Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on nectar (and pollen) of oil tea and are able to metabolize these galactose derivatives. We present the first next-generation genomes for five and one Andrena species that are respectively specialized and non-specialized oil-tea pollinators, and combining with published genomes of six other Andrena species which did not visit oil-tea, we performed molecular evolution analyses on genes involved in metabolism of galactose derivatives. Six genes (NAGA, NAGA-like, galM, galK, galT, and galE) involved in galactose derivatives metabolism were identified in the five oil-tea specialized species, but only five (with the exception of NAGA-like) were discovered in the other Andrena species. Molecular evolution analyses revealed that NAGA-like, galK and galT in oil-tea specialized species appeared under positive selection. RNASeq analyses showed that NAGA-like, galK, and galT were significantly up-regulated in the specialized pollinator A. camellia compared to the non-specialized pollinator A. chekiangensis. Our study demonstrated that the genes NAGA-like, galK, and galT had played an important role in the evolutionary adaptation of the oil-tea specialized Andrena species.

Chromosomal rearrangements in N. gonorrhoeae and N. meningitidis were studied with the determination of mobile elements and their role in rearrangements. The results of whole-genome sequencing and de novo genome assembly for 50 N. gonorrhoeae isolates collected in Russia were compared with 96 genomes of N. gonorrhoeae and 138 genomes of N. meningitidis from the databases. Rearrangement events with the determination of the coordinates of syntenic blocks were analyzed using the SibeliaZ software, the minimum number of events that allow one genome to pass into another was calculated using the DCJ-indel model using the UniMoG program. Population-level analysis revealed a stronger correlation between changes in the gene order and phylogenetic proximity for N. meningitidis in contrast to N. gonorrhoeae. Mobile elements were identified, including Correa elements, Spencer-Smith elements (in N. gonorrhoeae), Neisserial intergenic mosaic elements, IS elements of IS5, IS30, IS110, IS1595 groups, Nf1-Nf3 prophages, NgoФ1-NgoФ9 prophages, Mu-like prophages Pnm1, Pnm2, MuMenB (in N. meningitidis). More than 44% of the observed rearrangements most likely occurred with the participation of mobile elements, including prophages. No differences were found between the Russian and global N. gonorrhoeae population both in terms of rearrangement events and in the number of transposable elements in genomes.

Climate change poses a serious threat to global agricultural activity and food production. To address this issue, plant genome editing technologies have been developed to provide an alternative solution for crop improvement. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome to produce crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and possible gaps in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.

Enterovirus A71 (EV-A71) infection is a major cause of hand, foot and mouth disease (HFMD) which may be occasionally associated with severe neurological complications. There are currently a lack of treatment options for EV-A71 infection. The Raf-MEK-ERK signaling pathway, in addition to its critical importance in the regulation of cell growth, differentiation and survival, has been shown to be essential for virus replication. In this study, we investigated the anti-EV-A71 activity of vemurafenib, a clinically approved B-Raf inhibitor used in the treatment of late stage melanoma. Vemurafenib exhibits potent anti-EV-A71 effect in cytopathic effect inhibition and viral load reduction assays, with half maximal effective concentration (EC50) at nanomolar concentration. Mechanistically, vemurafenib interrupts both EV-A71 genome replication and assembly. These findings expand the list of potential antiviral candidates of anti-EV-A71 therapeutics.

The experiments described in this research article were designed to test the effect of rare variants into genomic prediction in dairy cattle. Common polymorphisms are able to explain only a small proportion of the underlying genetic variation of complex phenotypes. Variants representing functional mutations with large effects on complex phenotypes are expected to be rare due to natural (humans) or artificial (livestock) selection pressure. Therefore, it is important to check whether the use of rare variants could increase the accuracy of ranking of animals by providing the tool for more precise differentiation among the bulls with high additive genetic merit. The goal of our study was to verify whether including rare variants in a genomic selection model allows for a more accurate description of the additive genetic background of traits under selection in dairy cattle. We used the linear mixed model for comparison SNP estimates for Holstein-Friesian cattle of the two data sets – a set containing only single nucleotide polymorphisms defined by minor allele frequency ≥ 0.01, which is routinely used in the Polish genomic evaluation system (46,216 SNPs), and a set containing SNPs selected based only on the call rate (54,378 SNPs). Based on the SNP estimates we also calculated DGV and GEBV and compared them between both data sets. In all the analyses we used production, fertility, conformation and udder health traits. We also assessed the time required for the two most computationally demanding components of genomic selection: preparing genotype data, and estimation of SNP effects between those two data sets. The results of our study indicated that the analysis including rare variants resulted in changes in the individual ranking of the top 100 male and female candidates, but had no effect on the outcome of the quality of EBV prediction as expressed by the Interbull validation test.

Globally 390 millions of people are at risk of dengue infection; over the past 50 years the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases was noticed since 2017. In October 2018 an outbreak of DENV-2 was reported in Rosso area in the north of Senegal at the border with Mauritania. Out of the 187 blood specimen samples collected, 27 were positives by qRT-PCR and 8 were serologically positive for DENV IgM. Serotyping using qRT-PCR reveals that isolates were positive for DENV-2. A subset of DENV-2 positives samples was selected and subjected to full genome sequencing followed by phylogenetic analysis. Analysis of 06 nearly completed genome sequences (n= 6) revealed that isolates belong to the cosmopolitan genotype and are closely related to the Mauritanian strains detected between 2017 and 2018 and those detected in many West African countries such as Burkina Faso or Cote d’Ivoire. Our results suggest a transboundary circulation of the DENV-2 cosmopolitan genotype between Senegal and Mauritania and call for a need of coordinated surveillance of arboviruses between these two countries. Interestingly, high level of homology between West African isolates highlights endemicity and call for a set-up of sub-regional viral genomic surveillance which will lead to a better understanding of viral dynamic, transmission and spread across Africa.

Colletotrichum is one of the most important plant pathogenic genera of fungi due to its scientific and economic impact. Colletotrichum spp. can infect a wide range of hosts, causing losses in crops of major importance worldwide, such as soybean. In the past, soybean anthracnose was mainly caused by C. truncatum, but during the last decade, other species have been identified at an increasing rate, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight pathogens of other hosts. Our results show that the four species infecting soybean belong to two lineages and do not share any of the lineage specific effector candidates identified. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.

Eating disorders (ED) are characterized by alterations in eating behavior. The genetic factors shared between ED diagnoses have been underexplored. The present study aimed to perform a genome-wide association study on individuals with disordered eating behaviors in the Mexican population, blood methylation quantitative trait loci (blood-meQTL) analysis, and in silico function prediction by different algorithms. The analysis included a total of 1803 individuals. Genome-wide association study and blood-meQTL analysis were performed by logistic and linear regression. In silico functional variant prediction, phenome-wide, and transcriptome-wide association studies by different algorithms were analyzed. In the genome-wide association study, we identified 44 single-nucleotide polymorphisms (SNP) associated at a nominal value and 7 blood-meQTL at a genome-wide umbral. The SNPs were enriched in genome-wide associations of the metabolic and immunologic domains. In the in silico analysis, the SNP rs10419198 located on an enhancer mark could change the expression of PRR12 on blood, adipocytes, and brain areas that regulate food intake. The present study supports the previous associations of genetic variation in the metabolic domain with ED.

Komagataeibacter spp. have been used for the bioconversion of industrial wastes and lignocellulosic hydrolysates to bacterial cellulose (BC). Recently studies have demonstrated the capacity of Komagataeibacter spp. in the biotransformation of inhibitors found in lignocellulosic hydrolysates, aromatic lignin-derived monomers (LDMs) and acetate. In general, detoxification and BC synthesis from lignocellulosic inhibitors requires a carbon flow from acetyl-coA towards tricarboxylic acid and gluconeogenesis, respectively. However, the related molecular aspects have not yet been identified in Komagataeibacter spp. In this study, we isolated a cellulose producing bacteria capable of synthesizing BC in a minimal medium containing crude glycerol, a by-product from biodiesel production process. The isolate, affiliated to Komagataeibacter genus, synthesized cellulose in minimal medium containing glucose (3.3±0.3 g/L), pure glycerol (2.2±0.1 g/L) and crude glycerol (2.1±0.1 g/L). Genome assembly and annotation identified four copies of bacterial cellulose synthase operon and genes for redirecting the carbon from central metabolic pathway to gluconeogenesis. According to the genome annotations, a BC production route from acetyl-CoA, a central metabolic intermediate, was hypothesized and was validated using acetate. We identified that when K. rhaeticus ENS9b was grown in minimal medium supplemented with acetate, BC production was not observed. However, in presence of readily utilizable substrate, such as spent yeast hydrolysate, acetate supplementation improved BC synthesis.

Endometriosis is a chronic neuro-inflammatory disorder the defining feature of which is the growth of tissue (lesions) that resembles the endometrium in sites outside the uterus. Estimates of prevalence typically quote rates of ~10% of women of reproductive age, equating to ~190 million women world-wide. Three subtypes of endometriosis are usually considered when discussing the aetiology of the disorder - superficial peritoneal, ovarian (endometrioma cysts), and deep (infiltrating). Genetic, hormonal and immunological factors have all been proposed as contributing to risk factors associated with the development of lesions. Twin studies report the heritable component of endometriosis as ~50%. Genome wide association studies (GWAS) have been conducted allowing unbiased scanning of the genome for single nucleotide polymorphisms (SNPs) in many thousands of individuals. These studies have identified SNPs that appear over-represented in patients with endometriosis, particularly those with more extensive disease (stage III/IV). Amongst the larger scale GWAS there has been replication of SNPs near genes involved in oestrogen and other signalling pathways including ESR1 (oestrogen receptor alpha), GREB1, HOXA10, WNT4 and MAPK kinase signalling. The results from patients with endometriosis have also provided an opportunity to make comparisons with GWAS conducted on other patient cohorts including those with reproductive traits (age at menarche) and disorders (fibroids, endometrial and ovarian cancer) and conditions that are reported by women with endometriosis (migraine, depression). These comparative studies have highlighted some shared genetically-controlled biological mechanisms, including hormone-regulated pathways which might explain the co-occurrence of endometriosis with these disorders. In summary, unbiased genetic analysis has provided new insights into the genetic factors that may contribute to increased risk of developing endometriosis. New studies are needed to broaden the range of patients contributing to these datasets and to improve integration with non-genomic and tissue expression data before their full potential for diagnosis and improvements in patient care can be fully realised.

Abstract: Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.

Cas endonuclease-mediated genome editing provides a long-awaited molecular biological approach to the modification of predefined genomic target sequences in living organisms. Although cas9/guide (g)RNA constructs are straightforward to assemble and can be customized to target virtually any site in the plant genome, the implementation of this technology can be cumbersome, especially in species like Triticale that are difficult to transform, for which only limited genome information is available and/or which carry comparatively large genomes. To cope with these challenges, we have pre-validated cas9/gRNA constructs (1) by frameshift restitution of a reporter gene co-introduced by ballistic DNA transfer to barley epidermis cells, and (2) via transfection in Triticale protoplasts followed by either a T7E1-based cleavage assay or by deep-sequencing of target-specific PCR amplicons. For exemplification, we addressed the Triticale ABA 8’-hydroxylase 1 gene, one of the putative determinants of pre-harvest sprouting of grains. We further show that in-del induction frequency in Triticale can be increased by TREX2 nuclease activity, which holds true for both well- and poorly performing gRNAs. The presented results constitute a sound basis for the targeted induction of heritable modifications in Triticale genes.

