We utilize how Weber in 1961 initiated the process of quantization of early universe fields to the problem of what may be emitted at the mouth of a wormhole. While the wormhole models are well developed, there is as of yet no consensus as to how, say GW or other signals from a wormhole mouth could be quantized, or made to be in adherence to a procedure Weber cribbed from Feynman, in 1961. In addition, we utilize an approximation for the Hubble parameter parameterized from Temperature using Sarkar’s H ~ Temperature relations, as given in the text . Finally after doing this we go to the Energy as E also ~ Temperature, and from there use E (energy) as ~ signal frequency. This gives us an idea of how to estimate frequency generated at the mouth of a wormhole.

We reduplicate the Book “Dark Energy” by M. Li, X-D. Li, and Y. Wang, given zero-point energy calculation with an unexpected “length’ added to the ‘width’ of a graviton wave just prior to specifying the creation of ‘gravitons’, while using Karen Freeze’s criteria as to the breakup of primordial black holes to give radiation era contributions to GW generation. The GW generation will be when there is sufficient early universe density so as to break apart Relic Black holes of the order of Planck mass (10^15 grams) which isabout when the mass of relic black holes is created, 10^-27 or so seconds after expansion starts. Need to state a key result will be in the initial potential V calculated, in terms of other input variables

We reduplicate the Book “Dark Energy” by M. Li, X-D. Li, and Y. Wang, zero-point energy calculation with an unexpected “length’ added to the ‘width’ of a graviton wavefunction just prior to the entrance of ‘gravitons’ to a small region of space-time prior to a nonsingular start to the universe. We compare this to a solution worked out using Klauder Enhanced quantization, for the same given problem. The solution of the first Cosmological Constant problem relies upon the geometry of the multiverse generalization of CCC cosmology which is explained in this paper. The second solution, used involves Klauder enhanced quantization. We look at energy given by our methods and compare and contrast it with the negative energy of the Rosen model for a mini sub universe and estimate GW frequencies

Complex systems can be described as the network of interactions between their components. In directed networks, information, energy and matter flow in dominant directions. Undirected networks, on the other hand, cannot easily capture these asymmetries. The local flow of information depends on the node spin, which is a function of the number of incoming and outgoing links attached to it. And yet, how the heterogeneous association between in-degree and out-degree constraints global dynamics remains poorly understood. Here, we develop a new theoretical model to study the relationship between node directionality and global flow dynamics. Our computational analysis of random and scale-free directed networks indicates that structural diversity constrains the dimensionality of reachable dynamical space. These results suggest how local directionality might be an universal driver of global dynamics in many systems, from social networks, to technological systems to the connectome.

The hypothesis posed was whether participation in LaLiga Genuine Santander (competitive football) influenced the quality of life (QL) of the people who participated in it, since their perception of themselves is enhanced by all the aformentioned factors (self-determination, social inclusion, emotional well-being, physical well-being, material well-being, rights, personal development, interpersonal relationships). The objective was to evaluate the QL of people with Down's Syndrome (DS) using their self-perception (n=39) and the perception of the informants (family members, teachers) (n=39). The KidsLife-Down Scale, with a few modifications was used. In general, differences of opinion between the subgroups of participants with DS and informants showed that results were higher in terms of perception for participants in the DS subgroup. Scores for all variables were higher for those participants with DS who said they did engage in practicing competitive football. Despite the perception of informants provides a great deal of information regarding the QL of participants with DS, the latter should be involved in the evaluation process and their self perceptions taken into account. Our research shows that participation in the league modifies the perceptions of the participants with Down's Syndrome regarding their quality of life. However, these perceptions are not shared by the informants.

Nanoparticle (NP) transport is increasingly relevant to subsurface engineering applications such as aquifer characterization, fracture electromagnetic imaging and environmental remediation. An efficient field-scale simulation framework is critical for predicting NP performance and designing subsurface applications. In this work, for the first time, a streamline-based model is presented to simulate NP transport in field-scale subsurface systems. It considers a series of behaviors exhibited by engineered nanoparticles (NPs), including time-triggered encapsulation, retention, formation damage effects and variable nanofluid viscosity. The key methods employed by the algorithm are streamline-based simulation (SLS) and an operator-splitting (OS) technique for modeling NP transport. SLS has proven to be efficient for solving transport in large and heterogeneous systems, where the pressure and velocity fields are firstly solved on underlying grids using finite-difference (FD) methods. After tracing streamlines, one-dimensional (1D) NP transport is solved independently along each streamline. The adoption of OS enhances flexibility for the entire solution procedure by allowing different numerical schemes to solve different governing equations efficiently and accurately. For the NP transport model, an explicit FD scheme is used to solve the advection term, an implicit FD scheme is used for the diffusion term and an adaptive numerical integration is used to solve the retention terms. The model is implemented in an in-house streamline-based code, which is verified against analytical solutions, a commercial FD reservoir simulator (ECLIPSE) and an academic FD colloid transport code (MNMs). For a 1D homogeneous case, the effluent breakthrough curves (BTC) produced by the in-house simulator are in good agreement with the analytical solution and MNMs, respectively. For a two-dimensional (2D) heterogeneous case, the BTC and concentration pattern of the in-house simulator all match well with the solution produced by commercial simulator. Simulations on a synthetic three-dimensional (3D) nanocapsule application engineering design case, are performed to investigate the effect of fluid and NP properties on the displacement pattern of an existing subsurface fluid.

