Transcriptome assembly and functional annotation are essential for understanding gene expression and biological function. Nevertheless, many existing tools lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis. Here, we present TrAnnoScope, a comprehensive transcriptome analysis pipeline that provides a complete, customizable workflow capable of efficiently processing and integrating short- and long-read sequencing data to generate high-quality, full-length transcripts with detailed functional annotation. The pipeline encompasses steps from quality control to functional annotation, employing a range of tools and established databases, such as SwissProt, Pfam, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes. As a case study, TrAnnoScope was applied to RNA-Seq data from zebra finch brain, ovary, and testis tissues. TrAnnoScope produced comprehensive transcriptome, demonstrating strong alignment with the reference genome (99.63%) and capturing a significant proportion of nearly complete protein sequences (92.7%). The functional annotation process yielded extensive matches to known protein databases and successfully assigned relevant functional terms to majority of the transcripts. As such, TrAnnoScope successfully integrates multiple sequencing technologies to generate comprehensive transcriptomes with minimal user input. Its modular design, flexibility, and ease of use make it a valuable tool for researchers working with complex datasets, particularly for non-model organisms.

To guide analysts to select the right tool and parameters in differential gene expression analysis of single-cell RNA sequencing (scRNA-seq) data, we developed a novel simulator that recapitulates the data characteristics of real scRNA-seq datasets while accounting for all the relevant sources of variation in a multi-subject, multi-condition scRNA-seq experiment: the cell-to-cell variation within a subject, the variation across subjects, the variability across cell types, the mean/variance relationship of gene expression across genes, library size effects, group effects, and covariate effects. By applying it to benchmark 12 differential gene expression analysis methods (including cell-level and pseudo-bulk methods) on simulated multi-condition, multi-subject data of the 10x Genomics platform, we demonstrated that methods originating from the negative binomial mixed model such as glmmTMB and NEBULA-HL outperformed other methods. Utilizing NEBULA-HL in a statistical analysis pipeline (https://github.com/interactivereport/scRNAseq_DE) for single cell analysis will enable scientists to better understand cell-type specific transcriptomic response to disease or treatment effects and to discover new drug targets. Further, application to two real datasets showed the outperformance of our differential expression (DE) pipeline, with unified findings of differentially expressed genes (DEG) and a pseudo-time trajectory transcriptomic result. In the end, we made recommendations of filtering strategies of cells and genes based on simulation results to achieve optimal experimental goals.

: Since the COVID-19 pandemic, people have become aware that materials (products) can transmit infection and have begun to focus on questions such as how bacteria and germs, the sources of in-fection, maintain their infectivity on material surfaces, and the extent to which materials can or cannot prevent this. and to what extent materials can and cannot prevent it. The SIAA, a non-profit organization of many Japanese companies, had created an entirely separate interna-tional standard for materials' antibacterial, antiviral, and antibiofilm properties (products). The authors have studied the academic basis for the operation of the standards and were deeply in-volved as researchers in establishing one of the standards. This paper describes the interna-tional standards and some representative examples of the authors' actual use of these standards and explains the current status and future problems.

The Drosophila imaginal disc has been an excellent model for the study of developmental gene regulation. In particular, long non-coding RNAs (lncRNAs) have gained widespread attention in recent years due to their important role in gene regulation. Their specific spatiotemporal expressions further support their role in developmental processes and diseases. In this study, we explored the role of a novel lncRNA in Drosophila leg development by dissecting and dissociating w1118 third-instar larval third leg (L3) discs into single cells and single nuclei, and performing single-cell RNA-sequencing (scRNA-seq) and single-cell assays for transposase-accessible chromatin (scATAC-seq). Single-cell transcriptomics analysis of the L3 discs across three developmental timepoints revealed different cell types and identified lncRNA:CR33938 as a distal specific gene with high expression in late development. This was further validated by fluorescence in-situ hybridization (FISH). The scATAC-seq results reproduced the single-cell transcriptomics landscape and elucidated the distal cell functions at different timepoints. Furthermore, overexpression of lncRNA:CR33938 in the S2 cell line increased the expression of leg development genes, further confirming its important role in development.

Medical laboratories are perhaps the largest measurement industry in the world. The metrology terminology is relevant for effective and efficient communication, particularly where metrology activities are carried out by operators with different metrology skills. WASPaLM and SIPMeL have had some opportunities to propose changes to the documents in preparation to CLSI and ISO in order to harmonise the terminology with the Metrology Vocabulary (VIM). Many proposals have been accepted. Here we summarise some particularly critical points for metrological terms. The main terms discussed are: Measuring, measuring range, examination, pre-examination, post-examination, manufacturer, measuring instrument, quantitative, qualitative, semi-quantitative, processing, easurement error, maximum permissible error of measurement, total error of measurement, monitoring, variability, performance, reliability, influence, interference, selectivity, sensitivity, detection limit, reliability, pomparability, compatibility, control material. Despite all efforts to coordinate terminologies, it is inevitable that overlapping and inconsistent terminologies will continue to be used because documents and policies are produced in different contexts. In some ISO and CLSI documents, phenomena of magnetic attraction towards common words (such as “analysis” and derivatives), without any consideration of the true metrological meaning, are noted. The ISO and CLSI working groups show, alongside moments of openness, phenomena of true self-referential conservatism.

At present, business strategies in SMEs (Small and medium enterprises) are crucial for consolidation in highly competitive markets, in achieving a better image and in business profitability. One of the strategies that have the most success and business success are sustainable practices and social responsibility such as: ISO 14001 and ISO 26001. The literature related to sustainable business is based mainly on the theory of resources and capabilities, and in theory based on Stakeholders. These currents state that companies should focus on profitable strategies to ensure significant and long-term results, in order to achieve organizational and financial results for stakeholders. In this work, the sample consists of 215 companies from the commerce, services and industry sectors, located in the southern region of the State of Sonora in Mexico. The objective of the work is to analyze the influence of ISO 14001 and 26001 standards on the image and profitability of SMEs. The statistical analysis of the data has been carried out through the linear regression technique by OLS (Ordinary Least Squares). The findings prove that the ISO 14001 standard is the one that most influences the improvement of the business image and the level of profitability of the SME. In addition, we discovered that ISO 26001 has a partial influence on the image and profitability of the SME.

The evaluation of measurement uncertainty of natural gas properties calculated from composition data is an essential aspect of fiscal metering in the trade of natural gas. In particular in gas allocation, it is essential to have a reliable value for the uncertainty. This need is also reflected in the current edition of ISO 6976, the standard for computing natural gas properties, which follows much more closely the requirements of the “Guide to the expression of uncertainty in measurement”. A critical aspect in the uncertainty evaluation of natural gas properties is the fact that the amount fractions of the components of natural gas are always correlated after normalisation. A novel algorithm is provided to recover these correlations from the normalised fractions and associated standard uncertainties. The standard uncertainties are reproduced within 2 , which is acceptable for uncertainty calculations. The correlation coefficients obtained from the recovery algorithm agree with the ones obtained by normalisation. The algorithm requires only the data commonly stored by the natural gas industry as input and it enables providing values and credible associated uncertainties for natural gas properties calculated from composition.

The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic profiling in various fields, there is a need for optimized and reliable nuclei isolation methods, mainly for human tissue samples. Herein we compared different nuclei isolation methods for cell suspensions, such as peripheral blood mononuclear cells (PBMC, n=18) and a solid tumor type, ovarian cancer (OC) (n=18), derived from debulking surgery. Nuclei morphology and sequencing output parameters were used to evaluate the quality of preparation. Our results show that NP-40 detergent-based nuclei isolation yields better sequencing results than collagenase tissue dissociation for OC, significantly impacting cell identification and analysis. Given the utility of applying such techniques to frozen samples, we also tested frozen preparation and digestion (n=6). A paired comparison between frozen and fresh samples validated the quality of both specimens. Finally, we demonstrate the reproducibility of scRNA and snATAC + snRNA platform, by comparing the gene expression profiling of PBMC. Our results highlight how the choice of nuclei isolation methods is critical for obtaining quality data in multiomic assays. It also shows that the measurement of expression between scRNA and snRNA is comparable and effective for cell type identification.