Transposable elements (TEs) are mobile genetic elements capable of rapidly altering the genome through their movements. The importance of TE activity has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs results in the growing number of bioinformatics software to identify insertion events. However, the application of existing TE finding tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we report a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software dependencies using four inputs that can be easily generated with popular variant calling pipelines. The external software requirements are BEDTools, SAMtools, and Picard. Necessary inputs include TEs present in the reference genome, binary paired-end alignment, reference genome index, and a list of TE names. We tested TEfinder pipeline among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.

Astroviruses (AstVs) are occurs globally and are common causes of gastroenteritis in human and animals. The genetic diversity and epidemiology of AstVs in Africa is not well known, hence, we aimed to genetically characterize astroviruses in asymptomatic smallholder piglets in East Africa. Twenty-four samples randomly selected from 446 piglets (<6 months old), initially collected for rotavirus study, was sequenced for metagenomic analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of 7 strains with complete (or near complete) genome revealed variable nucleotide and amino acid sequence identities with known PoAstV strains. The U083 and K321 strains had nucleotide sequence similarities ranging from 66.4 to 75.4 % to the known PoAstV2 strains, nucleotide sequence similarity of U460 strain with known PoAstV3 ranged 57.0 to 65.1 % to the, while K062, K366, K451, and K456 strains showed nucleotide sequence similarities of 63.5 to 80 % to the known PoAstV4 strains. The low sequence identities (<90 %) indicate that novel genotypes of PoAstVs are circulating in the study area. Multiple recombination events were detected in our PoAstV4 strains, indicating that the genetic diversity observed in these strains may be due to recombination. Importantly, we identified potential candidate epitopes with conserved peptides in our PoAstV strains that could aid in the design of immune diagnosis tools and subunit vaccines. Our data provide new intuitions into the genetic structure of porcine astroviruses in East African.

In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.

The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled, complete, plastomed genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,198 base pairs (bp) to 154,361 bp and contained a pair of inverted repeats (IRa and IRb) of 25,027--25,071 bp that were separated by a large single-copy (LSC) region of 85,675--85,760 bp and a small single-copy (SSC) region of 18,457--18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastid genomes, which revealed close resemblance among the species. Both the substitution and insertion and deletion analyses confirmed that the IR region was significantly conserved compared with the LSC and SSC regions. Further comparative analysis among the Withania species highlighted 30 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification.

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

Appropriate vaccine selection is crucial in the control of foot-and-mouth disease (FMD). Vaccination can prevent clinical disease and reduces viral shedding, but there is a lack of cross-protection between the seven serotypes and their sublineages, making the selection of an adequately protective vaccine difficult. Since the exact composition of their vaccines is not consistently disclosed by all manufacturers, incompatibility of the strains used for vaccination with regionally circulating strains can cause vaccination campaigns to fail. Here, we present a deep sequencing approach for polyvalent inactivated FMD vaccines that can identify all component strains by their genome sequences. The genomes of all strains of a commercial pentavalent FMD vaccine were de-novo assembled and the vaccine composition determined semi-quantitatively. The genome assembly required high stringency parameters to prevent misassemblies caused by conserved regions of the genome shared by related strains. In contrast, reference-guided assembly is only recommended in cases where the number of strains is previously known and appropriate reference sequences are available. The presented approach can be applied not only to any inactivated whole-virus FMD vaccine, but also to vaccine quality testing in general and allows for better decision-making for vaccines with unknown composition.

Biological control is widely successful for controlling pests, but effective biocontrol agents are now more difficult to obtain due to more restrictive international trade laws. Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, applying genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them, incorporating evolutionary and ecological principles. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined to better target their selection, followed by how to implement this information into a breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depends on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci (QTL) analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices include marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

An outbreak of a virus-like disease has caused severe damage to noni plants (Morinda citrifolia L.) in Xishuangbanna area of China's southwestern Yunnan province since 2015. The diseased plants displayed typical mosaic symptom with light and dark green patches on leaves. Flexuous filamentous virus particles of about 800 nm in length were observed from the leaf saps by transmission electron microscope. Illumina transcriptomic sequencing further revealed the presence of a potyvirus and its near complete genome was obtained from de novo assembly. The complete genome of 9,659 nts was obtained by Sanger sequencing of eight amplicons generate by RT-PCR and 5’ and 3’ RACE. BLASTp analysis of the polyprotein sequence showed that the virus was most closely related to Tobacco vein banding mosaic virus (TVBMV), but these two viruses only shared 50.7% amino acid sequence similarity. Both phylogenetic analyses of the polyprotein and CP amino acid sequences indicated that this virus is a member of genus Potyvirus. However, the low sequence homology with all known potyviruses established this virus as a new species in the genus, tentatively named as Noni mosaic virus (NoMV). Our field surveys showed that 100% of the symptomatic samples and 28.57% of the asymptomatic samples were infected with this novel potyvirus. Aphids collected from diseased leaves were also detected carrying the virus. In summary, our data indicated that a novel species of potyvirus, NoMV, is prevalent in Yunnan, China and is associated with an emerging mosaic disease on M. citrifolia.

Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.

Background: Accurate diagnosis of the differentially aggressive fungus Leptosphaeria maculans and Leptosphaeria biglobosa causing Blackleg in crucifers is crucial. Available markers were designed decades ago which may become ineffective due to the ever evolving nature of the fungus, requiring the development of more precise molecular markers. Methods: The whole genomes of available isolates belonging to this two species were aligned using progressive MAUVE tool, species specific genomic regions were extracted and species specific primers were designed from the sequences that encode for effector proteins. Results: Three (Lm1, Lm2 and Lm5) and two (Lb3 and Lb3’) primer sets specifically detected the isolates of target species in PCR based assay, of which the primers Lm5 and Lb3’ were multiplexed for detection of Leptosphaeria maculans and Leptosphaeria biglobosa, generating PCR amplicons of 230 and 834 bp, respectively from a single PCR reaction. The markers were highly sensitive and were able to amplify target species from crude ‘pseudothecia and ascospores suspension’ without requiring DNA extraction. Conclusions: These markers, solitarily or in combination, designed from species specific genomic segments will serve as precise, sensitive and rapid detection of Leptosphaeria maculans and Leptosphaeria biglobosa species and will be helpful for surveillance, management and transboundary quarantine of the devastating disease.

Yeasts belonging to the Metschnikowia genus are particularly interesting for the unusual formation of only two needle-shaped ascospores during their mating cycle. Presently, the meiotic process that can lead to only two spores from a diploid zygote is poorly understood. The expression of fluorescent nuclear proteins should allow the meiotic process to be visualized in vivo; however, no large-spored species of Metschnikowia has ever been transformed. Accordingly, we aimed to develop a transformation method for Metschnikowia borealis, a particularly large-spored species of Metschnikowia, with the goal of enabling the genetic manipulations required to study biological processes in detail. Genetic analyses confirmed that M. borealis, and many other Metchnikowiacea, are CUG-Ser yeasts. Codon-optimized selectable markers lacking CUG codons were used to successfully transform M. borealis by electroporation and lithium acetate, and transformants appeared to be the result of random integration. Mating experiments confirmed that transformed-strains were capable of generating large asci and undergoing recombination. Finally, random integration was used to transform an additional 18 yeast strains, and all attempts successfully generated transformants. The results provide a simple method to transform many yeasts from an array of different clades and can be used to study or develop many species for various applications.

Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) >1 (but P values were non-significant) and 66 had Ka/Ks <1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.

Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (elovl2, elovl5 and fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, an essential resource for their effective conservation, management and sustainable exploitation.

A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.

Vehicle logo detection plays a crucial role in various computer vision applications, such as vehicle classification and detection. In this research, we propose an improved vehicle logo detection method leveraging the MAMBA structure. The MAMBA structure integrates multiple attention mechanisms and bidirectional feature aggregation to enhance the discriminative power of the detection model. Specifically, we introduce the Multi-Head Attention for Multi-Scale Feature Fusion (MHAMFF) module to capture multi-scale contextual information effectively. Moreover, we incorporate the Bidirectional Aggregation Mechanism (BAM) to facilitate information exchange between different layers of the detection network. Experimental results on a benchmark dataset (VLD-45 dataset) demonstrate that our proposed method outperforms baseline models in terms of both detection accuracy and efficiency. Furthermore, extensive ablation studies validate the effectiveness of each component in the MAMBA structure. Overall, the proposed MAMBA-based vehicle logo detection approach shows promising potential for real-world applications in intelligent transportation systems.

Electrolyte disturbances are common in patients with traumatic brain injury (TBI), particularly affecting sodium, potassium, chloride and calcium levels. This study aims to provide insights into these disturbances within the first 24 hours post-injury. We conducted a cross-sectional analysis of 50 TBI patients, excluding those with conditions affecting electrolyte balance. Electrolyte levels were measured, and correlations with demographic data, trauma mechanisms, imaging findings, and Glasgow Coma Scale (GCS) scores were analyzed. Results indicated that chloride levels inversely correlated with GCS scores (ρ = -0.515; p = 0.002), suggesting that elevated chloride may indicate severe neurological impairment. Potassium levels were significantly associated with subdural hematoma (p = 0.032) and subarachnoid hemorrhage (p = 0.043), highlighting their potential as markers for severe brain injuries. No significant associations were found between sodium or calcium levels and the studied variables. These findings underscore the importance of early monitoring of chloride and potassium levels in TBI patients to improve management and outcomes. Future research should focus on larger, multi-center studies to validate these findings and develop comprehensive guidelines for managing electrolyte imbalances in TBI patients.

Target detection technology plays a crucial role in fishery ecological monitoring, fishery diversity research, and intelligent aquaculture. Deep learning, with its distinct advantages, provides significant convenience to the fishery industry. However, it still faces various challenges in practical applications, such as significant differences in image species and image blurring. To address these issues, this study proposes a multi-scale, multi-level, and multi-stage cross-domain feature fusion model. In order to train the model more effectively, a new dataset called Fish52 (Multi-scene Fish dataset) was constructed, on which the model achieved an mAP of 82.57%. Furthermore, we compared prevalent one-stage and two-stage detection methods on the Lahatan (single-scene fish dataset) and Fish30 dataset and tested them on the F4k and FishNet dataset. The mAP of our proposed model on the Fish30, Lahatan, F4k, and FishNet datasets reaches 91.72%, 98.7%, 88.6%,and 81.5% respectively, outperforming existing mainstream models. Comprehensive empirical analysis indicates that our model possesses high generalization ability and has reached advanced performance levels. In this study, the depth of the model backbone is deepened, a novel neck structure is proposed, and anew module is embedded therein. To enhance the fusion ability of the model, a new attention mechanism module is introduced. In addition, in the adaptive decoupling detection header module, introducing classes with independent parameter sand regression adapters reduces interaction between different tasks. The proposed model can better monitor fishery resources and enhance aquaculture efficiency. It not only provides an effective approach for fish detection but also has certain reference significance for the identification of similar target sin other environments, and offers assistance for the construction of smart fisheries and digital fisheries.

