant Ca isotopes is revisited using DFT calculations on a 2c – double hexagonal superlattice. The introduction of superlattices is motivated by previous synchrotron absorption and Raman spectroscopy results on other superconductors that show evidence of superlattice vibrations at low (THz) frequencies. A 2c superlattice for CaC6 is illustrative of atomic orbital symmetry and periodicity, including bonding and antibonding s-orbital character implied by cosine modulated electronic bands. Inspection of the cosine band reveals that the cosine function has a small (meV) energy difference between bonding and antibonding regions relative to a midpoint non-bonding energy. Fermi surface nesting is apparent in an appropriately folded Fermi surface using a superlattice construct. Nesting relationships identify phonon vectors for conservation of energy and for phase coherency between coupled electrons at opposite sides of the Fermi surface. Detailed analysis of this Fermi surface nesting provides accurate estimates of the superconducting gaps for CaC6 with change in applied pressure. Recognition of superlattices within a rhombohedral or hexagonal representation provides consistent mechanistic insight on superconductivity and electron−phonon coupling in CaC6.

MicroRNAs (miRNAs), particularly miR-16 and miR-21, play a crucial role in mul-tiple myeloma (MM) pathogenesis by regulating gene expression. This study evalu-ated the prognostic significance of circulating miR-16 and miR-21 expression levels in 48 patients with MM at diagnosis treated with lenalidomide/dexamethasone (LD) compared with 15 healthy individuals (HI). All patients were treated with LD, 13 at first line and 35 at relapse, of whom 21 were tested twice at diagnosis and before LD initiation. The results revealed significantly lower levels of miR-16 and miR-21 in patients than in HIs, both at diagnosis and relapse, with decreased miR-16 levels at diagnosis, indicating improved overall survival (OS) (p value 0.024). Furthermore, miR-16 and miR-21 levels were associated with disease markers, while both corre-lated with the depth of response and mir-16 with sustained response to LD treatment. The ratios of both miR-16 and miR-21 expression levels (prior to LD treat-ment/diagnosis) below 2 predicted a shorter time to response (P = 0.027) and a longer time to next treatment (P = 0.042), respectively. These findings suggested a prognostic value for serum miR-16 and miR-21 levels in MM, as their expression levels corre-lated with disease variables and treatment outcomes.

Tidal notches, long regarded as reliable indicators of mean sea level, have been extensively studied along carbonate coasts in the central Mediterranean Sea. Previous studies revealed a correlation between the genesis of tidal notches and tidal range, lithology, cliff foot depth and wave energy. In the 2020 Geoswim campaign at Lampedusa, the southernmost island of the Pelagie archipelago (Italy), 'anomalous' tidal notches were identified. Unlike normal notches observed elsewhere, those in Lampedusa's southern bays exhibited a particular behavior —constantly deepening in the inner part of the bays, reaching a maximum depth of approximately 30 cm below sea level and narrowing inwards. Similar phenomena were previously observed by [1] near Marseille (France) and in Gozo Island (Malta). Time-lapse images, alongside measurements of morphometric param-eters, were collected during the survey. Despite the rapid morphological changes of the notches within the bay, the tectonic stability of the studied areas was confirmed by literature and data. Our hypothesis indicates that a combination of marine factors, influenced by local meteomarine conditions driven by the local morphology of the small bays exposed to southern quadrants con-tribute to the formation of these unique landforms. The latter manifest higher lowering erosion rates slightly below mean sea level in sheltered areas, challenging conventional notions about tidal notch formation.

One of the measures required by the European Green Deal to decarbonise the freight transport sector is the promotion of inland waterway transport (IWT), in particular intermodal transport in Europe. To facilitate intermodal transport on the Danube, we developed six new barge designs for the transport of 45' pallet-wide high-cube containers using a four-step approach. Our approach consisted of detailed desk research, followed by design and further analysis of the identified barge types, taking into account, for example, sight lines or stability. The container carrying capacity reaches up to 90 containers in three layers, which is double the capacity of existing standard barges on the Danube. Nevertheless, three-layer transport is hardly feasible in several cases, due to restrictions regarding sight lines and stability. We conclude that each loading condition must be evaluated separately to determine the best barge design option for each case. The study is limited by its geographical scope and the type of container used to develop the new barge designs. This could be a possible direction for further research on this topic: using other container types and/or extending the geographical scope.

The segmentation of abnormal regions is vital in smart manufacturing. However, the existing segmentation system for detecting sauce-packet leakage on intelligent sensors encounters an issue of imaging blurring caused by uneven illumination. This issue adversely affects segmentation performance, thereby impeding the rapid production of industrial assembly lines. To alleviate this issue, we propose the two-stage Illumination-aware Sauce-packet Leakage Segmentation (ISLS) method for intelligent sensors. The ISLS comprises two main stages: Illumination-aware region enhancement and leakage region segmentation. In the first stage, YOLO-Fastestv2 is employed to capture the Region of Interest (ROI), which reduces redundancy computations. Additionally, we propose an image enhancement to relieve the impact of uneven illumination, enhancing the texture details of ROI. In the second stage, we propose a novel feature extraction network. Specifically, we propose the Multi-scale Feature Fusion Module (MFFM) and the Sequential Self-Attention Mechanism (SSAM) to capture discriminative representations of leakage. The multi-level features are fused by MFFM with a small number of parameters, which capture leakage semantics at different scales. The SSAM realizes the enhancement of valid features and the suppression of invalid features by adaptive weighting of spatial and channel dimensions. Furthermore, we generated a self-built dataset of sauce-packets, including 606 images with various leakage areas. Comprehensive experiments demonstrate that our ISLS method shows better results than several state-of-the-art methods, with additional performance analyses deployed on intelligent sensors to affirm the effectiveness of our proposed method. Our code is available at https://github.com/LSJ5106/SauceDetect.

Development of the continental shelf has accelerated significantly as nations around the world seek to harness offshore renewable energy. Many areas marked for development align with submerged palaeolandscapes. Poorly understood and difficult to protect, these vulnerable, prehistoric landscapes provide specific challenges for heritage management. Indeed, there now appears to be a schism between what underwater cultural heritage policy intends and what it is achieving in practice. Shortcomings in international and national legislature ensures that large parts of the continental shelf, including areas under development, may have little or no legal protection.

