In this work we looked for a stable and accurate procedure to perform feature selection in datasets with a much higher number of predictors than individuals, as in Genome-Wide Association Studies. Due to the instability in feature selection when many potential predictors are measured, a variable selection procedure is proposed that combines several replications of shrinkage regression models. A weighted formulation is used to define the final predictors. The procedure is applied to investigate Single Nucleotide Polymorphisms (SNPs) predictors associated to Alzheimer’s disease in the Alzheimer’s disease Neuroimaging Initiative (ADNI) dataset. Two data scenarios are investigated: one considering only the set of SNPs and another with the covariates age, sex, educational level and APOE4 genotype. The SNP rs2075650 and the APOE4 genotype are given as risk factors for AD, which is in line with the literature, and other four new SNPs are pointed, opening new hypotheses for in vivo analyses. These experiments demonstrate the potential of the new method for stable feature selection.

Cercospora beticola Sacc. is an ascomycete pathogen that causes Cercospora leaf spot in sugar beets (Beta vulgaris L.) and other related crops. The disease symptoms are characterized by circular lesions with an ash-gray centre and dark brown to purple margins on the leaves. It can lead to significant yield losses if not effectively managed. This study aims to characterize and assess the impact of bacterial biological control agents against C. beticola. Following a dual-culture screening, 18 bacteria exhibiting over 50% inhibition were selected, with six of them demonstrating more than 80% control. Identification of the bacteria was carried out through sequencing of the16S rDNA, revealing potentially 12 species belonging to six genera including Bacillus which was represented by four species. Additionally, the bacteria underwent in-depth characterization of biochemical and molecular properties, as well as plant-growth promotion. PCR detection of genes responsible for producing antifungal metabolites revealed that 83%, 78%, 89%, and 56% of the selected bacteria possessed the bacillomycin, iturin, fengycin, and surfactin encoding genes, respectively. Infrared spectroscopy analysis confirmed the presence of lipopeptide structure in the bacteria supernatant filtrate. Subsequently, the bacteria were assessed for their effect on sugar beet plants in controlled conditions. The bacteria exhibited notable capabilities, promoting growth in both roots and shoots, resulting in significant increases in root length, weight, and shoot length. The field experiment with four bacterial candidates demonstrated good performance against C. beticola compared to difenoconazole fungicide. These bacteria played a significant role in disease control, achieving a maximum efficacy of 77.42%, slightly below the 88.51% efficacy attained by difenoconazole. Additional field trials are necessary to verify the protective and growth-promoting effects of these candidates, whether applied individually, combined in consortia, or integrated with chemical inputs in sugar beet crop production.

Nucleosome positioning plays an important role in crucial biological processes like replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes.

Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.

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

Background: RSV, or respiratory syncytial virus, is a deadly condition that is present all over the world today. The infection is initially contained in the lower respiratory tract without systemic transmission. The objective of the study: Bioinformatics was used in Egypt to create an mRNA vaccine against the Respiratory syncytial virus (RSV). Methodology: In the present screening experimental study, a lipid nanoparticles vaccine of mRNA of the surface fusion protein of Respiratory syncytial virus was manufactured. The present vaccine delivery system was lipid nanoparticles with a particle size of approximately 90 nanometres, manufactured by the hot micro-emulsion method. In stages 1 and 2 of clinical trials, the immunogenicity of the current mRNA RSV vaccine was evaluated. Results: The current vaccine demonstrated 81% immunogenicity in animal testing, but only 69% in stages 1 and 2 of clinical trials. Its side effects were manageable. The results persisted for a while. In the current trial, the vaccination proved effective as a preventative measure against RSV infection. The current vaccination lacked antibody-dependent enhancement, which causes non-protective antibodies to develop. These non-neutralizing antibodies exacerbate infection by activating cytokines and complement cascade through the formation of immune complexes or enhancement of the virus entry and replication in the host cells. On the other hand, the current RSV mRNA vaccine of the surface fusion protein consequent on the production of powerful neutralizing antibodies with prolonged immunity especially to infants and elderly candidates who received the optimal dosage regimen.

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

The basic helix-loop-helix (bHLH) transcription factor family is the second-largest transcription factor in plants. Members of this family are involved in the process of growth and development, secondary metabolic biosynthesis, signal transduction, and plant resistance. Loropetalum chinense var. rubrum is a critical woody plant with higher ornamental and economic values, which used as ornamental architecture and traditional Chinese herbal medicine plant. However, the bHLH transcription factor in the L. chinense var. rubrum (Loropetalum chinense var. Rubrum) have yet to be systematically demonstrated, and their role in anthocyanin biosynthesis remains secret. Here, we identified 165 potential LcbHLHs genes by two methods, and they were unequally distributed on chromosomes 1 to 12 of the L. chinense genome. Based on a phylogenetic comparison with proteins from Arabidopsis, these bHLH proteins were categorized into 21 subfamilies. Most LcbHLHs in a given subfamily had similar gene structures and conserved motifs. The gene ontology annotation and cis-elements predicted that the LcbHLHs had many molecular functions and were involved in plant growth processes, including flavonoid and anthocyanin biosynthetic processes, etc. Transcriptomic analysis revealed different expression patterns among different tissues and cultivars in L. chinense. Many LcbHLHs were expressed in leaves, and only a few genes were highly expressed in flowers. Six LcbHLH genes differentially expressed between species and periods in color variation, which may play a key role in anthocyanin synthesis. These further functional predictions of LcbHLHs were established by quantitative real-time PCR analysis and protein-protein interaction network. This study identified the six potential bHLH genes related to anthocyanin in L. chinense and created a solid framework for future research on the function and evolution of bHLHs.

This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes.” Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness.

Arboviruses are infections caused by arboviruses that may be either symptomatic or asymptomatic, according to individuals' resistance and immune response, which dietary patterns can influence. Thus, this study aimed to investigate the possible association between the occurrence of clinical manifestations of arboviruses and the dietary pattern of the population studied. The study was conducted in a rural population in the metropolitan area of Belém, Pará State, Brazil. The sampling consisted of 95 individuals during a febrile outbreak. Two investigations were conducted: clinical-epidemiological-dietary and laboratory investigation based on blood samples taken for arbovirus analysis. Out of the 95 individuals studied, more than half (57.89%) showed clinical manifestations. Following the laboratory serology (HI and IgM ELISA) analyses, viral isolation in C6/36 cells, and viral genome detection (RT-qPCR), the final diagnosis of the cases was 47.37% Oropouche Fever, 2.11% Oropouche Fever and Chikungunya Fever, and 1.05% Mayaro Fever. Regarding dietary pattern, as for the comparison analyses, statistical significance was observed between dietary pattern and classification regarding the presence of symptoms (p<0.05); after the correspondence analysis, symptomatic cases were more associated with a bad dietary pattern, while asymptomatic cases were more associated with a good dietary pattern.

Scientists can use the Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system, which is a powerful and flexible tool for changing the genome, to change only certain parts of the genome. This has helped researchers figure out how target genes work in biology and disease. CRISPR/Cas9 is made up of a sequence-specific CRISPR RNA (crRNA) set and a generic Cas9 nuclease. The crRNA set tells Cas9 where to cut DNA and cause double-strand breaks. In the next step of cellular DNA repair, insertions, deletions, and swaps are made at specific spots. For CRISPR/Cas9-mediated DNA cleavage to be specific, the target sequences must match the crRNA, and a protospacer nearby motif must be placed after the target sequences. In this article, we talk about how CRISPR/Cas9 works at the molecular level, what it can be used for, what it can't do, and what its future clinical treatment promise might be.

Diacylglycerol kinase (DGK) is a lipid kinase that phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Based on converting one important signaling molecule (DAG) to another (PA), DGK plays an important role in plant responses to abiotic stress including waterlogging stress. However, no studies have been reported on the characterization of the DGK gene family in the waterlogging-tolerant kiwifruit germplasm, Actinidia valvata Dunn. Here, we identified 18 AvDGK genes in the A. valvata genome. The phylogenetic analysis showed that AvDGKs can be classified into three clusters, and members within the same cluster have similar domain distribution, exon-intron structures and conserved motif compositions. Chromosome localization analysis revealed that all the AvDGK genes are located across 18 different chromosomes. There were 29 duplicated gene pairs in kiwifruit and all had undergone purifying selection during evolution. Promoter cis-element analysis revealed that the cis-elements within AvDGK genes are associated with multiple functions, including phytohormone signal transduction, stress response, and plant growth and development. The expression pattern analyses indicated that AvDGK play an important role in the fruit development and plant response to waterlogging stress. AvDGKs gene family in the tetraploid A. valvata genome might promote PA synthesis and subsequent signal transduction both under short-term and long-term waterlogging stress. These results provide information regarding the structural characteristics and potential function of DGK genes within kiwifruit and lay a fundamental basis for further research into breeding for enhancing the kiwifruit’s tolerance to waterlogging stress.

Genetic engineering has become an essential element in developing climate-resilient crops and environmental sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition rich, disease resistant, stress-tolerant “crops” fruits and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign DNA free or non-transgenic crops that could be easily regulated for commercialization in most countries.

Mulberry (Morus alba L), a significant fruit tree crop, requires magnesium (Mg) for its optimal growth and productivity. Nonetheless, our understanding of the molecular basis underlying magnesium stress tolerance in mulberry plants remains unexplored. In our previous study, we identified several differential candidate genes associated with Mg homeostasis via transcriptome analysis including xyloglucan endotransglucosylase/hydrolase (XTH) gene family. The XTH gene family is crucial for plant cell wall reconstruction and stress responses. These genes have been identified and thoroughly investigated in various plant species. However, there is no research pertaining to XTH genes within the M. alba plant. This research systematically examined the M. alba XTH (MaXTH) gene family at the genomic level using a bioinformatic approach. In total, 22 MaXTH genes were discovered and contained the Glyco_hydro_16 and XET_C conserved domains. The MaXTH’s were categorized into five distinct groups by their phylogenetic relationships. The gene structure possesses four exons and three introns. Furthermore, the MaXTH gene promoter analysis reveals a plethora of cis-regulatory elements; mainly stress responsiveness, growth and development, light responsiveness, and phytohormone responsiveness. GO analysis indicated that MaXTHs encode proteins that exhibit xyloglucan xyloglucosyl transferase and hydrolase activities in addition cell wall biogenesis as well as xyloglucan and carbohydrate metabolic processes. Moreover, a synteny analysis unveiled an evolutionary relationship between the XTH genes in M. alba and those in three other species: A. thaliana, P. trichocarpa, and Zea mays. Expression profiles from RNA-Seq data displayed distinct expression patterns of XTH genes in M. alba leaf tissue during Mg treatments. Real-time quantitative PCR analysis confirmed the expression of the MaXTH genes in Mg stress response. Overall, this research enhances our understanding of the characteristics of MaXTH gene family members and lays the foundation for future functional genomic study in M. alba.