Therapeutic proteins are used to successfully treat hemophilia, Crohn’s Disease, diabetes, and cancer. Recent product recalls have occurred because of sub-visible particle formation resulting from the inherent instability of proteins. It has been suggested that particle formation is associated with late stage processing steps of filling, shipping, and delivery. Previous works demonstrated that cavitation might occur in therapeutic vials subjected to agitation or accidentally dropped, but that mitigation can be achieved with fluid property manipulation. The goal of this research was to (1) assess the risk of cavitation under common pharmaceutical manufacturing conditions (i.e., pipe contraction and pumps), (2) establish a simple threshold criterion for when particulate will form, and (3) suggest a series of mitigation techniques based on these thresholds. To accomplish these tasks, computational fluid dynamic simulations for a variety of pipe contraction and fluid properties were performed. The results of this research show that reducing the turbulence in a fluid system will reduce the likelihood of cavitation. Additionally, threshold bounds were created that establish a definitive transition at which cavitation will occur.

Risk assessment management have been a hot topic for the researchers since a very long time. Software risk management is an important part of project management as it contains the identification, analysis, estimation and monitoring of different risks present in the system. This helps developers in decision making while assessing the problems that could arise in the software systems. Risk management is very complex in large scale system as these systems have very complex development. The paper describes risk management techniques for large scale system. Furthermore we have provided a detailed comparative analysis of these techniques with commonly identified risks in software systems and have provided a systematic order for risk management process to ensure risk mitigation.

Photoelectrochemical systems have the potential to contribute to de-carbonation of the energy system because solar energy can be directly converted to hydrogen which can be burnt without the release of greenhouse gases. However, meaningful deployment of photoelectrochemical (PEC) technology in the global energy system, even when highly efficient scaled up devices become available, shall only be a reality when their safe and reliable operation can be guaranteed over serveral years of service life. The first part of the review discusses the importance of hermetic sealing of up scaled PEC device provided by the casing and sealing joints from a reliability and risk perspective. The second part of the review presents a survey of fully functional devices and early demonstrators and uses this to establish the extent to which the state of the art in PEC device design address the issue of hermetic sealing. The survey revealed that current material choices and sealing techniques are still unsuitable for scale –up and commercialization. Accordingly, we examined possible synergies with related photovoltaic and electrochemical devices that have been commericalised and derived therefrom, recommendations for future research routes that could accelerate the development of hermetic sealings of PEC devices.

The technique of Faraday tomography is a key tool for the study of magnetised plasmas in the new era of broadband radio polarisation observations. In particular, observations at metre-wavelengths provide significantly better Faraday depth accuracies compared to traditional cm-wavelength observations. However, the effect of Faraday depolarisation makes the polarised signal very challenging to detect at metre wavelengths (MHz frequencies). In this work, Faraday tomography is used to characterise the Faraday rotation properties of polarised sources found in data from the LOFAR Two-Metre Sky Survey (LoTSS). Of the 76 extragalactic polarised sources analysed here, we find that all host a radio-loud AGN. The majority of the sources (∼64%) are large FRII radio galaxies with a median projected linear size of 710 kpc and median radio luminosity at 144 MHz of 4 × 10^26 W/Hz. In several cases, both hotspots are detected in polarisation at an angular resolution of ∼20". One such case allowed a study of intergalactic magnetic fields on scales of 3.4 Mpc. Other detected source types include an FRI radio galaxy and at least 8 blazars. Most sources display simple Faraday spectra, however, we highlight one blazar that displays a complex Faraday spectrum, with two close peaks in the Faraday dispersion function.