Background: Screening for postpartum depression can lower prevalence and ensure that mothers get adequate treatment and support. Yet, few practitioners screen.The present article is a brief review on barriers to screening and two screening scales that are validated for perinatal women. Findings: Despite recommendations from health organizations, most new mothers are not screened for depression. Providers cite lack of time, opening “Pandora’s box,” and lack of resources for mothers who screen positive as reasons for why they do not screen. The Edinburgh Postnatal Depression Scale and the Patient Health Questionnaires are brief screening scales that have been validated for new mothers and are widely available.Conclusions: Screening is the necessary first step to identifying new mothers who are depressed. Practitioners who screen need a clear plan, and to know how to access available community resources, so they will know what to do when a mother screens positive.

Typhoons bring great damages to transmission line systems located in coastal areas. Strong wind and extreme precipitation are the main sources of damaging effects. Transmission lines suffered from wind-driven rain exhibit more susceptibility to damage due to the coupled effect of wind and rain water. This paper presents an integrated numerical simulation framework based on mesoscale WRF model, multiphase CFD model and FEM model to analyze the motions of a transmission line subjected to coupled wind and rain loads during typhoon events. A full-scale transmission line in Zhoushan island is employed to demonstrate the effectiveness of the proposed framework by simulating typhoon evolution in terms of wind fields and rainfall, solving the coupled wind and rain fields around the conductor and predicting the dynamic responses of the transmission line during Super Typhoon Lekima (2019). The results show that the horizontal displacements of the transmission line under the joint actions of wind and rain increases approximately 17%~18% compared to those of wind loads only. It is important to consider the coupled effects of wind-driven rain on conductors in the design of transmission lines under typhoon conditions.

To conduct high-precision and high-resolution numerical simulation of complex flow structures in turbomachinery, a high-order finite volume weighted essentially non-oscillatory (WENO) scheme for the large eddy simulation (LES) is improved and embedded into the three-dimensional viscous unsteady CFD solver NUAA-Turbo. Firstly, the spectral characteristics and unsteady convergence of the improved WENO scheme are studied. Compared with the classical WENO scheme, the improved WENO scheme has better dissipation and dispersion characteristics and faster convergence speed. Then, the coefficient CW of the Wall-Adapting Local Eddy-viscosity (WALE) model is calibrated by decaying homogeneous isotropic turbulence (DHIT) test case. Finally, the scheme is applied to conduct high-precision LES calculations of turbulent boundary layer flow, supersonic compression corner flow, and low-pressure turbine cascade separation flow. The numerical simulation results show that this WENO scheme has excellent shock wave capture ability and turbulence resolution and can capture more flow field details with less mesh size, greatly reducing the computational cost and laying a foundation for large-scale engineering application of LES.

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.

The expansion of copper mining on the hyper-arid pacific slope of southern Peru has precipitated growing concern for scarce water resources in the region. Located in the headwaters of the Torata river, in the department of Moquegua, the Cuajone mine, owned by Southern Copper, provides a unique opportunity, in a little-studied region, to examine the relative impact of the landscape-scale mining on water resources in the region. Principal component analysis and cluster analysis of the water chemistry data from 16 sites, collected over three seasons during 2017 and 2018, show distinct statistical groupings indicating that, above the settlement of Torata, water geochemistry is a function of chemical weathering processes acting upon underlying geological units, and confirming that the Cuajone mine does not significantly affect water quality in the Torata river. Impact mitigation strategies that firstly divert channel flow around the mine and secondly divert mine waste to the Toquepala river and tailings dam at Quebrada Honda, below the Toquepala mine, in the department of Tacna, secure water quality in the Torata river for the foreseeable future. In the greater Moquegua river catchment, our results further suggest that water quality has been more significantly impacted by urban effluents and agricultural runoff than the Cuajone mine. The increase in total dissolved solids in the waters of the lower catchment reflects the cumulative addition of dissolved ions through chemical weathering of the underlying geological units, supplemented by rapid recharge of surface waters contaminated by residues associated with agricultural and urban runoff through the porous alluvial aquifer. Concentrations in some of the major ions exceeded internationally recommended maxima for agricultural use, especially in the coastal region. Occasionally, arsenic and manganese contamination also reached unsafe levels for domestic consumption. In the lower catchment, below the Cuajone mine, data and multivariate analyses point to urban effluents and agricultural run-off rather than weathering of exposed rock units, natural or otherwise, as the main cause of contamination.

This research explores the depolymerization of waste polymethyl methacrylate (PMMAW) from dental material in fixed-bed semi-batch reactors, focusing on three production scales: laboratory, technical, and pilot. The study investigates the thermal degradation mechanism and kinetics of PMMAW through thermogravimetric (TG) and differential scanning calorimetry (DSC) analyses, revealing a two-step degradation process. The heat flow during PMMAW decomposition is measured by DSC, providing essential parameters for designing pyrolysis processes. The results demonstrate the potential of DSC for energetic analysis and process design, with attention to standardization challenges. Material balance analysis across the production scales reveals a temperature gradient across the fixed bed negatively impacting liquid yield and methyl methacrylate (MMA) concentration. Reactor load and power load variables are introduced, demonstrating decreased temperature with increased process scale. The study identifies the influence of temperature on MMA concentration in the liquid fraction, emphasizing the importance of controlling temperature for efficient depolymerization. Furthermore, the research highlights the formation of aromatic hydrocarbons from the remaining char, indicating a shift in liquid composition during the depolymerization process. The study concludes that lower temperatures below 450 °C favor liquid fractions rich in MMA, suggesting the benefits of lower temperatures and slower heating rates in semi-batch depolymerization. The findings contribute to a novel approach in analyzing pyrolysis processes, emphasizing reactor design and economic considerations for recycling viability. Future research aims to refine and standardize the analysis and design protocols for pyrolysis and similar processes.

When describing the tribological behaviour of technical surfaces, the need for full length scale microtopographic characterization often arises. The self-affine of surfaces and the characterization of self-affine by a fractal dimension and its implantation into tribological models are commonly used. The goal of our present work was to determine the frequency range of fractal behaviour of surfaces by analysing the microtopographic measurements of a brake plunger. We also wanted to know if the bifractal and multifractal behaviour can be detected in real machine parts. As a result, we developed a new methodology for determining the fractal range boundaries to separate the nano- and micro-roughness. In order to reach our goals, we used atomic force microscope (AFM) and stylus instrument to provide measurements in wide frequency range (19 nm - 3 mm). As a result of the power spectral density (PSD) based fractal evaluation, it was found that the examined surface could not be characterized by a single fractal dimension and that we developed a methodology for stopping the margin of validity of each fractal dimension, and we also developed a methodology for determining the limits of validity of certain fractal dimensions.

In recent decades, porous scaffolds for bone tissue engineering (BTE) have gained significant attention. Considerable research efforts have been dedicated to investigating the impact of scaffold pore size on a diverse array of biological processes, including cell-scaffold interactions, substance transportation, and vascularization. However, the multi-scale hierarchical porosity, a key structural characteristic of natural bone, has rarely been replicated in BTE scaffolds due to the challenges of controlling the scaffold structure across multiple length scales. With the advancement of manufacturing technology, there has been increasing research on biomimetic multi-scale hierarchical materials, which are also gaining favor in the field of BTE. Therefore, there is an urgent need to review multi-scale hierarchical porous BTE scaffolds. This paper aims to review the role and fabrication methods of multi-scale porous BTE scaffolds at different length scales, the design and manufacturing of new BTE scaffolds for bone regeneration.

The papaya mealybug Paracoccus marginatus is an invasive, polyphagous pest and poses a quarantine threat to tropical and subtropical countries. Infested commodity internationally should be undergoing phytosanitary treatment, while irradiation is recommended to replace methyl bromide fumigation. Dose-response tests were conducted on the 2-, 4-, and 6-d-old eggs and gravid females of P. marginatus using the X-ray radiation doses of 15–105 Gy with an interval of 15 Gy, respectively. Radiotolerance was compared using fiducial overlapping and lethal dose ratio (LDR) test, resulting in insignificant difference except for LDR test at LD90 (leading 90% mortality at 95% confidence level (CL)); the estimated dose for 99.9968% mortality at 95% CL was 176.5–185.2 Gy, which was validated in the confirmatory tests using gamma irradiation because gammy and X-rays have equal biological effect on pests. Therefore, a total of estimating 60,386 gravid females of papaya mealybug irradiated with 146.8–185.0 Gy resulted in no F1 nymphs developing. Eggs can therefore be used as an alternative to gravid females for dose-response tests; the recommended minimum dose for phytosanitary treatment of P. marginatus on infested commodity is 185 Gy, with treatment efficacy ≥ 99.9950% at 95% CL.

Mercury emissions from small-scale coal-fired boilers are still a serious environmental problem in Poland and the Czech Republic. The publication presents the results of mercury emission tests conducted using five different small-scale coal-fired boilers and five different coal fuels. The research was carried out under laboratory conditions, but also using residential users' heating devices. They covered a wide range of operational parameters, both energy and emission. It was shown that more than 94% of the mercury contained in coal fuel undergoing combustion is emitted into the atmosphere with the volatile products of combustion (including dust), and the amount of emissions is strongly dependent on the original mercury content of the fuel. One solution to the problem of mercury emissions from small-scale coal-fired boilers may be to replace traditional coal with low-emission carbon fuels. The paper shows that mercury emissions from burning such fuels are many times lower than from burning coal. The widespread use of low-emission carbon fuels in individual heating systems in Poland and the Czech Republic would reduce mercury emissions to the atmosphere by up to 90% compared to the current level of emissions generated by individual heating systems in these countries.

To prevent CO2 leakage and ensure the safety of long-term CO2 storage, it is essential to investigate the flow mechanism of CO2 in complex pore structures at the pore scale. This study focuses on reviewing the experimental, theoretical, and numerical simulation studies on the microscopic flow of CO2 in complex pore structures during the last decade. For example, advanced imaging techniques, such as X-ray computed tomography (CT) and nuclear magnetic resonance (NMR), are used to reconstruct the complex pore structures of rocks. Mathematical methods, such as Darcy's law, Young–Laplace’s law, and the Navier-Stokes equation, are used to describe the microscopic flow of CO2. Numerical methods, such as the lattice Boltzmann method (LBM) and pore network (PN) model, are used for numerical simulation. The application of these experimental and theoretical models and numerical simulation studies is discussed, considering the effect of complex pore structures. Finally, future research is suggested to focus on: (1) Conducting real-time CT scanning experiments of CO2 displacement combined with the developed real-time CT scanning clamping device to realize real-time visualization and provide quantitative description of the flow behavior of CO2 in complex pore structures; (2) The effect of pore structures change on the CO2 flow mechanism caused by the chemical reaction between CO2 and the pore surface, the flow theory of CO2 considering wettability and damage theory in a complex pore structures; (3) The flow mechanism of multi-phase CO2 in complex pore structures; (4) The flow mechanism of CO2 in the pore structures at multiscale and the scale upgrade from microscopic to mesoscopic to macroscopic. Generally, this study focuses on reviewing the research progress of CO2 flow mechanisms in complex pore structures at the pore scale and affords an overview of potential advanced developments to enhance the current understanding of CO2 microscopic flow mechanisms.