This document introduces methods and algorithms to characterize a series of values as patterns of repeating symbols or sequences selected with the criterion to maximize the information retrieved. The method converts a series of real-number values into texts. Then, it interprets the text from a point of view specified by several parameters. Located patterns are linked nested, with shorter sequences within longer ones. Texts are then synthesized and organized in a tree-like structure, substantially reducing entropy. The characterization of processes serves as the basis for constructing models to estimate likely projected values. Alternative ways to assess the multiscale complexity of unidimensional processes are applications of the results obtained here.

Dietary patterns were recently applied to examine the relationship between eating habits and prostate cancer (PC) risk. While the associations between PC risk with glycemic index and Mediterranean score have been reviewed, no meta-analysis is currently available on dietary patterns defined by “a posteriori” methods. Search was carried out (PubMed, Web of Science) to identify studies reporting the relationship between dietary patterns and PC risk. Relevant dietary patterns were selected and the risk estimated were calculated by a random-effect model. Multivariable-adjusted odds ratios (ORs) for a 1st-percentile increase in dietary pattern score were combined by a dose response meta-analysis. 12 observational studies were included in the meta-analysis which identified “Healthy pattern” and “Western pattern”. The Healthy pattern was not related to PC risk (OR=0.96; 95% CI: 0.88-1.04) while the Western pattern significantly increased it (OR=1.34; 95% CI: 1.08-1.65). In addition, a “Carbohydrate pattern”, identified in four articles, was positively associated with a higher PC risk (OR=1.64; 95% CI: 1.35-2.00). A significant linear trend between the Western (p=0.011) and the Carbohydrate (p=0.005) pattern and the increment of PC risk was observed. The small numbers of studies included suggest that further investigations are necessary to support these findings.

In this paper the dynamics of spatially extended infected phytoplankton with the Holling type II functional response and logistically growing susceptible phytoplankton system is studied. The proposed model is an extension of temporal model available [6], in spatiotemporal domain. The reaction diffusion system exhibits spatiotemporal chaos in phytoplankton dynamics. This is particularly important for the spatially extended systems that are studied in this paper as they display a wide spectrum of ecologically relevant behavior, including chaos. In this system stability of the system is studied with respect to disease contact rate and the growth fraction of infected phytoplankton indirectly rejoin the susceptible phytoplankton population. The results of numerical experiments in one dimension and two dimensions in space as well as time series in temporal models are presented using MATLAB simulation. Moreover, the stability of the corresponding temporal model is studied analytically. Finally, the comparison of the three types of numerical experimentations are discussed in conclusion.

Aim: Streptococcus pneumoniae and influenza H1N1 virus are common organisms associated with human infections. These infections could play a significant role in immune regulation. The study was performed to analyse the genome sequences of these organisms with human genome and study its functional significance. Methods: The study was performed to analyse the overlapping of genome sequences in Streptococcus pneumoniae and Influenza (H1N1) virus against human genome sequences by BLASTn sequence analysis. The alignments are studied against the corresponding genes for their functional significance with DAVID and NDEx software.Results: Several hits or overlapping nucleotide segments were identified. Between streptococcus and homo sapiens 287 overlaps were identified, and among influenza and homo sapiens 124 hits were identified. A wide range of functional significance of these genes were identified, and the results are presented in this study. The results show insights into functional pathways and biological activities associated with the respective vaccinations or infections by these microorganisms. Conclusion: The common organisms like Streptococcus pneumoniae and Influenza H1N1 virus actively interact with the immune system and result in a wide range of immune regulations.

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.

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called “-omics”, have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated.

The main objective of this study is to conduct a bibliometric analysis of scholarly publications of Authorship Pattern. The present study covers 1723 research papers published in the area of authorship pattern and indexed in Scopus database from the year 2013 to 2022. These research publications considered for the present study have been analysed based on their year wise growth, pattern of authorship, times citations, type of publication, most productive publication source as well as countries and institutions. The study shows the positive growth of the literatures with collaborative authorship pattern and good citation status. This original research paper will be helpful to the researchers of library and information science, especially who are working in the area of bibliometrics studies.

Elevation has been a cornerstone of biodiversity research, and changes in the environmental factors behind it influence biodiversity and community patterns. Exploring the potential reasons behind liverwort community patterns has been a matter of multiplied interest for ecologists. In the present study, we assessed the liverwort plants of the Sygera Mountain from 3100 m to 4500 m decaying wood, tree, soil, and rock using complex field surveys in 2017 and 2019, and investigated the effects of altitude and various climatic factors on the diversity and community composition of the Sygera Mountain. Also, we used including ANOVA, mixed effects modeling, NMDS, ANOSIM, and CCA, which helped to critically assess the liverwort diversity with respect to environmental variables. The results of the study showed a bimodal variation in the richness of liverwort communities with altitude, with peaks occurring at 3500 m and 4100 m. The variation with altitude was significant, with communities at 4100 m and 4300 m being associated with arid environments, and those at 3100 m and 3300 m favoring areas of higher mean annual temperatures and precipitation. Among the climatic factors, the variation in mean diurnal rang, precipitation, and annual temperature was found to be the determinant of liverwort communities. The results suggest that elevation and daily temperature fluctuations play a crucial role in the distribution and community structure formation of mountain liverwort plants. This study deepens our understanding of liverwort ecology and emphasizes the importance of climatic variables in determining plant community composition.

In the investment casting process, the pattern made of wax is obtained in a die for further formation of shell mold. This work investigates commercial pattern waxes fluidity with a newly developed injection fluidity test. A good correlation between wax fluidity and its viscosity is observed, which is different from metallic alloys, where the solidification behavior is more critical. The difference in investigated filled waxes fluidity can be associated with the type and amount of filler.

MRI shows in-vivo the three archetypal patterns of CNS volume loss underlying progressive ataxias, namely spinal atrophy (SA), cortical cerebellar atrophy (CCA) and olivopontocerebellar atrophy (OPCA). The MRI-based CNS atrophy pattern was reviewed in 128 progressive ataxias. A CNS atrophy pattern was identified in 91 conditions: SA in Freidreich’s ataxia, CCA in 5 acquired and 72 (24 dominant, 47 recessive,1 X-linked) inherited ataxias, OPCA in Multi-System Atrophy and 12 (9 dominant, 2 recessive,1 X-linked) inherited ataxias. The MRI-based CNS atrophy pattern may be useful for genetic assessment, identification of shared cellular targets, and repurposing therapies or enlargement of drugs indications in progressive ataxias.

Abstract: The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes isolated from cattle farms, cattle abattoirs, and retail outlets in Gauteng province, South Africa. The isolates' sequence types (STs), clonal complexes (CCs), and lineages were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were 7 STs, 6 CCs, 44 putative virulence factors, 2 resistance genes, 1 plasmid with AMR genes and 3 with conjugative genes, 1 CRISPR gene, and all 60 isolates were positive for proviruses. Among the 7 STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p&lt;0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (P&lt;0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in 3 (5%) isolates. A CRISPR-Cas system was detected in 6 (10%), and all the isolates carried proviruses. Significant differences were detected in the frequencies of STs and virulence factors regarding the source and sample type of the L. monocytogenes isolates. The presence of both fosX and vga(G) genes in all the isolates from the three industries (cattle farms, abattoirs, and retail outlets) can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain in the country, provides the first evidence of the distribution of the pathogen with potential food safety and therapeutic implications.

Inflammation is the body’s response to infection, injury, or other stimuli. Acute inflammation is a crucial component of the immune system’s defense, aimed at eliminating infected or damaged cells and halting disease progression. A subtle interaction between pro- and anti-inflammatory processes determines its progression to inflammation resolution or to chronic inflammation. In this study, we propose a generic model of inflammation through a system of reaction-diffusion equations involving various inflammatory and anti-inflammatory cells and cytokines. We investigate the formation of patterns, determined by the emergence of Turing structures, through linear stability analysis and numerical simulations. These theoretical findings are further supported by observations of similar patterns in skin diseases.

This article introduces a novel approach, termed the Asymmetric Probabilistic Tsetlin (APT) Machine, which incorporates the Stochastic Point Location (SPL) algorithm with the Asymmetric Steps technique into the Tsetlin Machine (TM). APT introduces stochasticity into the state transitions of Tsetlin Automata (TA) by leveraging the SPL algorithm, thereby enhancing pattern recognition capabilities. To enhance random search processes, we introduced a decaying normal distribution into the procedure. Meanwhile, the Asymmetric Steps approach biases state transition probabilities towards specific input patterns, further elevating operational efficiency. The efficacy of the proposed approach is assessed across diverse benchmark datasets for classification tasks. The performance of APT is compared with traditional machine learning algorithms and other Tsetlin Machine models, including the Asymmetric Tsetlin (AT) Machine, characterized by deterministic rules for Asymmetric transitions, and the Classical Tsetlin (CT) Machine, employing deterministic rules for symmetric transitions. Strikingly, the introduced APT methodology demonstrates highly competitive outcomes compared to established machine learning methods. Notably, both APT and AT exhibit state-of-the-art performance, surpassing the Classical Tsetlin Machine, emphasizing the efficacy of asymmetric models for achieving superior outcomes. Remarkably, APT exhibits even better performance than AT, particularly in handling complex datasets.

Security patterns encompass security-related issues in secure software system development and operations that often appear in certain contexts. Since the late 1990s about 500 security patterns have been proposed. Although the technical components are well investigated, the direction, overall picture, and barriers to implementation are not. Here, a systematic literature review of 240 papers is used to devise a taxonomy for security pattern research. Our taxonomy and the survey results should improve communications among practitioners and researchers, standardize the terminology, and increase the effectiveness of security patterns.