Objective: The goal of this study was to analyse the attitudes and perceptions of emergency and mental health nurses through the validation of the SM-GIBED scale in specialised care in Spain on alcoholics and other drug-dependent patients. Design and Setting: This cross-sectional study was developed using the Spanish hospital version of the Seaman-Mannello scale to denominate the SM-GIBED scale. Participants: 170 Emergency and Mental Health Nursing from five Spanish Hospitals. Intervention: Self-administered questionnaire to analiyse the perceptions and attitudes about the drug addict and the alcoholic. Primary and Secondary Outcome Measures: A descriptive and inferential analysis of the study variables was carried out. A psychometric analysis was performed to validate the scale. Results: A total of 170 questionnaires were collected from 257 healthcare workers. Overall, 99.1% of the participants had contact with drug-dependent patients during their professional experience. Nearly 75% had difficulties in treating them. The psychometric analysis of the SM-GIBED scale in the Spanish context obtained values of KMO = 0.655 and Bartlett's test p < 0.000. Cronbach's alpha of 0.738 was obtained from the reliability analysis. A reliability analysis of each of the SM-GIBED questions found no case with an alpha lower than 0.71. In conclusion, positive aspects include an ingratiating attitude and subject-to-subject communication when nurses self-define as empathic and non-paternalistic. Among the negative aspects, there is a lack of communication skills and assertiveness with these patients. This highlights a certain degree of resignation and dissatisfaction when working with drug addicts.

Given the cross-scale interactions of agricultural ecosystems, it is important to collect ecosystem service data at the multiple spatial scales they operate at. Mapping of ecosystem services helps to assess their spatial and temporal distribution and is a popular communication tool of their availability and value. For example, maps can be used to quantify distance between areas of available ecosystem services and their beneficiaries and how services fluctuate with changes in land use patterns over time, allowing identification of synergies and trade-offs. However, a lack of local context and too large a resolution can reduce the utility of these maps, whilst masking heterogeneities in access due to equity dynamics. This review identifies and summarizes eight main methods of ESS mapping found in the literature—remote sensing, biophysical modelling, agent based modelling, economic valuation, expert opinion, user preference, participatory mapping, and photo-elicitation. We consider what spatial scales these methods are utilized at and the transferability of data created by each method. The analysis concludes with a methodological framework for mapping ecosystem services, intended to help researchers identify appropriate methods for a multi-scale research design. The framework is exemplified with an overview of a research project in Ethiopia.

In previous researches, Job Crafting questionnaire to develop is consists of 3 factors which are Task Crafting, Cognitive Crafting, and Relationship Crafting with 12 to 17 items. The purpose of study is to develop JCQ for leisure sports instructor of Korean. 274 valid samples are used for analysis. Data collecting is purposeful sampling. At result, for Korean Sports Instructor Job Crafting Scale is constructed 3 factors with 12 items is constructed by 3 step procedure. KSIJCQ is confirmed on convergent discriminant validity evidence. In conclusion, KSIJCQ is a valid scale of the measuring and distributes Job Crafting of generalization in sports.

We evaluated the potential of using fish species and functional traits as indicators of land use impacts to fish assemblages. We used environmental data collected at multiple spatial scales (local, reach, and upstream catchment) for 19 tributary and main stem sites in the Nolichucky River watershed in Tennessee. Canonical correspondence analyses showed that temperature, elevation, specific conductivity, sediment yield, impervious surfaces, and row crop cover at the catchment scale were strongly associated with fish assemblage structure, as well as forest cover from all three spatial scales. Blocked indicator species analysis, with stream size as the block, showed that significantly strong indicators of the least-impacted riparian land use condition (≥60% forest cover) were Saffron Shiner (Notropis rubricroceus), Rainbow Trout (Oncorhyncus mykiss), Longnose Dace (Rhynichthys cataractae), Creek Chub (Semotilus atromaculatus), and Mottled Sculpin (Cottus bairdi). Traits indicative of the least-impacted sites were the herbivorous trophic guild, mean female age-at-maturity, longevity, rock-gravel spawners, montane geology and pelagic swimmers. Specific conductivity was strongly related to multiple catchment-scale land use variables, and was a strong local-scale influence on fish assemblage structure. Our results show promise for using a relatively common but endemic southern Appalachian fish species, the Saffron Shiner, as an indicator for land-use related impacts to these streams.

Tobamoviruses are a group of plant viruses posing a significant threat to agricultural crops worldwide. In this review, we focus on plant immunity against tobamoviruses, including pattern-triggered immunity (PTI), effector-triggered immunity (ETI), RNA-targeting pathway, hormones and reactive oxygen species (ROS). Further, we highlight genetic resources for resistance against tobamoviruses in plant breeding and discuss future directions on plant protection against tobamoviruses.