Zoom dysmorphia (ZD) is a facial dysmorphia triggered or aggravated by frequent virtual meetings. The frequent use of videoconferencing platforms has been linked to a distorted perception of facial images as individuals have an increased awareness of their appearance, given constant video feedback. As a result, dysmorphic concerns can develop. It is crucial to identify ZD as the condition interferes with the individual’s life and can trigger or aggravate body dysmorphic disorder (BDD). A standardized approach for screening ZD in non-psychiatric settings has yet to be defined. We discuss the features of ZD and the challenges of screening for ZD in a virtual setting. To facilitate the recognition of ZD in telehealth consultations, we propose a comprehensive ZD screening questionnaire that includes questions related to typical ZD features and a BDD-focused question. The questionnaire is concise and allows the identification of individuals with a potential ZD. A BDD assessment in such individuals should follow.

This paper summaries the main findings from the full-scale CFD analyses conducted at SINTEF Ocean on the case of MV REGAL, which is one of the benchmark vessels studied in the ongoing joint industry project JoRes. The numerical approach is described in detail, and comparative results are presented regarding the propeller open water characteristics, ship towing resistance, and ship self-propulsion performance. The focus of numerical investigations is on the assessment of the existing simulation best practices applied to a ship scale case in a blind simulation exercise, and performance of thereof with different turbulence modelling methods. The results are compared directly with full-scale performance predictions based on model tests conducted at SINTEF Ocean and sea trails data obtained in the JoRes project.

Evaluating the performance of water indices and mapping the spatial distribution of water-related ecosystems are important for monitoring surface water resources. This is particularly the case for Ethiopia since there is limited information available on water resources development over time despite its relevance for the people and ecosystems. To address this problem, this paper evaluates the performance of seven water indices for country-scale surface water detection based on high spatial and multi-temporal resolution Sentinel-2 data, processed using the Google Earth Engine cloud computing system. Results show that the water index (WI) and automatic water extraction index with shadow (AWEIsh) are the most accurate ones to extract surface water. Comparisons are based on qualitative visual inspections and quantitative accuracy indicators. For the latter, WI and AWEIsh obtained kappa coefficients of 0.96 and 0.95, respectively, and an overall accuracy of 0.98 each. Both indices accounted for similar spatial coverages of surface waters with 82,650 km2 (WI) and 86,530 km2 (AWEIsh) for the whole of Ethiopia.

Target detection and segmentation in synthetic aperture radar (SAR) images are vital steps for many remote sensing applications. In the era of data-driven deep learning, this task is extremely challenging due to the limited labeled data. Few-shot Learning has the ability to learn quickly from few samples with supervised information. Inspired by this, a few-shot learning framework named MSG-FN is proposed to solve the segmentation of ship targets in heterologous SAR images with few annotated samples. The proposed MSG-FN adopts a dual-branch network consisting of a support branch and a query branch. The support branch is used to extract features with an encoder, and the query branch uses a U-shaped encoder-decoder structure to segment the target in the query image. The encoder of each branch is composed of well-designed residual blocks combined with filter response normalization to capture robust and domain-independent features. A multi-scale similarity guidance module is proposed to improve the scale adaptability of detection by applying hand-on-hand guidance of support features to query features of various scales. In addition, a SAR dataset named SARShip-4i is built to evaluate the proposed MSG-FN and the experimental results show that the proposed method achieves superior segmentation results compared with the state-of-the-arts.

Unmanned Aerial Vehicles (UAVs) image object detection has great application value in military and civilian fields. However, the objects in the captured images from UAVs have problems of large scale variation, complex backgrounds, and a large proportion of small objects. To resolve these problems, a multi-scale object detector based on coordinate and global information aggregation is proposed, named CGMDet. Firstly, a Coordinate and Global Information Aggregation Module (CGAM) is designed by aggregating local, coordinate, and global information, which can obtain features with richer context information. Secondly, a Multi-Feature Fusion Pyramid Network (MF-FPN) is proposed, which can better fuse features of different scales and obtain features containing more context information through repeated use of feature maps, to better detect multi-scale targets. Moreover, more location information of low-level feature maps is integrated to improve the detection results of small targets. Furthermore, we modified the bounding box regression loss of the model to make the model more accurately regress the bounding box and faster convergence. Finally, the proposed CGMDet was tested on VisDrone and UAVDT datasets and mAP0.5 of 50.9% and 48% was obtained, respectively. At the same time, our detector achieved the best results compared to other detectors.

Knowledge about ecological conditions and processes in centers of endemism (CoEs) is still limited with respect to various systematic groups of organisms, ecosystem types, ecological conditions and ecosystem functions. Endemics and CoEs play a prominent role in nature conservation monitoring and management, and in the organization of zoos, aquaria and botanical gardens. We review the meaning of different groups of organisms and indicators for the characterization of endemic-rich regions, the importance of heterogeneity in space, continuity in time, isolation and ex-situ management for the survival of endemic and threatened species. Currently, conversion of land cover and land use change are the most important causes of biodiversity decline and extinction risk of endemic and endangered species concentrated in CoEs. These are followed by climate change, including severe weather, and then natural processes such as volcanism, landslides or tsunamis. For conservation purposes the management of zoos, aquaria, botanical gardens, of regional land use, and social aspects of the diversity of endemics and CoEs have to be taken into account as well. We need better answers to questions about the relationship between ecoregions, CoEs and regional awareness of biodiversity, which is linked with human culture including the management of zoos, aquaria and botanical gardens, aesthetics, wellbeing, health and trade.

Calibration of flow devices is important in several areas of pharmaceutical, flow chemistry and microfluidic applications where dosage of process liquids or accurate measurement of the flow rate is important. The process-oriented liquid itself might influence the performance of the flow device and the simultaneous determination of the dynamic viscosity under flow conditions might be a valuable information for the process parameters. To offer the simultaneous calibration of the dynamic viscosity of the process-oriented liquid at the corresponding flowrate, METAS has built a pipe viscometer for the traceable in-line measurement of the dynamic viscosity in the current flow facilities for low flow rates from 1 L/min to 150 mL/min and pressure drops up to 10 bar. The traceability of all the measuring quantities as well as the geometrical dimensions of the micro tube guarantee the traceability of the pipe viscometer to SI units. The most challenging part is the traceable determination of the inner diameter of the micro tube. This can be achieved by measuring the pressure drop as a function of flow rate with the pipe viscometer and applying the law of Hagen-Poiseuille with a traceable dynamic viscosity of a reference liquid (water) or perform the measurements with the micro-CT at METAS, which determines the inner diameter by x-ray diffraction. The validation of the stated measurement uncertainty of the pipe viscometer has been performed by means of calibration of the dynamic viscosity of several reference liquids with traceable density and kinematic viscosity. The setup of the facility, the traceability as well as the uncertainty calculation of the pipe viscometer for the in-line measurement of the dynamic viscosity are discussed in this paper.

The gravitational constant is equivalent to natural units in its six unit dimensions. Evaluating the classical formulas in each of these dimensions shows that gravitational potentials are proportional to the Planck scale by the ratio of a body's radial density to a radial density limit in the ratio of Planck length to Planck mass.

Mechanical recycling of solid plastic wastes on a small-scale level can be accomplished with the correct approaches. Thermoplastics are mostly considered for mechanical recycling because of their physical properties and ease of reprocessing. This paper reviews the mechanical reprocessing techniques of selected thermoplastics (polyethylene terephthalate and polyolefins) since they constitute a significant proportion of plastics used commercially. Furthermore, necessary considerations for effective operation of small-scale plants, including energy requirements of machinery and optimisation in order to improve efficiency and product quality, are discussed. A clearer understanding and addressing of the process-related challenges will lead to successful establishment and management of small-scale mechanical recycling facilities to benefit communities. Efficient small-scale mechanical reprocessing establishments have become essential in reducing the environmental impacts of solid plastic wastes and for energy conservation.

We are using the book “Towards Quantum Gravity with an article by Claus Kiefer as to a quantum gravity interpretation of the density matrix in the early universe. The density matrix we are using is a one loop approximation, with inflaton value and potential terms, like V(phi) using the Padmanabhan values one can expect if the scale factor is a ~ a(Initial) times t ^ gamma , from early times . In doing so, we isolate out presuming a very small initial time step candidates initial time values which are from a polynomial for time values due to the Kiefer Density value.

In the last years, more and more studies highlight the advantages of complementing traditional master classes with additional activities that improve students´ learning experience. This combination of teaching techniques is specially advised in the field of structural engineering, where intuition of the structural response it is of vital importance to understand the studied concepts. This paper deals with the introduction of a new (and more encouraging) educational tool to introduce intuitively students in the dynamic response of structures excited with an educational shaking table. Most of the educational structural health monitoring systems use sensors to determine the dynamic response of the structure. The proposed tool is based on a radically different approach, as it is based on low-cost image-recognition techniques. In fact, it only requires the use an amateur camera, a black background and a computer. In this study, the effects of both the camera location and the image quality are also evaluated. Finally, to validate the applicability of the proposed methodology, the dynamic response of small-scale buildings with different typologies is analyzed. In addition, a series of surveys were conducted in order to evaluate the activity based on student´s satisfaction and the actual acquisition and strengthening of knowledge.

Recent analyses of cosmic microwave background (CMB) maps have been interpreted as demonstrating that the Universe was born without an initial rotation. However, these analyses are based on unrealistic models and do not contain essential ingredients such as quantum effects, the strong, weak and gravitational interactions between the components, their intrinsic spins and magnetic moments, as well as primordial black holes. If the Universe was born spinning these effects would distribute the initial spin angular momentum among its components long before the CMB forms at recombination. A primordial spin would now appear as a nonzero total angular momentum of its components along the direction of the original spin, and a primordial large-scale rotation would no longer be apparent. The existence of a special axis or direction would break a fundamental symmetry assumed in general relativity, cosmic isotropy, and a net angular momentum implies a cosmic parity violation.