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.

Recently, there have been revolutions in the development of both gene therapy and genome surgical treatments for inherited diseases. Much of this progress has been centered around hereditary retinal dystrophies, because the eye is an immune-privileged and anatomically ideal target. Gene therapy treatments, already demonstrated to be safe and efficacious in numerous clinical trials, are benefitting from the development of new viral vectors, such as dual and triple AAVs. CRISPR/Ca9, which revolutionized the field of gene editing, is being adapted into more precise “high fidelity” and catalytically dead variants. New CRISPR endonucleases, such as CjCas9 and Cas12a, are generating excitement in the field as well. Stem cell therapy has emerged as a promising alternative, allowing human embryo derived stem cells and induced pluripotent stem cells to be edited precisely in vitro and then reintroduced into the body. This article highlights recent progress made in gene therapy and genome surgery for retinal disorders, and it provides an update on precision medicine FDA treatment trials.

Ovarian tissue cryopreservation (OTC) or testicular tissue cryopreservation (TTC) are effective and often the only options for fertility preservation in female or male patients due to oncological, medical, or social aspects. While TTC and resumption of spermatogenesis, either in vivo or in vitro, has still be considered an experimental approach in humans, OTC and autotransplantation has been applied increasingly to preserve fertility with more than 200 live births worldwide. However, the cryopreservation of reproductive cells followed by the resumption of gametogenesis, either in vivo or in vitro, may interfere with sensitive and highly regulated cellular processes. In particular, the epigenetic profile, which includes not just reversible modifications of the DNA itself but also post-translational histone modifications, small non-coding RNAs, gene expression and availability, and storage of related proteins or transcripts, have to be considered in this context. Due to complex reprogramming and maintenance mechanisms of the epigenome in germ cells, growing embryos, and offspring, OTC and TTC are carried out at very critical moments early in the life cycle. Given this background, the safety of OTC and TTC taking into account the epigenetic profile has to be clarified. Cryopreservation of mature germ cells (including Metaphase II oocytes and mature spermatozoa collected via ejaculation or more invasively after testicular biopsy) or embryos has been used successfully for many years in Medically Assisted Reproduction (MAR). However, tissue freezing followed by in vitro or in vivo gametogenesis has become more attractive in the past, while few human studies have analysed the epigenetic effects, with most data deriving from animal studies. In this review, we highlight the potential influence of the cryopreservation of immature germ cells and subsequent in vivo or in vitro growth and differentiation on the epigenetic profile in humans and animals.

Footprints are powerful indicators for evaluating the impact of the bioeconomy of a country on environmental goods, domestically and abroad. In this study, we apply a hybrid approach combining a Multi-Regional Input-Output model and land use modelling to compute the agricultural land footprint (aLF). Furthermore, we added information on land-use change to the analysis and allocated land conversion to specific commodities. The German case study shows that the aLF abroad is larger by a factor of 2.5 to 3 than the aLF in Germany. In 2005 and 2010, conversion of natural and semi-natural land-cover types abroad allocated to Germany due to import increases was 2.5 times higher than the global average. Import increases to Germany slowed down in 2015 and 2020, reducing land conversion attributed to the German bioeconomy to the global average. The case study shows that the applied land footprint provides clear and meaningful information for policymakers and other stakeholders. The presented methodological approach can be applied to other countries and regions covered in the underlying database EXIOBASE. It can be adapted, also for an assessment of other ecosystem functions, such as water or soil fertility.

The effective management of Fusarium wilt of bananas (FW) depends on the knowledge of the disease dynamics in time and space. The objectives of this work were: To estimate disease intensity and impact, and to investigate the spatial and temporal dynamic of FW. Fields planted with Silk (n = 10), Pome (n = 17) or Cavendish (n = 3) banana subgroups were surveyed in Brazil, totaling 95 ha. In each field, all plants were visually assessed and diseased plants were georeferenced. The incidence of FW and the impact of the disease on yield on a regional scale were estimated. Spatial patterns were analyzed using quadrat- and distance-based methods. FW incidence ranged from 0.09 to 41.42%, being higher in Silk fields (median = 14.26%). Impacts of epidemics on yield ranged from 18.4 to 8,192.5 kg.ha-1.year-1, with a median of 935.2 kg.ha-1.year-1. The higher economic impact of the disease was observed on Silk cultivar with a median loss of US$ 910.5 ha-1.year-1. Overall, estimated losses increased on average by US$ 109.8 ha-1.year-1 at each 1% of incidence. Aggregation of FW was detected by all analytical methods in 13 fields (1 of Cavendish, 11 of Pome and 1 of Silk). In the other 17 fields, at least one analytical method did not reject the null hypothesis of randomness. One field (5 ha), composed of six plots, was selected for spatial and temporal studies during two years with bi-monthly assessments. A sigmoidal curve represented the FW progress and the Gompertz model best fitted disease progress. The level of aggregation varied over time, and evidence of secondary infection to neighboring and distant plants were detected. FW is a widespread problem in Brazil and yield losses can be of high magnitude. Epidemiology-based management strategies can now be better established.

The expression microarray technique was performed to investigate the differences in gene expression between Czech Large White pigs and wild boars in the longissimus lumborum et thoracis and biceps femoris muscle tissues. The NREP gene (neuronal regeneration related protein homolog) was selected for detailed study as an expressional and functional candidate gene. NREP plays a role in the transformation of neural, muscle and fibroblast cells and in smooth muscle myogenesis. Quantitative real-time PCR results confirmed that the porcine NREP gene was expressed in both skeletal muscles and significantly overexpressed in Czech Large White pigs compared to wild boars (P &lt; 0.05). We identified 9 polymorphic sites in genomic DNA of NREP gene. Six of these polymorphisms were in complete linkage disequilibrium and therefore only 4 polymorphisms were informative. Associations of these 4 polymorphisms (HF571253:g.103G&gt;A, HF571253:g.134G&gt;A, HF571253:g.179T&gt;C and HF571253:g.402_409delT) with meat performance traits were assessed in Czech Large White pigs. New polymorphisms in NREP gene were significantly associated with parameters of daily weight gain, lean meat and backfat thickness in Czech Large White pigs. Our primary study suggested that porcine NREP may play an important role in skeletal muscle growth, fat metabolism and meat performance traits.

Agriculture and farming worldwide are responsible for numerous environmental threats, including degradation of land and water resources depletion. Underlining the dynamic interaction between bio-physical and socio-economic drivers is the key towards a more sustainable land and water management. With regard to a highly developed agricultural area in southern Italy, multi-regression models were developed to interpret the observed inter-annual variability of cropped land. Main drivers related to Common Agricultural Policy support, product market prices, crop yield and irrigation water availability were investigated. The adopted models revealed the different weighs of each driver. The findings reported the role that direct payments played in supporting the extension of irrigated crops, such as processing tomato. Likewise, the models pointed to decoupled payment scheme as the most important driver of change in the crop pattern over the last years.

With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.

Generally, when cognitive radio users are in Underlay mode, through the analysis of the electromagnetic spectrum in time, frequency, space, and field of multiple dimensional data accounts for judging the inherent correlation of the radio spectrum used/idle state, this is the realization of cognitive radio users (secondary users, SUs) efficient access to the foundation of the limited spectrum resources. Therefore, how to efficiently use of spectrum status of each SU implementation of reception multidimensional combination forecasting is the core of this paper addressing the problem. In this paper, we propose a deep-learning hybrid model called TensorGCN-LSTM based on the tensor data structure. The model treats SUs deployed at different spatial locations under the same frequency and the spectrum status of SUs themselves under different frequencies in the task area as nodes and constructs two types of graph structures. Graph convolutional operations are used to sequentially extract corresponding spatial-domain and frequency-domain features from the two types of graph structures. Then, the long short-term memory (LSTM) model is used to fuse the spatial, frequency, and temporal features of the cognitive radio environment data. Finally, the prediction task of the spectrum distribution situation is accomplished through fully connected layers. Specifically, the model constructs a tensor graph based on the spatial similarity of SUs' locations and the frequency correlation between different frequency signals received by SUs, which describes the electromagnetic wave's dependency relationship in spatial and frequency domains. LSTM is used to capture the electromagnetic wave's dependency relationship in the temporal domain. To evaluate the effectiveness of the model, we conducted ablation experiments on LSTM, GCN, GC-LSTM, and TensorGCN-LSTM models using simulated data. The experimental results show that our model achieved better prediction performance in RMSE, and the correlation coefficient R2 of 0.8753 also confirmed the feasibility of the model.

Music acoustics is an interdisciplinary field and mathematics is the basis in the music art form. Music and mathematics correlation exist since the inception of music. Various philosophers, scientists, mathematicians and musicians have expressed their views about this relationship. This paper attempts to explore this association with focus on melodic pattern identification. Mathematics in Indian Classical music with raga as the basis and just intonation tuning system is discussed. Indian vocal music clips are used for different pitch estimation algorithms in the experimentation. Harmonic product spectrum and auto-correlation algorithms are tested for accurate pitch estimation. Enhanced auto-correlation function using audio segmentation is compared with other approaches for effective pitch extraction. Results indicate pitch extraction with enhanced auto-correlation function provides accurate results as compared with other approaches tested.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.

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

The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence is a major factor influencing the position of nucleosomes on genomes. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

Cardiomyopathies are diseases of heart muscle, a significant percentage of which are genetic in origin. Cardiomyopathies can be classified as dilated, hypertrophic, restrictive, arrhythmogenic right ventricular or left ventricular non-compaction, although mixed morphologies are possible. A subset of neuromuscular disorders, notably Duchenne and Becker muscular dystrophies, are also characterized by cardiomyopathy aside from skeletal myopathy. The global burden of cardiomyopathies is certainly high, necessitating further research and novel therapies. Genome editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as increasingly important technologies in studying this group of cardiovascular disorders. In this review, we discuss the applications of genome editing in the understanding and treatment of cardiomyopathy. We also describe recent advances in genome editing that may help improve these applications, and some future prospects for genome editing in cardiomyopathy treatment.