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Thus, specific breeding programs to incorporate these natural defences, that are common within the Solanum genus, might improve a more sustainable management. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. Two F2 mapping populations using two different parents have been developed, characterized and genotyped using a new genotype methodology, K-seq. We have been able to build an ultra-dense genetic map with 147,326 markers with an average distance between markers of 0.2 cM that has allowed us to perform a detailed mapping. We have used two different families and two different approaches, QTL mapping and QTL-seq, to identify several QTLs implicated in the control of trichome type IV developed in this accession on the chromosomes 5, 6, 9 and 11. The QTL located on chromosome 9 is a major QTL that has not been previously reported in S. pimpinellifolium that increases by a factor of 9 the density of trichomes.

To sustain and advance the development of our laboratory, it is imperative for the laboratory 1 personnel to consistently deliver high-quality products and services that meet customer expectations. 2 The progress of productivity and the pace of technological advancements result in constant evolution 3 of measurement procedures, analytical techniques, and overall work methods. Our research within 4 the Neutron Activation Analysis (NAA) laboratory is aimed at contributing to the establishment of 5 quality assurance that complies with the ISO 17025 standard. As such, the laboratory implements 6 quality-oriented approaches to foster a culture of continuous improvement in its detector operations 7 and enhance customer satisfaction.

1) Background: We analyzed the corpus of three geoscientific journals to investigate if there are enough locational references in research articles to apply a geographical search method, on the example of New Zealand. 2) Methods: Based on all available abstracts and all freely available papers of the New Zealand Journal of Geology and Geophysics, the New Zealand Journal of Marine and Freshwater Research, and the Journal of Hydrology, New Zealand, we searched title, abstracts and full texts for place name occurrences that match records from the official Land Information New Zealand (LINZ) gazetteer. We generated ISO standard compliant metadata records for each article including the spatial references and make them available in a public catalogue service. This catalogue can be queried for articles based on authors, titles, keywords, topics as well as by spatial reference. We visualize the results in a map to show which area the research articles are about. 3) Results: We outline the methodology and technical framework for the geo-referencing of the journal articles and the platform design for this knowledge inventory. The results indicate that the use of well-crafted abstracts for journal articles with carefully chosen place names of relevance for the article provides a guideline for geographically referencing unstructured information like journal articles and reports in order to make such resources discoverable through geographical queries. 4) Conclusion: This approach can actively support integrated holistic assessment of water resources and support decision making.

Circular RNAs are a special type of RNAs which recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes but are relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of CLIP-Seq experiments, RBP-circRNA interactions could also be identified through specialized analysis of CLIP-Seq datasets. However, many technical difficulties are involved in this process, such as the usually short read length of CLIP-Seq reads. In this study, we created a pipeline called Clirc specialized for profiling circRNAs in CLIP-Seq data and analyzing the characteristics of RBP- circRNAs interactions. In conclusion, this is one of the first few studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets to our knowledge, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs. Clirc software is available at https://github.com/Minzhe/Clirc

(1) Background: The study aimed to analyze and rank the benefits of adopting Artificial Intelligence (AI) in the logistics area, considering the opinion of professionals working in the Brazilian logistics sector through the implementation of ISO/IEC 42001; (2) Methods: The procedures adopted included a literature review to identify the benefits of the use and the application of a survey aimed at professionals in the logistics sector. The analysis used the TOPSIS method to identify and rank the most decisive benefits; (3) Results: Of the 15 benefits mapped in the literature, the professionals attributed the greatest importance to customer satisfaction, operational efficiency, incentives for innovation, and improving the company's image and competitive advantage. The results indicate that adopting ISO/IEC 42001 not only promotes process optimization and cost reduction, but also encourages innovation and strengthens competitiveness in the market; (4) Conclusions: the implementation of this standard is vital for companies in the logistics sector, especially in a Brazilian context of major infrastructural and regulatory challenges. The findings highlight the need for a strategic approach to the adoption of AI, emphasizing the importance of efficient logistics management and ethical practices in the application of this technology.

Preserving the Intangible Cultural Sound Heritage of Humanity is a crucial aspect of safeguarding a people’s culture and history. By employing objective acoustic and psychoacoustic parameters, we can effectively analyze and characterize these auditory environments based on objective, aesthetic, and emotional criteria. The ISO 12913 standard governs the depiction of soundscapes, while the evaluation of outdoor sites involves conducting sound-walks. This study focuses on assessing different soundscapes observed during festivities in Spain as sound walk (dynamic) and as in fireworks (static). The festivities assessed were: "Fallas" in Valencia, Sanfermines in Pamplona, "Festa de la Mare de Deu" in Algemesi, and "Moros y Cristianos" in Villena. To evaluate these soundscapes, we captured ambient sound recordings while traversing through or staying between the festival crowds. Subsequently, we employed various psychoacoustic metrics, such as loudness, sharpness, roughness, fluctuation stress, and tonality, and analyzed them using Zwicker models. Additionally, we conducted a subjective survey to compare the subjective responses with the psychoacoustic metrics obtained.

In response to the increasing importance of knowledge as a key competitive advantage, the role of knowledge management in value creation cannot be overstated. The International Standards Organization (ISO) has recognized this and announced a Management Standard for Knowledge Management Systems (KMS). This initiative is significant because, by viewing knowledge strategically, organizations are seeking ways to enhance their processes and align them to address their challenges. A synergistic effect can be achieved when another management system highly relevant to KMS is joined and later integrated. This new system is Artificial Intelligence Management (AIMS). The paper is structured as follows: Firstly, we explore knowledge and knowledge management (KM), along with the challenges companies face in implementing and operating KM. Next, we examine the ISO 30401:2018 standard as a guide for KM implementation. Finally, we discuss how ISO 30401:2018 and ISO/IEC 42001:2023 can help solve key organizational problems and support machine learning and knowledge extraction through AI. In conclusion, we summarize the key outcomes of the paper. The main purpose of the paper is to determine how these standards contribute to solving practical problems in the creation and development of a knowledge management system supported by artificial intelligence and to demonstrate their synergistic effect when used together.

Bamboo is considered a sustainable construction material due to its ability to grow quickly and its mechanical properties that are comparable to timber. Contributing to the current effort to establish the structural bamboo standards in the National Structural Code of the Philippines (NSCP), this study establishes the characteristic compressive strength of four bamboo species: Bambusa vulgaris (36 samples), Dendrocalamus asper (36 samples), Bambusa blumeana (94 samples), and Guadua angustifolia Kunth (30 samples). The samples were subjected to compressive loading following ISO 22157-1 (2017). The characteristic compressive strength values obtained, according to ISO 12122-1 (2014), were 40.35 MPa for B. vulgaris, 40.21 MPa for D. asper, 46.63 MPa for B. blumeana, and 36.99 MPa for G. angustifolia Kunth. Simple linear analysis, One-way ANOVA, and Welch’s t-Test were used to analyze the correlation models and establish a comparative analysis of the effect of nodes, and geometric and physical properties on the compressive strength of bamboos. Comparing the characteristic compressive strength obtained from this study to the strength of unseasoned structural timber of Philippine woods, all bamboo species showed higher strength values, and thus have great potential as an alternative construction material to timber.

The aim of this study was to develop, implement, and evaluate a new auxiliary enterprise risk management framework and process to serve as an enabler to the global ISO 31000 risk framework and ISO 31010 processes. This framework has been designed particularly for use within high-risk environments and those characterized by volatility, uncertainty, complexity, and ambiguity (VUCA). This paper proposes a methodology for optimization of structured sharing and grass-roots management of all available risk-sentience information with the assessed potential to develop into an identifiable risk in the future. The author introduces new risk terminology including risk-sentience, risk-sentience information, and risk-sentience management. The process involved the development of the Theory of Risk-Sentience (ToRS), Risk-Sentience Auxiliary Framework (RSAF) and a risk-sentience management process referred to as LUOMEAR (Learning from Uncertainties, Others Mistakes, Experiences and Anecdotal Reporting). Manchester Patient Safety Framework (MaPSaF), SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis, and a newly developed Risk-Sentience Fertility Checklist were used to conduct pre and post-trial evaluations. The findings include positive adjustments in safety culture, components of commitment to quality, communication and team-working around safety issues, access to evolving risk-information, and efficient sharing and management of recorded risk-information. Recommendations are made for more extensive application of both the proposed auxiliary risk framework and process within high-risk sectors to further explore its effectiveness and scope.