This paper proposes a mathematical model to simulate Day-ahead markets of large-scale multi-energy systems with high share of renewable energy. Furthermore, it analyses the importance of including unit commitment when performing such analysis. The results of the case study, which is performed for the North Sea region, show the influence of massive renewable penetration in the energy sector and increasing electrification of the district heating sector towards 2050, and how this impacts the role of other energy sources such as thermal and hydro. The penetration of wind and solar is likely to challenge the need for balancing in the system as well as the profitability of thermal units. The degree of influence of the unit commitment approach is found to be dependent on the configuration of the energy system. Overall, including unit commitment constraints with integer variables leads to more realistic behaviour of the units, at the cost of increasing considerably the computational time. Relaxing integer variables reduces significantly the computational time, without highly compromising the accuracy of the results. The proposed model, together with the insights from the study case, can be specially useful for system operators for optimal operational planning.

The world is currently, subjected to the worst health crisis documented in modern history; an epidemic led by the novel coronavirus disease 2019 (COVID-19). At the epicenter of this crisis, healthcare professionals continue working to safeguard our well-being. To the regular high levels of stress, COVID new heights even more to healthcare professionals so depending on the area, specialty, and type of work. Here we investigated what are the tendencies, or areas most affected. Through an adaptation of the original COVID-stress scale, we developed a remote, fast test designed for healthcare professionals of the Northeastern part of Mexico, an important part of the country with economic and cultural ties to the US. Our results showed 4 key correlations as highly dependent: Work area – Xenophobia (p &lt; 0.045), Work with COVID patients - Traumatic stress (p &lt; 0.001) and Total number of COVID patients per day – Traumatic stress (p &lt; 0.027), and Total number of COVID patients - Compulsive checking and reassurance. Overall concluding that normal levels of stress have increased (mild – moderate). Additionally, we further determine that the fear of being an asymptomatic patient (potential to spread without knowing) continues being a concern.

This paper presents a novel method to extract local features, which instead of calculating local extrema computes global maxima in a discretized scale-space representation. To avoid obtaining precise scales by interpolation and to achieve perfect rotation invariance, two essential techniques, increasing the width of kernels in pixel and utilizing disk-shaped convolution template are adopted in this method. Since the size of a convolution template is finite and finite templates can introduce computational error into convolution, we sufficiently discuss this problem and work out an upper bound of the computational error. The upper bound is utilized in the method to ensure that all features obtained are computed under a given tolerance. Besides, the technique of relative threshold to determine features is adopted to reinforce the robustness for the scene of changing illumination. Simulations show that this new method attains high performance of repeatability in various situations including scale change, rotation, blur, JPEG compression, illumination change and even viewpoint change.

Marine mortar was the goal material and its multi-scale physical-chemical-mechanical characteristics were the principal interest in this study. The on-line multi-scale damage detection experiments art was designed to quantify the characteristics mathematically and graphically. The normal cylinder specimen with 70-day age was produced and investigated by dynamically global MSHCT scan and local detection of EDS, SEM and XRD. The experiments results indicated that the marine mortar offered the appreciable strength at the early age at least, although some saline minerals were generated during the preparation. The micro-interfacial behavior and the parental foci controlled the damage development of the marine mortar the performance of which was still the adjustable one by the composition optimization.

After reviewing foundational literature by Snyder, I will demonstrate how hope theory has been used in psychological interventions and psychiatry, how hope influences learning and medical outcomes, and how hope can be applied to difficult life circumstances. Using this literature review, hope theory will be interrogated. I will argue that hope theory has developed its way through the years to garner many strengths, however a few weaknesses do exist and will be described. I will conclude with recommendations for using hope theory in practice, including the medical field, psychological interventions and counseling, and student development.

In a recent Foundations of Physics paper [5] by the current author it was shown that, when the self-force problem of classical electrodynamics is properly solved, it becomes a plausible ontology underlying the statistical description of quantum mechanics. In the current paper we extend this result, showing that ordinary matter, thus represented, possibly suffices in explaining the outstanding observations currently requiring for this task the contrived notions of dark-matter, dark-energy and inflation. The single mandatory 'fix' to classical electrodynamics, demystifying both very small and very large scale physics, should be contrasted with other adhoc solutions to either problems. Instrumental to our cosmological model is scale covariance (and 'spontaneous breaking' thereof), a formal symmetry of classical electrodynamics treated on equal footing with its Poincare covariance, which is incompatible with the (absolute) metrical attributes of the GR metric tensor.

According to the standard cold dark matter (CDM) cosmology, the structure of dark halos including those of galaxy clusters reflects their mass accretion history. Older clusters tend to be more concentrated than younger clusters. Their structure, represented by the characteristic radius $r_s$ and mass $M_s$ of the Navarro-Frenk-White (NFW) density profile, is related to their formation time. In this study, we show that $r_s$, $M_s$, and the X-ray temperature of the intracluster medium (ICM), $T_X$, form a thin plane in the space of $(\log r_s, \log M_s, \log T_X)$. This tight correlation indicates that the ICM temperature is also determined by the formation time of individual clusters. Numerical simulations show that clusters move along the fundamental plane as they evolve. The plane and the cluster evolution within the plane can be explained by a similarity solution of structure formation of the universe. The angle of the plane shows that clusters have not achieved “virial equilibrium” in the sense that mass/size growth and pressure at the boundaries cannot be ignored. The distribution of clusters on the plane is related to the intrinsic scatter in the halo concentration--mass relation, which is originated from the variety of cluster ages. The well-known mass--temperature relation of clusters ($M_\Delta\propto T_X^{3/2}$) can be explained by the fundamental plane and the mass dependence of the halo concentration without the assumption of virial equilibrium. The fundamental plane can also be used for calibration of cluster masses.

Earth's global surface temperature shows variability on an extended range of temporal scales and satisfies an emergent scaling symmetry. Recent studies indicate that scale invariance is not only a feature of the observed temperature fluctuations, but an inherent property of the temperature response to radiative forcing, and a principle that links the fast and slow climate responses. It provides a bridge between the decadal- and centennial-scale fluctuations in the instrumental temperature record, and the millennial-scale equilibration following perturbations in the radiative balance. In particular, the emergent scale invariance makes it possible to infer equilibrium climate sensitivity (ECS) from the observed relation between radiative forcing and global temperature in the instrumental era. This is verified in ensembles of Earth system models (ESMs), where the inferred values of ECS correlate strongly to estimates from idealized model runs. For the range of forcing data explored in this paper, the method gives best estimates of ECS between 2.3 and 3.4 K.

This is the second of a two-paper series describing a multi-scale modeling approach developed to simulate crack sensing in polymer fibrous composites by exploiting interruption of electrically conductive carbon nanotube (CNT) networks. The approach is based on the finite element (FE) method. FE models at three different scales, namely the micro-scale, the meso-scale and the macro-scale, have been developed using the ANSYS PDL environment. In the present paper, the meso- and macro-scale analyses are described. In the meso-scale, a two-dimensional model of the CNT/polymer matrix reinforced by carbon fibers is used to develop a crack sensing methodology from a parametric study which relates the crack position and length with the reduction of current flow. In the meso-model, the effective electrical conductivity of the CNT/polymer computed from the micro-scale is used as input. In the macro-scale, the final implementation of the crack sensing methodology is performed on a CNT/polymer/carbon fiber composite volume using as input the electrical response of the cracked CNT/polymer derived at the micro-scale and the crack sensing methodology. Analyses have been performed for cracks of two different lengths. In both cases, the numerical model predicts with good accuracy both the length and position of the crack. These results highlight the prospect of conductive CNT networks to be used as a localized structural health monitoring technique.

The role played by non extensive thermodynamics in physical systems has been under intense debate for the last decades. With many applications in several areas, the Tsallis statistics has been discussed in details in many works and triggered an interesting discussion on the most deep meaning of entropy and its role in complex systems. Some possible mechanisms that could give rise to non extensive statistics have been formulated along the last several years, in particular a fractal structure in thermodynamics functions was recently proposed as a possible origin for non extensive statistics in physical systems. In the present work we investigate the properties of such fractal thermodynamical system and propose a diagrammatic method for calculations of relevant quantities related to such system. It is shown that a system with the fractal structure described here presents temperature fluctuation following an Euler Gamma Function, in accordance with previous works that evidenced the connections between those fluctuations and Tsallis statistics. Finally, the fractal scale invariance is discussed in terms of the Callan-Symanzik Equation.

The physical and economic sustainability of using Built Environment Wind Turbine (BEWT) systems depends on the wind resource potential of the candidate site. Therefore, it is crucial to carry out a wind resource assessment prior to deployment of the BEWT. The assessment results can be used as a referral tool for predicting the performance and lifespan of the BEWT in the given built environment. To date, there is limited research output on BEWTs in South Africa with available literature showing a bias towards utility-scale or conventional ground based wind energy systems. This study aimed to assess wind power generation potential of BEWT systems in Fort Beaufort using the Weibull distribution function. The results show that Fort Beaufort wind patterns can be classified as fairly good and that BEWTs can best be deployed at 15m for a fairer power output as roof height wind speeds require BEWT of very low cut-in speed of at most1.2ms⁻¹.

Accurate assessment of the breast cancer deterioration degree plays a crucial role in making medical plan, and the important basis for degree assessment is the number of mitoses in a given area of the pathological image. We utilized deep multi-scale fused fully convolutional neural network (MFF-CNN) combing with conditional random felid (CRF) to detect mitoses in hematoxylin and eosin stained histology image. Analyze the characteristics of mitotic detection ----scale invariance and sparsity, as well as the difficulties ---- small amount of data , inconsistent image staining and sample class unbalanced. Based on this, mitotic detection model is designed. In this paper, a tissue-based staining equalization method is used, and to establish an effective training sample set, we select training samples by using CNN. A mitotic detection model fusing multi-level and multi-scale features and context information was designed, and the corresponding training strategy was made to reduce over-fitting. As preliminarily validated on the public 2014 ICPR MITOSIS data, our method achieves a better performance in term of detection accuracy than ever recorded for this dataset.

In 1990 the Malaysian Government launched Vision 2020 with the goal of Malaysia becoming a ‘fully developed country’ by the year 2020. In this drive for development the country has been examining many of its key natural assets, exploring how to both preserve them whilst ensuring that they make the maximum possible contribution to national development goals. Endau Rompin is one of these assets, being the second largest National Park in Peninsula Malaysia. The rich tropical rainforest flora and fauna of the Park and its hinterland, however, are threatened by various anthropogenic forces, most notably deforestation and poaching; both of which have taken the Park’s flagship species - the Tiger Panthera tigris jacksoni – towards the brink of local extinction. Malaysia’s statutory East Coast Economic Region Development Council commissioned a study to consider ways of increasing tourism revenues from the Park while at the same time reversing these threats. The key conclusion drawn is that a more holistic, landscape-scale approach should be adopted, with Endau Rompin forming part of a wider strategic economic zone based around sustainable tourism and land management. The proposed expanded zone extends eastwards beyond the confines of the Park, across the coastal plain to the South China Sea, and onwards to the neighbouring Mersing Islands. This expanded zone is referred to as Malaysia’s new ‘Rainforest to Reef Region’.