Despite increased protection globally, climate change and other anthropogenic factors have caused a significant decline in seagrass cover. Identifying the specific causes of this decline is paramount if they are to be addressed. Therefore, we identified the causes of long-term change in seagrass/submerged aquatic vegetation (SAV) percentage cover and extent in the Bluefields Bay Special Fish Conservation Area (BBSFCA), a marine protected area on Jamaica’s southern coast. We used two random forest regression (RFr) models that included 2013 hydroacoustic survey SAV percentage cover data (dependent variable), and auxiliary data, reflectance data from level 2 processed 2013 Landsat 7 and 8 images and image band texture statistics maps (mean and variance) as predictors to generate 24 SAV percentage cover maps for the period 1984 – 2021 (37 years) using data from Landsat 4-5, 7 and 8 images., from which benthic features maps (SAV present, absent and coral reef) were created. Rainfall and map data were used to determine if SAV extent/area (km2) and average percentage cover and annual rainfall changed significantly over time and to evaluate the influence of rainfall. Rainfall impact on the overall spatial patterns of SAV loss, gain, and percentage cover change was assessed using a pixel-based regression. Finally, the most important spatial pattern predictors (two rainfall proxies (distance and direction from river mouth), benthic topography, depth, and hurricane exposure (a measure of hurricane disturbance)) of SAV loss, gain, and percentage cover change during 23 successive 1-to-4-year periods were identified using spatial Bayesian INLA generalized linear mixed models. SAV area/extent was largely stable with &gt; 70% mean percentage cover for multiple years. However, Hurricane Ivan (in 2004) caused a significant decline in SAV area/extent (by 1.62 km2, or a 13%) during 2002 – 2006 and a second hurricane (Dean) in 2007 delayed recovery until 2015. Additionally, rainfall declined significantly by &gt;1000 mm since 1901, and mean monthly rainfall positively influenced SAV percentage cover change. The pixel-based regression highlighted areas where mean monthly rainfall had a positive overall effect on SAV cover percentage change (across the entire bay) and gain (closer to the mouth of a river). The most frequently selected important spatial pattern predictors were the two rainfall proxies (areas closer to the river mouth were more likely to experience SAV loss and gain) and depth, with shallow areas generally having a higher probability of SAV loss and gain. Three hurricanes had significant but different impacts depending on their distance from the southern coastline. Hurricane Gilbert, which made landfall in 1988, resulted in higher SAV percentage cover loss in 1987 - 1988. Benthic locations with a northwestern/northern facing aspect (the predominant direction of Ivan’s leading edge wind bands) experienced higher SAV losses during 2002 – 2006. Although some locations impacted by Ivan and not by Dean recovered during 2006 – 2008, exposure to Ivan explained percentage cover loss during 2006 – 2008 and average exposure to (the cumulative impact of) Ivan and Dean (both with tracks close to the southern coastline) explained SAV loss during 2013 – 2015. Therefore, despite historic lows in annual rainfall, overall, higher rainfall was beneficial, multiple hurricanes impacted the site, and despite two hurricanes in three years SAV recovered within a decade. Hurricanes and a further reduction in rainfall may pose a serious threat to SAV persistence in the future.

In offshore drilling, accidents such as gas invasion, overflow, and kicks are inevitable, and they can escalate into blowouts and other catastrophic events that result in casualties and substantial economic losses. Therefore, maintaining drilling safety requires accurate monitoring of gas invasion and overflow. The majority of overflow monitoring methods currently utilized at drilling sites are threshold-based. However, monitoring parameters acquired during actual drilling operations frequently contain noise signals, making it difficult for threshold-based methods to strike a balance between improving accuracy and minimizing false positives. In this paper, Pattern Recognition-based Kick Detection (PRKD) is proposed as a novel method for diagnosing overflow in offshore drilling. This method utilizes the overflow evolution process by integrating multi-phase flow calculations, data filtering theory, pattern recognition theory, the Bayesian framework, and other theoretical models. The PRKD effectively detects and monitors gas intrusion and overflow based on single parameters by analyzing the shape and wave characteristics of the curves. The case analysis demonstrates that the proposed method for monitoring drilling overflow achieves high precision while maintaining a low false positive rate. By combining advanced computational techniques with pattern recognition algorithms, the PRKD improves the accuracy and reliability of kick detection, enabling proactive responses to potential risks, protecting the environment and human lives, and optimizing drilling operations.

Ground penetrating radar (georadar, GPR), widely used in geology, archeology and road construction, is an efficient tool for searching and studying subsurface objects and structures. When planning GPR missions, it is necessary to predict the resolution of the device and the achievable probing depth. The article discusses the methods and results of assessing these characteristics of the Loza-V and Loza-N radars obtained in the course of archaeological and geographical expedition works.

For personalized recommender systems,matrix factorization and its variants have become mainstream in collaborative filtering.However,the dot product in matrix factorization does not satisfy the triangle inequality and therefore fails to capture fine-grained information. Metric learning-based models have been shown to be better at capturing fine-grained information than matrix factorization. Nevertheless,most of these models only focus on rating data and social information, which are not sufficient for dealing with the challenges of data sparsity. In this paper,we propose a metric learning-based social recommendation model called SRMC.SRMC exploits users' co-occurrence pattern to discover their potentially similar or dissimilar users with symmetric relationships and change their relative positions to achieve better recommendations.Experiments on three public datasets show that our model is more effective than the compared models.

Existing implementations of game design patterns have largely been confined to theoretical or research settings. Weaknesses in these implementations have prevented game design patterns from being properly evaluated as an educational and practical development tool. This paper examines these weaknesses, describes a method of developing and applying patterns that overcome the weaknesses, and evaluates use of the method for game design education and practice. Weaknesses in existing pattern implementations are: omission of design problems, presumption of functional completeness at the level of pattern languages, narrow topical focus, and lack of a concise, repeatable method for pattern production. Several features of the proposed method were specifically built to address these weaknesses, namely the pattern template, the process for connecting patterns into a language and assessing the language’s scope, a rubric for assessing pattern confidence and interconnectivity confidence, and pattern-building exercises. This method was applied in a classroom setting. Results, as assessed by the evaluation of student work, suggest that creating patterns/pattern languages is an effective pedagogical approach. De-signs produced using designer-created patterns closely align with existing design theory and are clearly understood by students. The above results may indicate that the path to gaining wider acceptance of pattern theory as a design framework within game design is not to produce a universal pattern language but to facilitate the creation of case-specific languages, by students and professional designers, that use a shared ontology and thus can be combined easily to solve the diverse sets of problems faced by these groups.

The study aimed to evaluate the association between the changes in ventilatory variables (tidal volume (Vt), respiratory rate (RR), and lung ventilation (VE)) and deoxygenation of m.intescostales (∆SmO2-m.intercostales) during a maximal incremental exercise in nineteen male competitive marathon runners. The ventilatory variables and oxygen-consumption (VO2) were recorded breath-by-breath by exhaled gas analysis. A near-infrared spectroscopy device (MOXY) located in the right-hemithorax allowed recording SmO2-m.intercostales. To explore changes in oxygen levels in muscles with high demand during exercise, a second MOXY records SmO2-m.vastus laterallis. The triphasic model of exercise intensity was used for evaluating changes in SmO2 in both muscle groups. We found that ∆SmO2-m.intercostales correlated with VO2-peak (r=0.65; p=0.002) and the increase of VE (r=0.78; p=0.001), RR (r=0.54; p=0.001), but not Vt (p=0.210). The interaction of factors (muscles X exercise-phases) in SmO2 expressed as an arbitrary unit (a.u) was significant (p=0.005). At VT1 were no difference (p=0.177), but SmO2-m.intercostales was higher at VT1 (p&lt;0.001) and VO2-peak (p&lt;0.001). In competitive marathon runners, the m.intercostales deoxygenation during incremental exercise is directly associated with the aerobic capacity and increased lung ventilation and respiratory rate, but not tidal volume. Besides, it shows less deoxygenation than m.vastus laterallis at intensities above the aerobic ventilatory threshold.

Recent advancements in web-based geospatial software and smartphone technology have popularized the process of voluntary production and sharing of geospatial data by individual citizens. Through such Volunteered Geographic Information (VGI) activities, people across the world participate in online mapping projects (such as OpenStreetMap) to insert their spatial information. The quality of data generated by such VGI activities has profound impacts on online mapping projects and their spatial database. In this study, we examine the VGI contribution pattern in OpenStreetMap through three case study neighborhoods located in three major cities: Tehran, London, and Los Angeles, and investigate how it might affect the process of quality assessment of VGI.

Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes.

A signal analysis of the genoma sequenced of coronavirus variants: B.1.1.7, B.1.135, B.1.429-B.1.427, B.1.525 and P1 is presented. We deal with a certain type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases A,C,G,T. This method provides additional information to conventional Similarity comparisons and Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of genomic sequences according to its progression along the nucleotide bases position. Hence, the method could be useful for survelliance of genoma variants.

Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type. This paper includes a broad and comparative review of the most recent short-read, long-read and hybrid assembly techniques. In this review, we provide (1) an algorithmic description of the important processes in the workflow that introduces fundamental concepts and improvements; (2) a review of existing software that explains possible options for genome assembly; and (3) a comparison of the accuracy and the performance of existing methods executed on the same computer using the same processing capabilities and using the same set of real and synthetic datasets. Such evaluation allows a fair and precise comparison of accuracy in all aspects. As a result, this paper identifies both the strengths and weaknesses of each method. This comparative review is unique in providing a detailed comparison of a broad spectrum of cutting-edge algorithms and methods.

Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r²≥0.8, while 2961 pairs of markers showed complete LD (r²=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

Background: Poisoning is a challenging medical condition facing health care providers, as it usually results in serious outcomes in terms of morbidities or mortalities. Poisoning is a challenging medical condition facing health care providers, as it usually results in serious outcomes in terms of morbidities or mortalities. The lack of or inadequate information about the circumstances, substances and populations at risk are considered barriers to the actual prevention of poisoning and effective intervention strategies in Saudi Arabia. The aim of the current study was to describe the pattern and determinants of chemical and drug overdose poisoning in Makkah.Subjects and methods: All reports of chemical and drug overdose poisoning delivered to the Environmental Health and Occupational Safety Department in Makkah over two years (2018-2019) were reviewed.Results: The total number of cases reported in 2018 was 209 cases, while it reached 42 cases in 2019. The overwhelming majority of the cases were Saudi (91.6%), with a slight predominance of males (57.4%) over females (42.6%). Generally, almost two-thirds of the cases occurred in children below 13 years (61.4%), most of the poisoning cases resulted from drug overdose (63.3%), while 34.7% were chemical poisoning. The most common drug poisoning was attributed to analgesics followed by antiepileptics, antihypertensive drugs, antipsychotics and antimicrobials, while cleaning and detergent agents were the most commonly poisoned chemicals. The majority of these agents were taken by the oral route. Children's chemical poisoning was significantly higher than that in older age groups (p<0.05). All intentional poisoning occurred in adults; the great majority of them (88.9%) used drug overdosing rather than chemical substances.Conclusion and recommendations: The current study results are consistent with most of the previous studies carried out in different regions of Saudi Arabia. Further in-depth studies are needed to elaborate other social and demographic factors associated with chemical and drug overdose poisoning. Public health plans, policies and legislations should be implemented to reduce these factors. Intensive supervision of children is needed. Suicidal poisoning patients should seek psychiatric help to limit the possibility of attempting suicide again in the future. Furthermore, efforts are needed to plan and implement health education programs about the factors proven in the current study to be significantly related to chemical and drug overdose poisoning.

Pressure drop and flow pattern of oil-water flows were investigated in a 19 mm ID clear polyvinyl chloride pipe consisting of U-bend with radius of curvature of 100 mm. The range for oil and water superficial velocities tested were and respectively. Measurements were carried out under different flow conditions in a test section that consisted of four different parts: upstream of the bend, at the bend and at two redeveloping flow locations after the bend. The result indicated that the bend had limited influence on downstream flow patterns. However, the shear forces imposed by the bend caused some shift flow pattern transition and bubble characteristics in the redeveloping flow section after the bend relative to develop flow before the bend. Generally, pressure gradient at all the test sections increased with both oil fraction and water superficial velocity and there was a sharp change of pressure gradient profile during phase inversion. The transition point where phase inversion occurred was always within the range of . Pressure losses differed at the various test sections and the difference was strongly linked to the superficial velocity of the phases and the flow pattern. At high mixture velocity, pressure losses at the redeveloping section after the bend were higher than that at the bend and that for fully developed flows. At low mixture velocity, pressure losses at the bend are higher than in the straight sections. Pressure drop generally decreased with level of flow development downstream of the bend.

Pregestational and gestational diabetes mellitus are relevant complications of pregnancy and antidiabetic drugs are prescribed to obtain glycemic control and improve perinatal outcomes. The objective of this study was to highlight the prescription pattern of antidiabetics before, during and after pregnancy in Italy and to evaluate its appropriateness. A multi-database cross sectional population study using a Common Data Model was performed. In a cohort of about 450,000 women, the prescribing profile of antidiabetics seemed to be in line with the Italian standards for the treatment of GDM which currently do not recommend the use of oral antidiabetics and non-insulin injection, even if a small share of new users (up to 3.8% in the third trimester) used oral antidiabetics. A substantial variability in the prescription pattern was observed among the Italian regions considered: the highest increase was registered in Tuscany (4.2%), Umbria (3.5%) and Emilia-Romagna (2.6%) while the lowest in Lombardy (1.5%), Veneto (1.7%) and Apulia (1.7%). Analysing the prevalence of use of antidiabetics between foreign women we observed that the consumption during pregnancy was higher than Italians (second trimester: 1,8% vs 0,9%, third trimester: 3,6% vs 1,8%).

Traditionally, neutron scattering is an essential method for the analysis of spin structures and spin excitations in bulk materials. Over the last 30 years, polarized neutron scattering in terms of reflectometry has also contributed largely to the analysis of magnetic thin films and magnetic multilayers. More recently it has been shown that polarized neutron reflectivity is, in addition, a suitable tool for the study of thin films laterally patterned with magnetic stripes or islands. We provide a brief overview of the fundamental properties of polarized neutron reflectivity, considering different domain states, domain fluctuations, and different domain sizes with respect to the neutron coherence volume. The discussion is exemplified by a set of simulated reflectivities assuming either complete polarization and polarization analysis, or a reduced form of polarized neutron reflectivity without polarization analysis. Furthermore, we emphasize the importance of the neutron coherence volume for the interpretation of specular and off-specular intensity maps, in particular when studying laterally non-homogeneous magnetic films. Finally, experimental results, fits, and simulations are shown for specular and off-specular scattering from a magnetic film that has been lithographically patterned into a periodic stripe array. These experiments demonstrate the different and mutually complementary information that can be gained when orienting the stripe array parallel or perpendicular to the scattering plane.

The human proteome is composed from diverse and heterogeneous gene products/proteoforms. Previously, we have been discussing the main technical aspects in developing for inventory of human proteoforms that would be visually attractive, clear, and easy to search (Naryzhny S. J. Proteomics 2018, S1874-3919(18) 30220-3). Here, we present our first draft of the database of proteoforms that is based on this discussion. The database principles and structure are described. The database is called “2DE-pattern” as it contains multiple isoform-centric patterns of proteoforms separated according to 2DE principles.

This paper presents a study and implementation of a convolutional neural network to identify and recognize humpback whale specimens from the unique patterns of their tails. Starting from a dataset composed of images of whale tails, all the phases of the process of creation and training of a neural network are detailed – from the analysis and pre-processing of images to the elaboration of predictions, using TensorFlow and Keras frameworks. Other possible alternatives are also explained when it comes to tackling this problem and the complications that have arisen during the process of developing this paper.

With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.

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

Forensic anthropologists play a key role in skeletal trauma analysis and commonly use macroscopic features to distinguish between trauma types. However, this approach can be challenging, particularly in cases of highly comminuted or incompletely recovered fractures. Histological analysis of microscopic fracture characteristics in fractured bones may thus help provide additional information on trauma type and bone fracture biomechanics in general. This study analysed the extent of microcrack damage to osteons in long bones with blunt force trauma (BFT) and gunshot trauma (GST), from both traumatic death cases and post-mortem experimental fractures. We identified four types of osteonal damage (OD). In traumatic death cases, OD affecting the inside of the osteon and compromising the Haversian canal (type 1) was found to be indicative of BFT. Moreover, OD affecting the cement line (type 3) and interstitial lamellae (type 4) was more common in the GST samples. OD affecting the inside of the osteon without compromising the Haversian canal (type 2) was not found to be indicative of either trauma type. In cases of experimental fractures, our study revealed that post-mortem fractures in dry bone samples featured the highest amount of OD, particularly of type 4. This study also found that the experimentally produced GST featured similar OD pattern to GST death cases. These findings support our hypothesis that there are distinct osteonal damage patterns in human long bones with BFT and GST, which are of relevant value for trauma analysis in forensic anthropology.

Background: Myocardial infarction (MI) is a major cause of mortality worldwide. Its presentation as ST-segment elevation MI (STEMI) and non-ST-segment elevation MI (NSTEMI) is influence by atherosclerosis risk factors. Aim: To assess the patterns of presentation and predicting risk factors of acute MI in Kosovo. Methods: This is a cross sectional study from the Clinic of Cardiology of the University Clinical Center of Kosovo, which included all patients hospitalized with acute MI over a period of 7 years (January 1st, 2014 to December 31st, 2020). Data was collected using a structured questionnaire and epidemiological patterns and risk factors were analyzed. Results: Among 7353 patients admitted with acute MI (age 63 ± 12 years, 29% female), 4366 (59.4%) patients had STEMI, and 2987 (40.6%) NSTEMI. Patients age was not different between the two groups (p=0.077). NSTEMI patients smoked less (48.3% vs. 54%, p<0.001), but were more diabetics (37.8% vs. 33.6%, p<0.001), more hypertensives (69.6% vs. 63%, p<0.001), frequently had family history for coronary artery disease (CAD) (40% vs 38%, p=0.009), and included more females compared to STEMI patients (32% vs 27%, p<0.001). The two groups of patients, did not differ in the prevalence of significant CAD on angiography (66.8% vs. 67.8%, p = 0.396), but NSTEMI patients underwent less primary percutaneous interventions compared with STEMI patients (43.6% vs. 55.2%, p < 0.001). Conclusion: In Kosovo, STEMI is commoner than NSTEMI, who were mostly males, more likely to have diabetes, hypertension and family history for CAD compared to those with NSTEMI. Smoking and arterial hypertension proved the strongest predictors of acute MI, in Kosovo, thus highlighting the urgent need for better atherosclerosis risk control and education strategy.

Galectins have been shown to have roles in cancer progression via contributions to angiogenesis, metastasis, cell division, and evasion of immune destruction. This study analyses galectin-1, -3, and -9 serum concentrations in breast cancer patients by enzyme-linked immunosorbent assay (ELISA) against the characteristics of the patient and tumor such as stage, molecular subtype, and receptor expression. Galectin-9 was found to be statistically significantly increased in HER2 enriched tumors as well as being reduced in patients with hormone receptor positive tumors and increased in patients with HER2 amplified tissues. Galectin-1 was found to be statistically significantly increased in the serum of patients who had undergone hormonal, immunotherapy, or chemotherapy. These findings provide insight as to the changes in galectin levels during cancer progress, response to treatment and molecular phenotype. These findings are valuable in the further understanding of the relationships of galectin and tumor biology and can inform future research on therapeutic targets for galectin inhibitors and the utility of galectin biomarkers.

The nutraceutical value of pomegranate in the treatment of many neoplastic, cardiovascular, viral, inflammatory, metabolic, microbial, intestinal, reproductive and skin diseases is well-documented and is linked to its richness in phenolic compounds. This study aims to evaluate nutraceutical and genetic diversity of novel pomegranate genotypes (G1-G5) in comparison to leading commercial pomegranate varieties i.e. ‘Wonderful’, ‘Primosole’, ‘Dente di Cavallo’ and ‘Valenciana’. Morphometric measurements were carried out on fruits, accompanied by chemical characterization and the development of four new polymorphic SSR markers involved in the flavonoid pathway. The cultivars displayed a marked variability in the weight and shape of fruits, as well as in the weight of arils and juice yield. The highest level of total phenolic content and antioxidant activity was found in ‘Wonderful’ and G4, while the lowest was in ‘Dente di Cavallo’. Furthermore, the results showed that the pomegranate juice, is an excellent source of minerals, especially potassium, which plays a key role in organ functioning. The new flavonoid-related markers effectively differentiated the cultivars with the same diversity pattern as morpho-chemical characterization, so the SSRs developed in the present study can be used as a rapid tool for the identification of pomegranate cultivars with relevant nutraceutical traits.

