Lasiodiplodia theobromae, as one of the causing agents associated with Chinese hickory trunk cankers, has caused huge economic losses to the Chinese hickory industry due to its extremely strong pathogenicity. Though the biological characteristics of this pathogen and the occurrence pattern of this disease have been reported, few studies have focused on investigating the mechanisms responsible for L. theobromae survival strategies and pathogenicity. The high-quality genome data and the efficient transformation system are the basis for researching above mechanism events. In this study we sequenced and assembled L. theobromae strain LTTK16-3, and established the first protoplasmic preparation method and polyethylene glycol (PEG) -mediated genetic transformation system for L. theobromae. These genetic information and transformation methods established the foundation for the future mechanisms study of L. theobromae and set up the possibility of targeted molecular improvements for Chinese hickory canker control.

During the recent pandemics of COVID-19, sequencing technics became powerful tool for gaining information about the SARS-CoV-2 virus and using this knowledge in our advantage. Thanks to this advantage, scientists over the world were able to search for emerging variations, watching the virus evolving in real time. Assembly of the virus genomes is crucial part of getting this kind of useful information. In our study, we sequenced 79 samples from nasopharyngeal swabs of COVID-19 patients. Positivity on disease was evaluated by qRT-PCR. By studying assembly success rate, we noticed, that Ct-value of qRT-PCR can predict success of genome assembly and SARS-CoV-2 lineage assignment. In this work we described the relationship between Ct-value and further steps of genome construction and its assignment to specific viral strain.

Poro-poro is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, there have been few genetic studies. The lack of genomic exploration limits the possibility of expanding our knowledge of its molecular evolution, new molecular pathways, genetic traits, and evolutionary relationships. Here, we report the plastid genome sequence of Passiflora tripartita var. mollissima and the reconstructed phylogenetic tree to infer the phylogenetic relationships among Passiflora species. Our phylogenetic analysis showed that poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study provides the basis for developing new molecular markers that constitutes a valuable resource for studying molecular evolution and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.

Fruit production is an important part of the gross domestic product for many countries around the world especially to those who have a strong focus on agriculture. However, long-term maintenance and yield stability of fruit production may be threatened by the ongoing climate change and its consequences like extended drought periods, heavy rain events, and floodings. Genome editing, with its progressive technological developments, offers opportunities to adapt relevant fruit plant species to new climatic conditions. Among modern genome editing techniques, CRISPR/Cas, in particular, has the potential to support breeding for those fruit plant species with extended breeding cycles, e.g., perennial fruits. In this review, we discuss CRISPR/Cas and other genome editing techniques in detail and how these techniques can be applied to support the breeding of fruit plant species for adaptation to changing climates. The chronological history of CRISPR/Cas9 systems, their associated computational tools, genomic data sources, transformation methods along with their delivery vehicles, quality improvement, environmental-stress resiliency, limitations, and future perspectives will also be discussed with respect to securing future global fruit production.

Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of the Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scab results in the development of black spots on the fruit surface, which considerably reduces its commercial value. Despite being an economic concern for Japanese apricot, there have been few reports on the phenotypic variation in scab resistance/susceptibility, the underlying genetic factors, and the development of DNA markers. Therefore, in this study, we performed a comprehensive trait analysis for scab resistance and susceptibility for four years and conducted a genome-wide association study (GWAS) to identify the associated loci. The results showed that significant GWAS peaks were detected in 2017 and 2018. Promising candidate gene encoding domains associated with disease resistance were found at the nine single-nucleotide polymorphisms (SNPs) identified in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on the mechanisms of scab resistance in P. mume and will assist future breeding programs to improve scab resistance in ‘Nanko’ lineages.

Advancement in biotechnology and genomics research have promoted access to DNA markers and their use in breeding programs. Genome-wide association study (GWAS), Genomic selection (GS) and Marker-Assisted Selection (MAS) are some of the applications of DNA markers in plant breeding. Researchers have suggested combining these individual applications for better selection accuracies. This study examines the potential advantages of incorporating GWAS-results into MAS and GS as well as the validity of the different methods for combining these approaches. From this study, it was concluded that number of QTNs have greater effects on prediction accuracies compared to heritability estimates. Also, the increase in prediction accuracy from the invalid method of incorporating GWAS results into GS and MAS model is similar to results recorded with using the valid approach. However, greater difference may be observed in another scenario which can lead to spurious results when used to make breeding decisions.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic still able to infect the population in many countries. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and the ability to evade immunity require a priority study of its properties in order to quickly create effective means of preventing it. The present work is devoted to the study of in silico interaction of piRNAs with the genome of the SARS-CoV-2 (gRNA) in order to identify endogenous piRNAs and propose synthetic piRNAs with high antiviral activity for drug development. The studies were carried out using proven bioinformatic methods of interaction of the entire SARS-CoV-2 genome with more than eight million piRNAs. Binding sites (BSs) of piRNAs in the 5'UTR were located with overlapping nucleotide sequences called clusters of BSs. Several clusters of BSs were found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a and nucleocapsid. 16 synthetic piRNAs have been proposed that interact with gRNA with free binding energy from -170 kJ/mol to -175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.

Infectious bronchitis virus (IBV) is a highly variable RNA virus that affects chickens worldwide. Due to its inherited tendency to suffer point mutations and recombination events during viral replication, emergent IBV strains have been linked to nephropathogenic and reproductive disease that are more severe than the typical respiratory disease, leading, in some cases, to mortality, severe production losses, and/or unsuccessful vaccination. QX and DMV/1639 strains are examples of the above-mentioned IBV evolutionary pathway and clinical outcome. In this study, our purpose was to systematically compare whole genomes of QX and DMV strains looking at each IBV gene individually. Phylogenetic analyses and amino acid site searches were performed in datasets obtained from GenBank accounting for all IBV genes and using our own relevant sequences as a basis. The QX dataset studied is more genetically diverse than the DMV dataset, partially due to the greater epidemiological diversity within the five QX strains used as a basis compared to the four DMV strains from our study. Historically, QX strains have emerged and spread earlier than DMV strains in Europe and Asia. Consequently, there are more QX sequences deposited in GenBank than DMV strains, assisting in the identification of a larger pool of QX strains. It is likely that a similar evolutionary pattern will be observed among DMV strains as they develop and spread in North America.

Cyanobacterial macrocolonies known as Llayta are found at Andean wetlands and consumed since pre-Columbian times in South America. Macrocolonies of filamentous cyanobacteria are niches for colonization by other microorganisms; however, the microbiome of edible Llayta has not been explored. Based on a culture-independent approach, we report the presence, identification and metagenomic genome reconstruction of Cyanocohniella sp. LLY associated to Llayta trichomes. The assembled genome of strain LLY is now available for further inquiries, and may be instrumental for taxonomic advances on this genus. All known members of the Cyanocohniella genus have been isolated from salty European habitats. A biogeographic gap for the Cyanocohniella genus is partially filled by the existence of strain LLY at Andes Mountains wetlands in South America as a new habitat. This is the first genome available for members of this genus. Genes involved in primary and secondary metabolism are described providing new insights on the putative metabolic capabilities of Cyanocohniella sp. LLY. The reconstructed genome of strain LLY is now available and instrumental for further inquiries and taxonomic advances on the genus Cyanocohniella.

Fracture is a global public health disease. Bone health and fracture risk have become the focus of public and scientific attention. Observational studies have reported that tea consumption is associated with fracture risk, but the results are inconsistent. The present study was conducted to evaluate whether tea consumption was causally associated with the risk of bone fracture through two-sample Mendelian Randomization (MR) analysis. We included a large genome-wide association study (GWAS) associated with tea consumption of 447,485 individuals and analyzed the effects of genetic instruments on fractures using fracture cases from the UK Biobank dataset (n=361,194). Inverse variance weighted (IVW) indicated no causal effects of tea consumption on fractures of the skull and face, shoulder and upper arm, hand and wrist, femur, calf, and ankle (odds ratio=1.000, P=0.881; OR=1.000, P=0.857; OR=1.002, P=0.339; OR=0.997, P=0.054; OR=0.998, P=0.569, respectively). Consistent results were also found in MR-Egger, weighted median, and weighted mode. Our research provided evidence that tea consumption is unlikely to affect the incidence of fractures.

Familial colorectal cancer (CRC) is only partially explained by known germline predisposing genes. We performed whole genome sequencing in 15 Polish families of many affected individuals, without mutations in known CRC predisposing genes. We focused on loss-of-function variants and functionally characterized them. We identified a frameshift variant in the CYBA gene (c.246delC) in one family and a splice site variant in the TRPM4 gene (c.25-1 G>T) in another family. While both variants were absent or extremely rare in gene variant databases, we identified four additional Polish familial CRC cases and two healthy elderly individuals with the CYBA variant (odds ratio 2.46, 95% confidence interval 0.48-12.69). Both variants led to a premature stop codon and to a truncated protein. Functional characterization of the variants showed that knockdown of CYBA or TRPM4 depressed generation of reactive oxygen species (ROS) in LS174T and HT-29 cell lines. Knockdown of TRPM4 resulted in decreased MUC2 protein production. CYBA encodes a component in the NADPH oxidase system which generates ROS and controls, e.g., bacterial colonization in the gut. Germline CYBA variants are associated with early onset inflammatory bowel disease, supported with experimental evidence on loss of intestinal mucus barrier function due to ROS deficiency. TRPM4 encodes a calcium-activated ion channel, which in a human colonic cancer cell line controls calcium-mediated secretion of MUC2, a major component of intestinal mucus barrier. We suggest that the gene defects in CYBA and TRPM4 mechanistically involve intestinal barrier integrity through ROS and mucus biology, which converges in chronic bowel inflammation.

In recent years, the role of non-coding RNAs (ncRNAs) in regulating cell physiology has begun to be better understood. Recent discoveries in viral molecular biology have revealed that such cellular functions are disturbed during viral infections mainly due to host cell ncRNAs, cellular factors, and virus-derived ncRNAs. Apart from the interplay between those molecules, other interactions derive from the specific folding of RNA virus genomes. These fulfill canonical regulation functions such as replication, translation, and viral packaging. In some cases, folds serve as precursors of small viral RNAs whose biogenesis is not yet clearly understood. Since ncRNAs and RNA viral genomes modulate complex molecular and cellular processes in viral infections, a new taxonomy is being proposed here overarching three main categories, considering the current information about ncRNA interactions in some well-known viral infections. The first category shows examples of host ncRNAs associated with the trigger of the immune response under viral infections. The second category describes interactions between the virus and host ncRNAs. The last category shows how the shape of the RNA viral genome is essential in processing RNAs derived from viruses. Finally, we introduce evidence of how these three categories can also work as a framework in order to organize known interactions of ncRNAs and cellular factors under DENV infection. This new taxonomy of interactions provides a comprehensive framework for organizing the ncRNA regulatory roles in the context of viral interactions and an RNA world.

Colorectal cancer (CRC) shows one of the largest proportions of familial cases among different malignancies, but only 5-10% of all CRC cases are linked to mutations in established predisposition genes. Thus, familial CRC constitutes a promising target for the identification of novel, high- to moderate-penetrance germline variants underlying cancer susceptibility by next generation sequencing. In this study, we performed whole genome sequencing on 3 members of a family with CRC aggregation. Subsequent integrative in silico analysis using our in-house developed variant prioritization pipeline resulted in the identification of a novel germline missense variant in SRC gene (V177M), a proto-oncogene highly upregulated in CRC. Functional validation experiments in HT-29 cells showed that introduction of SRCV177M resulted in increased cell proliferation and enhanced protein expression of phospho-SRC (Y419), a potential marker for SRC activity. Upregulation of paxillin, β-Catenin and STAT3 mRNA levels, increased levels of phospho-ERK, CREB and CCND1 proteins and downregulation of the tumor suppressor p53 further proposed the activation of several pathways due to the SRCV177M variant. The findings of our pedigree-based study contribute to the exploration of the genetic background of familial CRC and bring insights into the molecular basis of upregulated SRC activity and downstream pathways in colorectal carcinogenesis.

Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A-type and B-type lamins is localized in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilizes protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organization, the mechanical stability of the nucleus, genome organization, transcriptional regulation, genome stability, and cellular differentiation. Here we review recent research in the field of nuclear lamins and their role in modulating various nuclear processes and their impact on cell function.

Ploidy is a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.

The humpback puffer, Tetraodon palembangensis, also known as Pao palembangensis, is a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). Despite interesting biological features, such as its very inactive nature, tetrodotoxin production and body expansion mechanisms, molecular research on the humpback puffer is still rare because of the lack of a high-quality reference genome. Here, we reported a first chromosome-level genome assembly of an adult humpback puffer, of which the genome size is 362 Mb with ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50s. Based on the genome, ~61.5Mb (18.11%) repeat sequences were also identified, and totally 19,925 genes were annotated, 99.20% of which could be predicted with function using protein-coding function databases. Finally, a phylogenetic tree was constructed with single-copy gene families from ten teleost fishes. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance, providing clues for future detailed studies of biological toxins.

The severity of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), greatly varies from patient to patient. In the present study, we explored and compared mutation profiles of SARS-CoV-2 isolated from mildly affected and severely affected COVID-19 patients in order to explore any relationship between mutation profile and disease severity. Genomic sequences of SARS-CoV-2 were downloaded from GISAID database. With the help of Genome Detective Coronavirus Typing Tool, genomic sequences were aligned with the Wuhan seafood market pneumonia virus reference sequence and all the mutations were identified. Distribution of mutant variants was then compared between mildly and severely affected groups. Among the numerous mutations detected, 14,408C>T and 23,403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p<0.001). The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group. The 3,037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group. We concluded that RdRp P323L and spike protein D614G mutations predominate in severely affected COVID-19 patients. Further studies will be required to explore whether these mutations have any impact on the severity of COVID-19.

Development and deployment of wheat varieties with high yields, wide adaptability, good quality, multiple-resistance to abiotic and biotic stresses, and efficient response to fertilizers have greatly contributed to global wheat sustainable production. The genomic composition of key commercial wheat variety can help understand the genetic basis underlying the development of new variety and permit increased breeding efficiency. In this study, we report the chromosomal and genomic compositions of BN207, presently the leading wheat variety in the southern region of Huang-Huai River Valley, the most important wheat producing area in China through an integrated analysis using fluorescent in situ hybridization (FISH) and wheat 15 K SNP array. Our results showed that BN207 inherited 55.3% and 40.7% of its genome from its male parent BN64 and female parent ZM16, respectively, and generating 64 novel or recombined loci. Besides, we detected nine chromosomal variations in Bn207 and its parents and ten sister lines, and physically mapped two variations, the pericentric inversion of chromosome 6B, and large tandem repeat sequence block at the long arm of 5A, both had positive effects on agronomic traits, by integration of FISH and SNP loci recombination analyses. These results will provide a reference for breeding of high yield wheat varieties as BN207, and the application of founder parents BN64 and ZM16, which are being utilized frequently in wheat breeding programs in Henan Province and surrounding areas.

Fibrillin (FBN) is a plastid lipid-associated protein found in photosynthetic organisms from cyanobacteria to plants. In this study, 10 CsaFBN genes were identified in genomic DNA sequences of cucumber (Chinese long and Gy14) through database searches using the conserved domain of FBN and the 14 FBN genes of Arabidopsis. Phylogenetic analysis of CsaFBN protein sequences showed that there was no counterpart of Arabidopsis and rice FBN5 in the cucumber genome. FBN5 is essential for growth in Arabidopsis and rice; its absence in cucumber may be because of incomplete genome sequences or that another FBN carries out its functions. Among the 10 CsaFBN genes, CsaFBN1 and CsaFBN9 were the most divergent in terms of nucleotide sequences. Most of the CsaFBN genes were expressed in the leaf, stem, and fruit. CsaFBN4 showed the highest mRNA expression levels in various tissues, followed by CsaFBN6, CsaFBN1, and CsaFBN9. High-light stress combined with low temperature decreased photosynthetic efficiency and highly induced transcript levels of CsaFBN1, CsaFBN6, and CsaFBN11, which decreased after 24 h treatment. Transcript levels of the other seven genes were changed only slightly. This result suggests that CsaFBN1, CsaFBN6, and CsaFBN11 may be involved in photoprotection under high-light conditions at low temperature.

A little-known thermomechanical relation between entropy and action, originally discovered by Boltzmann in the classical domain, was later reconsidered by de Broglie in relation to the wave-particle duality in the free propagation of single particles. In this paper we present a version adapted to the phenomenological description of the hadronization process. The substantial difference with respect to the original de Broglie scheme is represented by the universality of the temperature at which the process occurs; this in fact coincides with the Hagedorn temperature. The main results are: 1) a clear connection between the universality of the temperature and the existence of a confinement radius of the color forces; 2) a lower bound on the hadronic mass, represented by the universal temperature, in agreement with experimental data; 3) a scale invariance which allows the reproduction of the well-known hadronic mass spectrum solution of the statistical bootstrap model. The approach therefore presents a heuristic interest connected to the study of the strong interaction.

In this paper we introduce the Adomian decomposition method for a class of first order fuzzy dynamic equations on arbitrary time scales for existence of solutions. The results are provided with suitable numerical examples.

This paper presents an enhanced Fully Connected Neural Network (FCNN) framework that incorporates manifold learning and Renormalization Group (RG) methods. By integrating Christoffel symbols, the model adapts to the curvature and topology of the data manifold, improving learning from geometrically complex data. Additionally, RG methods enable effective multi-scale data processing. We demonstrate the enhanced model’s performance on synthetic and real-world datasets, showing improved accuracy compared to standard FCNNs, particularly in complex systems simulation.

Vulnerabilities in smart contracts may trigger serious security events, and the detection of smart contract vulnerabilities has become a significant problem. In this paper, by using the multi-scale cascade encoder architecture as the backbone, we propose a novel Multi-scale Encoder Vulnerability Detection (MEVD) approach to detect well-known high-risk vulnerabilities in smart contracts. Firstly, we use the gating mechanism to design a unique Surface Feature Encoder (SFE) to enrich the semantic information of code features. Then, by combining a Base Transformer Encoder (BTE) and a Detail CNN Encoder (DCE), we introduce a dual-branch encoder to capture the global structure and local detail features of the smart contract code, respectively. Finally, to focus the model's attention on vulnerability-related characteristics, we employ the Deep Residual Shrinkage Network (DRSN). Experimental results on three types of high-risk vulnerability datasets demonstrate performance compared to state-of-the-art methods, and our method achieves an average detection accuracy of 90%.

This paper deals with the analysis of the cognitive functions of the cerebral cortex or cortex in the evolutionary context. The triune brain model is presented given its notorious popularity in fields that are not strictly neuroscientific, and its limitations and inaccuracies are also shown. Although it is an outdated theory, this one represented the passage to a new era, because it really was the model of the movement towards understanding the brain in evolutionary terms. Next, the paper illustrates the different areas of the cortex and their functions, as well as the evolution of the brain and the cortex in vertebrates. To date, the expansion of the cortex with the amniotes was placed 300 million years ago, although recent studies place it in the lampreys more than 500 million years ago. Evolutionary changes in mammalian brain and cortex size are discussed, showing the evolution from three to six cell layers and trends in different groups of mammals. Finally, the most recent contributions in the field of research are illustrated, such as the role of neurogenesis and the evolution of the connectivity of the cortex.

Background: Patients with allergic rhinitis (AR) have bothersome symptoms that may assess using the visual analog scale (VAS). Asthma frequently is associated with AR. The present study investigated the role of VAS in children with newly-diagnosed AR. Methods: Parameters were VAS for nasal and asthma symptoms, and doctor’s perception of these diseases, medication use, and asthma comorbidity. Results: 67% of AR children had asthma. Severity of perceived nasal symptoms was associated with more intense asthma symptoms and doctor’s perception of disease severity (p<0.001 and p=0.02, re-spectively. Conclusions: Allergic rhinitis frequently is associated with asthma in child-hood. Symptom perception assessment using VAS is a simple tool for assessing their intensity. Moreover, the severity of nasal symptoms is associated with asthma symptom severity. Therefore, asthma should be carefully considered in AR children and require appropriate symptom perception assessment.

We carry out in a thin heterogeneous porous layer, the multiscale analysis of Smoluchowski's discrete diffusion-coagulation equations describing the evolution density of diffusing particles that are subject to coagulate in pairs. Assuming that the thin heterogeneous layer is made of microstructures that are uniformly distributed inside, we obtain in the limit an upscaled model in lower space dimension. We also prove a corrector-type result very useful in numerical computations. In view of the thin structure of the domain, we appeal to a concept of two-scale convergence adapted to thin heterogeneous media to achieve our goal.

Interspecific competition between herbivorous insects is a major selection pressure affecting the distribution, abundance, and structure of their populations. Facilitator-mediated interactions, such as mutualism, can influence competition. Furthermore, the temporal dynamics of competitive relationships affect the interaction’s outcome. Here, we re-evaluated the data on the competition for space between two herbivorous insects commonly known as scales (Toumeyella martinezae and Opuntiaspis philococcus) in either the presence or absence of Liometopum apiculatum (a mutualistic species of T. martinezae) and its variations over time. We selected 27 Myrtillocactus geometrizans plants on which the studied insects were present; the plants were classified into one of five different conditions: either of the scale species were present on the plant, without its competitor; T. martinezae with neither its mutualistic species nor the competitor; and both scale species competing in either presence or absence of the mutualistic species. We kept a photographic record of each condition, measured the size of (as an indicator of the development stage) and area occupied by the individual scales, estimated the total coverage of each scale species, and assessed their relative occupation of space and their competitive intensity. We found temporal variations in competitive intensity. T. martinezae occupied more space during the first months, whereas O. philococcus did so towards the end of the study period. The population structure changed over time and between species, affecting the competitive interactions. In conclusion, the dynamics of competition change over time, and the mutualistic species has a positive effect on T. martinezae when the scales are in competition. However, temporal variations resulting from changes in the life cycle of the scales allow the two competitors to coexist in the same place at the same time.

Background: The adoption of self-care behaviors among patients with arterial hypertension (AH) plays an important role in the management of their health condition. However, a lack of scales assessing self-care is observed. We aimed to develop and validate the Hippocratic hypertension self-care scale. Methods: From a pool of questions derived from a literature review, 18 items were included in the scale and reviewed by a committee of experts. Participants indicate the frequency at which they follow the self-behavior prescribed in each statement on a five-point Likert scale. Data were collected between April 2019 and December 2019. Re-sults: 202 consecutive adult patients with AH were enrolled in the study. The internal consistency of the scale was found to be 0.807, using Cronbach’s alpha coefficient. An exploratory factor analysis identified two do-mains that accounted for 92.94% of the variance of the scale items; however, each sub-scale could not be used as an independent scale. Finally, the test- retest of the scale showed a significant strong correlation (r=0.0095, p<0.001). Conclusion: Our data indicate that the scale is a reliable and valid tool for assessing self-behaviors in patients with AH. Health professionals can use it in their clinical practice to improve the management of patients’ health condition.