Artisanal and small-scale gold mining (ASGM) has been an important source of income for communities in the Madre de Dios River Basin in Peru for hundreds of years. However, in recent decades, the scale of ASGM activities in the region has increased dramatically, and exposures to a variety of occupational and environmental hazards related to ASGM, including mercury, are becoming more widespread. The aims of our study were to: (1) examine patterns in the total hair mercury level of human participants in several communities in the region and compare these results to the 2.2 µg/g total hair mercury level equivalent to the World Health Organization (WHO) Expert Committee of Food Additives (JECFA)’s Provisional Tolerable Weekly Intake (PTWI); and (2), to measure the mercury levels of paco (Piaractus brachypomus) fish raised in local aquaculture ponds, in order to compare these levels to the EPA Fish Tissue Residue Criterion of 0.3 µg Hg/g fish (wet weight). We collected hair samples from 80 participants in four communities (one control and three where ASGM activities occurred) in the region, and collected 111 samples from fish raised in 24 local aquaculture farms. We then analyzed the samples for total mercury. Total mercury levels in hair were statistically significantly higher in the mining communities than in the control community, and increased with increasing distance away from the Madre de Dios headwaters (as the crow flies), did not differ by sex, and frequently exceeded the reference level. Regression analyses indicated that higher hair mercury levels were associated with residence in ASGM communities. The analysis of paco fish samples found no samples that exceeded the EPA tissue residue criterion. Collectively, these results align with other recent studies showing that ASGM activities are associated with elevated human mercury exposure. The fish farmed through the relatively new process of aquaculture in ASGM areas appeared to have little potential to contribute to human mercury exposure. More research is needed on human health risks associated with ASGM to discern occupational, residential, and nutritional exposure, especially through tracking temporal changes in mercury levels as fish ponds age, and assessing levels in different farmed fish species. Additionally, research is needed to definitively determine that elevated mercury levels in humans and fish result from the elemental mercury from mining, rather than from a different source, such as the mercury released from soil erosion during deforestation events from mining or other activities.

Escherichia coli is an indicator microorganism in One Health antibiotic resistance surveillance programmes. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harboured a richer diversity of antibiotic resistance genes, as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%; 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169) were detected at low frequencies. Sequence type complex (STc) 10 were the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2 to HC200 were observed. In conclusion, even though the isolates shared a spatio-temporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles, and cgMLST and HC according to the source of isolation.

Lecanicillium lecanii KMZW-1, is recognized for its potential as a bio-control agent against agricultural and forestry pests, particularly due to its compatibility with integrated pest management (IPM) strategies. This study aimed to investigate the complete genome of L. lecanii KMZW-1 and assess its pathogenicity against Bactrocera dorsalis. Whole genome sequencing revealed a genome size of 47,239,278 bp, comprising 27 contigs, with a GC content of 51.16%. The genome completeness was assessed as 97.93% using BUSCO analysis, AntiSMASH analysis identified 29 gene clusters associated with secondary metabolite biosynthesis providing insights into the genetic basis of its pathogenic mechanisms and biocontrol potential. The pathogenicity of L. lecanii KMZW-1 was assessed using concentrations ranging from 1×10^4 to 1×10^11 spores/mL. Higher-concentrations (1×10^10 to 1×10^11 spores/mL), resulted in significantly increased cumulative mortality rates of B. dorsalis adults compared to the control group. Notably, the pathogenicity was higher in male adults than in females. Probit regression analysis yielded LogLC50 values as 5.662 for female and 4.486 for male B. dorsalis adults. In summary, L. lecanii KMZW-1 exhibits strong insecticidal activity against B. dorsalis and shows potential as a biocontrol agent with IPM strategies. These findings provide robust genomic evidence supporting the use of L. lecanii KMZW-1in managing against B. dorsalis populations.

The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants is a challenge to public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4,213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 from California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage, or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.

Since the first reported case of COVID-19 in December 2019, several SARS-CoV-2 variants has evolved and some of them have shown higher transmissibility becoming the prevalent strains. Genomic epidemiological investigations into strains from different time points including the early stages of the pandemic are very crucial for understanding the evolution and transmission patterns. Using whole genome sequences, our study describes the early landscape of SARS-CoV-2 variants in central India retrospectively (including the first known occurrence of SARS-CoV-2 in Madhya Pradesh). We performed amplicon based whole genome sequencing of randomly selected SARS-CoV-2 isolates (n=38) collected between 2020-2022 at state level VRDL, ICMR-NIRTH, Jabalpur from 11899 RT-qPCR positive samples. We observed the presence of five lineages namely B.1, B.1.1, B.1.36.8, B.1.195 and B.6 in 19 genomes from the first wave cases and variants of concern (VOC) lineages i.e. B.1.617.2 (Delta), and BA.2.10 (Omicron) in the second wave cases. There was a shift in mutational pattern of SRAS-CoV-2 strains from the second wave in contrast to the first wave. We have identified five immune escape variants in the S gene: P681R, P681H, L452R, Q57H, and N501Y in the isolates collected during the second wave. Furthermore, these genomes were compared with 2160 complete genome sequences reported from central India that encompass 109 different SARS-CoV-2 lineages. Among them, VOC lineages Delta (28.93%), and Omicron (56.11%) were circulating predominantly in this region. This study provides useful insights into the genetic diversity of SARS-CoV-2 strains over the initial course of the COVID-19 pandemic in central India.

Habenaria, a member of Orchidaceae family is the cosmopolitan distributions, which has significant medicinal and ornamental values. Regardless of morphology and molecular data that have been studied in recent times, the phylogenetic relationship is still under debate. Here, we sequenced, assembled, and annotated the whole chloroplast (cp) genome of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and combined with seven already published cp genomes which may assist to uncover their genomic profiling. The two genomes ranged from 155259-155269 bp in length and both encoded 132 genes, including 86 protein, 38 tRNA and 8 rRNA. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions showed similarities among the species. Moreover, we identified 16 highly polymorphic regions with nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on the several genes such as cemA, petA, and ycf1. This may suggest that the important adaptation stratagem for two Habenaria species on the QTP. The phylogenetic relationship displayed that H.aitchisonii and H. tibetica have closer relationship than others and the rest seven species clustered in the other three groups. Our findings also supported the idea that Habenaria could be divided into different sections. This study enriched the genomics resources of Habenaria, which may be helpful for the conservation efforts of these endangered species.

Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and large extent of non-additive genetic variance associated with its autotetraploid genome. Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as autotetraploid and diploid dosage, plus allele ratios) and SNP marker subsetting (all available SNPs; only genic regions; only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used Genotyping by Sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and onset of flowering, assessed on 143 genotyped plants from a genetically-broad European reference population and their phenotyped half-sib progenies. Results: On average, allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), SNP subsetting offered an advantage compared with any tested subsettings (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting reached better performances. We also released Legpipe2, a SNP calling pipeline tailored for reduced representation (GBS, RAD) medium-sized genotyping experiments.

Abstract: CRISPR/Cas systems are used for genome editing, both in basic science and in bio-technology. At the same time, CRISPR/Cas editors have several limitations, including insufficient specificity leading to "off-targets" and the dependence of activity on chromatin state. A number of highly specific Cas9 variants have been obtained now, but most of them are characterized by reduced activity on eukaryotic chromatin. We identified a spatial cluster of amino acid residues in the PAM-recognizing domain of Streptococcus pyogenes Cas9, whose mutations restore the activity of one of the highly specific forms of SpyCas9 without reducing its activity in Saccharomyces cere-visiae. In addition, one of these new mutations also increases the efficiency of SpyCas9-mediated editing of a site localized on the stable nucleosome. The improved Cas9 variants we obtained, which are capable of editing hard-to-reach regions of the yeast genome, may help in both basic research and yeast biotechnological applications.

Here, we critically evaluate the communication and integrative mechanisms in ctenophores or comb jellies, the descendants of the earliest animal lineage. Ctenophores convergently evolved their neuro-muscular systems compared to other animals. Besides the canonical neural organization with distinct synapses, recent 3D electron microscopy reconstruction revealed unique syncytial-type connectivity in some neuronal populations, providing additional support for the independent origins of neurons in ctenophores. Furthermore, it was proposed that non-synaptic transmission is the distinct characteristic of ctenophores, in contrast to other metazoans and Cajal’s neuronal doctrine, highlighting Golgi’s reticular theory. However, the astonishing diversity and higher information capacity of classical synapses and volume transmission indicate that chemical signaling is the hallmark of neural and other integrative systems regardless of their origins.

Vancomisin resistant enterococcus(VRE), is a resistant microorganism which colonizates and causes infections in hospitalized patients. It was aimed to show the spread of vancomycin-resistant Enterococcus (fVREfm) step-by-step in all intensive care units, which started with the growth of vancomycin-resistant Enterococcus faecium (VREfm) on 02.12.2021 in the blood culture of a patient hospitalized in the anesthesia intensive care unit of our hospital and was found to have reached epidemic size in the surveys. Rectal swab samples were taken from all patients hospitalized in intensive care units, VRE colonization was determined and the VanA and VanB resistance genes associated with vancomycin resistance of VREfm isolates were determined by PCR method, and clonal association analysis was performed by Arbitrarily Primed-PCR (AP-PCR) and Pulsed-Field Gel Electrophoresis. In our study, VRE was detected in 61 of 2601 rectal swab samples. 54 (85.52%) of the VRE isolates were Enterococcus faecium, 3 (4.91%) was Enterococcus faecalis, 3 (4.91%) was Enterococcus gallinorum, 1 (1.63%) was Enterococcus casseliflavus. It was determined that all of the 54 VREfm isolates, which were the most detected among all VRE isolates, carried the vanA gene. In the clonal association analysis of the isolates by AP-PCR and PFGE methods, it was found that they had 12 different genotypes, 48 of them were included in any cluster, the clustering rate was 88.8%, and the largest cluster was genotype 1 cluster with 36 isolates. Of the 54 patients with VREfm isolated recently, 18.51 percent of the clinical samples were isolated before the survey, and 9.24% were isolated after the survey. It was determined that 100% of VREfm isolates were resistant to ampicillin, levofloxacin, ciprofloxacin, high-level gentamicin, trimethoprim-sulfamethoxazole, teicoplanin, 7.4% to tigecycline and 1.85% to linezolid. In our study, in the clonal association analysis performed by isolating VREfm in rectal swab samples, it was found that 88.8% of the samples were indistinguishably similar and the increase in the number of VREfm infections after the index case in our hospital was associated with the epidemic. VREfm infections cause long term hospitalization, costs and also deaths, which shows the seriousness of the event, and the importance of the combination of epidemiological and molecular analysis in epidemic research.

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

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of a first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: 1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; 2) a comprehensive variant calling pipeline; 3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequenc-ing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of the variant calling pipeline are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusion: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of up-to-date list of mutations, which can be incorporated into global efforts to sustainably prevent or treat infections.

Coronavirus disease 2019 (COVID-19), the emissary behind the worst global pandemic of the 21st century, is primarily a respiratory disease-causing virus called SARS-CoV-2 which is responsible for millions of new cases (incidence) and deaths (mortalities), worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. Nevertheless, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, was not properly discussed before. Therefore, an astounding issue arose when some developed countries experienced higher morbidity and mortality, compared with their relatively underdeveloped counterparts, despite having excellent medical health facilities. Hence this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, copy number variation, and how they could modulate the innate and adaptive immune systems, which put a particular ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.

Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent ge-nomic recombination. Here, we propose a new method, named coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic ori-gins. The results indicate that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed an-cestry originating from horseshoe bat (Rhinolophus) viruses. First, different regions of SARS-CoV share exclusive ancestry with five Rhinolophus viruses from Southwest China (RfYNLF/31C: 17.9%; RpF46: 3.3%; RspSC2018: 2.0%; Rpe3: 1.3%; RaLYRa11: 1.0%) and 97% of its genome can be related to bat viruses from Yunnan (China), supporting its emergence in Rhinolophus species of this province. Second, different regions of SARS-Cov-2 share exclusive ancestry with eight Rhi-nolophus viruses from Yunnan (RpYN06: 5.8%; RaTG13: 4.8%; RmYN02: 3.8%), Laos (RpBA-NAL103: 3.3%; RmarBANAL236: 1.7%; RmBANAL52: 1.0%; RmBANAL247: 0.7%), and Cam-bodia (RshSTT200: 2.3%), and 98% of its genome can be related to bat viruses from northern Laos and Yunnan, supporting its emergence in Rhinolophus species of this region. Although CGB barcodes are very useful to retrace the origins of human sarbecoviruses, further investigations are needed to better apprehend the diversity of coronaviruses in bats from Cambo-dia, Laos, Myanmar, Thailand and Vietnam.

Viroids are known the smallest plant pathogens, and although their genome sequences do not encode proteins, they can cause disease in economically important crops. In order to control viroid diseases and mitigate their damage, genetic resources used for breeding of the viroid-resistant crop have been searched, but the practical resistant trait has not been found in almost all viroid-crop combinations, as well as the tolerant trait. Due to the difficulty in exploiting naturally occurring resistance or tolerance, various effective strategies have been devised to control viroid diseases using non-transforming or transforming techniques. Meanwhile, extensive findings related to viroid resistance and tolerance may lead to confer resistance or tolerance to viroid infection by combining with the recently emerged new technologies (e.g., spray-induced gene silencing and genome-editing technologies), which are believed to be more environmentally viable and acceptable to the general public than previously reported approaches. In particular, some genome-modified crops produced by the latter technology are already on the market. In this review, we comprehensively summarize the current status about investigation of naturally occurring genetic traits for viroid resistance and tolerance, accumulating knowledge about host factors involved in viroid pathogenicity, and various basic technologies developed to try to possible viroid disease control strategies. Furthermore, we discuss prospects and challenges for the achievement of more effective, practical, and sustainable disease control of viroid.

Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the non-resistant but otherwise identical 20A>T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to Northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here we address this finding with the replacement hypothesis, according to which pre-existing genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, a gradual evolutionary process under selection can hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A>G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called Interaction-based Evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directional mutational responses to specific environmental pressures are possible. Such responses need to be further tested by future studies in natural and artificial settings.

Members of the insect ATP binding cassette transporter subfamily C2 (ABCC2) in several moth species are known as receptors for the Cry1Ac insecticidal protein from Bacillus thuringiensis (Bt). Mutations that abolish the functional domains of ABCC2 are known to cause resistance to Cry1Ac, although the reported levels of resistance vary widely depending on insect species. In this study, the function of the ABCC2 gene as putative Cry1Ac receptor in Helicoverpa zea, a major pest of over 300 crops, was evaluated using CRISPR/Cas9 to progressively eliminate different functional ABCC2 domains. Results from bioassays with edited insect lines support that muta-tions in ABCC2 was associated with Cry1Ac resistance ratios (RR) ranging from 7.3- to 39.8-fold. No significant differences in susceptibility to Cry1Ac were detected between H. zea with partial or complete ABCC2 knockout, although highest levels of tolerance were observed when knocking out half of ABCC2. Based on >500-1,000-fold RRs reported in similar studies for closely related moth species, the low RRs observed in H. zea knockouts support that ABCC2 is not a major Cry1Ac receptor in this insect.

Repetitive nature of the ribosomal DNA (rDNA) gene makes the sequencing of hundreds copies of mammalian 45S rDNA (about 45-kb per copy) extremely difficult and its assembly is often excluded. Increasing evidence shows that 45S rDNA variations (copy number or single nucleotide), structural ribosomal RNA (rRNA) transcript variants, and non-structural rRNA transcripts (sense and anti-sense long noncoding rRNAs that include promoter rRNAs, and rRNA-derived fragments) play essential roles in mammalian development and diseases. Complete pictures of the hundreds copies of 45S rDNA and their rRNA transcripts require further innovation in sequencing techniques that include bioinformatics. The advancements in mammalian rDNA and rRNA sequencings and the discoveries of novel functions of the rDNA variants and rRNA transcripts are discussed here.

To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in the GISAID repository, till 21 August 2020. Globally, nsp1/nsp2/nsp3/ nsp11 and orf7a/orf3a/S were the most mutation-ridden non-structural and structural genes respectively. Phylogeny based on 4,618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries (including India, the biggest hotspot of the pandemic) whereas the recently-derived lineages are more globally distributed. Of the total 16,602 polymorphism-bearing sites in the pan-genome, 11,037 and 4,965 involved transitions and transversions, which in turn were predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host’s metabolic system, while it is still redefining virulence/transmissibility strategies at the molecular level.

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

Triploidy in cancer is associated with poor prognosis but its origins remain unclear. Here, we attempted to differentiate between random chromosomal and whole-genome origins of cancer triploidy. In silico meta-analysis was performed on 15 male malignant and 5 benign tumour cohorts (2928 karyotypes) extracted from the Mitelman Database, comparing their ploidy and combinations of sex chromosomes. A distinct near-triploid fraction was observed in all malignant tumour types, being especially high in seminoma. For all tumour types, X-chromosome doubling, predominantly observed as XXY, correlated strongly with the near-triploid state (r≈0.9, p<0.001), negatively correlated with near-diploidy, and did not correlate with near-tetraploidy. A smaller near-triploid component with a doubled X-chromosome was also present in 3 of 5 benign tumour types, especially notable in colon adenoma. Principal Component Analysis revealed a non-random correlation structure shaping the X-chromosome disomy distribution across all tumour types. We suggest that doubling of the maternal genome followed by pedogamic fusion with a paternal genome (a possible mimic of the fertilization aberration, 69, XXY digyny) associated with meiotic reprogramming may be responsible for the observed rearrangements of genome complements leading to cancer triploidy. The relatively frequent loss of the Y-chromosome results secondary from chromosome instability.

A double-stranded RNA (dsRNA) virus was isolated and characterized from a strain EW220 of the phytopathogenic fungus Botryosphaeria dothidea. The full-length cDNAs of dsRNAs were 6,434 bp and 5,986 bp in size, respectively. The largest dsRNA of BdBRV1 encodes a cap-pol fusion protein that contains part coat protein gene and a RNA-dependent RNA polymerase (RdRp) domain, and the second dsRNA encodes a hypothetical protein. The dsRNA virus was named Botryosphaeria dothidea botybirnavirus 1 (BdBRV1). BdBRV1 contains spherical virions that are 37 nm in diameter consisting of two segments. The structural proteins of BdBRV1 virus particles were 110 kDa, 90 kDa, and 80 kDa, which encoded by dsRNA1 and 2-ORFs. The analysis of genome sequences revealed that the sequences of BdBRV1 shared 99% identity with Bipolaris maydis botybirnavirus 1(BmBRV1). Phylogenetic reconstruction indicated that BdBRV1 and BmBRV1 are phylogenetically related to the genus Botybirnavirus. Importantly, BdBRV1 influences the growth of B. dothidea and confers hypovirulence to the fungal host. BdBRV1 and BmBRV1 were two strains of the same virus. To our knowledge, this is the first report of a botybirnavirus in B. dothidea and our result might be the first funding in the different fungi infected by the same virus.

With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.

Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultivars to be machine harvested. Fruit softening naturally occurs during berry development, maturation, and postharvest ripening. However, some genotypes are better at retaining firmness than others, and some are crispy, which is a putatively extra-firmness phenotype that provides a distinct eating experience. In this review, we summarized important studies addressing the firmness trait in blueberry, focusing on physiological and molecular changes affecting this trait at the onset of ripening and also the genetic basis of firmness variation across individuals. New insights into these topics were also achieved by using previously available data and historical records from the blueberry breeding program at the University of Florida. The complex quantitative nature of firmness in an autopolyploid species such as blueberry imposes additional challenges for the implementation of molecular techniques in breeding. However, we highlighted some recent genomics-based studies and the potential of a QTL mapping analysis and genome editing protocols such as CRISPR to further assist and accelerate the breeding process for this important trait.

The Hyper-Torus Universe Model (HTUM) proposes a novel framework to unify quantum mechanics, cosmology, and consciousness. This paper introduces HTUM's core concept: a higher-dimensional hyper-torus encompassing all possible states of existence. HTUM suggests that the universe functions as a quantum system where all outcomes are inherently connected, with consciousness playing a significant role in actualizing reality. The model introduces several key innovations, including the universe's 4-dimensional toroidal structure (4DTS), providing a new geometric interpretation of spacetime. HTUM presents dark matter and dark energy as nonlinear probabilistic phenomena within this toroidal framework, offering a unique perspective on their nature and interactions. The model proposes a mechanism for wave function collapse through universal self-observation, bridging quantum mechanics and gravity. It introduces a Topological Vacuum Energy Modulator (TVEM) function, offering a potential resolution to the cosmological constant problem. Furthermore, HTUM integrates consciousness as a fundamental aspect of the universe, influencing quantum state actualization and potentially resolving the hard problem of consciousness. The model explores the implications of a timeless singularity and the emergence of time as a product of causal relationships within the toroidal structure. This framework addresses critical challenges in modern physics, including the nature of quantum entanglement, the origin and fate of the universe, and the relationship between mind and matter. The paper discusses the mathematical formulation of HTUM, its implications for quantum mechanics and cosmology, and its potential to bridge the gap between science and philosophy. We present detailed predictions for the cosmic microwave background (CMB) power spectrum, gravitational wave signatures, and large-scale structure formation, demonstrating how HTUM differs from the standard ΛCDM model. Our analysis reveals distinctive oscillatory patterns in the relative difference between HTUM and ΛCDM predictions, with deviations reaching up to ±20% at certain scales. The paper also explores the unification of fundamental forces within the HTUM framework, proposing novel approaches to particle physics and quantum field theory. It introduces the concept of unified mathematical operations, suggesting a more holistic approach to mathematical thinking that aligns with the model's interconnected view of the universe. Additional testable predictions and proposed experimental approaches are discussed, including advanced space-based tests and laboratory experiments probing quantum gravity effects. These specific, quantifiable predictions offer multiple avenues for empirical validation, highlighting HTUM's potential to be distinguished from ΛCDM and other alternative cosmological models. HTUM represents a significant new perspective in our understanding of the universe, inviting further research and exploration into the nature of reality, consciousness, and the fundamental structure of the cosmos. By providing a comprehensive framework that unifies various aspects of physics, cosmology, and consciousness studies, HTUM offers a promising path toward a more complete understanding of our universe.