Purposes: Engaging in regular physical activity has been consistently linked to improved physical health and academic performance. Despite its known benefits, there is a concerning trend of decreased physical activity among children globally. The study primarily aims to investigate the level of physical activity among junior high school students in Taiyuan and analyze the main affecting factors from a socio-ecological perspective. Methods: A cross-sectional study was conducted, involving 650 junior high school students from 7 schools in Taiyuan, and 648 valid questionnaires were collected. Physical activity levels were assessed using the Children’s Leisure Activities Study Survey Questionnaire. Factors influencing physical activity were evaluated through the Student Perceived Factors Affecting Physical Activity Questionnaire. Results: In this study, students from the 7th, 8th, and 9th grades participated in physical activities, averaging 214.5 minutes per week in moderate-intensity and 25 minutes in high-intensity activities, cumulatively averaging 280 minutes weekly. Notably, a significant disparity (p<0.05) was observed in the combined duration of moderate and high-intensity activities, with male students engaging more time compared to their female counterparts (307.500 vs 255.000 minutes). This variance extended across different grades, particularly evident in 8th graders who recorded the highest weekly high-intensity activity duration (31.000 minutes) and overall physical activity time (320.500 minutes), surpassing the 7th graders. Furthermore, an exploratory factor analysis of a 32-item questionnaire, designed to identify determinants of physical activity, revealed six principal components. These components were found to positively correlate with both moderate and high-intensity physical activities. Conclusion: This study emphasizes the necessity for educational institutions and community programmes to provide engaging physical activities, especially during weekends. It highlights the importance of tailoring physical education curricula to address gender and grade differences and investing in quality sports equipment and facilities by schools and local governments.

When it comes to financial transactions and counterfeit detection systems, banknote classification is crucial. In this paper, we propose an approach for the classification of Kazakhstan banknote images integrating Learning Vector Quantization (LVQ) with Statistical Texture Feature Extraction using the Gray Level Co-occurrence matrix (GLCM). Our methodology demonstrates effectiveness in accurately classifying banknote images, as evidenced by experimental results. The comprehensive testing scenarios show promising outcomes, with the combination of GLCM and Color Histogram under the LVQ algorithm achieving a high accuracy of 94.87 percent at distance 1 and 90°. These findings indicate the robustness and practical viability of the proposed method for authenticating banknotes.

In this paper, we present a groundbreaking methodology in the realm of aspect-level sentiment analysis, which capitalizes on the advanced capabilities of graph-based neural networks. Our approach, distinguished as the Aspect Correlation Graph Network (ACGN), represents a significant departure from conventional models. These traditional models often analyze aspects in isolation, failing to capture the intricate web of sentiment relationships that may exist within a single sentence. ACGN, however, is designed to address this gap by employing a sophisticated bidirectional attention mechanism, integrated with positional encoding. This unique combination not only enhances the model's ability to focus on relevant parts of the sentence but also aids in constructing detailed, aspect-focused representations. These representations are particularly crucial for understanding the nuanced interplay of sentiments associated with different aspects. Central to our model's architecture is the incorporation of a graph convolutional network. This network serves as a pivotal component in mapping and analyzing the complex network of sentiment correlations that can exist among various aspects within sentences. Through this integration, ACGN is able to unearth and interpret the subtle and often overlooked sentiment dynamics that traditional models might miss. Our comprehensive evaluations of the Aspect Correlation Graph Network, conducted using the SemEval 2014 datasets, have yielded promising results. These findings demonstrate a clear and significant advancement over the capabilities of existing models. Particularly, the results underscore the critical importance and utility of recognizing and understanding the connections between sentiments of different aspects in text analysis. This insight opens new avenues in the field of sentiment analysis, suggesting a broader application potential of ACGN in various contexts where understanding nuanced sentiment relationships is key. Overall, our study not only introduces a novel approach in aspect-level sentiment analysis but also sets a new standard for future research in this area. By highlighting the integral role of inter-aspect sentiment connections, ACGN paves the way for more sophisticated and accurate sentiment analysis tools, capable of handling the complexities of natural language with greater finesse and precision.

In this paper, we delve into the realm of aspect-level sentiment analysis, a sophisticated analytical task focused on pinpointing and interpreting the sentiment directed towards specific elements within a sentence. Traditional methods in this domain, primarily based on neural networks, have often overlooked the critical role of syntactic structures in sentences. To bridge this gap, we have developed the Syntax-Enhanced Sentiment Graph Network (SentiSyn). This pioneering model represents a significant step forward in aspect-level sentiment analysis, bringing to the forefront the utilization of word dependency relationships to enrich sentiment analysis. SentiSyn stands out by its innovative use of a dependency graph, a tool that meticulously maps out the intricate web of syntactic relationships surrounding a target aspect in a sentence. This approach allows SentiSyn to effectively capture and channel sentiment-related characteristics that are deeply rooted in the syntactic context of the aspect target. By doing so, SentiSyn unlocks a deeper understanding of sentiment dynamics in textual content, enabling a more nuanced and accurate sentiment analysis. Our comprehensive experimental evaluation of SentiSyn showcases its remarkable capabilities. When combined with advanced embedding techniques like GloVe and BERT, SentiSyn demonstrates a superior performance edge over several existing sentiment analysis methods. This performance leap is not just incremental; it represents a significant enhancement in the field of sentiment analysis, underscoring the importance of syntactic context in understanding sentiments. Furthermore, our analysis delves into how SentiSyn effectively leverages these embeddings to gain a more profound and contextually rich insight into sentiment dynamics. The results from our tests indicate that SentiSyn, with its unique approach to integrating syntactic structures and advanced embeddings, sets a new benchmark in aspect-level sentiment analysis, offering both enhanced accuracy and deeper sentiment understanding.

Background:This study evaluated the effect of low-level laser therapy on postoperative pain and wound healing in children undergoing primary molar extractions.Methods:40children,6-10years of age, systemically healthy, and had atraumatic extraction indications of bilateral primary molar teeth were included in the study. First session randomly selected tooth was extracted under local anesthesia. In the control group, only the clot formation on the socket was observed and photographed. Other group extraction's performed 2weeks later. The LLLT group treated with980nm wavelength Doctor Smile Wiser diode laser and photographed. Non-epithelialized surface measurements performed with the ImageJ program. Pain assessment was performed with Wong-Baker Pain Scale. Statistical analyzes were performed with SPSS software.Results: There was no statistically significant difference in Wong-Baker values(p&gt;0.05). The laser group had more '0' values on days 1 and7; same values as the control group were recorded on other days. In soft tissue healing 3rd day evaluations, non-epithelialized surface of laser socket was found to be smaller than control group, and measurement results were found to be statistically significant(p&lt;0.05). The other days' measurement results were not statistically significant(p&gt;0.05).Conclusions:Although LLLT not found to be very effective in reducing postoperative discomfort after extraction of primary molars, it provides better wound healing in extraction sockets.