Introduction: Lack of certainty or knowledge in health professions generates uncertainty, affecting clinical practice in decision-making (diagnostic or therapeutic), intervention design and therapeutic communication. In nursing, the lack of information to predict prognosis and outcome of interventions generates uncertainty: recognizing and managing it is essential for individualized, safe, and effective care. Objective: to assess uncertainty and the perception of a debriefing within the same shift ("intrathoracic pass") as a proposal for improvement. Method: ad-hoc survey of nursing professionals and Auxiliary Nursing Care Technicians (ANC). Variables: age, work experience, PRU scale (Physisicians' Reactions to Uncertainty) and additional question on intrathoracic pass. Results: Sample: 61 nurses and 10 TCAE (90.14 % female, 9.86 % male; mean age 35.18, standard deviation SD=13.04). Mean professional experience 11.74 years (SD=12.21); 56.33% had ≤4 years of experience. Origin: 49.30% Intensive Care Units (ICU), 11.27% Hospitalization, 7.04% Emergency, 1.41% Primary Care and 30.99% Other Services. The mean level of uncertainty was 27.99 points (max. possible 75; SD=7.50), with stress (mean=25.55, max. possible: 40; SD=5.24) and anxiety (mean=15.80, max. possible: 25; SD=3.05) as major manifestations. The association uncertainty-age (r=0.339; p=0.004) and uncertainty-experience (r=0.391; p=0.001) correlated negatively (the older and more experienced, the less uncertainty), with no significant differences between degrees or services. 91.55% stated that the intra-day pass was useful to reduce uncertainty during the working day. Conclusion: Uncertainty is frequent in nursing, and implementing the intrashift pass is perceived as a competent strategy.

AbstractPurpose: This study aimed to perform a psychometric evaluation of the preliminary preterm birth risk assessment scale (PBRAS-K) of 32-item. Method(s): There were 299 subjects, 167 in the exploratory factor analysis (EFA) group and 132 in the confirmatory factor analysis (CFA) group, who delivered before 37⁺⁰ weeks after having preterm symptoms and were admitted to high-risk pregnancy maternal-fetal intensive care units (MFICU). After an item reduction process in EFA, the psychometric property scales were assessed using SPSS 26, and CFA was accomplished using AMOS 27. Results: The Kaiser-Meyer-Olkin measure (KMO) and Bartlett’s χ² test of sphericity confirmed the adequacy of the sample for factor analysis (KMO = .81 (> .80), χ² = 1841.38, p < .001). The final version of the PBRAS-K was comprised of 23 items within seven dimensions. Factor analysis identified items explaining 65.9% of the total variance. The PBRAS-K had a mean score of 35.58 (±10.35) and showed a high internal consistency and satisfactory reliability with a Cronbach’s alpha of .85. The PBRAS-K had a low correlation with risk scoring of preterm delivery (RPD) for discriminant validity (r = .45, p < .001), a positive, high correlation with the Somatic Awareness Scale with Spontaneous Preterm Labor (SPL-SAS) for criterion validity (r = .65, p < .001), and with pregnant stress for convergent validity (r = .57, p < .001). RPD and SPL-SAS were moderately correlated (r = .53, p < .001). Conclusion(s): The PBRAS-23-K is a valid and reliable instrument for assessing pregnant women’s risk of preterm birth. Clinical nurses are encouraged to apply and obtain information for effective interventions in MFICU. This scale has meaningful results and reflects the voices of women who had a preterm birth. The scale should be evaluated for standardization and cut-off scores using larger subject sizes in the future.

The paper shows an analysis of the large-scale distribution of galaxy spin directions of 739,286 galaxies imaged by DES. The distribution of the spin directions of the galaxies exhibits a large-scale dipole axis. Comparison of the location of the dipole axis to a similar analysis with data from SDSS, Pan-STARRS, and DESI Legacy Survey shows that all sky surveys exhibit dipole axes well within 1$\sigma$ error from each other. While non-random distribution is unexpected, the findings are consistent across all sky surveys, regardless of the telescope or whether the data were annotated manually or automatically. Possible errors that can lead to the observation are discussed. The paper also discusses previous studies showing opposite conclusions, and analyzes the decisions that led to these results. Although the observation is provocative, and further research will be required, the existing evidence justifies to consider the contention that galaxy spin directions as observed from Earth are not necessarily randomly distributed. Possible explanations can be related to mature cosmological theories, but also to the internal structure of galaxies.

An accurate understanding of jointed rock mass behavior is important in many applications ranging from deep geological disposal of nuclear waste to deep mining to urban geoengineering projects. The roughness of rock fractures and the matching of the fracture surfaces are the key contributors to the shear strength of rock fractures. In this research, push shear tests with three normal stress levels of 3.6, 6.0, and 8.5 kPa were conducted with two granite samples with artificially induced well-matching tensile fractures with sizes of 500 mm × 250 mm and 1000 mm × 500 mm. The large sample reached on average a -60 % weaker peak shear stress than the medium-sized sample, and a strong negative scale effect was observed in the peak shear strength. The roughness of the surfaces was measured using a profilometer and photogrammetry. The scale-corrected profilometer-based method (JRC) underestimates the peak friction angle for the medium-sized slabs by -27 % for the medium sample and -9 % for the large sample. The photogrammetry-based (Z’2) method produces an estimate with -7% (medium) and +12 % (large) errors. The photogrammetry-based Z’2 is an objective method that consistently produces usable estimates for the JRC and peak friction angle.

The present paper investigates numerically the resistance at full-scale of a zero-emission, high-speed catamaran in both deep and shallow water, with the Froude number ranging from 0.2 to 0.8. The numerical methods are validated by two means: a) comparison with available model tests; b) a blind validation using two different flow solvers. The resistance, sinkage and trim of the catamaran, as well as the wave pattern, longitudinal wave cuts and cross-flow fields, are examined. The total resistance curve in deep water shows a continuous increase with the Froude number while in shallow water, a hump is witnessed near the critical speed. This difference is mainly caused by the pressure component of total resistance, which is significantly affected by the interaction between the wave systems created by the demihulls. The pressure resistance in deep water is maximised at a Froude number around 0.58, whereas the peak in shallow water is achieved near the critical speed (Froude number ≈ 0.3). Insight into the underlying physics is obtained by analysing the wave creation between the demihulls. Profoundly different wave patterns within the inner region are observed in deep and shallow water. Specifically, in deep water, both crests and troughs are generated and moved astern as the increase of the Froude number. The maximum pressure resistance is accomplished when the secondary trough is created at the stern, leading to the largest trim angle. In contrast, the catamaran generates a critical wave normal to the advance direction in shallow water, which significantly elevates the bow and creates the highest trim angle as well as pressure resistance. Moreover, significant wave elevations are observed between the demihulls at supercritical speeds in shallow water which may affect the decision for the location of the wet deck.

Shrinking farm size and fragile farm resources pose a significant challenge to the sustainability of small-scale farms. Efficient resource utilization in small-scale farms is crucial to achieving farm sustainability through endogenous mechanisms. However, the precise mechanisms to integrate physical resources to achieve farm sustainability are not very clear yet. By capturing the interaction among farm resources as a network phenomenon, we identify the discrete resource interactions (RIs) in different types of small-scale farms of Indian Sundarbans, which are associated with higher farm sustainability. Thirty-two linkages, 11 reciprocal linkages, 22 triads, and three ‘core elements’ that occurred and cooccurred on highly sustainable farms are found to be critical in achieving farm sustainability. Using the properties of resource interaction networks as explanators of farm sustainability, we anticipate that sustainability in small-scale farms can be achieved by strategically creating new RIs on the farm. However, there may be limitations to such achievement depending on the nature of RI and type of farm. The analytical approach helps to understand the structural basis of sustainability in small-scale farms, and this approach can be used to achieve farm sustainability through the strategic integration of existing farm resources in the smallholder systems.

Perovskite based solar cells have achieved tremendous progress reaching record efficiency in the past 5 years. Numerous new processes and chemistry have been reported and contribute to the perovskite rapid progress. Continuous efficiency improvements are still necessary for perovskite solar cells, and an exploratory data analysis on devices performance over multiple studies could boost the technology development. Such analysis could identify patterns or provide insights that are not obvious in a single study. Here we present a high quality dataset containing only independently certified Pb-based perovskite solar cells summarizing their efficiency, relevant I-V metrics, manufacturing processes and materials used. Analysis over the dataset provides insights on how aperture size, perovskite deposition methods and materials used in each functional layer affect the final solar cell efficiency and I-V metrics. Future directions are also suggested for efficiency improvements.

From physics to the social sciences, information is now seen as a fundamental component of reality. However, a form of information seems still underestimated, perhaps precisely because it is so pervasive that we take it for granted: the information encoded in the very environment we live in. We still do not fully understand how information takes the form of cities, and how our minds deal with it in order to learn about the world, make daily decisions, and take part in the complex system of interactions we create as we live together. This paper addresses three related problems that need to be solved if we are to understand the role of environmental information: (1) the physical problem: how can we preserve information in the built environment? (2) The semantic problem: how do we make environmental information meaningful? And (3) the pragmatic problem: how do we enact environmental information in our daily lives? Attempting to devise a solution to these problems, we introduce a three-layered model of information in cities, namely environmental information in physical space, environmental information in semantic space, and the information enacted by interacting agents. We propose forms of calculating entropy in these different layers, and apply these measures to archetypal urban cases and simulated scenarios. Our results suggest that ordered spatial structures and diverse land use patterns encode information, and that aspects of physical and semantic information affect coordination in interaction systems.

Abstract: Comparing outcrop data to laboratory results is important to verify and validate experiments of analogue and reservoir materials especially regarding conditions for deformation experiments. This is important better understand highly complex carbonate reservoir strata and their response to changes in subsurface conditions, reducing subsurface uncertainty. This study develops methods to allow for a more straightforward comparison of outcrop data (m-scale) with experimentally created fracture arrays developed in cylindrical samples (cm-scale). The main objective is to assess usefulness of experimentally-produced fracture networks as analogues for subsurface structures, typically at the meter and above scale by developing new techniques to use the lab deformation. It analyses key characteristics of laboratory-induced fracture networks by adapting scanline methods to use with x-ray tomography (XRT) images to allow for comparison with outcrop and field data. To test and verify these new methods two low permeability carbonate samples were used for deformation testing and analysis. Applying the different scanline methods we show that they can be used to analyse lab induced fractures (mm to cm-scale) identified in XRT images for comparison with outcrop data (m-scale). In addition, these methods also allow for quantification of fracture network attributes e.g. fracture spacing, fracture apertures, orientation. This new data bridges the gap between micro-scanlines using thin sections and outcrop scanlines.

Auricular keloids pose significant aesthetic and functional challenges, and traditional treatments often fall short in ad-dressing these. Our study presents an innovative combined approach of ablative CO2 and dye laser therapy for improved keloid management. This treatment protocol was applied to 15 patients with auricular keloids after an initial multispec-tral analysis to assess keloid composition. The laser sequence was tailored per patient based on this analysis. Evalua-tions using the Vancouver Scar Scale and Patient and Observer Scar Assessment Scale were carried out at baseline and at 3-week intervals post-treatment. The results showed a significant reduction in these scores at the final follow-up (p<0.05), suggesting improvements in keloid color, texture, and pliability, with minimal adverse events. Additionally, no recur-rence of keloids was observed. Our findings indicate that this novel methodology of multispectral analysis followed by tailored laser therapy may offer a safe and effective solution for auricular keloids, promising enhanced keloid treatment and prevention of recurrence. However, further investigations, including randomized controlled trials, are needed to confirm and optimize this treatment protocol.