Data on the KIT mutation rate in skin melanoma in the central European region is missing. Accordingly, in a cohort of 79 double wild type (BRAF/NRAS) skin melanoma KIT mutation was assessed by Sanger sequencing of exons 9,11,13,17 and 18. In this skin melanoma cohort KIT mutation frequency was found to be 34/79 (43%) with a significantly higher rate in acrolentiginous melanoma (ALM) as compared to UV-induced common variants (20/34, 58.8% versus 14/45, 31.1%, p=0.014). Exon 11 was the most frequent mutation site (44.7%) followed by exon 9 (21.1%) equally characterizing UV-induced common histotypes and ALM tumors. KIT mutation hotspots were identified in exon 9 (c491/492), in exon 11 (c559,c572, c570), in exon 13 (c642), in exon 17 (c822) and in exon 18 (c853). The relatively high KIT mutation rate in skin melanoma in this central-European cohort justifies regular testing of this molecular target.

The effect of divergence of chute sidewalls with three different baffle block geometries namely USBR, trihedral and semicircular blocks, as well as the depth and dimensions of the scour hole downstream of the chute were studied using a physical model. For this purpose, 9 models of baffled chutes were designed and constructed with divergence ratios of 1.45, 1.75, and 2.45 and without divergence (with a divergence ratio of 1). Comparing the results on the effect of block geometry at different divergence ratios revealed that the use of blocks proposed in this study instead of standard USBR blocks reduced the mean and maximum scour hole by 50%. For a given block geometry, the mean depth, maximum depth, and length of scour hole were reduced by 75%, 58%, and 50%, respectively.

Stingless bee beekeeping provides new opportunities to improve the incomes of many households in Malaysia through the sale of honey and other bee products. While Heterotrigona itama is one of the most commonly cultured species of stingless bees, its behavior is not very well understood. Hence, we conducted this study to investigate the behavior of H. itama in exploiting food sources by ascertaining the nectar sugar concentration preferred by the bee. We also aimed to determine the preferred distance of food source from the bee hive. Our results suggest that H. itama prefers high sugar concentrations of 35% and above, and they would fly up to 7 m from the hive to collect food. We discuss how nectar concentration and food distance influence the number of bees exploiting food sources and the overall foraging pattern of H. itama.

This paper aims to investigate carbon monoxide (CO) concentrations on roadways of Karachi, potential blood levels carboxy-hemoglobin (COHb) in Karachi. Geographical information system (GIS) was used for spatial analysis of diseases potentiality while an interpolation technique has been applied for surface generation with town boundaries and later evaluates risk areas.The higher concentration of carbon monoxide in the ambient is mainly due to automobile emissions. The City center and CBD areas are more perilous.

With recent advancements in network technology and spread of Internet, use of social network services and Internet of Things devices has flourished, leading to a continuous generation of large volumes of graph stream data, where changes, such as additions or deletions of vertices and edges occur over time. Additionally, owing to the need for efficient use of storage space and security requirements, graph stream data compression has become essential in various applications. Even though various studies on graph compression methods have been conducted, most of them do not fully reflect the dynamic characteristics of graph streams and complexity of large graphs. In this paper, we propose a compression scheme using provenance data to efficiently process and analyze large graph stream data. It obtains provenance data by analyzing graph stream data and builds a pattern dictionary based on this to perform dictionary-based compression. By improving the existing dictionary-based graph compression methods, it enables more efficient dictionary management through tracking pattern changes and evaluating their importance using provenance. Furthermore, it considers the relationships among sub-patterns using an FP-tree and performs pattern dictionary management that updates pattern scores based on time. Our experiments show that the proposed scheme outperforms existing graph compression methods in key performance metrics, such as compression rate and processing time.

As the world increasingly becomes more interconnected, the demand for safety and security is ever-increasing, particularly for industrial networks. This has prompted numerous researchers to investigate different methodologies and techniques suitable for intrusion detection systems (IDS) requirements. Over the years, many studies have proposed various solutions in this regard including signature-based and machine-learning (ML) based systems. More recently, researchers are considering deep learning (DL) based anomaly detection approaches. Most proposed works in this research field aimed to achieve either one or a combination of high accuracy, considerably low false alarm rates (FARs), high classification specificity and detection sensitivity, achieving lightweight DL models, or other ML and DL-related performance measurement metrics. In this study, we propose a novel method to convert a raw dataset to an image dataset to magnify patterns. Based on this we devise an anomaly detection for IDS using a lightweight convolutional neural network (CNN) that classifies denial of service and distributed denial of service. The proposed methods were evaluated using a modern dataset, CSE-CIC-IDS2018, and a legacy dataset, NSL-KDD. We have also applied a combined dataset to assess the generalization of the proposed model across various datasets. Our experimental results have demonstrated that the proposed methods achieved high accuracy and considerably low FARs with high specificity and sensitivity. The resulting loss and accuracy curves have also demonstrated the excellent generalization of the proposed lightweight CNN model, effectively avoiding overfitting. This holds for both the modern and legacy datasets, including their mixed version.

The fate of critically sick patients with infections in intensive care units (ICUs) is significantly influenced by antimicrobial resistance, which has become a serious concern in developing nations. This observational study was conducted at the IBN Sina Specialised Hospital in Dhaka, Bangladesh, over a 12-month period from January 2021 to December 2021, in order to track the pattern of antibiotic resistance among the patients admitted to the intensive care unit (ICU). Aspiration pneumonia (29%) and diabetes mellitus (24%), among 200 patients, were the most common main diagnoses. 65 samples (or 26%) of the 250 samples had 85 bacteria identified from them. Urine (14.12%) and tracheal aspirate (64.71%) were the most frequently found sites of infection. In the sample from the tracheal aspirate, Pseudomonas spp. (30.59%), Escherichia coli (24.71%), Acinetobacter spp. (20%), and Klebsiella spp. (14.12) were the most frequently isolated microorganisms. The following antibiotics were shown to have the highest overall patterns of resistance: levofloxacin (68.24), amikacin (64.71), meropenem (49.41), ceftazidime (75.29), ciprofloxacin (78.82), and gentamicin (82.35). The most effective antibiotic against Klebsiella species was meropenem (64.61%), while Acinetobacter species were mostly susceptible to cotrimoxazole (64.67%) and piperacillin + tazobactam (60.50%). Most susceptible to netilmicin (70.48%) and meropenem (49.32%) were Escherichia coli, while Pseudomonas spp. were mostly responsive to colistin (55.14%) and netilmicin (52.25%). Antibiotic resistance is common among intensive care unit (ICU) patients, and most isolated microbes have resistance to traditional medicines.

E-commerce recommendation systems usually deal with massive customer sequential databases, such as historical purchase or click stream sequences. Recommendation systems’ accuracy can be improved if complex sequential patterns of user purchase behavior are learned by integrating sequential patterns of customer clicks and/or purchases into the user-item rating matrix input of collaborative filtering. This reviews focuses on algorithmic techniques of existing E-commerce recommendation systems that are sequential pattern based such as ChoRec05, ChenRec09, HuangRec09, LiuRec09, ChoiRec12, Hybrid Model RecSys16, Product RecSys16, SainiRec17, HPCRec18 and HSPCRec19. It provides a comprehensive and comparative performance analysis of these systems, exposing their methodologies, achievements, limitations, and potentials for solving more important problems in this domain. The review showed that integrating sequential pattern mining of historical purchase and/or click sequences into user-item matrix for collaborative filtering (i) improved recommendation accuracy (ii) reduced user-item rating data sparsity (iii) increased novelty rate of recommendations and (iv) improved scalability of the recommendation system.

The popularity of online retail is followed by decreasing transactions at shopping centres. Leisure and companionship trips to restaurants and cafés are replacing the frequency of intra-urban shopping trips. Several studies demonstrated a notable trend in urban commercial areas, wherein functionality has shifted from shopping centres to primarily focused on restaurants and cafes. Leisure and companionship places in the urban south have greater diversity than formal restaurants and cafés. This article employs a comprehensive framework to examine the categorization of restaurants and cafés in the urban south, referred to as food services. This study aims to investigate the spatial pattern of food service in Surabaya and ascertain whether there is a concentration of all food service variants around existing shopping centres. This research employs the POI of food service units gathered through web scraping from Google Maps. Applying the k-means cluster analysis demonstrates that the spatial pattern of food services is categorized into several distinct clusters. This article discloses five types of urban spaces characterized by varying compositions of food service variants within them. These spaces include the city centre, sub-city centre, areas along main roads, residential neighbourhoods, and peri-urban areas.

Life in the modern century is heavily reliant on an enormous amount of electricity consumption as technology has become the most integral part of daily life. In this context, smart grid systems play a pivotal role to maintain the uninterrupted power supply which needs to be monitored in a timely fashion to keep track of the electric consumers’ usage pattern. The smart meter is the one of smart applications of the smart grid that collects huge amounts of consumer load data on a daily basis which has become a focus for various researchers and analyzers to study load characterization. In this paper, an approach has been proposed to recognize the energy consumption patterns among diverse types of consumers ranging from residential to industrial levels. This approach is worth considering not only for load pattern recognition but also for involving customers in different events such as demand response or peak shaving. In such a way, this analytical mechanism certainly assists in reducing power wastage and saving costs. The proposed methodology is based on a two-fold clustering algorithm with the use of state-of-the-art technology, machine learning. The primary goal is to classify electric customers' data collected from smart meters. Then, analyzing the classified results with an aim to predict power consumption patterns for the customers in the future and making the right energy policy that will benefit both the grid operator and consumers as well.