Natural killer cells are associated with the pathogenesis of ulcerative colitis (UC), but their precise contributions remain unclear. The present study sought to investigate the diagnostic value of activated NK-associated genes (ANAGs) in UC. Bulk RNA-seq and scRNA-seq datasets were obtained from the Gene Expression Omnibus (GEO) and Single Cell Portal (SCP) databases. In the bulk RNA-seq, 92 differentially expressed genes (DEGs) were screened out by the “Batch correction” and “Robust rank aggregation” (RRA) methods. The immune infiltration landscape was estimated by single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT, which revealed a higher abundance of activated NK cells in noninflamed UC tissues. 54 DEGs correlated with activated NK cells were identified as ANAGs. Protein-protein interaction (PPI) analysis and least absolute shrinkage and selection operator (LASSO) regression were utilized to screen out 4 key ANAGs (SELP, TIMP1, MMP7, and ABCG2) and establish an activated NK-associated gene score (ANAG score). The ANAG score demonstrated excellent diagnostic value and was validated in three external datasets. The expression of the 4 key ANAGs was validated in UC patients and healthy controls (HC) samples. Through scRNA-seq data analysis, higher expression levels of SELP, TIMP1, MMP7, and ABCG2 were observed in post-capillary venules, inflammatory fibroblasts, enterocytes, and immature enterocytes. The cell scores based on the ANAGs showed enrichment in endothelial cells and fibroblasts. In conclusion, we established and validated an ANAG score with the ability to precisely diagnose UC. The 4 key ANAGs have the potential to serve as therapeutic targets in UC.

Flood forecasting helps anticipate floods and evacuate people, but due to the access of a large number of iot data acquisition devices, the explosive growth of multidimensional data and the increasingly demanding prediction accuracy, classical parameter models and traditional machine learning algorithms are unable to meet the high efficiency and high precision requirements of prediction tasks. In recent years, deep learning algorithms represented by convolutional neural networks, recurrent neural networks and Informer models have achieved fruitful results in time series prediction tasks. The Informer model is used to predict the flood flow of the reservoir. At the same time, the prediction results are compared with the prediction results of the traditional method and the LSTM model, and how to apply the Informer model in the field of flood prediction to improve the accuracy of flood prediction is studied. The data of 28 floods in the Wan 'an Reservoir control basin from May 2014 to June 2020 were used, with areal rainfall in five subzones and outflow from two reservoirs as inputs and flood processes with different sequence lengths as outputs. The results show that the Informer model has good accuracy and applicability in flood forecasting. In the flood forecasting with sequence length of 4, 5 and 6, Informer has higher prediction accuracy, and the prediction accuracy is better than other models under the same sequence length, but the prediction accuracy will decline to a certain extent with the increase of sequence length. The Informer model stably predicts the flood peak better, and its average flood peak difference and average maximum flood peak difference are the smallest. As the length of the sequence increases, the number of fields with a maximum flood peak difference less than 15% increases, and the maximum flood peak difference decreases. Therefore, the Informer model can be used as one of the better flood forecasting methods, and it provides a new forecasting method and scientific decision-making basis for reservoir flood control.

The exogenous application of phenolic compounds is increasingly recognized as a valuable strategy for promoting growth and mitigating the adverse effects of abiotic stress. However, the biostimulant effect under optimal conditions have not been thoroughly explored. In this study, we investigated the impact of foliar application of flavonoids, specifically Crop Bio Life (CBL), on tomato plants grown under controlled conditions. Our study focused on determining growth parameters, such as cell size, and assessing the concentration of hormones. Principal component analysis (PCA) from all physiological variables were determined. Additionally, we utilized high-throughput mRNA sequencing technology and bioinformatic methodologies to robustly analyze the transcriptomes of tomato leaves regulated by flavonoids. The findings revealed that CBL primarily influenced cells enlargement, leading to increased growth. Furthermore, CBL-treated plants exhibited higher concentrations of the hormone zeatin but lower concentrations of IAA. Moreover, RNAseq analysis indicated that CBL-treated plants required increased mineral transport and water uptake, as evidenced by gene expression patterns. Genes related to pathways such as fatty acid degradation, phenylpropanoid biosynthesis, and ABC transporters showed regulatory mechanisms governing internal flavonoid biosynthesis, transport, and tissue concentration, ultimately resulting in higher flavonoid concentrations in tomato leaves.

As the number of Small and Medium Enterprises (SMEs) rises in the world, the amount of sensitive data used also increases, making them targets for cyberattacks. SMEs face a host of issues such as lack of resources, and poor cybersecurity talent, resulting in multiple vulnerabilities that increase overall risk. Cybersecurity risk assessment frameworks have been developed by multiple organizations such as the National Institute of Science and Technology (NIST) and the International Organization for Standardization (ISO), but they are complicated to understand, and challenging to implement. This research aimed to create an effective cybersecurity risk assessment framework specifically for SMEs while considering their limitations. This was achieved by first identifying common threats and vulnerabilities and categorizing them according to their importance, and risk. Secondly, popular frameworks like the NIST CSF and ISO 27001/2 were analyzed for their proficiencies and deficiencies while identifying relevant areas for SMEs. Finally, novel techniques catered to SMEs were explored and incorporated to create an effective framework for SMEs. This framework was also developed in the form of a tool, providing an interactive and dynamic environment. The tool was effective and the framework is a promising start but requires more quantitative analysis.

Energy management, especially in communities, is attracting growing interest, but is often marred by confusion between the terms "Energy Information System" (EIS) and "Energy Man-agement System" (EMS). This ambiguity hinders understanding of their use and role in improv-ing energy performance. Our objective is to clarify these terms and their contribution to energy management. We used a mixed qualitative and quantitative approach to evaluate and compare the criteria of definition, objective, functionality, role, as well as correlated elements such as or-ganizational structure, responsibilities, planning and policy, according to the requirements of ISO 50001, in addition to criteria specific to the two systems. The study reveals differences in the roles of the EIS and the SME, with a complementarity of 40% between the two systems, depend-ing on the positioning of the EIS in relation to the elements of the SME process. The EIS plays a crucial role in facilitating the implementation of the EMS according to ISO 50001. This clarifica-tion contributes to a better understanding of the respective roles of these systems in energy management, thus helping communities to improve their energy performance in an effective manner.

Directive 2018/844/EU on energy efficiency claims almost 80% of final energy consumption in EU is used within the buildings. Subsequent Directive (EU) 2023/1791 introduced in 2023 expected 68% of the World population living in urban areas. Both Directives enhanced the role of energy management (EM) applied on the city buildings. The study introduces the development of energy management in Czech municipalities between the years 2009 and 2023. The main goal of this article is to present selected results of the unique national survey focused on the energy management in Czech municipalities conducted in 2023 and compare it with results of national surveys implemented in 2009 and 2018. The main method is the evaluation of deep survey conducted among the municipal representatives or energy managers in the past with the new survey conducted in 2023. The results show that EM became notably more important issue for the most Czech municipalities. The number of cities implementing EM significantly grew and the number of city energy managers increased too. On the other hand, the used potential of energy savings triggered by establishing EM is insufficient. This article should be applied to stress power of municipal EM in performing energy efficiency and RES projects and encouraging government to support municipal energy managers in their complex role.