Background: Depending on the phase of the menstrual cycle the athlete is in, some kinetic, physiological and fatigue variables will show differences. The aim of this study is to analyze whether there are changes in these variables over the course of the menstrual cycle. Methods: Eight regular female runners and triathletes performed a maximal treadmill test, as well as a submaximal test (6’ stages at 50%, 60% and 80% of maximal aerobic speed) in each of the phases of the menstrual cycle: bleeding phase (day 2.4 ± 0.7), follicular phase (day 10.4 ± 2.2) and luteal phase (day 21.8 ± 2.1). Running dynamics were measured (using RunScribe) at the end of each test, as were lactate concentration, heart rate and fatigue (evaluated on a scale of 0 to 5). Results: Higher shock (G) values were recorded in the bleeding phase and higher vertical spring stiffness (kN/m) in the follicular phase. The phase of the menstrual cycle had a significant effect on average and peak heart rate, which was significantly higher in the follicular phase. Conclusions: Higher vertical spring stiffness was observed in the follicular phase, as well as higher peak and average heart rate.

This study evaluates the agricultural carbon emission efficiency of Shandong Province from 2011 to 2020 using the DEA-SBM model. The nexus between endogenous and exogenous variables is estimated using the Tobit model. The findings reveal an overall increasing trend in agricultural carbon emissions, with significant variations in efficiency values among different cities, leading to a severe polarization. Spatial evaluation shows a high distribution trend in the central region and low in the eastern and western regions of Shandong Province. The empirical tests conducted for Shandong Province and its three regions indicate that urbanization plays a major role in sup-porting the growth of agricultural carbon emission efficiency, while the education level of the la-bor force has a suppressive impact. Economic development and crop cultivation structure, how-ever, have no significant influence. The impact of these variables varies across the eastern, central, and western regions. The proposed countermeasures include improving planting structure and reducing brain drain in the eastern region, strengthening agricultural and rural inputs and in-creasing the added value of agricultural products in the central region, and intensifying the link-age between urbanization and industrial layout in the western region to reduce agricultural car-bon emissions efficiency in Shandong Province.

Speech emotion recognition is a critical component for achieving natural human-robot interaction. The modulation-filtered cochleagram is a feature based on auditory modulation perception, which contains multi-dimensional spectral-temporal modulation representation. In this study, we propose an emotion recognition framework that utilizes a multi-level attention network to recognize emotions from the modulation-filtered cochleagram. The channel-level attention and spatial-level attention modules are used to capture emotional saliency maps of channel and spatial feature representations from the 3D convolution feature maps, respectively. Furthermore, the temporal-level attention module captures significant emotional regions from the concatenated feature sequence of the emotional saliency maps. Our experiments on the IEMOCAP dataset demonstrate that the modulation-filtered cochleagram significantly improves the prediction performance of categorical emotion compared to other evaluated features. Moreover, our emotion recognition framework achieves a better unweighted accuracy of 71% in categorical emotion recognition than several existing approaches in the experiments. In summary, our study demonstrates the effectiveness of the modulation-filtered cochleagram in speech emotion recognition, and our proposed multi-level attention framework provides a promising direction for future research in this field.

When the image quality is evaluated, the human visual system (HVS) infers the details in the image through its internal generative mechanism. In this process, the HVS integrates both local and global information of the image, utilizes contextual information to restore the original image information, and compares it with the distorted image information for image quality evaluation. Inspired by this mechanism, a no-reference image quality assessment method is proposed based on a multitask image restoration network. The multitask image restoration network generates a pseudo-reference image as the main task and produces structural similarity index measure map as an auxiliary task. By mutually promoting the two tasks, a higher quality pseudo-reference image is generated. In addition, when predicting the image quality score, both the quality restoration features and the difference features between the distorted and reference images are used, thereby fully utilizing the information from the pseudo-reference image. To enable the model to focus on both global and local features, a multi-scale feature fusion module is proposed. Experimental results demonstrate that the proposed method achieves excellent performance on both synthetically and authentically distorted databases.

The article is devoted to solving the problem of searching for universal explainable features that can remain explainable for a wide class of objects and phenomena and become an integral part of Explainable AI (XAI). The study is implemented on the example of an applied problem of early diagnostics of plant stress, using Thermal IR (TIR) and HSI, presented by 8 vegetation indices/channels. Each such index was presented by 5 statistical values. A Single-Layer-Perceptron classifier was used as the main instrument. TIR turned out to be the best of the indices in terms of efficiency in the field and sufficient to detect all 7 key days with 100% accuracy. Our study shows also that there are a number of indices, inluding NDVI, and usual color channels Red, Green, Blue, which are close to TIR possibilities in early plant stress detection with 100% accurasy or near, and can be used for wide class of plants and in different conditions their treatment. The stability of the stress classification in our study was maintained when the training set was reduced up to 10% of the dataset volume. The entropy-like feature of (max-min) for any indices/channels have determined as a leadersheep universal high-level explainable feature for the plant stress detection, which used in interaction with some of other statistical features.

Sexual vs asexual reproduction—unisexual vs bisexual populations—diploid vs polyploid biotypes—genetic vs environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. Two Carassius entities with completely different biological characteristics exist: one globally widespread and invasive Carassius gibelio, and the other C. carassius with decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance advantages of highly invasive and disadvantages of threatened species. For example, benefits of a wide-ranged colonization can lead toward extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Also, the review focuses on consequences of co-occurrence of native and non-native species and outlines future perspectives of Carassius research.