Genome-wide association studies (GWAS) have successfully revealed many disease-associated genetic variants. For a case-control study, the adequate power of an association test can be achieved with a large sample size, although genotyping large samples is expensive. A cost‐effective strategy to boost power is to integrate external control samples with publicly available genotyped data. However, the naïve integration of external controls may inflate the type I error rates if ignoring the systematic differences (batch effect) between studies, such as the differences in sequencing platforms, genotype calling procedures, population stratification, and so forth. To account for the batch effect, we propose an approach by integrating External Controls into the Association Test by Regression Calibration (iECAT-RC) in case-control association studies. Extensive simulation studies show that iECAT-RC not only can control type I error rates but also can boost statistical power in all models. We also apply iECAT-RC to the UK Biobank data for M72 Fibroblastic disorders by considering genotype calling as the batch effect. Four SNPs associated with Fibroblastic disorders have been detected by iECAT-RC and the other two comparison methods. However, our method has a higher probability of identifying these significant SNPs in the scenario of an unbalanced case-control association study.

Control of Tropical Theileriosis, a tick-borne disease with a strong impact on cattle breeding, can be facilitated by using marker-assisted selection in breeding programs. Genome-wide association studies (GWAS) using high-density arrays are extremely important for the ongoing process of identifying genomic variants associated with resistance to Theileria annulata infection. In this work, Single Nucleotide Polymorphisms (SNPs) were analyzed in the Portuguese autochthonous cattle breeds Alentejana and Mertolenga. In total, 14 SNPs suggestive of significance (p ≤ 10-4) were identified for Alentejana cattle and 20 SNPs for Mertolenga cattle. The genomic regions around these SNPs were further investigated for annotated genes and Quantitative trait loci (QTLs) previously described by other authors. Regarding the Alentejana breed, the MAP3K1, CMTM7, SSFA2, and ATG13 genes are located near suggestive SNPs and appear as candidate genes for resistance to Tropical Theileriosis, considering its action the immune response and resistance to other diseases. On the other hand, in the Mertolenga breed, the UOX gene is also a candidate gene due to its apparent link to the pathogenesis of the disease. These results may represent a first step towards the possibility of including genetic markers for resistance to Tropical Theileriosis in current breed selection programs.

Recent successes in the field of evolutionary cancer cell biology (ECCB) have brought to a head two of the most important controversies regarding cancer origin. The first concerns the question of whether carcinogenesis is initiated only by genetic alterations, mutations, and driver genes, as the mutational theory teaches. The ECCB, claims that a large number of polyploidy-related cancers (PGCC cancers) are not due to mutations, but rather to inadequate ancient repair mechanisms used by DNA-damaged stem cells for their repair. Somatic mutations are merely secondary. The second controversy, described in the previous article, concerns the non-mutational theory itself: Are non-mutational polyploid cancers an atavism - as previously thought - or rather the effect of an ancient gene regulatory network aGRN that controls genome reprogramming in precancerous DNA-damaged cells as well in the transformed cells. Finally, the unicellular gene module of cancer, of which the aGRN is a part, has evolved along with the multicellular genome during the last 1000 My of evolution. and non-mutated cancer cell systems are under the control of the aGRN. The atavistic theory relies on phylostratigraphic evidence to determine the age of cancer genes. It states that most cancer-like genes arose during the transition period from unicellularity to multicellularity, but also during the early metazoan era. In our opinion, the atavistic theory is flawed and suffers from many misunderstandings. It provides little insight into the origin and coevolution of the cancer cell system and its control by the ancient gene regulatory network aGRN.

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

Recent developments in artificial nucleic acid and drug delivery systems (DDS) present possibilities for the symbiotic engineering of oligonucleotide therapeutics, such as antisense oligonucleotides (ASOs), and small interfering RNA (siRNA). These technologies can also be applied for triplex-forming oligonucleotides (TFOs) to develop symbiotic genome-targeting tools and a new class of oligonucleotide drugs. Many reports have described the functionalization of TFOs and the enhancement of TFO activities. In particular, the tethering of crosslinking groups to TFOs enables irreversible triplex formation and is frequently exploited for antigene and genome-editing experiments. These crosslinkable TFOs have shown considerable potential for therapeutic application. In this review, we revisit these crosslinking techniques and explore the combination of these techniques with recent artificial oligonucleotide and DDS technologies.

The genome sequencing technologies reveal the molecular mechanisms of differentiated thyroid cancer (DTC). Unlike somatic mutation analysis from thyroidectomy samples, germline mutations showing genetic susceptibility to DTC are less understood. The study aimed to assess the prevalence of germline mutations predisposing to DTC in a cohort of Polish individuals based on their whole genome sequencing (WGS) data. We analyzed sequencing data from 1076 unrelated individuals, released openly for academic and clinical research as The Thousand Polish Genomes database (https://1000polishgenomes.com). The list of genes chosen for further analysis was based on the review of previous studies. The cohort contained 104 variants located within the coding and noncoding DNA sequences of 90 genes selected by ClinVar classification as pathogenic and potentially pathogenic. The frequency of variants in the Polish cohort (our study) was compared to the frequency estimated for the non-Finnish European population, obtained from the gnomAD database (gnomad.broadinstitute.org). Statistically significant variants included 23 genes. Even though the Polish population is genetically similar to other European populations, there are significant differences in variant frequencies contributing to the disease development and progression, such as RET, CHECK2, BRCA1, SLC26A4 or TERT. Further studies are needed to identify genomic variants associated directly with DTC.