Crops obtained by genome editing (GE) technologies represent a notable and disruptive shift from genetically modified or transgenic plants, outpacing public perception and regulatory frame-works. Multiple aspects of GE are contributing to the advancement of modern agriculture, in-fluencing the market structure by introducing specific changes within the existing genetic blue-print of an organism. Generally, the GE toolbox includes distinct technologies able to incorporate site-specific and pre-determined genomic modifications, exploiting well-established genetic modification strategies. For these reasons, GE-derived approaches are considered new plant breeding methods, known as new breeding techniques (NBTs). Particularly, CRISPR/Cas-based technologies represent a considerable improvement over prior techniques, being more precise, accurate and straightforward for targeted gene editing, in a reliable and reproducible way, with numerous applications. CRISPR/Cas system exploitation for non-editing purposes has also been widely documented, ranging from cell imaging to expression regulation and DNA assembly. Recently, CRISPR/Cas systems have been employed for target detection and could be used to ef-ficiently identify multiple organic chemicals. High-sensitivity and high-specificity detection are two main points of the CRISPR/Cas technology, without needing complex expertise or technical pipelines. This manuscript aims to provide an overview of the main advances of CRISPR/Cas-based systems into new frontiers of non-editing. The associated implications (e.g., molecular traceability) and their relative impacts are also presented and discussed.

Garcinia indica (Thouars) Choisy (commonly known as Kokum) is an important medicinal plant in Ayurvedic medicine and belonging to the Clusiaceae family. Kokum is a highly traded medicinal plant species of India, dried rind of fruits and butter from seeds are traded in the markets. This study aimed to assemble the complete chloroplast (cp) genome of G. indica and compare it with the previously published cp genome within the Garcinia taxa to identify the potential species-specific barcode marker for Kokum authentication. The assembled cp genome, with a size of 1,56,891 bp, exhibits a typical quadripartite structure. The large single-copy (LSC) region spans 85,580 bp, and the small single-copy (SSC) region spans 17,181 bp, together comprising 64.5% of the genome. The pair of inverted repeats (IRA and IRB) are each 27,065 bp, covering the remaining 35.5% of the genome. A total of 126 unique genes were identified, including 86 protein-coding genes, 32 tRNA genes, and 8 rRNA genes. Phylogenetic analysis using complete cp genomes from 12 species in the Clusiaceae family indicated that 10 Garcinia species form a sister clade. Notably, the ycf1 gene in the LSC region was more divergent within the Garcinia species. This study presents the first report on the chloroplast genome of G. indica. This chloroplast genome resource provides a basis for identifying new DNA barcode marker as well as species-specific marker for herbal drug authentication of Kokum, and species delineation within the Garcinia genus.

In genomics analysis, with the development of sequencing technology and the rapid growth of data volume, how to effectively identify and analyze important information in genomic data from massive data has become an important challenge. Identify key patterns and features in genomic data through advanced community testing methods. First, genomic data often contains a lot of noise and redundant information that needs to be processed through steps such as normalization, filtering, and dimensionality reduction. Normalization makes data at different scales comparable, filtering out data points with low quality or missing values, and dimensionality reduction reduces data dimensions through principal component analysis (PCA) and retains the main information. The gene co-expression network establishes the connection relationship between genes by calculating the expression similarity matrix between genes, and applies the Louvain algorithm to maximize the modularity of the network, aggregate nodes layer by layer, form a community structure, and identify the complex relationship and potential structure between genes. Finally, we utilize the cancer dataset to evaluate the proposed model. From our extensive experimental results, we can observe that Louvain's algorithm indicates outperformances and accuracy in the recognition and analysis of genomic data.

Relationships of the three bryophyte lineages (liverworts, mosses, and hornworts) to vascular plants is a pivotal question in the study of origin and evolution of land plants. In recent decades, this question has been subject to intense phylogenetic analyses using morphological characters, multigene DNA sequences, and genome structural characters. A tentative consensus reached ten years ago suggested that bryophytes are a paraphyletic group, with liverworts being sister to all other land plants and hornworts being sister to vascular plants. However, several more recent nuclear phylogenomic studies have concluded that bryophytes represent a monophyletic group that is sister to vascular plants. A discussion is presented here on strengths and weaknesses of different types of characters (morphological traits, nucleotide sequences, and genome structural arrangements), and their suitability for resolving deep phylogenetic relationships. Moreover, several criteria for credible phylogenetic reconstruction are proposed. Strong statistical support for reconstructed relationships should be derived from high quality, independent characters selected for suitability to the particular question being addressed. The relationships inferred in a study should be congruent with those from as many other lines of phylogenetic evidence as possible. Any incongruities should be explicable by well-understood biological mechanisms. It is concluded that the relationships of the three bryophyte lineages to vascular plants should currently be viewed as unresolved. This is a difficult phylogenetic problem; the land plants underwent a rapid radiation a long time ago. Yet, further exploration of analytical methods and careful choice of characters should lead to eventual elucidation of diversification patterns among early land plants.

Genome-wide association studies (GWAS) have accelerated the exploration of genotype-phenotype associations, facilitating the discovery of replicable genetic markers associated with specific traits or complex diseases. This narrative review explores the statistical methodologies developed using GWAS data to investigate relationships between various phenotypes, focusing on endometrial cancer, the most prevalent gynecological malignancy in developed nations. Advancements in analytical techniques such as genetic correlation, colocalization, cross-trait locus identification, and causal inference analyses have enabled deeper exploration of associations between different phenotypes, enhancing statistical power to uncover novel genetic risk regions. These analyses have unveiled shared genetic associations between endometrial cancer and many phenotypes, enabling identification of novel endometrial cancer risk loci and furthering our understanding of risk factors and biological processes underlying this disease. The current status of research in endometrial cancer is robust; however, this review demonstrates that further opportunities exist in statistical genetic that hold promise for advancing the understanding of endometrial cancer and other complex diseases.

A fully automated bacteria whole genome sequencing (WGS) assay was evaluated to characterize Mycobacterium tuberculosis (MTB) and non-tuberculosis Mycobacterium (NTM) clinical isolates. Results generated were highly reproducible with 100% concordance in species and sub-lineage classification, and 92% concordance between antimicrobial resistance (AMR) genotypic and phenotypic profiles. These findings demonstrate that a fully automated WGS assay, with a short turnaround time of 24.5 hours, provides timely and valuable insights into MTB outbreak investigation while providing reliable genotypic AMR profiling consistent with traditional antimicrobial susceptibility tests (AST). This study establishes a favorable proposition in the adoption of an end-to-end fully automated WGS solutions for decentralized TB diagnostics, thereby aiding in WHO’s vision of tuberculosis eradication.

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

Heteroresistance (HR) to colistin is especially concerning in settings where multi-drug resistant (MDR) K. pneumoniae are prevalent and empiric use of colistin might lead to treatment failures. This study aimed to assess the frequency of occurrence of colistin HR (CHR) among (MDR) K. pneumoniae (n=676) isolated from patients hospitalized in 13 intensive care units (ICUs) in 6 European countries in a clinical trial assessing the impact of decolonization strategies. All isolates were whole-genome-sequenced and studied for in vitro colistin susceptibility. Majority were colistin-susceptible (CS) (n=597, MIC 2 µg/ml). 288 CS isolates were randomly selected for population analysis profiling (PAP) to assess CHR prevalence. CHR was detected in 108/288 CS K. pneumoniae. No significant association was found between the occurrence of CHR and country, MIC-value, K-antigen type and O-antigen type. Overall, 92% (618/671) of the K. pneumoniae were MDR with high prevalence among CS (540/592) and CR (98.7%, 78/79) isolates. In contrast, proportion of carbapenemase-producing K. pneumoniae (CP-Kpn) was higher among CR (72.2%, 57/79) than CS isolates (29.1%, 173/594). Proportions of MDR and CP-Kpn were similar among CHR (MDR: 85%, 91/107; CP-Kpn: 29.9%, 32/107) and CS isolates (MDR: 91%, 539/592; CP-Kpn: 29.1%, 153/59). WGS analysis of PAP isolates showed diverse insertion elements in mgrB or even among technical replicates underscoring the stochasticity of the CHR phenotype. CHR isolates showed high ST diversity (Simpson’s diversity index, SDI: 0.97, in 52 of the 85 STs tested). CR (SDI: 0.85) isolates were highly associated with specific STs (ST101, ST147, ST258/ST512, P ≤ 0.003). The widespread nature of CHR among MDR K. pneumoniae in our study urge the development of rapid HR detection methods to inform on the need for combination regimens.

Whole genome alignment (WGA) is a critical process in comparative genomics, facilitating the detection of genetic variants and aiding our understanding of evolution. This paper offers a detailed overview and categorization of WGA techniques, encompassing suffix tree-based, anchors-based, and graph-based methods. It elaborates on the algorithmic properties of these tools, focusing on performance and methodological aspects. The paper underscores the latest progress in WGA, emphasizing the increasing capacity to manage the growing intricacy and volume of genomic data. However, the field still grapples with computational and biological hurdles affecting the precision and speed of WGA. We explored these challenges and potential future solutions. This paper aims to provide a comprehensive resource for researchers, deepening our understanding of WGA tools and their applications, constraints, and prospects.

Opossums, native to the Americas, are unique marsupials with over 100 species. The Common Opossum and Virginia Opossum are notable species. They are nocturnal, omnivorous, and adapt to various habitats. Their reproduction involves a short gestation and marsupial pouch development. Despite their ecological benefits like seed dispersal and insect control, their proximity to human habitats exposes them to pathogens, posing public health risks. These include protozoa, helminths, and arthropods that can spread zoonotic parasites and vector-borne diseases. The marsupial immune system, including opossums, is complex, rivaling eutherian mammals. Key immune genes were identified in the grey short-tailed opossum genome. CD1 protein and VpreB surrogate light chain were also found. Marsupials are proposed as ideal models for studying developmental immunology. A West Indian opossum (Didelphis marsupialis) was found and examined. Blood tests revealed abnormalities, including a low white blood cell count and signs of anemia. The results contribute to understanding the species’ health and adaptability in the wild.

Gene editing is now easy to make new disease models through in-vivo and in vitro tests. It can potentially be used to make animals with single-gene or multiple-gene changes. The mutant strains with changed germlines are no longer needed with in vivo gene editing, which uses the CRISPR-Cas9 system to target cells of interest in their normal tissues. Whereas, the AAVs and other viral vectors have made it possible to change cells selectively. Gene editing hade made it possible to use human induced pluripotent stem cells (iPSC) to model diseases that run in families. Researchers can compare and contrast the human genomes of many different ethnic and racial groups using this method. Scientists may be able to make a disease in a lab dish using iPSCs from a patient. Using CRISPR, iPSCs made from patient cells can be fixed if they have certain problems. This shows that gene therapy is possible and shows what happens when cells aren't working right. The fact that CRISPR-Cas9 can change the DNA by just one nucleotide has had a huge effect on biological studies. CRISPR is becoming more and more popular, which shows how useful, easy, and effective it is. With the broad use of CRISPR-based apps, the tool is now used for much more than just changing genes. This method can be used to screen the whole genome, control the translation of genes based on their sequence, and edit several genes at the same time. Scientists can now model diseases in different species and learn more about how genes work because of these advances. Genome-wide association studies and genome-editing tools like CRISPR are giving us a good look at the future of personalized medicine.

Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene Ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, associated with the significant SNP chr6.S_155668107 of axis tissue, encodes a cysteine proteinase inhibitor, suggesting its potential role in alleviating Hg toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.

Background: Genome-wide association studies (GWAS) have shed light on various complex diseases and traits, by detecting more than 400,000 associated genetic loci. This number is expected to drastically increase because of the use of novel artificial intelligence methods offering new ways to study the effects of variants. Deep learning using artificial neural networks (ANN) is a sub-field of artificial intelligence, which simulates how the human brain learns. We aimed at assessing the potential of deep learning in human genetic studies of Alzheimer’s Disease (AD) and how these compare to the traditional statistical methods used in GWAS, by simultaneously testing the two approaches on the same dataset, while discovering new genetic loci associated to AD. Methods: To address this aim, phenotypic and genome-wide SNP data from the UK Biobank was analysed on a binary outcome, AD diagnosis, in two different data balance options, of one-to-one and one-to-two case-control datasets, using 2,764 cases vs 2,764 controls and 5,528 controls respectively matched on gender, age, ethnicity, PC1-20 and genotyping array. Genetic data handling and GWAS were performed using PLINK, whereas neural networks were trained using GenNet, a new ANN tool, with the same datasets, separated into training (60%), validation (20%) and test (20%) sets. Neural network layers were determined using biological knowledge, by annotating SNPs to genes and genes to AD related pathways, using ANNOVAR annotations followed by GeneSCF and KEGG. Results: Significant associations were detected between four SNPs linked to two different genes and AD for the 1 to 1 case-control study design and six SNPs linked to four different genes for the 1 to 2 case-control study design by using PLINK. All identified regions have been previously associated to AD. GenNet identified twelve SNPs on seven genes to be associated with AD, all with biological plausibility, achieving an AUC of 0.80 when using three biologically determined layers and 0.73 when using two layers at the neural networks. No common top SNPs were identified between the machine learning and GWAS models. Conclusion: This is one of the first studies attempting to compare the traditional GWAS to more sophisticated state-of-art methods for understanding the genetic architecture of complex phenotypes using the same dataset. More systematic comparisons with such approaches on real data are needed to enable best practises for machine learning in the analysis of genome-wide genetic data.

Goji berries, long valued in Chinese medicine and cuisine for their wide range of medicinal benefits, are considered a 'superfruit' and functional food. Out of the nearly 100 Lycium species known for their genetic diversity, L. barbarum and L. chinense currently dominate the market. Due to increasing market demand and concerns about food safety and sustainability, Europe and the Americas are expanding the local goji berry production, using as starting material plants originated from China. European breeding programs are focusing on Lycium to develop varieties adapted to local conditions, especially in response to climate change. By 2023, Romania registered seven goji berry varieties, both from L. barbarum and L. chinense species, without incorporating local germplasm. Advanced genomic studies, including NGS sequencing of five cultivated and three wild goji berry plant genomes, have been conducted to analyse their genetic variation, with a particular focus on the BODYGUARD 3 and 4 genes. This research uncovered significant differences between cultivated and wild genotypes, both in the entire genome and specifically in the BODYGUARD genes, providing crucial insights for goji berry breeders to support the development of goji berry cultivation in Romania.

In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings. While this abundance of data offers invaluable insights, it also places a pressing responsibility on genetic professionals and researchers to stay informed about the latest findings and their clinical significance. Genomic variant interpretation is currently facing a challenge in identifying the most up-to-date and relevant scientific papers, while also extracting meaningful information to accelerate the process from clinical assessment to reporting. Computer-aided literature search and summarization can play a pivotal role in this context. By synthesizing complex genomic findings into concise, interpretable summaries, this approach facilitates the translation of extensive genomic datasets into clinically relevant insights. To bridge this gap, we present VarChat (varchat.engenome.com), an innovative tool based on generative AI, developed to find and summarize the fragmented scientific literature associated with genomic variants into brief yet informative texts.VarChat provides users with a concise description of specific genetic variants, detailing their impact on related proteins and possible effects on human health. Additionally, VarChat offers direct links to related scientific trustable sources, and encourages deeper research. Availability: VarChat is freely available at varchat.engenome.com

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China in December 2019, it has spread rapidly, and many coronavirus disease (COVID-19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID-19 epidemic have increased interest in the characteristics of epidemics in this region, and pathogen genetic analysis is required for infection control and prevention. In this study, SARS-CoV-2 whole-genome analysis was performed on samples from patients with COVID-19 in Gwangju from 2020 to 2022 to identify the trends in COVID-19 prevalence and to analyze the phylogenetic tree of dominant variants. B.41 and B.1.497 prevailed in 2020, the early stage of the COVID-19 outbreak; then, B.1.619.1 mainly occurred until June 2021. B.1.617.2, classified as sublineage AY.69 and AY.122, occurred continuously from July to December 2021. Since strict measures to strengthen national quarantine management had been implemented in South Korea until this time, mutations phylogenetic analysis was also able to infer the epidemiological relationship between infection transmission routes. Since the first identification of the Omicron variant in late December 2021, the spread of infection has been very rapid, and weekly whole-genome analysis of specimens has enabled us to monitor new Omicron sublineage occurring in Gwangju. Our study suggests that conducting reginal surveillance in addition to nation-level genomic surveillance will enable more rapid and detailed variant surveillance, which will be helpful in the overall prevention and management of infectious diseases.

Standardized protocols were specifically designed and developed for clinical information collection and obtaining trio genomic information from infants affected with congenital anomalies (CA) and their parents, as well as securing human biological resources. Two large areas of these protocols include clinical and genomic information collection on CA which were difficult to diagnose using pre-existing screening methods. The following are three essential items for the clinical information collection protocol: establishment of a consent system for collecting and utilizing research resources, establishment of criteria for target patient selection, and collection of clinical and epidemiological information. A total of 138 cases consisting of 45 families of infants with CA and their parent trios have provided human-derived resources and genomic information. Whole genome sequencing data have been generated for all participants, and standardized protocols for resource collection and manufacturing have been developed. Phenotype information according to the Human Phenotype Ontology term and major test findings were recorded. It is important to keep updating and recording clinical symptoms and genetic diagnosis that are newly added or changed over time. The unique significance of this study is to develop a protocol that enables long-term tracking by adding growth and development tests that reflect important characteristics of newborns. By using these clinical and genetic information collection protocols for CA, it will be possible to establish an essential platform for early genetic diagnosis and diagnostic research, and further present new genetic diagnostic guidelines in the near future.

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H+ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont's orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor.

Vernonia amygdalina is an important nutritional and medicinal plant that is used to treat various diseases such as malaria and diabetes in Nigeria. In this study, we sequenced, assembled, and annotated the complete nucleotide sequence of the chloroplast genome of a V. amygdalina species isolated in Awka, Nigeria. The chloroplast genome is 153 149 bp in length and has a conserved structure that includes the LSC (84261 bp) region, the SSC (13152 bp) region, and the IR (27868 bp) regions. A total of 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis of the genome revealed species variations in the LSC region associated with the geographical location of the V. amygdalina plant. Phylogenetic analysis of the chloroplast genomes using FastTree showed that V. amygdalina clustered closest to the chloroplast of the Crepidiastrum genus. This study identifies the characteristics of the V. amygdalina chloroplast genome, which will improve our understanding of intraspecies diversity and the identification of potential molecular markers to determine geographical origin.

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is picking up, however, current pipelines are failing to identify a significant proportion of divergent repeats in non-model organisms. The order Decapoda, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied on 20 Decapoda and 6 other crustacean genomes. With our new tool we identify 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other crustaceans, with an incredibly large number of highly repeated satDNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and a different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using genome sequences from Davao City and nearby provinces. We adapted the RABV ARTIC Protocol for Oxford Nanopore High-Throughput Sequencing to optimize workflow efficiency under limited resources. Comparing new virus samples collected from June 2019 to June 2021 (n=38) with baseline samples from June 2018 to May 2019 (n=49), new sub-clades were observed in the phylogenetic tree, suggesting divergence from older variants that were previously undetected. Most of the new viruses belonged to the Asian SEA4_A1.1.1 lineage, but new (SEA4_B1 and SEA4_B1.1) and emerging (SEA4_B1.1_E1) lineages that have never been reported in the Philippines were also identified. The baseline study reported phylogeographic clustering of RABV isolates from the same areas. However, this pattern was disrupted in the current biosurveillance, with variants detected in areas outside the original cluster. Furthermore, our findings revealed significant transmission routes between Davao City and neighboring provinces, contrasting with the predominantly intra-city transmission observed in the baseline study. These results underscore the need for ongoing and timely genomic surveillance to monitor genetic diversity changes and the emergence of novel strains, as well as to track alterations in transmission pathways. Implementing cost-effective next generation sequencing workflows will facilitate the integration of genomic surveillance into rabies control programs, particularly in resource-limited settings. Collaborations between different sectors can empower local laboratories and experts in genomic technologies and analysis.

Ningxiang pig is renowned breed for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 minutes and 24 hours) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30 ~ 0.80) for carcass traits and from low to high (0.11 ~ 0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the HMGA1 gene emerged as a pleiotropic gene correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs.

In this study, we de novo assembled whole genomes of two small body-sized West Pacific sciaenids (Larimichthys polyactis and Collichthys lucidus) and compared them with published genome data of two closely-related, large body-sized species (Larimichthys crocea and Miichthys miiuy) and one distantly-related, large body-sized outgroup species (Dicentrarchus labrax). The phylogeny constructed using 7,403 single-copy orthologs shared among the five species indicated that L. crocea and L. polyactis diverged about 42 MYA. The two sibling taxa are more closely-related to C. lucidus than M. miiuy. We further identified four growth-related genes (CDHR2, PGC, PTN and PDGFA) that host five diagnostic amino acid variants on body size traits in the fishes, splitting small-body sized L. polyactis and C. lucidus from large-body sized L. crocea, M. miiuy and D. labrax. The results provide new genomic resources and guidelines to facilitate future endeavors in studying functional genomics and developing selective breeding programs for desirable growth traits in sciaenids.

The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures and for this propose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanism leading to the creation of genomic heterogeneity by altering the number of chromosomes as well as changing their structures. In this review we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, human genome shows induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as whole genome doubling to more discrete changes as indels as well as the recent discovered complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double strand breaks (DSB) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar pattern observed during tumorigenesis. Then, we will also list several diseases associated to CIN resulting in fertility issue, miscarriage, genetic rare diseases and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.

Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multi-drug resistant (MDR) pathogen. Further, Carbapenem-Resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases in Kp isolates from India, (2) determine the most prevalent sequence type (ST) & plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n=65) were collected from various pathology lab, drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was done for (n=22) resistant isolates and WGS analysis was performed using various bioinformatics tools. Additional Indian MDR Kp genomes (n=187) were retrieved using Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location, plasmid replicons, and ST type of genomes were carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST respectively. All data were analyzed and summarized using iTOL tool. ST231 was highest, followed by ST147, ST2096 & ST14 among Indian isolates. blaAmpH was detected as the most prevalent gene followed by blaCTX-M-15, blaTEM-1. Among carbapenemase genes, blaOXA-232 was prevalent and associated with ST231, ST2096 and ST14, which was followed by blaNDM-5 which was observed to prevalent in ST147, ST395 &ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col (BS512) was abundantly present in ST147 genomes. One Kp isolate with novel MLST profile was identified, which carried blaCTX-M-15, blaOXA-1 and blaTEM-1. ST16 &ST14 from this study, which is mostly dual producer of carbapenem and ESBL genes, could be emerging high-risk clones in India.