The orthodontic treatment brings numerous benefits and, in most cases, the benefits outweigh the possible disadvantages. Root resorption (RR) is a common adverse phenomenon associated with orthodontic treatment. This study evaluates the role of low-level laser emission / Photobiomodu-lation (LE/P) in quantitative measurements of root resorption (QRR). The application of LE/P was done after each orthodontic activation with 4 types of treatment intervention (TI) on the RR after fixed orthodontic treatment (FOT) of the upper arch with ectopic eye tooth/teeth [EET]. 32 Orthodontic patients scheduled for FOT were selected and assigned to the 4 groups. These were LE/P+Self ligating bracket (SLB), LE/P+Conventional bracket (CB), Non-Photobiomodulation (non-LE/P)+SLB, and non-LE/P+CB. Standard management stages of FOT were followed in the maxilla. Each patient received a single application of LE/P labially/buccally and palatally, a total of 5 different points during each activation or appointment. The main outcome measure was QRR in maxillary anteriors before and after FOT assessed via cone-beam computed tomography (CBCT) using 3D OnDemand software. Insignificant QRR was found between before and after FOT in SLB, CLB, and LE/P, non-LE/P groups (p > 0.05). QRR in the SLB vs CB and LE/P vs non-LE/P group was significantly different in 11, 13, and 23 (p < 0.05). QRR in the LE/P+SLB group (p < 0.05) was significantly different in 11, 13, and 23 than that in the other groups. The most severe QRR was found on the 13 (0.88 ± 0.28mm and 0.87±0.27mm) and 23 (1.19 ± 0.14 mm and 1.16±0.13mm) in the CB and non-LE/P group (p < 0.001). LE/P+SLB showed highly significant superior outcome (p < 0.001) in relation to non-LE/P+CB, the QRR of 23 were 0.813± 0.114mm and 1.156± 0.166mm respectively. Significantly higher amount of QRR found in EET patients after FOT treated with the CB, non-LE/P, and non-LE/P+CB system and warrants further investigation to explore potential specific causes.

A simple underwater noise model suitable for use with explosives in the decommissioning of oil and gas subsea structures is introduced and evaluated against data from five projects in the US. The performance of the model is compared to four existing models for open water blasts, and for the severance of well conductors and piles. Simulated received underwater sound pressure levels were significantly correlated with measurements for all scenarios. The maximum total error achieved between simulations and measurements was 3.5%, suggesting that predictions are accurate to within 4% of the average measurement. A low relative bias was observed in the simulations when compared to measured values, suggesting only a small systematic underestimate (≤ 1% of average measurement) for most severance operations and a small overestimate (1.34%) for open water blasts.

Understanding the processes that govern the transformation of the landscape through time is essential for exploring the evolution of a coastal area. Coastal landscapes are dynamic sites, with their evolution strongly linked with waves and sea-level variations. Geomorphological features in the coastal area, such as beachrock formations and dune fields, can function as indicators of the coastal landscape evolution through time. However, our knowledge of the chronological framework of coastal deposits on the Aegean coasts is limited. Optically stimulated luminescence dating techniques are deemed to be very promising indirect dating of the coastal sediments, especially when they are linked with archaeological evidence. The dating of the sediments from different sediment core depths, as they are determined by the method of luminosity, allows us to calculate the rate of sediment deposition over time. Additionally, the coastal evolution and stability were studied from 1945 until today, with the use of aerial photographs and satellite images. This paper presents the 6000 ka years evolution of a coastal landscape based on geomorphological, archaeological, and radio-chronological data. Based on the results, the early stages of the Ammoudara beach dune field appear to be formed ~9.0 – 9.6 ka BP, while the OSL ages from 6 m depth represented the timing of its stabilization (OSL ages ~5–6 ka). This indicates that the dune field appears to already have been formed long before the Bronze Age (5-10 ka BP) and became stabilized with only localized episodes of dune reactivation occurring, while high coastal erosion rates are found in modern times.

The supposition is that the usage of fibrin rich in leukocytes and platelets advanced (A-PRF) in ulcerative osteomyelitis of the diabetic foot allows rehabilitation from this critical illness. In this investigation, the focus was to normalize the use of PRF in patients with osteomyelitis not amputated, to use this second generation platelet concentrate as a regeneration enabler. The researchers submitted and utilized A-PRF membranes (1300 g × 8 min) in 7 patients (all diabetics) with osteomyelitis and cutaneous injury for 6 months. The membranes, in combination with the supernatant fluid produced by stress, have been integrated into the skin lesion down to the bone after surgical debridement. The advancement of the lesions after some period of time has been analyzed. All seven subjects had a Probe-to-Bone positive assay; MRI indicated a cortico-periosteal coagulation and/or foci of cortico-spongeous osteolysis contiguous to the lesion. Gram-positive bacterium were identified in our procedures in 52% of cases. Gram+ Cocci, for example, S. Aureus (15.6%), S. Hemolytic (12.1%), S. Viridans (7.1%), and Gram-negative Bacteria, for example, Pseudomonas (10.6%), Proteus (7.8%), Enterobacter (5.7%) are present. Candida Albicans is active in 2.8%. The blood count shows no relevant differences. To date, cutaneous lesions have cured in 6 of the seven subjects treated (one patient for more than five years) without any evidence of infection or recurrence. The results obtained on our subjects indicate that PRF membranes may be a therapeutic option in this problematic disease.

Green Stormwater Infrastructure (GSI), a sustainable engineering design approach for managing urban stormwater runoff, has long been recommended as an alternative to conventional conveyance-based stormwater management strategies to mitigate the adverse impact of sprawling urbanization. Hydrological and hydraulic simulations of small-scale GSI measures in densely urbanized micro watersheds require high-resolution spatial databases of urban land use, stormwater structures, and topography. This study presents a highly resolved Storm Water Management Model developed under considerable spatial data constraints. It evaluates the cumulative effect of the implementation of dispersed, retrofitted, small-scale GSI measures in a heavily urbanized micro watershed of Costa Rica. Our methodology includes a high-resolution digital elevation model based on Google Earth information, whose accuracy was sufficient to determine flow patterns and slopes, as well as to approximate the subsurface stormwater structures. The model produced satisfactory results in event-based calibration and validation, which ensured the reliability of the data collection procedure. Simulating the implementation of GSI shows that dispersed, retrofitted, small-scale measures could significantly reduce impermeable surface runoff (peak runoff reduction up to 40%) during frequent, less intense storm events and delay peak surface runoff 5-10 minutes. The presented approach can benefit stormwater practitioners and modelers conducting small scale hydrological simulation under spatial data constraint.