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

A strong correlation between karyotype diversity and species richness in mammals was first reported over forty years ago: in mammalian phylogenetic clades, standard deviation of karyotype diversity (KD) closely corresponds to the standard deviation of species richness (SR). These initial studies, however, did not control for phylogenetic signal, raising the possibility that the correlation was due to phylogenetic relatedness among species in a clade. Accordingly, karyotype diversity trivially reflects species diversity simply as a passive consequence of adaptive radiations. A more recent study in mammals has controlled for phylogenetic signal and established the correlation as phylogenetically independent, suggesting that species diversity cannot, in itself, explain the observed corresponding karyotype diversity. The correlation is therefore remarkable because the mechanisms contributing to karyotype diversity are evolutionarily independent of the mechanisms contributing to species diversity. Recently, it was shown in salamanders that the two processes generating genetic diversity and species diversity are indeed independent and operate in parallel, suggesting a potential non-adaptive and non-causal relationship between the two fundamental variables involved in adaptive radiations. The following will examine the relationship between KD and SR in the context of Motoo Kimura’s theory of non-adaptive radiation.

Ribosomal proteins (RPs) mediate protein synthesis and stability of the ribosomal complex. RPs and rRNA form ribosomal subunits and ri-bosomes, the cellular machinery for protein synthesis, a fundamental biological process related to cell growth and proliferation. The differ-ences between paralogs within the same RP family have led them to ac-quire extraribosomal functions involved in plants' growth, develop-ment, and biotic and abiotic stresses. From transcriptomic analysis, it has been revealed that ribosomal proteins have a crucial role during MTs development. The RPLs; RPL11, RPL29 and RPL40 interact with PEBP family members (Phosphatidylethanolamine-binding proteins), poten-tial activators in the MTs development. In potatoes, genome editing is a promising technology to introduce crop breeding traits. Recently, the edition of the genome through the CRISPR/Cas9 system has made it the most efficient and powerful genetic modification method. Based on this, the gene modulation by overexpression and silencing in RPL11, RPL29 and RPL40 will guide us to understand the effect on the microtuberiza-tion process and produce improved potato plants with the capability of growing under adverse environments (biotic and abiotic stresses). By understanding the molecular biology mechanisms that RPs govern, we can improve crops under today's changing climatic conditions.

At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in male and female patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33×10^-8 calculated with the Yates-corrected Chi-square test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWAS of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network. This study indicates that a number of genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The results also suggest the genetic basis of sex-specific psychiatric comorbidities of AD.

Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut. An in-depth assessment was carried out on safety properties (antibiotic resistance profiling, β-haemolytic, DNAse and gelatinase activities and virulence factor presence) and other properties (antimicrobial activity, auto-aggregation, co-aggregation and hydrophobicity). Based on phenotypic and genotypic characterization, both strains satisfied all the safety requirements. More specifically, genome analysis showed the absence of genes encoding for glycopeptide (vanA, vanB, vanC-1, vanC-2, vanD, vanE, vanG), resistance to tetracycline (tet-M, tet-L and tetO), and virulence genes (asa1, gelE, cylA, esp, hyl).

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing posttranslational modifications as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl-linkage between two aromatic amino acids. Recent genomic analyses revealed the minimal biosynthetic prerequisite of biarylitide biosynthesis consisting of only one ribosomally synthesized pentapeptide precursor as substrate and a modifying cytochrome P450 dependent enzyme. In silico analyses revealed that the minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH termed Myxarylin from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide surprisingly exhibiting a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides featuring a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.

Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in Salmonella entericasubspecies I. The motif differed between cother taxonomic classes but not between Salmonella enterica serovars. The motif in plasmids was associated with serovar. Approximately 12.3% of the S. enterica motif loci had mutations. Mutability of AT 8+mers suggests that genomes undergo frequent repair to maintain optimal gene content, and that the motif facilitates self-recognition; in addition, serovar diversity is associated with plasmid content. A theory that genome regeneration accounts for both persistence of predominant Salmonella serovars and serovar diversity provides a new framework for investigating root causes of foodborne illness.

Clustered regularly interspaced short palindromic repeats or CRISPR, one of the major technological tools from nature's toolbox, has revolutionized the scientific world with its potential use in humans and plants. CRISPR Cas9 was first known as an adaptive immune system of bacteria. It is a system that cleaves foreign DNA. It has been exploited to be used as a genome editing tool for correcting genetic diseases in humans, for plants to create stress-resistant plants, and for a variety of different purposes. This review provides a basic overview of its applications in different areas of biological research. It has immense potential for a variety of researches, but it's still a mystery for science. It feels like scientists just know a tip of an iceberg.