Chagas disease is a Neglected Tropical Disease with limited and ineffective therapy. In a search for new antitrypanosomal compounds, we investigated the potential of metabolites from bacteria living in corals and sediments of the Southeastern Brazilian coast. Three corals Tubastraea coccinea, Mussismilia hispida, Madracis decactis and sediments yielded 11 bacterial strains, that were fully identified by MALDI-ToF/MS or gene sequencing, resulting in six genera - Vibrio, Shewanella, Mesoflavibacter, Halomonas, Bacillus and Alteromonas. To conduct this study, EtOAc extracts were prepared and tested against Trypanosoma cruzi. Crude extracts showed IC50 values ranging from 15 to 51 μg/mL against trypomastigotes. The bacterium Mesoflavibacter zeaxanthinifaciens was selected for fractionation, resulting in an active fraction (FII) with IC50 values of 17.7 μg/mL and 23.8 μg/mL against the trypomastigotes and amastigotes, respectively, with neither mammalian cytotoxicity nor hemolytic activity. Using NMR and ESI-HRMS analysis, FII revealed the presence of unsaturated iso-type fatty acids. Its lethal action was investigated, leading to a protein spectral profile of the parasite altered after treatment. FII also induced a rapid permeabilization of the plasma membrane of the parasite, leading to cell death. These findings demonstrate these unsaturated iso-type fatty acids as possible new hits against T. cruzi.

The integration of artificial intelligence (AI) into the European Foundation for Quality Management (EFQM) business excellence model is a promising approach to improve the efficiency and effectiveness of excellence in organizations. This research paper’s integrated framework follows the ISO/IEC 23053 standard in addressing some of the concerns related to time and cost associated with the EFQM model, achieving higher EFQM scores, hence operational excellence. A case study involving a UAE government organization serves as a sample to train the AI framework. Historical EFQM results from different years are used as training data. The AI framework utilizes the unsupervised machine learning technique known as k-means clustering (with k=2). This technique follows the ISO/IEC 23053 standard to predict EFQM output total scores based on criteria and sub-criteria inputs. The research paper's main output is a novel AI framework that can predict EFQM scores for organizations at an early stage. If the predicted EFQM score is not high enough, then the AI framework provides feedback to decision makers regarding the criteria that need reconsideration. Continuous use of this integrated framework helps organizations attain operational excellence. This framework is considered valuable for decision makers as it provides early predictions of EFQM total scores and identifies areas that require improvement before officially applying for the EFQM excellence award. This approach can be considered as an innovative contribution and enhancement to knowledge body and organizational practices.

Wounds are breaks in the continuity of the skin and the underlying tissues, due to external causes, such as cuts, blows and impacts, or even, during surgical interventions. Millions of people suffer minor or serious injuries, sometimes ending in death. Today, there are many commercially available products that promote healing from wounds. The high demand from the healthcare industry has created a huge market that continues to grow, fueling research and development of new wound healing products. In the present article, we review recent advances in wound healing products based on natural biopolymers, stem cells, and microRNAs. We analyze the advances of both, the commercial products and the products that are still in research phase, and we also include an overview of the opportunities, barriers, and regulatory issues for the commercialization of these products in the European, American, and Asian markets.

The success of a software product depends on several factors. Given that different organizations and institutions use software products, the need to have a quality and desirable software according to the goals and needs of the organization makes measuring the quality of software products an important issue for most organizations and institutions. To be sure of having the right software. It is necessary to use a standard quality model to examine the features and sub-features for a detailed and principled study in the quality discussion. In this study, the quality of Word software was measured. Considering the importance of software quality and to have a good and usable software in terms of quality and measuring the quality of software during the study, experts and skilled in this field were used and the impact of each factor and quality characteristics. It was applied at different levels according to their opinion to make the result of measuring the quality of Word software more accurate and closer to reality. In this research, the quality of the software product is measured based on the fuzzy inference system in ISO standard. According to the results obtained in this study, it is understood that quality is a continuous and hierarchical concept and the quality of each part of the software at any stage of production can lead to high quality products.

In this short paper we study some properties of the lines associated with van Aubel’s theorem in the special case when squares are replaced with equilateral triangles constructed on the sides of an arbitrary quadrilateral.

The increasing demand for sustainable products and services has become a constant requirement by the different stakeholders in an organization. Higher Education Institutions (HEI) have a crucial role in training conscious and competent professionals to lead these changes. Chemical analyses laboratories bring together the proper mix, where the adoption of mature and efficient management systems proves to be crucial not only to better train the institutions´ human resources but also to cooperate in recruiting research projects and other services to benefit society. Maturity models assist in the needed stages for sustainable growth to take place. This paper proposes a Maturity Model based on standardized norms to guide adjustments related to quality, risks, safety, and environment of chemical analyses laboratories in public higher education institutions. This research was done in four stages: theoretical research about Maturity Models, sustainability, and integrated management systems; survey with laboratories; case study at a chemical analyses laboratory of an HEI; and structuring and validating a maturity model. As a result of this, the model includes eight dimensions (Strategy, Leadership, Management, Operations, Continuous Improvement, Sustainability, Culture, and Integration), 31 subdimensions, and 204 management practices to assess and guide chemical analyses laboratories to sustainable maturity levels.

As smoke toxicity is unregulated outside of the mass transport industry, there is no set methodology for assessing smoke toxicity of construction products, like OSB, on a large-scale. This research aims to assess the novel design of a modified ISO 9705 room corner test designed for smoke toxicity quantification. Three tests conditions will be assessed to determine if restriction of ventilation is enough to force a fire to transition to under-ventilated flaming, or if the fuel loading is much more important in affecting the fire severity and fire condition. The research found that fuel loading and test geometry has more significant impact on the fire condition than restricting the ventilation. While imposing restrictions on the test rooms ventilation did increase the equivalence ratio, it was not sufficient enough to force the transition into under-ventilated flaming. The addition of a door to the test room did not force the fire to transition to under-ventilated flaming. When doubling the fuel loading, there was sufficient fuel for the fire to transition to under-ventilated flaming. This research has provided the experimental methodologies to assess smoke toxicity at a range of ventilation conditions on a large-scale.

Magnesium (Mg)-based biomaterials are promising candidates for bone and tissue regeneration. Alloying and surface modifications provide effective strategies for optimizing and tailoring their degradation kinetics. Nethertheless, biocompatibility analyses of Mg-based materials are challenging due to its special degradation mechanism with continous hydrogen release. In this context, the hydrogen release and the related (micro-) milieu conditions pretend to strictly follow in vitro standards based on ISO 10993-5/-12. Thus, special adaptions for the testing of Mg materials are necessary, which have been described in a previous study from our group. Based on these adaptions, further developments of a test procedure allowing rapid and effective in vitro cytocompatibility analyses of Mg-based materials based on ISO 10993-5/-12 are necessary. The following study introduces a new two-step test scheme for rapid and effective testing of Mg. Specimens with different surface characteristcis were produced by means of plasma electrolytic oxidation (PEO) using silicate-based and phosphate-based electrolytes. The test samples were evaluated for corrosion behavior, cytocompatibility and their mechanical and ostogenic properties. Thereby, two PEO ceramics could be identified for further in vivo evaluations.

A simple method for the determination of caffeine in coffee grains by GC-FID is presented in the current work. The method was fully validated according to ISO 17025 requirements and European Commission regulation. The accuracy, as provided by recovery experiments was higher than 93%, and the precision, as provided by the (%)Relative standard deviation under reproducibility conditions, was lower than 5%. All independent parameters that lead in the increase of methods uncertainty were investigated. In the present work all special precautions were taken into account in order to avoid the use of an internal standard. The method was applied in real samples and possible health claims were investigated.