The conservation of coastal wetland ecosystems, like mangrove forests and salt marshes, represents a critical strategy for mitigating atmospheric emissions and climate change in the 21st century. Yet the existence of these environments is threatened by human-induced disturbances, namely deforestation and accelerated sea-level rise. Coastal systems maintain surface elevation in response to sea-level rise through a combination of physical and biological processes both above and below the ground surface. The quantification and relative contribution of belowground process controls (e.g., seasonal water content, organic matter decomposition) on surface elevation change is largely unexplored but crucial for informing coastal ecosystem sustainability. To address this knowledge deficit, we integrated measurements of surface elevation change of the live root zone (0.5 to 1 m depth) with geotechnical data from co-located sediment cores in the Sundarbans mangrove forest (SMF) of southwest Bangladesh. Core data reveal that the primary belowground controls on surface elevation change include seasonal fluctuations in pore-water content and the relative abundance of fine-grained sediments capable of volumetric expansion and contraction, supporting an elevation gain of ~2.42 ± 0.26 cm yr⁻¹. In contrast to many mangrove environments, the soils of the SMF contain little organic matter and are dominantly composed (>90%) of inorganic clastic sediments. The mineral-rich soil texture likely leads to less compaction-induced subsidence as compared to organic-rich substrates and facilitates surface equilibrium in response to sea level rise. Despite a relatively high soil bulk density, soil carbon (C) density of the SMF is very low owing to the dearth of preserved organic content. However, rates of C accumulation are balanced out by locally high accretion rates, rendering the SMF a greater sink of terrestrial C than the worldwide mangrove average. The findings of this study demonstrate that C accumulation in the SMF, and possibly other alluvial mangrove forests, is highly dependent on the continued delivery of sediment to the mangrove platform and associated settings.

An improved FSM method is used in geophysical and environmental corrections to enhance the final product of the along track Jason-2 SLA data and extend it near the Red Sea borders. In this study the ionospheric correction range, wet tropospheric correction range, sea state bias correction range and dry tropospheric correction range are enhanced and improved using FSM01, which helped to retrieve three more tracks (106, 170 and 234), earlier neglected by the distribution centers, and extend the tracks towards the coast. The FSM01 SLA is compared with Jason-2 SLA and AVISO SLA for the available 5 tracks, in which the FSM01 SLA show a good agreement and higher correlation with the Jason-2 SLA compared with that of AVISO, in addition to that it fills the gaps in the times series of all tracks. The new retrieved tracks also compared with those retrieved by AVISO, both data show similar variability, with FSM01 SLA show no gaps in the time series. The FSM01 SLA also extended towards the coast and show high correlation with the coastal tide measurements.

A new formulation for a proposed solution to the 3D Navier-Stokes Equations in cylindrical co-ordinates coupled to the continuity and level set convection equation is presented in terms of an additive solution of the three principle directions in the radial, azimuthal and z directions of flow and a connection between the level set function and composite velocity vector for the additive solution is shown. For the case of a vertical tube configuration with small inclination angle, results are obtained for the level set function defining the interface in both the radial and azimuthal directions. It is found that the curvature dependent part of the problem alone induces sinusoidal azimuthal interfacial waves wheras when the curvature together with the equation for the composite velocity is considered oscillating radial interfacial waves occur. The implications of two extremes indicate the importance of looking at the full equations including curvature.

The main objective of this paper is to find a close link between the adaptive level of significance, presented here, and the sample size. We, statisticians, know of the inconsistency, or paradox, in the current classical tests of significance that are based on p-value statistics that is compared to the canonical significance levels (10%, 5% and 1%): "Raise the sample to reject the null hypothesis" is the recommendation of some ill-advised scientists! This paper will show that it is possible to eliminate this problem of significance tests. The Bayesian Lindley's paradox – "increase the sample to accept the hypothesis" – also disappears. Obviously, we present here only the beginning of a possible prominent research. The intention is to extend its use to more complex applications such as survival analysis, reliability tests and other areas. The main tools used here are the Bayes Factor and the extended Neyman-Pearson Lemma.

(1) Background: Multiple alterations of cellular metabolism have been documented in experimental studies of autosomal dominant polycystic kidney disease (ADPKD) and are thought to contribute to its pathogenesis. (2) Methods: To elucidate the molecular pathways and transcriptional regulators associated with the metabolic changes of renal cysts in ADPKD, we compared global gene expression data from human PKD1 renal cysts, minimally cystic tissues (MCT) from the same patients, and healthy human kidney cortical tissue samples. (3) Results: We found PKD1 renal cysts displayed the Warburg effect with gene pathway changes favoring increased cellular glucose uptake and lactate production, instead of pyruvate oxidation. Additionally, mitochondrial energy metabolism was globally depressed, associated with downregulation of gene pathways related to fatty acid oxidation (FAO), branched-chain amino acid (BCAA) degradation, the Krebs cycle, and oxidative phosphorylation (OXPHOS) in renal cysts. Activation of mTORC1 and its two target proto-oncogenes, HIF-1α and MYC, was predicted to drive the expression of multiple genes involved in the observed metabolic reprogramming (e.g., GLUT3, HK1/HK2, ALDOA, ENO2, PKM, LDHA/LDHB, MCT4, PDHA1, PDK1/3, MPC1/2, CPT2, BCAT1, NAMPT); in-deed, their predicted expression patterns were confirmed by our data. Conversely, we found AMPK inhibition was predicted in renal cysts. AMPK inhibition was associated with decreased expression of PGC-1α, a transcriptional coactivator for transcription factors PPARα, ERRα, and ERRγ, all of which play a critical role in regulating oxidative metabolism and mitochondrial biogenesis. (4) Conclusions: These data provide a comprehensive map of metabolic pathway re-programming in ADPKD and highlight nodes of regulation that may serve as targets for therapeutic intervention

1) Background: carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic Gram-negative pathogen that has a significant role in healthcare-associated infections. Unlike several studies on the antibiotic-resistant epidemiology of A. baumanni, virulence molecular epidemiology was less studied. This study aimed to investigate CRAB virulence genes and their ability to form biofilms, and to correlate their biofilm formation ability with both; biofilm-encoding virulence genes and carbapenemase-encoding resistance genes. 2) Methods: 107 CRAB clinical isolates were collected from two hospitals in Jordan between 2018 and 2019 and were screened for virulence genes using PCR. In addition, biofilm formation ability was assessed using the microtiter plate method. 3) Results: the frequencies of the bap, OmpA, surA, PLD, paaE, basD, and traT virulence genes were 99.10%, 98.20%, 98.20%, 95.50%, 89.10%, 86.40%, and 8.20%, respectively. Overall, 86.4% of the tested isolates were biofilm formers with varying degrees; weak (28.2%), moderate (36.4%) and strong (21.8%). A significant relationship was found between the carbapenemase-encoding gene (OXA-23 gene) and biofilm production. 4) Conclusion: to the best of our knowledge, this is the first study in Jordan that inspected CRAB virulence genes and highlighted the importance of improving infection control measures to avoid CRAB outbreaks.