The analysis of curated genomic, metagenomic, and proteomic data are of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw form in free international repositories, its access requires plenty of computing, storage, and processing capacities for the domestic user. The purpose of the study is to offer a comprehensive set of genomic and proteomic reference data, in an accessible and easy-to-use form to the scientific community. A representative type material set of genomes, proteomes and metagenomes were directly downloaded from the site: https://www.ncbi.nlm.nih.gov/assembly/ and from Genome Taxonomy Database, associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy raw reduced representations, by using Mash software. Our dataset contains near to 100 GB of space disk reduced to 585.78 MB and represents 87,476 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with computational resources. Potential uses of this dataset include but are not limited to, microbial species delimitation, estimation of genomic distances, genomic novelties, paired comparisons between proteomes, genomes, and metagenomes.

The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis.

Summary CoV-GLUE is an online web application for the interpretation and analysis of SARS-CoV-2 virus genome sequences, with a focus on amino acid sequence variation. It is based on the GLUE data-centric bioinformatics environment and provides a browsable database of amino acid replacements and coding region indels that have been observed in sequences from the pandemic. Users may also analyse their own SARS-CoV-2 sequences by submitting them to the web application to receive an interactive report containing visualisations of phylogenetic classification and highlighting genomic variation of potentially high impact, for example linked to primer mismatches.Availability and implementation Available at http://cov-glue.cvr.gla.ac.uk. Implemented using GLUE, an open source framework for the development of virus sequence data resources. Contact [email protected]

The success of many viruses depends upon cooperative interactions between viral genomes. For example, viruses that coinfect the same cell can share essential gene products, such as replicase, the enzyme that replicates the viral genome. However, when cooperation occurs, there is the potential for ‘cheats’ to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, evolutionary theory developed to explain cheating offers a conceptual framework for understanding and manipulating viral dynamics. At the same time, viruses offer unique opportunities to study how cheats evolve, because cheating is relatively common in viruses, compared with taxa where cooperation is more usually studied, such as animals.

The type of tail of sheep is an important economic trait. However, the candidate genes associated with the tail type are uncertain. The objective of this study was to identify the genetic region and genotype responsible for the tail type phenotype. Here we perform a genome-wide association study (GWAS) in 40 large tailed Han sheep and 40 Altay sheep as case and 40 Tibetan sheep as control. The results indicated that a total 31 genome-wide significant SNPs associated with type of tail traits were detected. For significant SNPS loci, determine its physical location, and screening of candidate genes within section. By combining information of previously reported and annotated biological functional genes, we identified SPAG17, Tbx15, VRTN, NPC2, BMP2 and PDGFD as the most promising candidate genes for type of tail traits. Based on the above identified candidate genes on type of tail traits, we selected BMP2 and PDGFD to conduct the genetic effect analysis in a large Altay sheep and Tibetan sheep population. Rs119 T>C in the exon1 of BMP2 gene and 1 SNPs in the exon4 (rs69 C>A) of PDGFD gene were detected, rs119 that located on exon1 of BMP2 gene was TT genotype in Altay sheep, while with CC genotype in Tibetan sheep. On rs69 of PDGFD gene, Altay sheep with CC genotype, however, Tibetan sheep with AA genotype. These results indicated that the significant associations of SNPs detected in GWAS were indirectly caused by the genetic effects of BMP2 and PDGFD on sheep tail fat deposition.

The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.

Maintenance of the human chromosomes stability requires a tight regulation of DNA replication to duplicate once and only once the entire genome of a single cell. In mammalians cells, origin activation is controlled in space and time by a cell specific and robust program called replication timing. About 100 000 of potential origins are loaded onto the chromatin at the G1 phase but only 20-30% are selected and active during the replication of a given cell. When the replication fork is slowed down by exogenous or endogenous sources, the cell need to activate more origins to complete the replication on time. Thus, the large choice of origins that can be activated may be a key player in the protection of the genome. The aim of this review is to discuss about the role of these dormant origins as housekeepers of the human genome in response to replicative stress.

The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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.