Mulberries is a type of fruit tree that is rich in nutrients and possesses both medicinal and dietary properties, deeply loved by consumers. The fragrance is a significant factor in the sensory quality of mulberries, playing a crucial role in consumer purchasing behavior. 'Baichang' mulberry is a unique variety of mulberry that emits a strong, creamy-like fragrance, which has enormous potential market value. However, the key metabolites and mechanisms responsible for the formation of this fragrance are still unclear. In this study, we utilized GC-MS technology and RNA-seq to examine the Volatile Organic Compounds (VOCs) and gene expression in 'Baichang' (Morus macroura) mulberries and 'Hongchang' (Morus laevigata) mulberries, the latter of which do not have a distinct fragrance. The results showed that 661 volatile metabolites were detected in both mulberry varieties. Most of these were found in higher relative amounts in the 'Baichang' mulberry variety, with 47 types being present only in the 'Baichang' mulberries, suggesting a rich composition of VOCs in the 'Baichang' mulberry. 312 metabolites were identified as differential metabolites; combining the sensory annotation information and relative content of VOCs, 70 candidate VOCs were annotated as related to the formation of 'sweet, waxy, coconut, and oily' sensations. They could potentially be the key metabolites contributing to the unique aroma of 'Baichang' mulberries. The relative odor activity value (rOAV) analysis revealed that 2(3H)-Furanone, 5-hexyldihydro- was the key VOC contributing to the formation of the special aroma of 'Baichang' mulberries. By RNA-seq, 19 key structural genes related to ester synthesis were identified, including AAT , ACX , ALDH, CYP, EHL, FAD, HPL, and LOX. The high expression of these structural genes in the "Baichang" mulberry fruit is the main reason for its unique creamy aroma. This study provides insights into the aroma differences among different kinds of mulberrie.

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and validation by PCR and RT-PCR were used. Single and mixed infections with Tomato mosaic virus (ToMV), Tomato golden mosaic virus (ToGMoV), and Pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR of Mexican ToMV isolates suggest the need to evaluate known resistance genes against these viral variants. The precise identification and characterization of viruses that naturally infect tomato germplasm could be used as a strategy for selecting the appropriate disease management and guiding breeding efforts.

This study explored the effects of pBD114 (porcine β-defensin 114) on inflammatory response. The results in RAW264.7 cells showed that 100 μg/mL of pBD114 significantly increased the concentrations of TNFα and IL-10, and 10 μg/mL of pBD114 significantly decreased the concen-tration of TNFα in LPS-induced RAW264.7 cell cultures at 10 ng/mL. These results suggest that pBD114 can exhibit pro-inflammatory or anti-inflammatory activities under certain conditions. RNA-seq analysis was performed to gain further insight into the effects of pBD114 on the in-flammatory response. Among pBD114 promoting RAW264.7 pro-inflammatory response, pBD114 significantly up-regulated 1170 genes and down-regulated 724 genes. KEGG enrichment found that the DEGs were significantly enriched in immune- and signal-transduction-related signaling pathways. PPI and KDA analyses revealed that Bcl10 and Bcl3 were the key genes. In addition, pBD114 significantly up-regulated 12 genes and down-regulated 38 genes in the an-ti-inflammatory response. KEGG enrichment analysis revealed that the DEGs were mainly en-riched in the "Cytokine-cytokine receptor interaction" signaling pathway, and PPI and KDA analyses showed that Stat1 and Csf2 were the key genes. The results of qRT-PCR verified those of RNA-seq. In vivo mice tests also confirmed the pro- or anti-inflammatory activity of pBD114. Although the inflammatory response is a rapid and complex physiological reaction to noxious stimuli, this study found that pBD114 plays an essential role in the inflammatory response mainly by acting on genes related to immunity, signal transduction, signaling molecules, and interactions.

Cervical cancer presents a significant global health concern with high-risk human papilloma-viruses (HPVs) being identified as the cause of this cancer. Although current treatment methods for cervical cancer can eliminate lesions, preventing metastatic spread and minimizing tissue damage remains a major challenge. Therefore, the development of a safer and innovative thera-peutic approach is of utmost importance. Natural products like Fig latex, derived from the Ficus Carica tree, have demonstrated promising anti-cancer properties when tested on cervical cancer cell lines. However, the specific mechanisms by which Fig latex exerts its effects are still un-known. In this study, we conducted RNA-seq analysis to explore how Fig latex may counteract carcinogenesis in HPV-positive cervical cancer cell lines, namely CaSki (HPV type 16-positive) and HeLa (HPV type 18-positive). Our data from this investigation indicates that Fig latex influ-ences the expression of genes associated with the development and progression of cervical can-cer, including pathways related to " Nonsense-Mediated Decay (NMD) "cell cycle regulation" and Transcriptional Regulation by TP53. This selective impact of Fig latex on cancer-related pathways suggests a potential novel therapeutic approach for HPV-related cervical cancer.

Alternative splicing can produce transcripts that affect cancer development and shows potential for cancer diagnosis and treatment. However, intron retention (IR), a type of alternative splicing, has been less systematically studied in cancer biology research. Here, we generated a pan-cancer IR landscape for more than 10,000 samples across 33 cancer types from The Cancer Genome Atlas (TCGA). We characterized differentially retained introns between tumor and normal samples and identified retained introns associated with survival. We discovered 988 differentially retained introns in 14 cancers, some of which demonstrated diagnostic potential in multiple cancer types. We also inferred a large number of prognosis-related introns in 33 cancer types, and the associated genes included well-known cancer hallmarks such as angiogenesis, metastasis, and DNA mutations. Notably, we discovered a novel intron retention event inside 5′UTR of STN1 that is associated with the survival of lung cancer patients. The retained intron reduces translation efficiency by producing upstream open reading frames (uORFs) and thereby inhibits colony formation and cell migration of lung cancer cells. Besides, the IR-based prognostic model achieved good stratification on certain cancers, as illustrated in acute myeloid leukemia. Taken together, we performed a comprehensive IR survey at a pan-cancer level, and the results implied that IR has the potential to be diagnostic and prognostic cancer biomarkers, as well as new drug targets.

The transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. In this study, we selected Baghlani Nangarhar, an extremely fast dehydration material, and Saturn, a slow dehydration material, based on the results of the previous studies of screening of 165 germplasm materials for dehydration rate phenotypes. Fast dehydration experiment on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified by transcriptome sequencing and quantitative real-time PCR (qRT-PCR). GO and KEGG analyses were carried out. The results showed that in Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. Similarly, in Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 down-regulated. The results of the GO analysis showed that the sites of action of the differentially expressed genes enriched in the fast dehydration modes were concentrated in the cytoplasm, internal components of the membrane and nucleosomes. They play regulatory roles in catalysis, binding, translocation, transcription, protein folding, degradation and replication. They are involved in adaptive responses to adverse external environments such as reactive oxygen species and high temperature. The KEGG analysis showed that the main metabolic pathways enriched are protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation. The key differentially expressed genes and the most important metabolic pathways in the rapidly and slowly dehydrated materials obtained in this study were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism, which are presumed to have important regulatory roles in stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during dehydration and drying of mature seeds. The results of this study could potentially provide a valuable reference for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.

Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated). Infection influenced numerous immunoregulatory interactions between lymphoid and nonlymphoid cells in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T-lymphocyte mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signalling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signalling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of Binding and Uptake of Ligands by Scavenger Receptors in EP and p53 signalling in the EN group was found. In conclusion, this study provides new insights into the disease course and host‒pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.

Brown-marbled grouper is one of the most important mariculture species in China, which is used as an important crossbreeding parent in grouper industry. Enhancing growth rates is a key target in fish breeding, and gaining insight into the underlying mechanisms responsible for growth differences among individuals can aid in the improvement of grouper growth rates. However, the mechanism behind this difference in growth in this fish is unclear. The difference of transcriptome profiles of muscle tissue between fast- and slow-growing brown-marbled grouper was analyzed by RNA-Seq. 77 significantly up-regulated genes and 92 significantly down-regulated genes were identified in the growth extreme groups. The up-regulated of ghr and tnni2 and the down-regulated of stc2 led to the growth advantages of brown-marbled grouper. The differently expressed genes (DEGs) were used for GO and KEGG enrichment analysis. The results of GO enrichments indicated that the significantly upregulated genes in the fast-growing group were involved in protein folding, actin cytoskeleton, myosin complex, etc. The results of KEGG enrichments indicated that the significantly upregulated genes in the fast-growing group were involved in glycolysis/ gluconeogenesis, adipocytokine signaling pathway, MAPK signaling pathway, carbon metabolism, PI3K-Akt signaling pathway, etc. To analysis the difference gene sets between fast- and slow-growing group, the RNA-seq data were used by gene set enrichment analysis (GSEA). The results showed that the PI3K/AKT/mTOR pathway was up-regulated in the fast-growing group. The up-regulated of this pathway could lead to higher nutrient absorption efficiency and lead to muscle growth in the fast-growing group. These results contribute to understanding of the molecular mechanisms of fast growth and regulative pathways regulating growth in brown-marbled grouper.