Originating in the Mediterranean, B. oleracea is grown all over the world and is highly valued for its nutritional value and variety in cooking. Its susceptibility to pests, diseases, and environmental stressors, however, poses significant challenges to sustaining consistent crop quality and productivity. The BASIC PENTACYSTEINE gene significantly impacts plant growth and responses to abiotic stresses. Nevertheless, little is known about its precise role and the underlying biological processes in B. oleracea. Eleven BPC genes in B. oleracea were identified by a thorough genome-wide investigation and categorized into three categories according to their structural traits and gene motifs. There were eight different chromosomes on which these BoBPCs were located. Comparative synteny analysis was used to reveal the evolutionary traits of potatoes, Arabidopsis, and B. oleracea. The BoBPC family genes in B. oleracea were found to have specific cis-elements linked to growth, stress responses, and hormone regulation when their promoter regions were studied. Cuticular wax synthesis expression revealed that all BoBZR1 genes, from wild to mutant, expressed at varied amounts in distinct types. Moreover, distinctive BoBPC gene expression patterns were found in the seven distinct tissues that were studied. Our thorough analysis shows that the BoBPC family is widely involved in B. oleracea developmental processes. The present findings provide an established theoretical basis for further exploration into the composition and roles of BoBPC in B. oleracea.

Bergamot flavonoids have been shown to prevent metabolic syndrome, non-alcoholic fatty liver disease (NAFLD) and stimulate autophagy in animal models and patients. To investigate further the mechanism of polyphenol-dependent effects, we performed RT2-PCR array analysis on 168 metabolism, transport and autophagy-related genes expressed in rat livers exposed for 14 weeks to different diets: standard, cafeteria (CAF) and CAF diet supplemented with 50 mg/kg of Bergamot Polyphenol Fraction (BPF). CAF diet caused a strong upregulation of the gluconeogenesis pathway (Gck, Pck2) and a moderate (>1.7 fold) induction of genes regulating lipogenesis (Srebf1, Pparg, Xbp1), lipid and cholesterol transport or lipolysis (Fabp3, Apoa1, Lpl) and inflammation (Il6). However, only one -oxidation gene (Cpt1a) and a few autophagy genes were modulated in the CAF group compared to controls. While most of these transcripts were significantly modulated by BPF, we observed a particularly potent effect on lipogenesis genes, like Acly, Acaca, Fasn and Scd1, which were suppressed far below the mRNA levels of control livers as confirmed by alternative primers-based RT2-PCR analysis and western blotting. These effects were accompanied by downregulation of pro-inflammatory cytokines (Il6, Tnfa, and Il10) and diabetes-related genes. Few autophagy (Map1Lc3a, Dapk) and no -oxidation gene expression changes were observed, suggesting minor transcriptional effects on autophagy. In conclusion, chronic BPF supplementation efficiently prevents NAFLD by modulating hepatic energy metabolism and inflammation gene expression programs, with no effect on -oxidation, but profound suppression of de-novo lipogenesis.

Human Epidermal Growth Factor Receptor 2(HER2) is a transmembrane glycoprotein receptor with intracellular tyrosine kinase activity. It is generally considered as a poor prognostic marker. Targeted therapies, such as small molecule tyrosine kinase inhibitors (TKIs), showed limited efficacy in HER2-mutant advanced Non-Small Cell Lung Cancer (NSCLC). In the 2023 NCCN guidelines for NSCLC, Antibody-Drug Conjugate(ADC) Trastuzumab emtansine (T-DM1) is recommended for the treatment of HER2-mutant Lung Cancer (LC). However, this medication is currently not approved in certain regions.So it is necessary to explore alternative treatment options for HER2-mutant NSCLC patients.In our study of a patient with HER2 exon 20ins Lung Adenocarcinoma who had previously failed multiple TKI treatments, we discovered that Sunvozertinib could stabilize the patient's condition, achieving a progression-free survival (PFS) of 87 days. This is a novel finding that may provide new treatment options for HER2 exon 20ins patients who have failed TKI therapy.

Abstract: There are a large number of cross-linked chemical bonds such as tight disulfide bonds, hydrogen bonds,and salt bonds in keratin, which makes it difficult to break the structural stability of the protein using conventional methods. The degradation of feather waste using keratinases produced by microorganisms has the advantage of being efficient and environmentally friendly. In this study, 23 strains capable of producing transparent circles were obtained via preliminary screening with skim milk as the sole carbon and nitrogen source, and 9 strains capable of degrading feathers were obtained via rescreening with feathers as the sole carbon and nitrogen source. Finally, through the determination of enzyme activity, the strain CY-A with a high ability to degrade feathers was obtained. The strain was identified as Bacillus tequilensis via morphological observation, physiological and biochemical identification, and 16 S rRNA molecular biology. The keratinase gene (bta) of Bacillus tequila was cloned, and its full-length gene sequence was 1110 bp, containing an open reading frame of 1089, encoding 369 amino acids (GeneBank accession number OR733336). The physicochemical properties, secondary structure, and tertiary structure of the recombinant protein were analyzed using bioinformatics tools such as ProtParm, SOPMA, MEGA, and SWISS-MODELS. It was found that the relative molecular mass was 37.953 kD and that the isoelectric point was 8.48. The protein was a hydrophilic protein. The keratinase bta gene was ligated to the expression vector pET28a(+) using T4 ligase, and the recombination expression plasmid pET28-bta was constructed and transformed into E. coli BL21(DE3) to obtain recombinant engineered bacteria. The expressed keratinase was purified using a Ni2+ affinity chromatography column to obtain recombinant bta keratinase bta with a molecular weight of 37.953 kD. The identification and characterization of this keratinase gene provides some theoretical basis for the further enhancement of keratinase activity by means of genetic engineering.

Background A diet rich in red meat, and poor in fruits and vegetables, can hinder the body's ability to detoxify, therefore, an alternative vegetarian diet maintained over a certain period, determines the elimination of excess toxins and accumulated residues, helping the body to regenerate and recharge energy. Following this simple rule, there are a multitude of benefits for our health. Significance of the autophagy process An even better regeneration of the body takes place during the black fast, in which senescent cells, (dead cells that no longer exercise any function, but instead produce inflammation in the body), are eliminated by autophagy, and in their place, the cells are stimulated stem. Aging can be associated with various pathological conditions if autophagy is not promoted by a healthy lifestyle. In elderly people, cells can show DNA mutations and accumulations of protein aggregates that impair the body's physiological processes. Several studies have shown that the activation of autophagy slows down the ageing process. Conclusions Aging, and its associated conditions of illness, are due to genomic instability caused by DNA damage, telomere shortening and epigenome changes that modulate gene expression.