Due to an increase in the consumption of food, feed, and fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to obtain high-yielding crops that can adapt to future climate changes. Currently, the main feed source used for ruminant livestock production is forage grasses. In temperate climate zones, perennial grasses grown for feed are widely distributed and tend to suffer under unfavorable environmental conditions. Gene editing has been shown to be an effective tool for the development of abiotic stress-resistant plants. The highly versatile CRISPR-Cas system enables increasingly complex modifications in genomes while maintaining precision and low off-target frequency mutations. In this review, we provide an overview of forage grass species that have been subjected to gene editing. We offer a perspective view on the generation of plants resilient to abiotic stresses. Due to the broad factors contributing to these stresses the review focuses on drought, salt, heat, and cold stresses. The application of new genomic techniques (e.g., CRISPR-Cas) allows addressing several challenges caused by climate change and abiotic stresses for developing forage grass cultivars with improved adaptation to the future climatic conditions. Gene editing will contribute towards developing safe and sustainable food systems.

Abstract. The increasing frequency of isolation of methicillin-resistant Staphylococcus aureus (MRSA) limits the chances of effective antibacterial therapy of staphylococcal diseases and results in development of persistent infection such as bacteremia and osteomyelitis. The aim of this study was to identify features of the MRSAST239 0943-1505-2016 (SA943) genome, that contribute to the formation of both acute and chronic musculoskeletal infections. The analysis was performed using comparative genomics data of the dominant epidemic S. aureus lineages namely ST1, ST8, ST30, ST36, ST239. SA943 genome encodes proteins that provide resistance to the host immune system, suppress immunological memory and form biofilms. The molecular mechanisms of adaptation responsible for development of persistent infection were as follows: amino acid substitution in PBP2 and PBP2a, providing resistance to ceftaroline; loss of a large part of prophage DNA and restoration of nucleotide sequence of beta-hemolysin, that greatly facilitates escape of phagocytosed bacteria from phagosome and formation of biofilms; dysfunction of the AgrA system due to the presence of psm-mec and several amino acid substitutions in the AgrC; partial deletion of nucleotide sequence in genomic island vSAβ resulting in the loss of two proteases of Spl - operon; deletion of SD repeats in SdrE amino acid sequence.

The emergence of drug-resistant parasitic nematodes of both humans and livestock calls for development of alternative and cost-effective control strategies. For the economically important ruminant strongylid Haemonchus contortus, Barbervax® remains the only registered vaccine available. Here we compared the microbiome, genome-wide diversity and transcriptome of H. contortus adult male populations that survived vaccination with an experimental vaccine after inoculation in sheep. Our genome-wide SNP analysis revealed 16 putative candidate vaccine evasion genes. However, we did not identify any evidence for changes in microbial community profiling based of 16S rRNA gene sequencing results of vaccine surviving parasite populations. A total of 58 genes were identified as significantly differentially expressed with six being long non-coding (lnc) RNAs and no putative candidate SNP associated genes. The genes highly upregulated in surviving parasites from vaccinated animals were associated with GO terms belonging to predominantly molecular function and a few biological processes that may have facilitated evasion or potentially lessened the effect of the vaccine. These included five targets: astacin (ASTL), carbonate dehydratase (CA2), phospholipase A2 (PLA2), glutamine synthetase (GLUL) and fatty acid-binding protein (FABP3). We searched all five DEG targets against the proteomes of selected Nematoda (Clades III, V, IV, C, I) and Platyhelminthes (Clades Monogenea, Trematoda, Cestoda, Rhabditophora) to determine homologs within the H. contortus NZ_HCO_NP v1.0 genome and identified single-copy orthologous groups (OGs) in selected proteomes. All but one (FABP3) demonstrated high levels of duplication and wide-spread occurrence in closely related Caenorhabditis elegans and Pristionchus pacificus, with complete absence of all five gene targets among other Clade III (Toxocara canis) and V (Ascaris suum, Ascaris lumbricoides and Parascaris univalens) nematodes, further supporting their vital biological functions in nematodes. Phylogenetic analyses inferred the presence of only ASTL and CA2 in almost all Nematoda, platyhelminthes and metazoans examined, with loss of GLULs observed among all outgroup vertebrate species and the presence of FABP3 in only three other species (Schmidtea mediterranea, Fasciola gigantica and F. hepatica). Our tertiary structure predictions and modelling analyses were used to perform in silico searches of all published and commercially available inhibitor molecules or substrate analogues with potential broad-spectrum efficacy against nematodes of human and veterinary importance.

From the hospital wastewater, a novel bacteriophage was isolated and characterized. According to characterization properties, this bacteriophage belongs to the Siphoviridae family, the maximum bacteriophage titer was recorded at 37°C and a pH of 7.2, had a 44,789 bp linear double-strand DNA genome, and within the genome sequence, there are 61 genes, all of which are encoded into proteins. Although this bacteriophage does not have any virulence factors or antimicrobial resistance genes and had specific lytic activity against some antimicrobial resistance S. aureus clinical isolates.

Understanding extremophiles and their usefulness in biotechnology involves studying their habitat, physiology and biochemical adaptations , as well as their ability to produce biocatalysts, in environments that are still poorly explored. In northwestern Peru, which saline lagoons of marine origin Pacific Ocean, the other site from the coast of Brazil of the Atlantic Ocean. Both environments are considered extreme. The objective of the present work was to compare two different strains isolated from these extreme environments at the metabolic level using molecular network methodology through the Global Natural Products Molecular Social Network (GNPS). In our study, the MS/MS spectra from the network were compared with GNPS spectral libraries, where the metabolites were annotated. Differences were observed in the molecular network presented in the two strains of Streptomyces spp. coming from these two different environments. Within the annotated compounds from marine bacteria, the metabolites characterized for Streptomyces sp. B-81 from Peruvian marshes were lobophorins A (1) and H (2), as well as divergolides A (3), B (4) and C (5). Streptomyces sp. 796.1 produced different compounds, such as glucopiericidin A (6) and dehydro-piericidin A1a (7). The search for new metabolites in underexplored environments may therefore reveal new metabolites with potential application in different areas of biotechnology.

To assess the genetic diversity of circulating dengue virus 2 in Senegal in 2018 we performed molecular characterization by complete genome sequencing and performing phylogenetic analysis. Sequenced strains belong to Cosmopolitan genotype of DENV-2 we observed intra-genotype variability leading to a divergence in two clades with differential geographic distribution. We report two variants namely; the “Northern variant” harbouring three nonsynonymous mutations (V1183M, R1405K, P2266T) located respectively on NS2A, NS2B and NS4A and the “Western variant” with two nonsynonymous mutations (V1185E, V3214E) located respectively in the NS2A gene and the NS5 gene. Findings calls for in depth in vitro and functional study to elucidate the impact of observed mutations on viral fitness, spread, epidemiology and disease outcome.

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

The article is devoted to the new results of the author, which add his previously published ones, of studying hidden rules and symmetries in structures of long single-stranded DNA sequences in eukaryotic and prokaryotic genomes. The author uses the existence of different alphabets of n-plets in DNA: the alphabet of 4 nucleotides, the alphabet of 16 douplets, the alphabet of 64 triplets, etc. Each of such DNA alphabets of n-plets can serve for constructing a text as a chain of these n-plets. Using this possibility, the author represents any long DNA nucleotide sequence as a bunch of many so-called n-texts, each of which is written on the basis of one of these alphabets of n-plets. Each of such n-texts has its individual percents of different n-plets in its genomic DNA. But it turns out that in such multi-alphabetical or multilayer presentation of each of many genomic DNA, analyzed by the author, universal rules of probabilities and symmetry exist in interrelations of its different n-texts regarding their percents of n-plets. In this study, the tensor product of matrices and vectors is used as an effective analytical tool borrowed from the arsenal of quantum mechanics. Some additions to the topic of algebra-holographic principles in genetics are also presented. Taking into account the described genomic rules of probability, the author puts also forward a concept of the important role of stochastic resonances in genetic informatics.

During the last decades West Nile Virus (WNV) outbreaks have continuously occurred in the Mediterranean area. In August 2020 a new WNV outbreak affected 71 people with meningoencephalitis in Andalusia and 6 more cases in Extremadura (south-west of Spain), causing a total of eight deaths. The whole genomes of four viral isolates were obtained and phylogenetically analyzed in the context of recent outbreaks. The Andalusian viral samples belonged to the lineage 1 and were relatively similar to previous outbreaks occurred in the Mediterranean region. Here we present a detailed analysis of the outbreak, including an extensive phylogenetic study.

Polyploidy means having more than two basic sets of chromosomes. Polyploid plants may be artificially obtained through chemical, physical and biological (2n gametes) methods. This approach allows an increased gene scope and expression, thus resulting in phenotypic changes such as yield and product quality. Nonetheless, breeding new cultivars through induced polyploidy should overcome deleterious effects that are partly contributed by genome and epigenome instability after polyploidization. Furthermore, shortening the time required from early chromosome set doubling to the final selection of high yielding superior polyploids is a must. Despite these hurdles, plant breeders have successfully obtained polyploid bred-germplasm in broad range of forages after optimizing methods, concentration and time, particularly when using colchicine. These experimental polyploids are a valuable tool for understanding gene expression, which seems to be driven by dosage dependent gene expression, altered gene regulation and epigenetic changes. Isozymes and DNA-based markers facilitated the identification of rare alleles for particular loci when compared with diploids, and also explained their heterozygosity, phenotypic plasticity and adaptability to diverse environments. Experimentally induced polyploid germplasm could enhance fresh herbage yield and quality, e.g. leaf protein content, leaf total soluble solids, water soluble carbohydrates and sucrose content. Offspring of experimentally obtained hybrids should undergo selection for several generations to improve their performance and stability.

Whole genome pooled sequence data of 12 Pakistani Teddy goats is analyzed for positive selection signatures as their breed defining characteristics. Selection imprints left in the Teddy genome are unveiled by genomic differentiation after the successful paired-end alignment of 635,357,043 reads with (ARS1) reference genome assembly. Pooled-heterozygosity ( ) and Tajima’s D (TD) are applied for validation and getting better hits of selection signals, while pairwise F_ST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation. Annotation of regions under positive selection reveals 59 genes underlying production and adaptive traits. score ≥ 5 detected six windows having highest scores on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, TD value of ≤ -2.2 showed 4 windows with very strong hits on Chr.5 & 9 harbor STIM1 and ADM genes related to body mass and weight. Lastly, F_ST analysis generated three strong signals with threshold ≤ 0.42 on Chr.12 & 5 harbor ITGB1 gene associated with milk production & lactation traits. Other significant selection signatures encompass genes associated with wool production, prolificacy, immunity and coat colors. In brief, this study identified the genes under selection in this Pakistani goat breed that will be helpful to refining future breeding policies and converging required productive traits within and across other goat breeds and to explore full genetic potential of this valued livestock species.

Proteins are the primary effectors of function in biology, and thus complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is expressed in their many proteoforms, which result from combinations of genetic polymorphisms, RNA splice variants and post-translational modifications. This knowledge is foundational for the biological complexes and networks that control biology, yet remains largely unknown. We propose here an ambitious initiative to define the human proteome; that is to generate a definitive reference set of the proteoforms produced from the genome. Several examples of the power and importance of proteoform-level knowledge in disease-based research are presented, along with a call for improved technologies in a two-pronged strategy to accomplish the Human Proteoform Project.