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during plant growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula. Background and Objectives: The cell cycle factors not only influence cell cycle progression together, but also regulate accretion, division and differentiation of cells, and then regulate growth and development of plant. In this study, we identified the putative cell cycle genes in B. pendula genome, based on the annotated cell cycle genes in A. thaliana. It could serve as a foundation for further functional studies. Materials and Methods: The transcript abundance was determined for all the cell cycle genes in xylem, root, leaf and flower tissues using RNA-seq technology. Results: We identified 59 cell cycle gene models in the genome of B. pendula, 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1 and BpWEE1. Conclusions: We identified 17 core cell cycle genes in the genome of birch by combining phylogenetic analysis and tissue specific expression data.

RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA (cDNA) library construction. Here we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance.

This paper aims to explore the relationship between airfoil deformation and airfoil aerial-aquatic adaptation. The form of “flexible skin and rigid drive structura” holds immense potential for various applications. In this study, we utilize the B-spline method to parametrically describe the airfoil shape. An airfoil deformation parameterization method is proposed based on the isogeometric method. This method allows us to depict airfoil deformation as the position and displacement of the driving point, enabling an expression of the flexible skin's deformation driven by the internal structure. We utilize the Xfoil application and Gaussian regression method to elucidate the relationship between driving point position and displacement and the airfoil's dynamic performance. Additionally, we employ the Sobol method to assess the sensitivity of the driving point variables to the airfoil's dynamic performance. Our findings indicate that the attack angle of the airfoil exhibits the highest sensitivity index to the airfoil's dynamic performance. Furthermore, variables of the driving point situated at the leading and trailing edges of the lower surface significantly impact the airfoil lift coefficient, those located at the mid-section of the upper surface have a considerable effect on the airfoil drag coefficient.

The purpose of this paper is to propose a tool to measure the performance of a Strategic Asset Management Plan (SAMP) based on a Balanced Scorecard (BSC). The SAMP converts organizational objectives into asset management objectives, also specifies the role of the asset management system and brings support to achieve asset management objectives. The SAMP becomes the heart of the organization and integrates with long-term, medium-term, and short-term financial plans integrated with same term activity plans. In the SAMP, the balance among performance, costs and risks is also taken into consideration in order to achieve the organization’s objectives. On the other side, the SAMP is a guide to set the asset management objectives while describing the role of the Asset Management System (AMS) in meeting those objectives. While SAMP is the central figure of AMS, it is important to measure its performance and needs to be build and improved through an iterative process, what means that is not just a document, it is “the document”, and should be treated as a “living being” that needs to adapt to internal and external changes quickly. The BSC is an excellent tool where, through the appropriate Key Performance Indicators (KPIs), the progress can be measured, and is supported by four perspectives: Financial; Customer; Internal Process; and Learning and Growth.

Computer systems are involved in many critical human applications today, so that a small error can lead to serious and dangerous problems. These errors can be from an error in the incorrect design of the user interface to an error in the program code. The success of a software product depends on several factors. Given that different organizations and institutions use software products, the need to have a quality and desirable Software according to the goals and needs of the organization makes measuring the quality of software products. an important issue for most organizations and institutions, To be sure of having the right software. It is necessary to use a standard quality model to examine the features and sub-features for a detailed and principled study in the quality discussion. In this study, the quality of Word software was measured by Adaptive Neural Fuzzy Inference System. In recent years, powerful systems called fuzzy inference systems on The basis of adaptive neural network (ANFIS) has been used in various sciences. Using the power of neural network training and the linguistic advantage of fuzzy systems, these types of systems have been able to realize the advantages of the two in terms of analyzing very powerful complex processes. Considering the importance of software quality and to have a good and usable software in terms of quality and measuring the quality of software during the study. It was applied at different levels to make the result of measuring the quality of Word software more accurate and closer to reality. In this research, the quality of the software product is measured based on the adaptive neural-fuzzy inference system in ISO standard. According to the results obtained in this study, it is understood that quality is a continuous and hierarchical concept and the quality of each part of the software at any stage of production can lead to high quality products.

This study contributes to the literature by exploring challenges to implementing ISO 20000-1 in an emerging economy context, and suggests ways to overcome these challenges. A survey-based methodology was adopted. The data were analyzed using principal component analysis. The results indicated that senior management support was the most significant challenge for the successful implementation of IT Service Management (ITSM) systems. Other significant challenges were the justification of significant investment, premium customer support, co-operation and co-ordination among IT support teams, proper documentation, and effective process design The findings help managers introduce IT service management system (ISO 20000-1:2011) as well as improving IT service delivery system in IT support organizations for managing big data in an emerging economy. In the future, cross-firm and cross-country studies on challenges to ISO 20000 can be conducted. Also, interpretive structural model (ISM) can be formulated to examine the interrelationships among the identified challenges to ISO 20000.

Polyploidy, a prevalent event in plant evolution, drives phenotypic diversification and speciation. While transcriptional changes and regulation in polyploids have been extensively studied, the translational level impact remains largely unexplored. To address this gap, we conducted a com-parative transcriptomic and translatomic analysis of cotton leaves from allopolyploid species G. hirsutum (AD1) and G. barbadense (AD2) relative to their model A-genome and D-genome diploid progenitors. Our data revealed that while allopolyploidization significantly affects the transcrip-tional landscape, its impact on translation was relatively modest, evidenced by a narrower ex-pression range and fewer expression changes in ribosome-protected fragments than in mRNA levels. Allopolyploid-specific changes commonly identified in both AD1 and AD2 were observed in 7,393 genes at either transcriptional or translational levels. Interestingly, the majority of translational changes exhibited concordant down-regulation in both ribosome-protected fragments and mRNA, particularly associated with terpenoid synthesis and metabolism. Regarding translational efficiency (TE), at least one-fifth of cotton genes exhibit translational level regulation, with a general trend of more down-regulation than up-regulation of TE. The magnitude of translational regulation was slightly reduced in allopolyploids compared to diploids, and allopolyploidy tends to have a more profound impact on genes and functional associations with ultra-low TE. Moreover, we demonstrated a reduced extent of homeolog expression biases during translation compared to transcription. In conclusion, our study provides insights into the regulatory consequences of allopolyploidy post-transcription, contributing to a comprehensive understanding of regulatory mechanisms of duplicated gene expression evolution.

Comparative metatranscriptomics of bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, and differing in rheological features and organic acid amounts production was carried out to figure out the relation between differences in physicochemical and rheological properties of kefir and the microbial active profile associated with each product. The dominance of lactic acid bacteria and yeast and a marginal amount of acetic acid bacteria marked the microbiome. The bacterial families Lactobacillaceae and Streptococcaceae account for almost all bacterial gene transcripts, with Lactobacillus helveticus, L. kefiranofaciens, L. gallinarum and Lactococcus lactis being most frequent in the microbiome of MKAA1 beverage, and L. kefiranofaciens, Lc. lactis and Leuconostoc mesenteroides being most prevalent in the MKAA2. Dipodascaceae and Saccharomycetaceae were the leading yeast families represented by Yarrowia lipolytica, Saccharomyces unisporus, and Kluyveromyces marxianus. The MKAA1 and MKAA2 shared >75% KEGG Ortologs (KO) in bacteria and yeast libraries. Considerable decreases in total expressed genes (KEGG Ortolog) assigned to Lactobacillus helveticus and L. gallinarum might be related to the variations in rheological features of the beverages, probably by compromising the interrelations with L. kefiranofaciens which might explain the variations in rheological features of the beverages.