The key to ensuring the sustainability of transportation operations on the roads is to manage traffic flows homogeneously. By homogenizing the behavior of various drivers, traffic operation can be optimized, and traffic safety can be improved. However, the advent of autonomous vehicles is expected to have a major impact on the homogeneity of sustainable transportation operations. In this study, a method of driving in harmony with surrounding vehicles was studied to minimize the impact of autonomous vehicles on current traffic operation. In particular, in this study, a methodology was developed to optimize the driving behavior of autonomous vehicles by analyzing the driving behavior of following vehicles using spectrum analysis. Specifically, a method for calculating three indicators that can analyze the driving behavior of a following vehicle, such as reaction time, stimulus adaptation index, and collision risk avoidance index, was proposed. These indices produced consistent and robust results for all traffic conditions. If these indicators are used, it is expected that sustainable traffic management will be possible even when autonomous vehicles and human drivers are mixed on the road.

Brugada Syndrome is a cardiac channelopathy closely related to lethal arrhythmias and sudden death in people without underlying structural pathology. The diagnosis is usually assumed with electrocardiographic patterns strictly limited to the right precordial leads, V1 or V2; but this is not so at all. In our article, we describe the clinical case of a patient with a novel and different electrocardiographic presentation: the typical diagnostic pattern was presented in a lower lead of the electrocardiogram, and next to it, another pattern was presented in a contiguous lead. In addition, we propose the possible association of a structural pathology (non-compaction cardiomyopathy) with Brugada Syndrome, since both share a possible common genetic origin in the SCN5A gene.

Food security is a matter of global interest, as the provision of food resources is the primary determinant of human existence. Food is one of the basic needs, ensuring the survival of the species. The trend of globalization and development of the global economy has shifted the responsible local consumption patterns to an increased homogeneity of diets, food products being disconnected from their source. This disconnection led to two major results: (1) increased global consumption, with seasonal foods now available throughout the year, and a decrease in food prices on the global market, and (2) increased uncertainty in the supply chain, susceptible to disruptions, as was the case during the Covid-19 pandemic. The present study, based on the research and analysis of third-party data on food security, sustainable diets, consumption patterns and recommended actions to change the current unsustainable consumer behaviour towards a careful approach to food, environment and personal health, aims to identify consumption patterns that have the potential to increase the sustainability of the food system and a positive correlation with food security. Adopting sustainable dietary patters, based on short supply chains and mindful consumption, has great potential in restoring food security and resilience to adversity.

In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species.

The Oriental ratsnake Ptyas mucosa is a common non-venomous snake of the colubrid family, with a wide geographic range spanning much of South and Southeast Asia. P. mucosa is widely cultivated dut to it used in traditional medicine, scientific research, and handicrafts. Therefore, genome resources could play an important role in the efficacy of traditional medicine and the analysis of the living environment of the species. We collected a snake sample in Hezhou, Guangxi, China, which was identified as P. mucosa by morphological identification. Here we present a highly continuous P. mucosa genome with a genome size of 1.74Gb. The scaffold N50 length is 9.57Mb and the maximal length of scaffold is 78.3Mb, the P. mucosa genome has a CG content of 37.9% and the integrity of the gene reached 86.6%.Assembled using long-reads, the total length of the repeat sequence in the genome reached 735 Mb, and its repeat content was as high as 42.19%. A total of 24,869 functional genes were annotated. This study will assist in the understanding of the P. mucosa, and also provide a basis for medicinal research.

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

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

The growing population meet the challenge for agricultural production. CRISPR/Cas9 technology is based on plant research for the development of the new varieties as well as disease resistance crops. In addition the deletion of significant characters makes the new alleles from the CRISPR/Cas9. Recent and reliable molecular scissor for genetic engineering. The review is focused on the various application of the CRISPR/Cas9 technology in plant enhancement of plant disease resistance, stress burden in plant, nutritional improvement, and quality of crops from the CRISPR/Cas9 system. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (cas9) is adopted from the prokaryotic type II system. CRISPR/Cas9 is simplicity and efficiency than ZENs and TALENs for the genome engineering. Due to rapid growing of the CRISPR/Cas9 system has been formulate the adaptation of many plant species. The current advancement of plants and future schemes of improve of CRISPR technology has been presented in contest of multiplex editing, knowledge on induced mutation whether the factor effect in CRISPR/Cas9 technology in plant. Remarkable perspective and challenges of CRISPR/Cas9 technology in significance of plant genetic modification.

Single-stand selective monofunctional uracil DNA glycosylase 1 (SMUG1) works to remove uracil and certain oxidized bases from DNA during base excision repair (BER). This review provides a historical characterization of SMUG1 and 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) one important substrate of this enzyme. Biochemical and structural analyses provide remarkable insight into the mechanism of this glycosylase revealing SMUG1 has a unique helical wedge which influences damage recognition during repair. Rodent studies suggest that, while SMUG1 shares substrate specificity with another uracil glycosylase UNG2, loss of SMUG1 can have unique cellular phenotypes. This review highlights the multiple roles SMUG1 may play in preserving genome stability, and how the loss of SMUG1 activity may promote cancer. Finally, we discuss recent studies indicating SMUG1 has moonlighting functions beyond BER, playing a critical role in RNA processing including the RNA component of telomerase.

Due to the growth of tourism, mining and manufacturing, economy of the Hainan Island, southern China has swiftly expanded, but also poses a risk of soil pollution by mercury (Hg) due to the traffic and mineral processing. In order to investigate the characteristics of soil Hg pollution in the Hainan Island and assess the health risk, a total of 239 samples were gathered from five representative regions across the island. A vehicle-mounted potable mercury analyzer was used to measure the atmospheric Hg and soil Hg concentrations in the collected samples. The results indicate that the soil Hg concentration of the five sub-study areas exhibits notable fluctuations, which was found to be influenced by various factors, including wind direction, mining activities, and economic development conditions. The degree of Hg pollution was assessed using both the Single Pollution Index Method and the Geoaccumulation Index Method. The results showed that although nearly half of the sampling points were contaminated, the current soil Hg level does not pose a non-carcinogenic risk to human health.

In our work, using the analysis of DNA barcodes and morphology (wing color, male genitalia, sphragis shape in females), we show that the group of species close to P. mnemosyne is represented by two phylogenetic lineages, the western and eastern ones. The eastern lineage includes P. stubbendorfii, P. glacialis and P. hoenei. The western lineage includes three morphologically similar species, P. mnemosyne (Western Eurasia), P. turatii (southwestern Europe) and P. nubilosus stat. nov. (Turkmenistan and NE Iran), as well as P. ariadne (Altai). The latter species differs from the rest of the group in the presence of red spots on the wings. Parnassius mnemosyne s.s. is represented by four differentiated mitochondrial clusters that show clear association with specific geographic regions. We propose to interpret them as subspecies: P. mnemosyne mnemosyne (Central and Eastern Europe, N Caucasus, N Turkey), P. mnemosyne adolphi (the Middle East), P. mnemosyne orientalis (Tian Shan) and P. mnemosyne gigantea (Gissar-Alai in Central Asia). We demonstrate that in P. ariadne the red spots on the wing evolved as a reversion to the ancestral wing pattern. This reversion is observed in Altai, where the distribution areas of the western lineage, represented by P. ariadne, and the eastern lineage, represented by P. stubbendorfii, overlap. These two species hybridize in Altai, and we hypothesize that the color change in P. ariadne is the result of reinforcement of prezygotic isolation in the contact zone. Lectotype of Parnassius mnemosyne var. nubilosus Christoph, 1873 is designated.

Background: Scaffold (SCA) functionalization with aptamers (APT) provides adsorption of specific bioactive molecules on biomaterials surface. The aim of this study was to observe if SCA enriched with anti-fibronectin APT can favor coagulum (PhC) and osteoblasts (OSB) differentiation. Methods: 20 ug of APT was functionalized on SCA by simple adsorption. For PhC formation, SCAs were inserted into rat calvaria defects for 17 hours. Following proper transportation (Buffer solution-PB), OSB (UMR-106 lineage) were seeded over PhC + SCAs with and without APT. Cells and PhC morphology, PhC cell population, protein labelling and gene expression were observed in different time points. Results: The APT induced higher ALP and BSP immunolabeling in OSB. CD90, CD45 and CD44 expression was more detected in APT group than when scaffolds were not functionalized. Additionally, an enriched and dense fibrin network and different cell types were observed, with more OSB and white blood cells in PhC formed on SCA with APT. The gene expression showed higher TGF-β1 detection in SCA with APT. Conclusions: The SCA functionalization with fibronectin aptamers provides a selective expression of proteins related to coagulation pattern and osteo differentiation. Additionally, aptamers increase TGF-β1 gene expression, which is highly associated with improvements in regenerative therapies.

Cardiovascular disease (CVD) may sometimes unexpected loss of life. It affects the heart and blood vessels of body. CVD plays an important factor of life since it may cause death of human. It is necessary to detect early of this disease for securing patients life. In this chpter two exclusively different methods are proposed for detection of heart disease. The first one is Pattern Recognition Approach with grammatical concept and the second one is machine learning approach. In the syntactic pattern recognition approach initially ECG wave from different leads is decomposed into pattern primitive based on diagnostic criteria. These primitives are then used as terminals of the proposed grammar. Pattern primitives are then input to the grammar. The parsing table is created in a tabular form. It finally indicates the patient with any disease or normal. Here five diseases beside normal are considered. Different Machine Learning (ML) approaches may be used for detecting patients with CVD and assisting health care systems also. These are useful for learning and utilizing the patterns discovered from large databases. It applies to a set of information in order to recognize underlying relationship patterns from the information set. It is basically a learning stage. Unknown incoming set of patterns can be tested using these methods. Due to its self-adaptive structure Deep Learning (DL) can process information with minimal processing time. DL exemplifies the use of neural network. A predictive model follows DL techniques for analyzing and assessing patients with heart disease. A hybrid approach based on Convolutional Layer and Gated-Recurrent Unit (GRU) are used in the paper for diagnosing the heart disease.

We previously showed that, based on the frequency and distribution of specific cell types, rainbow trout (RT) intestinal mucosa is divided in two regions that form a complex nonlinear 3D pattern and have a different renewal rate. This work had two aims. First, to investigate whether the unusual distribution of cell populations reflects a similar distribution of functional activities. To this end, we determined the protein expression pattern of three well defined enterocytes functional markers: Peptide Transporter 1 (PepT1), Sodium-Glucose/Galactose Transporter 1 (SGLT-1) and fatty acid-binding protein 2 (Fabp2). Second, to characterize the structure of RT intestinal stem cells (ISC) niche and to determine whether the different proliferative rates correlate with a different organization and/or extension of the stem cells population. We studied the expression and localization of well-characterized mammal ISC markers: LGR5, HOPX, SOX9, NOTCH1, DLL1 and WNT3A. Our results indicate that morphological similarity is associated with similar function only between the first portion of the mid-intestine and the apical part of the complex folds in the second portion. Mammal ISC markers are all expressed in RT but their localization is completely different suggesting also substantial functional differences. Finally, higher renewal rates are supported by a more abundant ISC population.