COVID-19 manifests regarding extreme acute respiratory conditions caused by a novel beta coronavirus (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But specific furin site in the spike protein, mutation prone and phylogenetically mess Orf1ab separates SARS-CoV-2 from other RNA viruses. Since, the outbreak (February - March 2020) which originated in China, researchers, scientists, and medical professionals are inspecting all possible facts from every possible aspect including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural based functional information of proteins, and strategies to prevent its spread. Due to the rapid mutation rate, the functional characterization of a few proteins is still lagging. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.

Chickens have extensive phenotypic variation. The Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken in China, characterized by white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of traits associated with WHYC is still poorly understood. In this study, whole genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 SNPs and 1,069,574 InDels were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. A comparative genomic analysis of WHYC and other yellow-feathered chicken showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interaction. Several genes associated with disease resistance were identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, PMEL and TYRP1 may contribute to the coloring of white feathers in WHYC. These findings improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.

Background: SARS-CoV-2 infection has spread to over 200 countries since it was first reported in December of 2019. Significant country-specific variations in infection and mortality rate have been noted. Although country-specific differences in public health response have had a large impact on infection rate control, it is currently unclear as to whether evolution of the virus itself has also contributed to variations in infection and mortality rate. Previous studies on SARS-CoV-2 mutations were based on the analysis of ~ 160 SARS-CoV-2 sequences available until mid-February 2020.^{2, 3, 4, 5} By mid-April, > 550 SARS-CoV-2 sequences had been deposited in GenBank, and over 8,200 in the GISAID database. Methods: We performed a sequence analysis on 474 SARS-CoV-2 genomes submitted to GenBank up to April 11, 2020 by multiple alignment using Map to a Reference Assembly and Variants/SNP identification. The results were verified on a larger scale, 8,126 hCoV-19 (SARS-CoV-2) sequences from GISAID database. Results: We identified 5 recently emerged mutations in many isolates (up to 40%). Our analysis highlights 5 frequent new mutations that have emerged since late February 2020. These mutations are: one each missense (non-synonymous) mutation in orf1ab (C1059T), orf3 (G25563T) and orf8 (C27964T), one in 5’UTR (C241T), one in a non-coding region (G29553A). The final mutation (G29553A) was found to be almost exclusive to the US isolates. The first 3 mutations are non-synonymous, leading to amino acid substitutions in the viral protein sequence. Except for C241T, all the novel mutations identified are absent in the isolates from Italy and Spain in the SARS-CoV-2 genomes deposited in GenBank and GISAID by April 13, 2020. Conclusion: The results of current study indicate that new mutations are emerging as COVID-19 pandemic are spreading to different countries and that geography specific mutants may exist. The findings of current study lay the foundation for further investigation into the impact of SARS-CoV-2 mutations on disease incidence, severity, and host immune response. In addition, it may also provide insights into vaccine development and serological response detection for the virus.

A novel coronavirus COVID-19 was first emerged in Wuhan city of Hubei Province in China in December 2019. The COVID-19, since then spreads to 213 countries and territories, and has become a pandemic. Genomic analyses have indicated that the virus, popularly named as corona, originated through a natural process and is probably not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Genome-wide annotation of thousands of genomes revealed that more than 1,407 nucleotide mutations and 722 amino acids replacements occurred at different positions of the SARS-CoV-2. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, rapid, and specific diagnostic tools targeting IgM/IgG or newly developed plug and play methods should be available for resource-poor developing countries. Some drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools and the preventive or therapeutic remedies of the COVID-19, and discusses on scopes for further research and effective management and surveillance of COVID-19.

The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active / inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase separated nuclear bodies possibly contributes to mammalian genome organization and gene expression.

Beta-lactam resistant bacteria, commonly resident in tertiary hospitals, have emerged as a worldwide health problem because of ready-to-eat vegetable intake. We aimed to characterize the genes providing resistance to beta-lactam antibiotics in Enterobacteriaceae, isolated from five commercial salad brands for human consumption in Mexico City. 25 samples were collected, grow in blood agar plates, the bacteria were biochemistry identified and antimicrobial susceptibility testing was done, the carried family genes were identified by endpoint PCR and the specific genes were confirmed with WGS by NGS. 12 positive cultures were identified and their microbiological distribution was as follows, 8.3% for Enterobacter aerogene (n=1), 8.3% for Serratia fonricola (n=1), 16.7% for Serratia marcesens (n=2), 16.7% for Klebsiella pneumoniae (n=2), and 50% (n=6) for Enterobacter cloacae. The endpoint PCR results showed 11 colonies positive for blaBIL (91.7%), 11 for blaSHV (91.7%), 11 for blaCTX (97.7%), 12 for blaDHA (100%),4 for blaVIM (33.3%), 2 for blaOXA (16.7%), 2 for blaIMP (16.7%), 1 for blaKPC (8.3%) and 1 for blaTEM (8.3%) gene, all samples were negative blaROB, blaCMY, blaP, blaCFX and blaLAP gene. The sequencing analysis revels a specific genotypes for Enterobacter cloacae (blaSHV-12, blaCTX-M-15, blaDHA-1, blaKPC-2); Serratia marcescens (blaSHV-1, blaCTX-M-3, blaDHA-1, blaVIM-2); Klebsiella pneumoniae (blaSHV-12, blaCTX-M-15, blaDHA-1); Serratia fonticola (blaSHV-12, blaVIM-1, blaDHA-1) and Enterobacter aerogene (blaSHV-1, blaCTX-M-1, blaDHA-1, blaVIM-2, blaOXA-9). Our results indicate that beta-lactam resistant bacteria have acquired integrons with a different number of genes that providing panresistance to beta-lactam antibiotics, including penicillins, oxacillins, cefalosporins, monobactams, carbapenems and imipenems.

We describe the genomes of two Echovirus isolates from Nigeria as reference enterovirus species B genomes for the region. These Echovirus 7 and 19 genomes have 7,411nt and 7,426nt, and were recovered from sewage contaminated water (in 2010) and an acute flaccid paralysis case (in 2014), respectively.

Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.

Light pollution of the night sky is a phenomenon increasingly observed around the world and reported in the form of thematic maps. The major contributor to light pollution is ill-adjusted or inappropriately designed artificial lighting by outdoor light sources. The phenomenon occurs mainly over urban areas, but affects both the urban environment and the areas adjacent to it. The problem of excessive artificial light emission at night and the negative effects it causes has already become so serious and global in its impact that effective and comprehensible methods of cartographic presentation of this phenomenon have been explored. The literature on the subject provides examples of how to present the results of measurements of light pollution of the night sky, but these have been developed using different colour scales, often in discretionary ranges and units of measurement. This paper presents an overview of the measurement scales and units found in the literature to describe the phenomenon of light pollution that obscures the night sky. A proposal of the author’s color scale for the presentation of the phenomenon was proposed and shown by example. The differences between measurement scales and how they affect interpretation of results are discussed. Furthermore, a recommendation is made for a standardised method of cartographic visualisation of the spatial distribution and presentation of light smog measurement results.

This study investigated whether positive self-talk (ST) over 4 weeks would improve standing long jump (SLJ) performance in men and women in their 20s. The participants of this study were 36 men and 28 women, selected through interviews with male and female students. The test subjects’ performance was measured 10 times over a 4-week period, 2-3 sessions per week. In the experimental group, participants performed SLJ while reciting positive ST; the control group performed SLJ without any specific conditions. A pre-and post-intervention survey was conducted using the Rosenberg Self-Esteem Scale (RSE). The results revealed a significant difference in the performance of experimental group (p < 0.05), while no significant difference was observed in the control group. RSE survey results also showed a significant difference only in the experimental group (p < 0.05). These findings indicate that self-affirmation yields positive effects on SLJ performance.

Weak signal spectral detection is a serious problem in many applications, especially the target possesses certain frequency band and under low signal-to-noise ratio (SNR). A kind of novel technique based on pre-whitening scale-transformation symmetric bistable parallel stochastic resonance (SR) is proposed to solve the problem. Firstly, the pre-whitening can ensure the even distribution of the receiving signal to fit the requirement of SR processing. Secondly, the scale- transformation can help to utilize the weak signal improvement property especially under low frequency band more effectively. Thirdly, the symmetric bistable parallel SR can try to reduce the variance of the clutter and additive noise fluently. Fourthly, by subtracting the steady state re-sponse of the selected symmetric bistable SR system from the parallel SR output, the weak signal spectral detection objective can be realized successfully. Simulation results based on the real sea clutter radar data guarantee the effectiveness and applicability of the proposed symmetric bistable PSR processing approach.

Involving local people in natural area management is very important to address the complexity of environmental management issues for sustainable use of local resources. Participatory methods require the contribution of local stakeholders in decision making. Mapping the environmental views of local communities allows for detecting aspects that could facilitate management efforts. This research – in the frame of the Skyros LIFE project and the PAMNATURA project - measures local acceptability of the conservation actions proposed by the LIFE project in Skyros Island (Greece) in relation with recording local people’s environmental orientation using the 15-item revised New Ecological Paradigm (NEP) scale. The research was carried out by means of questionnaires. The LIFE project proposed actions were grouped into three categories according to their theme, i.e. promoting (a) Nature protection, (b) Agro-pastoralism and (c) Ecotourism. The sample seems to largely agree with the LIFE project proposals, while the results showed high scores for most of the NEP scale items, implying pro-environmental beliefs, though there appears disagreement or neutrality regarding a few items. Local acceptability of the proposed actions was found to correlate to local people’s environmental concern measured through the NEP scale. Drawing on the results, implementation of actions related directly or indirectly to economic activities, preservation of traditional activities, as well as environmental education, interactive informing and consultation could enhance local participation. Skyros island seems to offer an appropriate social background for applying participatory and adaptive management and implementing conservation programs.

The study focused on the technical and scale efficiency of smallholder pineapple farmers in the Central Region of Ghana. The input-oriented Data Envelopment Analysis (DEA) was used to estimate technical, pure and scale efficiencies of the smallholder pineapple farmers, of which a random sampling procedure was used to select 320 respondents. The study revealed that the farmers were technically inefficient with mean technical efficiency under Constant Returns to Scale (CRS), pure efficiency under Variable Returns to Scale (VRS) and the Scale Efficiency levels of 0.505, 0.641 and 0.772, respectively, due to farmers’ inability to exploit fully the available technology while experiencing evident post-harvest losses resulting from low adoption of post-harvest technologies. Such findings are meaningful and could help the farming communities and relevant policymakers to understand the issues in farming production and hence undertake necessary actions to potentially improve farmers’ technical and scale efficiencies in the study area.

Background: The adoption of self-care behaviors among patients with congestive heart failure (CHF) is essential for the management of their health condition. However, there is a lack of tools for estimating self-care in CHF patients. We aim to develop and validate the Hippocratic heart failure self-care scale (HHFSCS). Methods: the scale includes 22 items which are reviewed by a committee of experts. Individuals indicate the frequency at which they follow each self-behavior on a five-point Likert scale. Adult patients with CHF (n=250) from a General Hospital, in Athens, were participated in the study from June 2020 to March 2021. Reliability coefficients and Explanatory Factor Analysis (EFA), using a Varimax rotation and the Principal Components Method were used to assess the psychometric measurements. Results: The Cronbach’s alpha coefficient of the HHFSCS was 0.807. The exploratory factor analysis identified two domains that accounted for 88.44% of the variance of the scale items; however, each sub-scale could not be used as an independent scale. Finally, the test-retest showed a significant strong correlation (r=0.973, p&lt;0.001). Conclusions: The HHFSCS is a reliable and valid tool for assessing self-behaviors in CHF patients. Health professionals can use it in their clinical practice to improve the management of patient’s health conditions.