The Jeryak, a hybrid offspring of Gannan yak and Jersey cattle, exhibits evident hybrid advantages over the Gannan yak in terms of production performance and other various aspects. The small non-coding RNAs known as miRNAs exert a significant regulatory influence on gene expression post-transcriptionally. However, the regulatory mechanism of miRNA associated with muscle development in Jeryak remains elusive. To elucidate the regulatory role of miRNAs in orches-trating the skeletal muscle development in Jeryak, we selected dorsal longissimus muscle tissues from Gannan yak and Jeryak for transcriptome sequencing analysis. A total of 230 (DE)miRNAs and 1819 differentially expressed mRNAs (DEMs) were identified in the longest dorsal muscle of Gannan yak and Jeryak. The functional enrichment analysis revealed a significantly enrichment of target genes from differentially expressed (DE)miRNAs and DEMs in signaling pathways associ-ated with muscle growth, such as the Ras signaling pathway and the MAPK signaling pathway. The network of interactions between miRNA and mRNA suggested that some differentially ex-pressed miRNAs, including miR-2478-z, miR-339-x, novel-m0036-3p and novel-m0037-3p, played a pivotal role in facilitating muscle development. These findings help us to deepen our under-standing of the hybrid dominance of Jeryaks and provide a theoretical basis for further research on the regulatory mechanisms of miRNAs associated with Jeryak muscle growth and development.

The A. japonicus industry has expanded significantly, but no research has focused on how to de-termine the age of A. japonicus during farming. Correctly estimating the age of A. japonicus can provide a decision-making basis for the breeding process, and data for the protection of A. japonicus aquatic germplasm resources. DNA methylation levels in the body wall of Apostichopus japonicus at 4 months, 1 year, 2 years, and 3 years old were determined by MethylRAD-Seq, and differentially methylated genes related to age were screened. The results of the study found that 441 and 966 differentially methylated genes were detected at CCGG and CCWGG sites, respectively. As-partate aminotransferase, succinate semialdehyde dehydrogenase, isocitrate dehydrogenase, the histone H2AX, heat shock protein Hsp90, aminopeptidase N, cell division cycle CDC6, Ras GTPase activating protein (RasGAP), slit guidance ligand slit 1, integrin linked kinase ILK, mechanistic target of rapamycin kinase Mtor, protein kinase A Pka, and autophagy-related 3 atg3 these genes may play key roles in the growth and aging process of A. japonicus. This study provided data for identifying the age of A. japonicus.

The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. However, the regulatory mechanisms underlying the growth and development are still unclear. In this study, we used autotetraploid potato JC14 as experimental subject to analyze the transcriptome of root, stem and leaf at seedling, tuber formation and tuber expansion stages to explore the spatio-temporal expression pattern of genes and genetic development characteristics. The results identified thousands of differentially expressed genes and KEGG pathway enrichment analysis showed that these genes were mainly involved in defense response and carbohydrate metabolism pathways. A total of 12 co-expressed Gene modules were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and 4 modules were screened out with the highest correlation with potato stem developmental traits. Core genes in the network were further investigated and functionally annotated by computing the connectivity of genes within the module. The results unveiled number of hub genes in stems at different developmental stages, including carbohydrate metabolism related genes, the defense response related genes, and transcription factors. These findings provide important leads for further understanding of the molecular regulation and genetic mechanisms of potato tissue development.

Iron is the most abundant micronutrient in plant mitochondria and it has a crucial role in biochemical reactions involving electron transfer. It has been described in Oryza sativa that Mitochondrial Iron Transporter (MIT) is an essential gene and that knockdown mutant rice plants have a decreased amount of iron in mitochondria, strongly suggesting that OsMIT is involved in mitochondrial iron uptake. In Arabidopsis thaliana, two genes encode MIT homologues. In this study, we analyzed different AtMIT1 and AtMIT2 mutant alleles, confirming that individually AtMIT1 nor AtMIT2 genes are essential. When we generated crosses between Atmit1 and Atmit2 alleles we were able to isolate homozygous double mutant plants. Interestingly, homozygous double mutant plants were obtained only when mutant alleles of Atmit2 with the T-DNA insertion in the intron region were used for crossings, and in these cases a correctly spliced AtMIT2 mRNA was generated, although at a low level. Atmit1 Atmit2 double homozygous mutant plants, which were knockout for AtMIT1 and knockdown for AtMIT2, were grown and chacterised in iron sufficient conditions. Pleiotropic developmental defects were observed including abnormal seeds, increased number of cotyledons, slow growth rate, pinoid stems, defects in flower structures and reduced seed set. We observed a possible phenomenon of T-DNA suppression in the next generation of Atmit1 Atmit2 double homozygous mutant plants, correlating with an increased splicing of the AtMIT2 intron containing the T-DNA. Molecular analysis of gene expression markers for mitochondrial and oxidative stress showed that Atmit1 Atmit2 double homozygous mutant plants express a degree of mitochondrial perturbation. A RNA-Seq study was performed and we could identify more than 760 genes differentially expressed in Atmit1 Atmit2, including genes involved in iron transport, coumarin metabolism, and hormones metabolism, transport and signaling. Our data suggest that some of the phenotypes observed in Atmit1 Atmit2 double homozygous mutant plants are mediated by defects in auxin homeostasis.

The mosaic disease in maize is caused by Sugarcane mosaic virus (SCMV), a member of the Potyviridae family. The best strategy to cope with viral infections is the use of disease-resistant maize lines. To better understand the resistance response to SCMV, we analyzed differentially expressed genes among a resistant line (CI-RL1), a susceptible line (B73), and the F1 progeny from a cross between both lines using RNA-Seq data. We also analyzed transcript expression pattern clustering to allocate previously reported resistance candidate genes. GO enrichment analysis of biological processes highlighted a strong regulation in ROS detoxification in both the susceptible and resistant lines. The enrichment of cellular components led to the identification of an integral component of the plasma membrane in the RL line. Transcript expression patterns provide evidence of the importance of host translation in virus response, showing the diverse and complex behavior of eIF4E homologs and the presence of eleven eEF1α factors in maize. In addition, we identified two genes putatively implied in long-distance movement: ZmPiezo and ZmPVIP1. Finally, we propose an ABC transporter to be associated with viral resistance.

The major threats to the sustainable supply of forest tree products are adverse climate, pests and diseases. Climate change, exemplified by increased drought, poses a unique threat to global forest health. This is attributed to the unpredictable behavior of forest pathosystems, which can favor fungal pathogens over the host under persistent drought stress conditions in the future. Currently, the effects of drought on tree resistance against pathogens are hypothetical, thus research is needed to identify these correlations. Norway spruce (Picea abies) is one of the most economically important tree species in Europe, and is considered highly vulnerable to changes in climate. Dedicated experiments to investigate how disturbances will affect the Norway spruce - Heterobasidion sp. pathosystem are important, in order to develop different strategies to limit the spread of H. annosum s.l. under the predicted climate change. Here, we report a transcriptional study to compare Norway spruce gene expressions to evaluate the effects of water availability and the infection of Heterobasidion parviporum. We performed inoculation studies of three-year-old saplings in a greenhouse (purchased from a nursery). Norway spruce saplings were treated in either high (+) or low (-) water groups: high water group received double the water amount than the low water group. RNA was extracted and sequenced. Similarly, we quantified gene expression levels of candidate genes in biotic stress and jasmonic acid (JA) signaling pathways using qRT-PCR, through which we discovered a unique preferential defense response of H. parviporum-infected Norway spruce under drought stress at the molecular level. Disturbances related to water availability, especially low water conditions can have negative effects on the tree host and benefit the infection ability of the pathogens in the host. From our RNA-seq analysis, 114 differentially expressed gene regions were identified between high (+) and low (-) water groups under pathogen attack. None of these gene pathways were identified to be differentially expressed from both non-treated and mock-control treatments between high (+) and low (-) water groups. Finally, only four genes were found to be associated with drought in all treatments.