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

Streptococcus thermophilus is widely used as a starter culture in the dairy industry and has garnered attention as a beneficial bacterium owing to its health-promoting functionalities in humans. In this study, the probiotic potential of S. thermophilus MCC0200, isolated from a dairy product, was investigated through a combinatorial approach of in-vitro and in-silico studies. MCC0200 demonstrated the ability to survive harsh gastro-intestinal transit (GIT), adhere to intestinal mucosa and exert health-promoting traits in in-vitro studies. These findings were corroborated with in-silico evidence, wherein MCC0200 genome harboured genes associated with tolerance to GIT conditions, intestinal adhesion and colonization. Genome mapping also highlighted the ability of MCC0200 to produce compounds advantageous for host (folate, bacteriocins), to release enzymes that can reinforce the host ability (antioxidative enzymes), to metabolize food components that can be harmful to sensitive people (lactose). MCC0200 also demonstrated a positive effect on reducing cholesterol levels, proving to be a potential candidate for food and pharmaceutical applications. Absence of transmissible antibiotic resistance genes and virulence genes underscored the GRAS nature of MCC0200. This study explored the potential of Streptococcus thermophilus for its probable applications as a probiotic beyond the dairy industry.

Plant protein phosphatase 2Cs (PP2Cs) serve as negative regulators of protein kinase cascades activated in different processes and play important roles in plant development and abiotic-stress-mediated signaling pathways. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physical and chemical feature, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structure, conserved motif and all the CqPP2C proteins had the type 2C phosphatase domains. Gene duplication revealed that segmental duplication was the major driving force for CqPP2Cs expansion and all duplicated CqPP2Cs evolved from purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The results revealed that CqPP2C genes were involved in regulating development and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s, but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities to respond to various biological processes and stresses. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.

In Poland, the mountainous and hilly regions until recently were territories with unbalanced and poor diet quality, especially in early spring. Wild edible plants were or still are influential in supplementing a human diet. One of the earliest wild edible plants to appear in the growing season, characteristic of a broad swath of Europe from Ukraine to Germany, remains wild (bear) garlic (Allium ursinum L.). This paper assesses the impact of the vegetation site and preservation methods on selected parameters of the chemical composition of bear garlic. In addition, the connection between its genome pattern and chemical composition was assessed. The plants were collected in three locations in the Carpathian foothills, and the reference sample was plants collected in the lowlands. The site from which the raw material was harvested has a statistically significant effect on the chemical composition of the preserved leaves of bear garlic. The profiles of the analysed components differed in the material from a different site. Bear garlic leaves from mountainous areas had more analyzed components than those obtained from the lowland sites. Moreover, the material from the lowlands had a different genetic pattern from the leaves from the mountainous areas..

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most destructive diseases in maize that severely reduces grain yield and contaminates several potential mycotoxins. However, few efforts had been devoted to dissect the genetic basis of maize GER resistance. In the present study, a genome-wide association study (GWAS) was conducted in a maize association panel consisting of 303 diverse inbred lines. The phenotypes of GER severity were evaluated using kernel bioassay across multiple time points in the laboratory. Then, three models including fixed and random model circulating probability unification model (FarmCPU), general linear model (GLM) and mixed linear model (MLM), were conducted simultaneously in GWAS to identify single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance. A total of four individual significant association SNPs with the phenotypic variation explained (PVE) ranging from 3.51 to 6.42% were obtained. Interestingly, the peak SNP (PUT-163a-71443302-3341) with the greatest PVE value, was co-localized in all models. Subsequently, 12 putative genes were captured from the peak SNP that several of these genes were directly or indirectly involved in disease resistance. Overall, these findings contribute to understand the complex plant-pathogen interactions in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the kernel bioassay that can be used for evaluating and selecting elite germplasm resources with GER resistance in maize.

Ornamental kale (Brassica oleracea var. acephala) is an attractive ornamental plant with a range of leaf colors and shapes. Breeding new varieties of ornamental kale has proven challenging due to its lengthy breeding cycle and the limited availability of genetic markers. Microspore culture is an effective approach to generate new materials and genetic maps are a prerequisite for quantitative trait loci analysis, MAS, fine gene mapping, and genome sequence assembly. In this study, a F1DH ornamental kale population comprising 300 DH lines was constructed using microspore culture. A high-density genetic map was developed by conducting whole-genome sequencing on 150 individuals from the F1DH population. The genetic map contained 1,696 bin-markers with 982,642 single-nucleotide polymorphisms (SNPs) spanning a total distance of 775.81 cM on all nine chromosomes with an average distance between markers of 0.46 cM. The ornamental kale genetic map contained substantially more SNP markers compared with published genetic maps for other B. oleracea crops. The F1DH progenies provide an excellent resource for germplasm innovation and breeding new varieties of ornamental kale. The high-density genetic map provides crucial insights for gene mapping and unraveling the molecular mechanisms behind important agronomic traits in ornamental kale.