Small scale carp polyculture plays a key role for food supply in Bangladesh, however, factors including water pollution, limited infrastructure and inadequate disease management hinder its sustainability. This paper reports on a survey of 231 farmers across the 6 major carp producing regions in Bangladesh, analyzing factors including, farmers’ social aspects, farm characteristics, information on disease and approaches adopted to combat them, and biosecurity practices. Almost half (46.8%) of the farms surveyed experienced disease in carp species, with clear regional variations. Eighty four percent of farms reported carp mortalities during disease outbreak, with an average mortality level 10.23±11.81%. Clinical signs during outbreaks lasted between a week and a month, and there was a peak in disease outbreaks in two seasonal periods between June to July and October to December. Disease incidence was related to a range of factors including the farmer experience, ponds/farm type, stocked species, and biosecurity practice. A combination of disinfecting measures during pond preparation and measures during stocking, including discarding fingerling transport water off-farm, fingerling disinfection and check the health of fingerlings before stocking significantly reduced disease occurrence. Treatments involving the antibiotics, ciprofloxacin, erythromycin, and azithromycin were reported as ineffective, raising concerns about non-prudent use, inadequate dosing (perhaps without appropriate veterinary guidance) and the potential for further driving antimicrobial resistance in the environment. The research unveils a concerning pattern of disease high disease incidence across small-scale carp farms in Bangladesh and the significant potential for disease spread highlights the need for responsible disposal practices. The study emphasizes the need for improving training and awareness programs are vital for addressing biosecurity and disease management challenges, ensuring sustainable aquaculture and community well-being.

One of the current challenges in Higher Education is the development of students’ emotional competencies, and consequently, how these competencies can be trained. Moreover, this must be addressed within the UN framework of inclusive, equitable, quality education (United Nations Agenda 2030) (SDG 4). To address this challenge, the present study set the following objectives: (1) to analyze pre-service teachers’ level of interest in EI and their perceived level of general EI knowledge, (2) to examine their self-perception of certain variables of emotional knowledge, according to their degree program and year of studies, (3) to analyze the relationship between these emotional knowledge variables and perceived emotional intelligence (EI); and (4) to study the predictive capacity of the study variables on future teachers' emotional knowledge variables. The study sample contained a total of 434 university students from three degree programs at two universities in Spain, of which 82.70% were women, and the mean age was 20.91 years. Two instruments were used: an ad hoc questionnaire, which assessed perceived emotional knowledge according to three variables (General knowledge of EI, where level of training in EI is considered; Intrapersonal knowledge of EI; and Theoretical-practical knowledge related to teaching), and the Trait Meta-Mood Scale (TMMS-24), which assesses metaknowledge of emotional states across three variables (Attention, Clarity, and Repair). Results of the study suggest that there are differences in perceived EI knowledge according to students' year of studies and according to their degree, and indicate that students present high interest, while their perceived level of knowledge is low. In addition, emotional clarity is the EI variable that was identified as being important in the emotional knowledge of future teachers. This study shows evidence of the importance of social-emotional competencies in initial teacher training.

The grinding process by friction at the micro-scale in a mill with stones is considered a variable combination of contacts: with two-body (the asperities of lower millstone in direct contact with the asperities of upper millstone) and the three-body (micro-particles of ground seeds trapped between the asperities of lower and the upper stones of the mill). Three elements are described: (1) the mechanic contact of the asperities of the lower and upper millstone, to predict pressures on asperities, by modeling; (2) tests on a millstone sample covered with grinding particles, and (3) tests on a wafer sample formed by the millstones with the grinding particles between them. The paper highlights the combined effects of the micro-scale friction by individual measurements and to sum these effects an analytical model was used, and to validate the model, several experiments were performed. A suitable grind by friction assumes the grain’s movement and the interaction between the seeds and solid surfaces and is highlighted through theoretical and experimental studies. Topography analysis of the surface of the millstones revealed the model of microscopic frictional force. Endpoint measurements (the traces of the surface topography evolution), enable model verification in the grinding process.

Thanks to its valuable assessment possibilities (subjective complaints and changes in nasal patency in the course of the examination), nasal provocation test may serve as an alternative tool for oral food challenges in the future. However, this test requires successive attempts to regulate its methodology in order to develop a standardized lyophilisate form and determine the threshold dose for a positive result. The study objective was to present the methodological foundation for nasal food allergen provocation tests induced by freeze-dried powdered chicken egg white. A control group of 25 individuals with no history of allergy to chicken eggs or any other allergy was included in the study. Optical rhinometry and visual analog scale were used to assess the response of nasal mucosa to local allergen challenge. Minor variations in nasal flows as measured by optical rhinometry were observed in the provocation tests. The mean optical density measurements (as measured regardless of the allergen dose used) varied from positive to negative values and vice versa; e.g., amounting to 0.018 OD (standard deviation 0,095) at 15 minutes and −0.011 OD (standard deviation 0,090) at 30 minutes. No significant differences were observed with regard to the perceived nasal discomfort using the visual analog scale. Due to the absence of nasal mucosal reactivity, nasal challenge is an excellent methodological tool for implementing food allergen tests.

Pain is a complex multidimensional feeling combined with sensorial and emotional features. The majority of patients undergoing orthodontic treatment reported various degrees of pain, which is perceived as widely variable between individuals, even when the stimulus is the same. Orthodontic pain is considered the main cause of poor-quality outcomes, patients' dissatisfaction, and lack of collaboration up to the interruption of the therapy. A deep understanding of pain and how it influences the patient’s daily life is fundamental to establishing proper therapeutic procedures and obtaining the correct collaboration. Because of its multifaced and subjective nature, pain is a difficult dimension to measure. The use of questionnaires and their relative rating scales is actually considered the gold standard for pain assessment. Depending on the patient’s age and cognitive abilities is possible to choose the most appropriate instrument for self-reported pain records. Although several scales have been proposed and a lot of them are applied, it remains uncertain which of these tools represents the standard and performs the most precise, universal, and predictable task. This review aims to give an overview of the aspects which describe pain, specifically the pain experienced during orthodontic treatment, the main tool to assess self-perceived pain in a better and more efficient way, the different indications for each of them, and their correlated advantages or disadvantages.

Innovation and technology are important tools of minerals sector efficiency and productivity im-provement. The uptake of technologies has proven important levelrs to improve the productivity of mining sector. This paper provides a comprehensive analysis of mine-level productivity by using a global data of copper, gold, and platinum from 1991-2020. Various drivers of proioductivity have been analysed to draw policy insights. Empirical findings reveal significant disparities in technical efficiency and productivity across mines and regions. A further decomposition of TFP into its different components suggest that the adoption of innovative practices and investment in technology adoption could improve the overall productivity of these commodities. The findings also suggest that an appropriate input mix and optimal scale of production could boost platinum mining productivity. Regional disparities in productivity in different commodities (e.g., South Africa vs. Zimbabwe) give policymakers with insights into how to support production scale and productivity through appropriate input mixtures.

Although the Geriatric Depression Scale (GDS) is a well-established instrument for the assessment of depressive symptoms in older adults, this has not been validated specifically for Portuguese cognitively impaired persons. The objective of this study was to analyze the psychometric properties of two Portuguese versions of the GDS (GDS-27 and GDS-15) in a Portuguese mild-to-moderate cognitively impaired sample. Clinicians assessed for major depressive disorder and cognitive functioning in 117 participants with mild to moderate cognitive decline (76.9% female, Mage = 83.66 years). The internal consistency of GDS-27 and GDS-15 were 0.874 and 0.812, respectively. There was a significant correlation between GDS-27 and GDS-15 with Beck Depression Inventory-II GDS-27: rho = 0.738, p < 0.001; GDS-15: rho = 0.760, p < 0.001), suggesting good validity. A cutoff point of 15/16 in GDS-27 and 8/9 in GDS-15 resulted in identification of persons with depression (GDS-27: sensitivity 100%, specificity 63%; GDS-15: sensitivity 90%, specificity 62%). Overall, the GDS-27 and GDS-15 are reliable and valid instruments for the assessment of depression in Portuguese-speaking cognitively impaired persons.

Considering the differences between the European and African continents concerning the management of the mining production sector, we decided to carry out this study with the main objective of demonstrating that, in Africa, mining can positively change the quality of life of the populations where it develops and, at the same time, it is possible to respect the environment, which is our main wealth. To achieve these objectives, it is necessary to present the mining activity of the continent, emphasizing both the negative aspects and its strong points. The most important thing is to make a good diagnosis of the situation, which will allow us to cure our "patient", that is, African mining production.

Marketing is the manner of how to make our sales the best in the market, our prices the most accessible, our clients satisfactory, and thus our brand is the largest distributed. This needs sophisticated and advanced understanding of the total network related. Indeed, marketing data may be seen in different forms such as qualitative and quantitative. However, in the literature, it is easily noticed that large bibliography may be collected about qualitative studies, against few studies on the quantitative point of view. This is a major drawback that makes the marketing science still focusing on the design, although the market is strongly depending on quantities such as money and time. Indeed, marketing data may be a time series such as brand sales per specified periods, brand related-prices over specified periods, market shares, ..., etc. The purpose of the present work is to investigate some marketing models based on time series due to brands. We will precisely study the effect of the time scale on the persistence of brands sales in the market and on the forecasting of such a persistence according to the characteristics of the brand and the related market competition or competitors. Our study is acted on a sample of Saudi brands during the period November 22, 2017 to December 30, 2021.

Background This paper draws learnings and successes based on field implementation experience spanning four years (2016–2019) of implementing CLTS by Prince of Peace Orphans and Widows Vision, a community-based organization located in Kaberamaido district in eastern Uganda. Methods The study aimed to document, disseminate and inform from an evidence-based point of view how adaptation and collaborative engagements triggers learning from mistakes to inform iterative changes from improvements and success.This is a descriptive paper that used project documents review based on field implementation experience. Existing project reports were synthesised, collated and curated for evidence. Data were drawn from project reports and records to inform narratives in writing. Implementation of the project was executed in homogenous rural communities occupied by people of the same dialect, cultural and social settings. Results We note that success in CLTS implementation can hardly be achieved by merely following prescriptions in handbooks and guidelines but rather by devising innovative community engagement and other participatory and community-driven techniques that foster adaptive management, promote ownership, and buy-in.Having learned from our failures, we used data to inform decisions and transformatively deviated from traditional CLTS implementation and introduced high impact and innovative approaches such as the use of CLTS helpdesks and Situation room, the Pamoja approach, learning labs and iterative feedback loops, innovatively tackling slippage and carefully introducing the follow-up mandona approach. These enhanced experiential learning and ultimately resulted in sustained sanitation behaviour. Conclusions The CLTS approach as outlined in the handbook needs to be flexibly adapted to address contextual needs. Reflective and learning sessions reinforced with routine feedback loops from implementers and beneficiaries yields tremendous results, propagates experiential learning, and ultimately results in a transformative deviation from undesirable to desired sanitation behaviours. These innovative approaches once carefully blended have proved to be sustainable, are adaptable and can work in an even larger scale and in a variety of contexts.