As motor capacity and rated voltage increase, the demand for motor insulation also increases. Additionally, the electric field distribution at the end of a large-scale hydro generator is extremely non-uniform, and corona discharge readily occurs. This destroys the main insulation, which significantly affects the service life of electrical machinery. Thus, the regulation of the electric field concentration at the end of a large-scale hydro generator needs to be addressed. There are many problems in resistance–capacitance chain model research. Particularly, these models cannot accurately reflect the insulation, corona structure, and electric field distribution in electrical machinery. Additionally, the corner electric field and loss distributions cannot be obtained, leading to a higher calculation error. The electric field distribution at the motor end and the loss distribution were analyzed using the finite-element method. First, by applying the basic principles of electric circuits and electromagnetic field theory, we calculated the electric field distribution at the stator bar end. Second, a 3D model of the stator bar was built using Creo Parametric, yielding a model that is more closely related to the prototype wirebar model. Then, the potential, electric field, and loss distributions around the stator bar were simulated by using COMSOL simulation software. The effects of the circular arc corner, nonlinearity coefficient, anti-corona coating length, and resistivity of the stator bar on the electric field distribution at the motor end were explored.

After an earthquake, assessing the seismic vulnerability of buildings is essential for prioritizing emergency response, guiding reconstruction, and ensuring public safety. Accurate and timely evaluation of structural damage plays a vital role in mitigating further risks and facilitating in-formed decision-making during disaster recovery. This study investigates the performance of various Generative Artificial Intelligence (GAI) models, developed by different companies with diverse model sizes and context windows, in analysing post-earthquake images. The primary objective was to evaluate the models' effectiveness in classifying structural damage according to the EMS-98 scale (with 5 levels of damage), which ranges from minor damage to total destruction. For masonry buildings, the correct classification rates varied widely across models, from 28.6% to 64.3%, with mean damage grade errors ranging from 0.50 to 0.79. In the case of reinforced concrete buildings, correct classification rates ranged from 37.5% to 75.0%, with mean damage grade errors between 0.50 and 0.88. The use of fine-tuning could probably improve the results substantially. Improving the accuracy of GAI models could significantly reduce the time and resources needed to assess post-earthquake damage, namely when comparing with more traditional approaches. The results achieved thus far demonstrate the promise of GAI models for rapid, automated, and ac-curate damage evaluation, which is critical for expediting decision-making in disaster response scenarios.

An optical fiber scale sensor based on the detection principle of surface plasmon resonance (SPR) was developed for the rapid, high-sensitivity real-time evaluation of scale precipitation from geothermal fluids. The optical fiber SPR scale sensor was fabricated by depositing a gold thin film on the surface of an optical fiber with an exposed core. The optimal gold film thickness of the sensor was determined to be 30 nm, which achieved a refractive index sensitivity of 2140 nm per refractive index unit. A field test was conducted using geothermal brine from the Obama Binary Geothermal Power Plant in Unzen, Nagasaki Prefecture. A conventional optical fiber scale sensor and the SPR sensor were simultaneously assessed using raw and pH-adjusted brines. For the SPR sensor, a peak shift of 0.27 nm/min was observed at a response time of 1 min, whereas no change in transmittance was observed for the conventional sensor until 180 min. After the experiments, scanning electron microscopy–energy-dispersive spectroscopy analysis was conducted on the sensors, and findings showed that the deposition of Mg–SiO2 scale did not significantly differ between the two sensors. The developed SPR sensor achieved faster scale precipitation detection (tens of minutes to hours) than the conventional sensor.

Tourism Geographers in Anglo-American geographical departments migrate to teach and research tourism in applied schools and departments such as business, resource and environment, and even cultural and creative industry. Under national research assessment and funding pressures, tourism geographers are not encouraged to keep on undertaking serious theoretical researches related to their mother discipline and transferred to research applied researches and publish in hybrid journals. Such changes in tourism geographers` research behavior have not been tested and reported in Asian academic contexts, especially Taiwan while frequently being discussed internationally. This research aims to investigate the differences in the research behavior of tourism geographers between those who are staffed in geography departments and those who migrate to applies departments such as tourism and recreation, resource and environment, and others in terms of publishing journals, paradigmatic approaches, research types(qualitative, quantitative, and mixed), research methods and geographical scales conducted based on content analysis of articles published by tourism geographers in geography and tourism and recreation departments. This study revealed that there are significant differences in the research behavior of tourism geographers between different department. Finally, this paper explains the differences in terms of Taiwan changing social and economic conditions, academic traditions and politics of geography and applied departments, research habits and preferences of tourism geographers among departments and other aspects. This study can help international tourism geography academic circles to understand the complexity and diversity of tourism geography academic landscape of the Chinese language.

(1) Background: The rapid development of information technology has changed the traditional concept of space, gradually shifting the "container space" to the "relational space" . The constraints of geographical spatial elements are diminishing, and the theory of virtual agglomeration is gaining attention. (2) Methods: In this study, we constructed an evaluation system for virtual agglomeration, comprising four primary indicators: virtual infrastructure level, virtual output level, virtual input level, and virtual service level. The TOPSIS method was used to calculate the virtual agglomeration level for each province, and the DEA-Malmquist method was employed to measure provincial total factor productivity (TFP) in China. Using panel data from 30 provincial regions in China from 2013 to 2021, we examined the mechanism and impact path of virtual agglomeration on TFP. (3) Result: There is an inverted U-shaped relationship between virtual agglomeration and TFP in China. The overall development level of virtual agglomeration is relatively low, within the range where the marginal effect of virtual agglomeration on TFP is positive but diminishing, indicating significant potential for further development. The impact of virtual agglomeration on TFP is stronger in the Yangtze River Economic Belt compared to non-Yangtze River areas, and the highest stable point of TFP is higher in central provinces than in eastern and western provinces. (4) Conclusions: This study provides a theoretical basis and practical reference for improving the level of virtual agglomeration.

Objective biomarkers have been a critical challenge for the field of psychiatry, where diagnostic, prognostic and theranostics assessments are still based on subjective narratives. Psychopathology operates with idiographic knowledge and subjective evaluations incorporated into clinical as-sessment inventories, but is considered to be a medical discipline and, as such, uses medical in-tervention methods (e.g., pharmacological, ECT; rTMS; tDCS), and therefore is supposed to oper-ate with the language and methods of nomothetic networks. The idiographic assessments are pro-visionally “quantified” into “structured clinical scales” to in some way resemble nomothetic measures. Instead of fostering data merging and integration, this approach further encapsulates the clinical psychiatric methods, as all other, biological tests (molecular, neuroimaging) are per-formed separately, only after the clinical assessment has provided diagnosis. Translational cross-validation of clinical assessment instruments and fMRI is an attempt to address the gap. The aim of this approach is to investigate whether there exist common and specific neural circuits, which underpin differential item responses to clinical self-rating scales during fMRI session in pa-tients suffering from the two main spectra of mental disorders: schizophrenia and major depres-sion. The current status of this research program and future implications to promote the devel-opment of psychiatry as a medical discipline are discussed.

Commercial production of Choromytilus meridionalis (black mussel) and Mytilus galloprovincialis (Mediterranean mussel) contributes to half of the South African marine aquaculture production per year. However, limited ready-to-eat black mussel products are available. The aim of this preliminary study was to investigate the effects of storage (15 days at room temperature) on the total viable counts (TVC), coliforms, proximate composition, and fat oxidation (TBARS) of a small-scale kitchen-based ready-to-eat hot smoked black mussel product preserved with vegetable oil. Three batches of black mussel meat were smoked at 80ºC for 15 minutes. Half of each batch were packaged in sterile glass jars with heated (50ºC) vegetable oil and half without oil. Microbiological analyses were done at days 1, 3, 9 and 15. Proximate composition was determined at day 1 and TBARS at days 1 and 15. Coliforms for all samples throughout the storage period were undetected. TVC plates for mussels stored without oil had no growth at days 1 to 5, however, reached TVC > 5 log10.g-1 at day 15. TVC for mussels with oil increased from 0 at day 1 to > 5 log10.g-1 at day 3 and remained at counts > 5 log10.g-1. There was no significant difference (P > 0.05) in moisture, protein, and ash for mussels stored with oil and those without oil, while significant differences (P < 0.001) in total fat and carbohydrates (10.27 ± 2.10% and 6.80 ± 2.22% with oil, and 5.05 ± 1.49% and 10.59 ± 3.00% without oil) were detected. These differences were due to the presence of additional fats from the vegetable oil. TBARS at day 15 showed no significant difference (P > 0.05) between mussels stored with oil and those without oil. There were no significant differences in TBARS from day 1 to 15 for both oil and without oil. Small-scale kitchen-based smoked black mussels preserved without vegetable oil could be stored for up to 9 days at room temperature.

A two scalar field model that incorporates non Riemannian Measures of integration or usually called Two Measures Theory (TMT) is introduced, in order to unify the early and present universe. In the Einstein frame, a K-essence is generated and as a consequence for the early universe, we can have an Inflation for the very early universe and then, after inflation, an early dark energy period and a late dark energy period for the present universe dark, both dark energy epochs have a consistent generation of dark energy (DE), dark matter (DM) and stiff matter. This is obtained when the scale invariance is introduced and then is spontaneously broken from the integration of the degrees of freedom associated with the modified measures. The resulting effective potentials and K-essence in the Einstein frame produce the three flat regions corresponding to the different epochs mentioned before. For the first flat region, we can associate an inflationary universe. Also assuming this first plateau, we study the inflation in the framework of the slow-roll approximation. In this scenario under the slow roll approximation, we obtain a linear combination that is a constant. The corresponding cosmological perturbations in our model are determined and we also obtain the different constraints on the parameter-space from the Planck data. The slow roll approximation can be arranged so that the transition from inflation to the next flat region can be achieved without problems. In the following two flat regions, in addition to the inflation phase, representing the Early Dark Energy and Late Dark Energy Periods, with DE and also the DM, do not need to be introduced separately, they are instead a result of a K-essence induced by the multi measures, multi field theory. Therefore the scalars generate both the DE and the DM . Also a stiff matter component is automatically generated from the K-essence theory from two scalar fields. From the perturbative analysis associated to the perturbation solution of background, we find a correlation between the two scalars. Besides, we obtain that our model during the dark epoch has a behaviour of tracking freezing mode

This paper aims to demonstrate that, beyond the small world of Riemann-Liouville and Caputo derivatives, there is a vast and rich world with many derivatives suitable for specific problems and various theoretical frameworks to develop, corresponding to the different paths taken. Notions of time and scale sequences are introduced and general associated basic derivatives, namely right/stretching and left/shrinking, are defined. A general framework for fractional derivative definitions is reviewed and applied to get both known and new fractional order derivatives. Several fractional derivatives are considered, mainly: Liouville, Hadamard, Euler, bilinear, tempered, q-derivative, and Hahn.