Deeper understanding of biological processes, disease mechanisms, and prospective therapeutic targets can be attained by Gene Expression Network Analysis (GENA), which offers a potent framework for revealing the intricate regulatory mechanisms controlling gene expression. GENA is a computational method used to understand the intricate interactions and relationships between the genes in a biological system. It entails using network theory, statistical analysis, and gene expression data to pinpoint functional modules, regulatory linkages, and important genes or pathways involved in a particular biological process or illness. This chapter broadly outlines the principles and practice of GENA, to an novice reader and outlines a simple method of performing a GENA using online Rice gene expression datasets available in various websites.

Background: Eukaryotes whole-genome sequencing is crucial for species identification, gene detection and protein-annotation. Oxford Nanopore sequencing serves as an affordable and rapid platform for sequencing eukaryotes, however the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryotes genome completeness, gene detection and protein-annotation. Methods: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. Results: genome completeness was dependent on assembly method rather than read correction tool, however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. Conclusion: We show that three rounds of read correction significantly affects gene detection and protein-annotation which are dependent on assembly quality in preference to assembly completeness.

Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host and the possible outcomes of host-pathogen interaction.

Nitrogen (N) is an important mineral nutrient for plant growth, as well as a limiting factor for crop yield, and how to improve the utilization efficiency of N fertilizer by plants is currently a research hotspot. This article uses bioinformatics methods to identify and analyze members of the glutamine synthetase (GS) and glutamate synthase (GOGAT) gene families in pecan. A total of 6 GS genes and 4 GOGAT genes were identified, and their physicochemical properties, gene structures, and homologous evolutionary relationships were analyzed. Analysis of tissue-specific expression of GS and GOGAT genes based on transcriptome data from pecan. The enzyme activities of GS and GOGAT and the gene expression were quantitatively analyzed under different N form ratios in pecan. According to the results, the promoter cis-acting elements of GS and GOGAT genes can be roughly divided into three types: light-responsive elements, hormone-responsive elements, and stress-responsive elements. The results of homologous evolution showed that there was no tandem duplication event for the two gene families, and GS and GOGAT have undergone purification during the evolutionary process. CiGS2s and CiFd-GOGATs were expressed mainly in leaves, and CiNADH-GOGATs were expressed mainly in fruits. The qPCR analysis results showed that T4 treatment significantly increased the expression levels of CiGS and CiGOGAT genes in the leaves. The enzyme activities of GS and GOGAT in pecan were significantly increased under T3, T4, and T5 treatments. In summary, a higher proportion of ammonium nitrogen (NH4+) in the nutrient solution was profit to pecan NH4+ assimilation. This study determined the appropriate nitrogen ratio for pecan, promoting a theoretical basis for reducing environmental pollution caused by nitrogen fertilizer and improving the nitrogen utilization efficiency of pecan. In summary, both CiGSs and CiGOGATs exhibit tissue specificity, and an ammonium-nitrate mixture with a higher proportion of NH4+ is more favorable for NH4+ assimilation in pecan. This study provides a reference basis for further understanding the functions of CiGSs and CiGOGATs in pecan, and offers a theoretical foundation for improving N use efficiency in pecan.

The MLL1 gene located on chromosome 11q23, is crucial for histone lysine-specific methylation and is frequently implicated in various leukemia types. Despite prior in silico investigations into non-synonymous single nucleotide polymorphisms (nsSNPs) associated with leukemia in the MLL1 gene, there is a dearth of comprehensive studies evaluating their impact on the protein's structure, function, and post-translational modifications. Addressing this, our study screened 2049 nsSNPs from the dbSNP database, identifying 62 high-risk variants. A thorough domain analysis revealed that these nsSNPs are distributed across seven domains of the MLL1 protein, potentially affecting their functions. Our conservation analysis highlighted 31 nsSNPs as deleterious, suggesting their potential effects on protein stability and function. Furthermore, utilizing the MutPred2 tool, we identified mutations affecting metal-binding, protein loop structures, and post-translational modifications, which could alter the MLL1 protein's native functionality. Interaction network analysis underscored the role of MLL1 in hematopoietic cell development, implying that mutations may influence hematological malignancies. Additionally, a subset of non-coding SNPs was found to possess regulatory capabilities, potentially affecting gene expression and chromatin modification. Most significantly, using CScape and CScape-somatic tools, four nsSNPs were predicted to be oncogenic, with two classified as cancer drivers, underscoring their potential role in leukemia development. The oncogenic nsSNP, D2724G, located between the FY-rich N and FY-rich C domain of the MLL1 protein, has raised significant interest due to its potential impact on proteolytic cleavage. Predictive analyses, such as those by Mutpred2, suggest a loss of cleavage at D2724 caused by this mutation, potentially affecting the formation of essential MLL1 fragments, p320 and p180. These fragments play a crucial role in creating a stable multiprotein complex that localizes to a specific subnuclear region. Therefore, mutations like D2724G can potentially alter gene expression patterns, influencing cellular behavior and possibly fostering a cancer-prone environment. In conclusion, our research provides an in-depth assessment of the effects of nsSNPs in the MLL1 gene on leukemia, offering potential avenues for personalized treatment strategies, early detection, prognosis, and a better understanding of hematological malignancy genesis.

CXCL14 is one of the most evolutionarily conserved members of the chemokine family and is constitutionally expressed in multiple organs, suggesting that it is involved in the homeostasis maintenance of the system. CXCL14 is highly expressed in colon epithelial cells and shows obvious gene silencing in clinical colon cancer samples, suggesting that its silencing is related to the immune escape of cancer cells. In this paper, we analyzed the expression profiles of multiple human clinical colon cancer datasets and mouse colon cancer models to reveal the variation trend of CXCL14 expression during colitis, colon polyps, primary colon cancer, and liver metastases. The relationship between CXCL14 gene silencing and promoter hypermethylation was revealed through the colorectal carcinoma methylation database. The results suggest that CXCL14 is a tumor suppressor gene in colorectal carcinoma, which is activated first and then silenced during the process of tumor occurrence and deterioration. Promoter hypermethylation is the main cause of CXCL14 silencing. The methylation level of CXCL14 is correlated with the anatomic site of tumor occurrence and positively correlated with patient age, and associated with prognosis. Reversing the hypermethylation of CXCL14 may be an epigenetic therapy for colon cancer.

Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which N6-Methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as therapeutic approach. In this review, we overview the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.

Background: The COMT gene polymorphism is associated with neurological and psychiatric disorders and pain perception. This study aimed to determine the relationship between the COMT (catechol-O-methyltransferase) gene polymorphism, pain perception in parturients with inhaled nitrous oxide during labour, and anxiety as a personality trait. Methods: A total number of 181 woman who chose vaginal birth were enrolled in this study. To present the difference in pain perception, the parturients were divided into one group (n=80) that chose labour analgesia with inhaled nitrous oxide (50% nitrous oxide and 50% oxygen) and one group without analgesia. The blood samples were taken during the pregnancy as a part of routine pregnancy controls in the hospital. The COMT gene polymorphism was detected with the PCR technique. Pain perception of labouring women was self-evaluated two times according to the VAS (Visual Analogue Scale) and anxiety as a personality trait was determined with STAI-T (State Trait Anxiety Inventory). Pain perception as well as anxiety were compared according to COMT genotypes. Results: In the 181 pregnant women there were 40 women (22%) of wild homozygotes (GG) of COMT, 95 women (53%) of mutant heterozygotes (GA), and 46 women (25%) of mutant homozygote (AA). A negative association of pain perception with the GA (mutant heterozigote) polymorphism of the COMT gene versus the wild type (GG polymorphism) was observed. The GA polymorphism of the COMT gene was associated with 0.46 units lower pain perception compared to the wild type (GG). The anxiety trait score in group AA was lower than in groups GA and AA. The difference reached statistical significance only when comparing AA versus GA (P&gt;0.042). Analgesic efficacy of nitrous oxide was noticed in 22% of labouring women who reported moderate pain (VAS score 4-7). Conclusions: The COMT gene polymorphism was associated with pain perception and anxiety among labouring women. The COMT gene polymorphism GA was associated with negative pain perception among labouring women. Nitrous oxide showed statistical significance in anxiolytic efficacy during labour in women with mild anxiety as a personality trait. Anxiolytic efficacy of nitrous oxide has shown better efficacy in labouring women with the COMT gene polymorphism AA.

Buffalo are silent breeders, therefore detecting estrus is a serious challenge. There is a rising need for sensitive and precise biomarkers in this scenario. Recent research on miRNA has demon-strated the importance of these molecules as biomarkers. Though there have been miRNA studies in saliva during the estrous cycle, there have been few miRNA research in blood samples. The current study was designed to look at blood miRNAs during the oestrous cycle in heifers (n=5) to address the issue of silent estrus. On the day of estrus and diestrus, blood samples from 60 heifers were obtained and pooled into (n=5) separate samples. Ultrasonography and progesterone assay was performed to confirm estrus. Then, employing particular miRNA adapters, small RNA se-quencing of miRNA was performed using the Illumina Miseq 2500. The UEA sRNA bioinfor-matics workbench identified 94 substantially differently expressed miRNAs (p>0.05) from these data. In estrus, 63 miRNA were upregulated and 31 miRNA were downregulated. When fold change was increased to (log2foldchange >1; q value less than 0.05), 25 miRNAs were elevated during estrus. miR-497, miR-582, miR-10174, miR-23, miR-223, miR-1296 were upregulated, whereas miR-10167, 671, 1246,122 were downregulated. miR-497 is unusually elevated (log2 foldchange>5) when compared to another miRNA (log2 foldchange >5) miRNet 2.0, Cytoscape, and MIENTURNET network software found that miR-497 has more degree centrality, above 60; it is associated with more than 60 nodes, followed by miR-93

Cell identity is determined by chromatin structure and the profiles of gene expression, which are dependent on chromatin accessibility and DNA methylation of regions critical for gene expression, such as enhancers and promoters. These epigenetic modifications are required for mammalian development and are essential for the establishment and the maintenance of the cellular identity. DNA methylation was once thought to be a permanent repressive epigenetic mark, but systematic analysis in various genomic contexts reveals a more dynamic regulation than previously thought. In fact, both active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. To link methylation signatures of specific genes to their expression profiles, we have determined the methyl-CpG configurations of the promoters of five genes switched on and off during murine postnatal brain differentiation by bisulfite-targeted sequencing. We report here the structure of significant, dynamic and stable methyl-CpG profiles associated with silencing or activation of expression of genes during neural stem cell and brain postnatal differentiation. Strikingly, these methylation cores mark different mouse brain areas and cell types derived from the same areas during differentiation.

Chromatin structure plays a fundamental role in regulating gene expression, with histone modifiers shaping the structure of chromatin by adding or removing chemical changes to his-tone proteins. The p53 transcription factor controls gene expression, binds target genes, and regulates their activity. While p53 has been extensively investigated in the context of cancer research, its association with histone modifiers has received limited attention. This review ex-plores the interplay between histone modifiers and p53 in regulating gene expression. We discussed how histone modifications can influence how p53 binds to target genes and how this interplay can be disrupted in cancer cells. This study provides insights into the complex mechanisms underlying gene regulation and their implications for potential cancer therapy.

Recently, a database of human piRNAs has been created, which allows studying the binding of many piRNAs to mRNAs of genes involved in many diseases, including cancer. In the present work, we investigated what piRNAs can interact with candidate esophageal squamous cell carcinoma (ESCC) genes. The binding of 480 thousand piRNAs with mRNAs of 66 candidate ESCC genes was studied. Bioinformatic studies found that piRNAs bind only to the mRNAs of nine candidate genes: AURKA, BMP7, GCOM1, ERCC1, MTHFR, SASH1, SIX4, SULT1A1, and TP53. It has been shown that piRNAs can bind to mRNA by overlapping nucleotide sequences in limited 3'UTR and 5'UTR regions called clusters of binding sites (BSs). The existence of clusters of piRNA BSs significantly reduces the proportion of nucleotide sequences of these sites in the mRNA of target genes. Competition between piRNAs occurs for binding to the mRNA of target genes. Individual piRNAs and groups of piRNAs that have separate BSs and clusters of BSs in the mRNAs of two or more candidate genes have been identified in the mRNAs of these genes. This organization of piRNAs BSs indicates the interdependence of the expression of candidate genes through piRNAs. Significant differences in the ability of genes to interact with piRNAs avoid the side effects of piRNAs on genes with the lack of binding of such piRNAs. Individual piRNAs and sets of piRNAs are proposed and recommended for the diagnosis and therapy of ESCC.