Methanotrophic bacteria that possess a unique ability of using methane as a sole source of carbon and energy have attracted considerable attention as potential producers of a single-cell protein. So far, this biotechnology implied using freshwater methanotrophs, although many regions of the world have limited freshwater resources. This study aimed at searching for novel methanotrophs capable of fast growth in saltwater comparable in composition with seawater. A methane-oxidizing microbial consortium containing Methylomarinum- and Methylotuvimicrobium-like methanotrophs has been enriched from a sediment of the river Chernavka (water pH 7.5, total salt content 30 g L-1), a tributary river of the hypersaline Lake Elton, southern Russia. This microbial consortium, designated Ch1, demonstrated stable growth on natural gas in a bioreactor in media with a total salt content of 23 to 35.9 g L-1 at a dilution rate of 0.19-0.21 h-1. The highest biomass yield of 5.8 g CDW/L with a protein content of 63% was obtained during continuous cultivation of the consortium Ch1 in a medium with a total salt content of 29 g L-1. Isolation attempts resulted in obtaining a pure culture of methanotrophic bacteria, strain Ch1-1. The 16S rRNA gene sequence of strain Ch1-1 displayed 97.09-97.24% similarity to the corresponding gene fragments of characterized representatives of Methylomarinum vadi, methanotrophs isolated from marine habitats. The genome of strain Ch1-1 was 4.8 Mb in size and encoded 3 rRNA operons, and about 4400 proteins. The genome contained the gene cluster coding for ectoine biosynthesis, which explains the ability of strain Ch1-1 to tolerate high salt concentration.

The emergence of new SARSCoV-2 variants can affect vaccine efficacy, laboratory diagnosis and therapies already available, triggering interest in the search for antiviral agents for SARSCoV-2 infections. Ribavirin (RBV) is a broad-spectrum antiviral with demonstrated in vitro activity against multiple viruses, including SARSCoV-2. Methods. This retrospective study evaluated the dynamic and viral clearance of SARSCoV-2 in hospitalized adult participants (PTs) with COVID-19 pneumonia who received RBV aerosol within a compassionate use study. Was also assessed the impact of RBV on the clinical outcome and the mutational profile of SARSCoV-2. Results. The median RNA values measured in nine PTs included in the study de-creased from baseline to discharge (at BL, threshold cycle (Ct)=22.4, IQR 19.84-5.07; at discharge, Ct=27.92, IQR 26.43-36.11). Seven/9 PTs experienced a clinical improvement, while two PTs deceased during hos-pitalization. In PTs with a favorable outcome the virus clearance rate at discharge was 28.6%. The cumulative clearance rate was 71.4% within day 14th from discharge. A mutational pattern after RBV was detected in 3/5 PTs in whom was available whole genome sequencing. Conclusions. RBV may limit SARSCOV-2 replication resulting in a favorable clinical outcome. Ribavirin may also contribute to the mutational spectrum of SARSCoV-2.

Chicken infectious anemia (CIA) poses a significant threat to the chicken industry in China. De-spite its non-specific symptoms, the disease is often overlooked. This study aimed to conduct a comprehensive analysis of the etiology and pathology of CIA in Guangxi Province, China. Three strains of the chicken infectious anemia virus (CIAV) were isolated from liver samples of diseased 20-week-old chickens. The complete genomes of these strains were sequenced, and experiments on specific pathogen-free (SPF) chicks revealed that the GX21121 strain exhibited high virulence. Histopathological examination of the deceased chicks showed liver cell necrosis, fibrous-serous exudation, inflammatory cell infiltration, hemorrhage in liver tissues, as well as congestion in lung and renal tissues. Phylogenetic analysis of the genome revealed that the three strains had a close genetic relationship to the Heilongjiang wild-type (GenBank KY486144). The genetic evolu-tion of their VP1 genes indicated that all three CIAV isolates belonged to genotype IIIc. In sum-mary, this study demonstrated the genomic diversity of three CIAV strains in adult layer hens. The isolation and characterization of the GX21121 strain as a highly virulent isolate provide val-uable information for further investigations into the etiology, molecular epidemiology, and viral evolution of CIAV.

Begomovirus infection in plant causes a great economic loss in many countries every year. Increasing rate of the infectivity of this single stranded DNA virus forces to study of its transmission in detail for the necessary researches regarding the control of this disease. This pathogenic virus is whitefly vector borne and transferred from one plant to another plant during the suckling of phloem sap by that vector. Viral transmissibility through this insect vector may depend on the genetic variations within the cryptic species groups. Two distinct categories of begomoviruses viz., bipartite and monopartite types consist of different genome organization. Virion particles modify the intracellular environment of the host according to their need of replication and survival. Viral replication takes place through RCR as well as RDR methods. Interplay among host, vector and pathogen is crucial for the establishment of infection. Several endosymbiotic organisms living within the insect vector also have vital role here. Being infected with this virus, host plant responds with defensive activities like TGS, PTGS, autophagy, hormonal regulation, metabolic alteration etc. However, virus also counteracts those through the manipulation of several pathways of cellular events. It is necessary to study in different directions and utilize advanced molecular biological techniques to develop begomovirus resistance within plants.

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.