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

Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 genomes in Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species and performed a phylogenetic analysis to determine their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasica and Apis mellifera mellifera and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD30D/Tigger, DD33D/Tigger and DD34D/mariner may have experienced horizontal transfer events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

In this study, we aimed to determine the trend of antimicrobial resistance pattern of pathogens isolated in samples collected from patients hospitalized in the intensive care unit (ICU), in selected periods before and after COVID-19. A retrospective study of bacterial pathogens was performed on 1267 patients. The resistance patterns were analyzed using Vitek 2 Compact system. Positive-bacterial culture data of 1695 samples from pre-COVID-19 period and 1562 from post-COVID-19 period were obtained. The most frequently isolated in both periods were Staphylococcus aureus and Klebsiella spp. Klebsiella spp. had a statistically significant increase in resistance rates in the post COVID-19 period, against colistin, gentamicin and aztreonam. For E. coli strains, it was registered a significant increase against colistin and a significant decrease against levofloxacin and imipenem. For Acinetobacter spp. strains it was observed a significant increase against colistin. More than 50% from the Staphylococcus aureus strains were MRSA with statistically significant increases in antimicrobial resistance rate in the post-COVID-19 period against doxycycline, linezolid, rifampicin and teicoplanin. The study revealed a significantly increasing trend of the antimicrobial resistance rate of Gram-negative pathogens (Klebsiella spp., Acinetobacter spp.) against certain antibiotics, including those used only in cases where there are no other therapeutic options.

Healthy eating behaviour of women is critical not only for their health but also for their children's health and well-being. The present study examined the dietary pattern, nutrition knowledge and attitudes of working women in Western Province, Sri Lanka. In addition, identify the factors associated with Dietary Diversity Score (DDS). A cross-sectional study was conducted among 300 working women, aged 20-60 years, in Western Province, Sri Lanka. The data on so-cio-demography, dietary patterns, and nutrition-related knowledge and attitudes were collected. Overall, 38% of the women were overweight and 13% were obese. The median frequency of intake of chicken, fish, eggs, milk and milk products, green leafy vegetables and fruits were 2, 5, 2, 9, 5 and 10 respectively, per week. A large majority of the women (70%) had tea/coffee with sugar and snacks (60%) at least four times a week. Only a third of the women met the minimum DDS, while more than half of the women had good nutrition-related knowledge and attitudes. Multiple regression analysis showed that age and household income were significantly independently related to DDS, while attitudes were negatively associated. While there was a trend, the association of nutrition-related knowledge with DDS was not statistically significant (p=0.057). The overall F ratio (8.46) was highly significant (p=0.000) and the adjusted R2 was 0.093. The results demonstrated that a significant proportion of working women have good basic nutrition-related knowledge and attitudes, while two-thirds of them do not meet the minimum DDS. Furthermore, age, family income and knowledge were positively associated with DDS, while attitudes were negatively associated. Before designing any intervention, further research is needed using a qualitative approach to understand how nutrition knowledge and eating behaviour are related in this population group.

Understanding the spatial distribution pattern and evolution characteristics of the elderly population in urban areas is of great significance for the development of urban planning and the implementation of public management policies in the context of rapid aging. Accurately identifying the spatial distribution and evolution characteristics of the elderly population in the city requires a comprehensive analysis of multiple indicators and large-scale data. Taking Wuhan city as an example, this article measures the spatial distribution characteristics and evolution trend of the elderly population from 2000 to 2020 at the street/township level, based on the fifth, sixth, and seventh census data, using methods such as kernel density hotspot detection, spatial clustering analysis, and standard deviation ellipse analysis. The results show that: ① there are significant differences in the aging spatial pattern between the central area and the suburban areas of Wuhan; ② overall, Wuhan's aging rate shows a typical "core-periphery" growth mode in space, while the density of the elderly population has significant spatial aggregation characteristics and shows an evolution trend of "centralized concentration, peripheral outliers, axial development, and near-field growth"; ③the center of gravity of the elderly population remains relatively stable over time.

Background: Patients hospitalized in the intensive care unit (ICU) have a higher susceptibility to infections. Respiratory infections are the most common nosocomial infections. Rising antibiotic resistance due to indiscriminate use of antibiotics and poor adherence to standard precaution in healthcare facilities compounds the problem. The main aim of this study is to assess microbial patterns and antibiotic resistance from bronchoalveolar lavage specimens in severe pneumonia patients. Methods: This retrospective study was conducted in an Indonesian tertiary care hospital from January 2016-December 2020. Written and verbal informed consent was obtained prior to bronchoscopy procedures. Patients were enrolled if they had severe community-acquired pneumonia (CAP) according to American Thoracic Society (ATS)/Infectious Disease Society of America (IDSA) criteria, had high-risk hospital-acquired pneumonia (HAP), late-onset ventilator-associated pneumonia (VAP), or pneumonia caused by Coronavirus disease (COVID-19). Respiratory specimens via bronchoscopy were inoculated on general semi-sloid thioglycolate media. Testing for antibiotic susceptibility was done using the disk diffusion method. Results: Two hundred and one patients’ data were analyzed. The majority of patients were males (65,17%) and above 60 years of age. The most common type of pneumonia was CAP (39,3%). Neurologic/cerebrovascular disease was the most common comorbidity (35,32%). Acinetobacter baumannii was the most frequently isolated microorganism. Ampicillin/sulbactam and amikacin were found to yield lower microbial resistance. Conclusion: Combination of ampicillin/sulbactam and amikacin appeared effective as initial empirical therapy in severe pneumonia patients. Further studies are needed to evaluate the feasibility and effectiveness of this combined therapy.

Unhealthy diet can lead to the development of metabolic disorders, and studies have shown strong associations between those conditions and biomarkers, such as c-reactive protein (CRP) and adiponectin. Recently, marine algal biomaterials have been investigated extensively due to their health benefits. We report on associations between metabolic markers and bioactive nutrients from diet and Sujiaonori algal biomaterial (SBM), a natural adiponectin modulation inducer (NAMI) containing 60% of ulvan-rich fiber, in a sample of Japanese women. The study comprised dietary survey and intervention conducted in Kochi, Japan (2016-2017), involving 31 women who completed a dietary survey and provided biospecimen for CRP and adiponectin measurement using ELISA. Sixteen women received 3g SBM daily for one month and 15 others (controls) received 3g of corn starch. In SBM group, mean age was 23.06 (2.21) years [vs. 23.06 (1.55)], BMI was 21.11 (0.59) kg/m² [vs. 21.43 (0.60) in controls], and daily intake of n3-PUFA [3.83 (0.24) vs. 2.21 (0.33) mg/day; p=0.042] and total fiber [364.12 (2.45) vs. 48.13 (1.57) mg/day in controls; p=0.000] were markedly higher. Furthermore, CRP was inversely associated with total fiber, total n3-PUFA, SBM-n3PUFA, vitamin D and vitamin B6, whereas adiponectin was strongly and positively associated with SBM-fiber and total n3-PUFA. Thus ulvan-rich SBM supplement, which contains ulvan-rich fiber and n3-PUFA, might be beneficial in reducing metabolic risk.

To address the expression pattern of the SARS-CoV-2 receptor ACE2 and the viral priming protease, TMPRSS2, in the respiratory tract, this study investigated RNA sequencing transcriptome profiling of samples of airway and oral mucosa. As shown, ACE2 has medium levels of expression in both small airway epithelium and masticatory mucosa, and high levels of expression in nasal epithelium. The expression of ACE2 is low in mucosal associated invariant T (MAIT) cells, and can’t be detected in alveolar macrophages. TMPRSS2 is highly expressed in small airway epithelium and nasal epithelium, and has lower expression in masticatory mucosa. Our results provide the molecular basis that the nasal mucosa is the most susceptible locus in the respiratory tract for SARS-CoV-2 infection and consequently for subsequent droplet transmission and should be the focus for protection against SARS-CoV-2 infection.

DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under conditions of relaxed selection, and results in a balance between rates of mutation and rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the tree of life, and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.

During the progression of cancer cells, the degree of genome instability increases leading to genome chaos in populations of malignant cells. While normally chaos is associated with er-godicity, i.e., the state when the time averages of relevant parameters is equal to their phase space averages, the situation with cancer propagation is more complex. Chromothripsis, a catastrophic massive genomic rearrangement, is observed in many types of cancer leading to increased mu-tation rates. We present an entropic model of genome chaos and ergodicity and experimental evidence that increasing the degree of chaos beyond the non-ergodic threshold may lead to the self-destruction of the tumor cells. We study time and population averages of chromothripsis frequency in cloned rhabdomyosarcoma from rat stem cells. Clones with frequency above 10% result in cell apoptosis possibly due to mutations in the BCL2 gene. Potentially this can be used for suppressing cancer cells by shifting them into a non-ergodic proliferation regime.

Concatemeric viral DNA is packaged into Bacteriophage P22 procapsids via a headful packaging mechanism mediated by a molecular machine consisting of small (gp3) and large (gp2) terminase subunits. Although a negative stain reconstruction exists for the terminase holoenzyme, it is not clear how this complex binds dodecameric portal protein located at a 5-fold mismatch vertex. Herein, we describe new assemblies for the holoenzyme. Both native mass spectrometry and transmission electron microscopy reveal that the P22 terminase complex adopts three main assemblies, which include a nonameric S-terminase bound to two L-terminase 1(gp3)9:2(gp2), two nonameric S-terminase bound to five L-terminase 2(gp3)9:5(gp2), and three nonameric S-terminase bound to seven L-terminase 3(gp3)9:7(gp2). Native agarose gel electrophoresis shows that the terminase complex interacts with procapsid with mild crosslinking. These results herein illustrate the P22 terminase complex can adopt a variety of confirmations and assembly states.