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from liver, muscle, hypothalamus, pituitary and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

In December 2019, a novel coronavirus (SARS-CoV-2) was identified in patients with pneumonia (called COVID-19) in Wuhan, Hubei Province, China. SARS-CoV-2 shares high sequence similarity and uses the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), as does severe acute respiratory syndrome coronavirus (SARS-CoV). Several studies have provided bioinformatic evidence of potential routes for SARS-CoV-2 infection in respiratory, cardiovascular, digestive and urinary systems. However, whether the reproductive system is a potential target of SARS-CoV-2 infection has not been determined. Here, we investigate the expression pattern of ACE2 in adult human testis at the level of single-cell transcriptomes. The results indicate that ACE2 is predominantly enriched in spermatogonia, Leydig and Sertoli cells. Gene ontology analyses indicate that GO categories associated with viral reproduction and transmission are highly enriched in ACE2-positive spermatogonia while male gamete generation related terms are down-regulated. Cell-cell junction and immunity related GO terms are increased in ACE2-positive Leydig and Sertoli cells, but mitochondria and reproduction related GO terms are decreased. These findings provide evidence that human testes are a potential target of SARS-CoV-2 infection which may have significant impact on our understanding of the pathophysiology of this rapidly spreading disease.

Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.

Removal of the proliferation component of gene expression by PCNA adjustment has been addressed in numerous survival prediction studies for breast cancer and all cancers in the TCGA. These studies indicate that widespread co-regulation of proliferation upwardly biases survival prediction when gene selection is performed on a genome-wide basis. In addition, removal of the correlative effects of proliferation does not reduce the random bias associated with survival prediction using random gene selection. Since most cancers become addicted to DNA repair as a result of forced cellular replication, increased oxidation, and repair deficiencies from oncogenic loss or genetic polymorphisms, we pursued an investigation to remove the proliferation component of expression in DNA repair genes to determine survival prediction. This translational hypothesis-driven focus on DNA repair genes is directly amenable to finding new sets of DNA repair genes that could potentially be studied for inhibition therapy. Overall survival (OS) prediction was evaluated in 18 cancers by using normalized RNA-Seq data for 126 DNA repair genes with expression available in TCGA. Transformations for normality and adjustments for age at diagnosis, stage, and PCNA metagene expression were performed for all DNA repair genes. We also analyzed genomic event rates (GER) for somatic mutations, deletions, and amplification in driver genes and DNA repair genes. After performing empirical p-value testing with use of randomly selected gene sets, it was observed that OS could be predicted significantly by sets of DNA repair genes for 61% (11/18) of the cancers. Interestingly, PARP1 was not a significant predictor of survival for any of the 11 cancers. Results from cluster analysis of GERs indicates that the most opportunistic cancers for inhibition therapy may be AML, colorectal, and renal papillary, because of potentially less confounding due to lower GERs for mutations, deletions, and amplifications in DNA repair genes. However, the most opportunistic cancer for inhibition therapy is likely to be AML, since it showed the lowest GERs for mutations, deletions, and amplifications in DNA repair genes. In conclusion, our hypothesis-driven focus to target DNA repair gene expression adjusted for the PCNA metagene as a means of predicting OS in various cancers resulted in statistically significant sets of genes.

Peanut (Arachis hypogaea) is a crop plant with high economic value, but the epigenetic regulation of its growth and development has only rarely been studied. The peanut histone deacetylase 1 gene (AhHDA1) has been isolated and is known to be ABA- and drought-responsive. In this paper, we investigate the role of AhHDA1 in more detail, focussing on the effect of altered AhHDA1 expression in hairy roots at both the phenotypic and transcriptional levels. Agrobacterium rhizogenes-mediated transformation of A. hypogaea hairy roots was used to analyse how overexpression or RNA interference of AhHDA1 affects this tissue. In both types of transgenic hairy root, RNA sequencing was adopted to identify genes that were differentially expressed, and these genes were assigned to specific metabolic pathways. AhHDA1-overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and superoxide anions and hydrogen peroxide accumulated to a greater extent than in control or RNAi groups. Overexpression of AhHDA1 is likely to accelerate flux through various secondary synthetic metabolic pathways in hairy roots, as well as reduce photosynthesis and oxidative phosphorylation. Genes encoding the critical enzymes caffeoyl-CoA O-methyltransferase (Araip.XGB85) and caffeic acid 3-O-methyltransferase (Araip.Z3XZX) in the phenylpropanoid biosynthesis pathway, chalcone synthase (Araip.B8TJ0) and polyketide reductase (Araip.MKZ27) in the flavonoid biosynthesis pathway, and hydroxyisoflavanone synthase (Araip.0P3RJ) and isoflavone 2'-hydroxylase (Araip.S5EJ7) in the isoflavonoid biosynthesis pathway were significantly upregulated by AhHDA1 overexpression, while their expression in AhHDA1-RNAi and control hairy roots remained at a lower level or was unchanged. Our results suggest that alteration of secondary metabolism activities is related to overexpression of AhHDA1, which is mainly reflected in phenylpropanoid, flavonoid and flavonoid biosynthesis. Future studies will focus on the function of AhHDA1 interacting proteins and their action on cell growth and stress responses.

Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Piertain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-beta signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.

COVID-19 was an inflammatory pneumonia caused by a respiratory infection with a coronavirus named SARS-CoV-2. Severely ill COVID-19 patients could die of acute pulmonary and systemic inflammation. Thus, there was a theory that long COVID-19 shared many similarities with systemic autoimmune diseases. There was also a theory that the SARS-CoV-2 virus could infect many cell- and tissue-types distributed throughout multiple organ systems of the body. I aim to review the above theories using unbiased high-throughput datasets cataloguing gene expression. Studies reviewed used the technology of next generation sequencing, either as bulk tissue RNA sequencing, or as single-cell RNAs sequencing; ingenious methods for signal deconvolution were then used to identify individual cell types. Datasets reviewed suggested that severe COVID-19 induced expression of genes associated with pro-inflammatory signaling, tissue development or remodeling, scarring, or cell death. The datasets also provided evidence for several inflammatory syndromes associated with COVID-19, such as neuronal COVID, acute respiratory disease syndrome, vascular inflammation, or multisystem inflammatory syndrome. Indeed, inflammatory signal during severe COVID-19 was reported in many cell types, for example in structural cells, in infiltrating immune cells, in the vascular system, or in circulating cells in the blood. There was also frequently a change in proportions of immune cell-types in the blood, epithelial cells in the lungs, or among infiltrating immune cells.

In this paper the thermodynamic and reactivity study of light alcohol fuels was prepared, based on experimental and numerical results. We also tested the influence of water addition on fundamental properties of the combustion reactivity dynamics in closed vessels, like the maximum explosion pressure, maximum rate of pressure rise and the explosion delay time of alcohol-air mixtures. Substances that we investigated were: methanol, ethanol, n-propanol and iso-propanol. All experiments were conducted at initial conditions of 323.15 K and 1 bar in a 20 dm3 closed testing vessel. We investigated the reactivity and thermodynamic properties during the combustion of liquid fuel-air mixtures with equivalence ratios between 0.3-0.7 as well as some admixtures with water, to observe water mitigation effects. All light alcohols samples were prepared at the same initial conditions on a volumetric basis by mixing the pure components. The volumetric water content of the admixtures was varied from 10 to 60 vol%. The aim of water addition was to investigate the influence of thermodynamic properties of light alcohols and to find out to which extent a water addition may accomplish mitigation of combustion dynamics and thermodynamic reactivity.

Iron ore processing involves critical steps that affect the quality of the final product. Determining the diameter of the pellets is the necessary initial step for volume measurement and, ultimately, for porosity and bulk density measurement, crucial characteristics for optimizing the burning process in the blast furnace. Traditional measurement methods using mercury present issues related to operator safety and environmental preservation, while the practices described in ISO 4698 standard require lengthy preparation and execution time. In light of environmental needs, operator safety, and the time consumed in tests, implementing a new method based on digital image processing and convolutional neural networks for measuring the diameter of burnt iron ore pellets is proposed. The methodology involves capturing images of the pellets using a high-resolution camera and utilizing digital image processing and neural networks capable of performing pixel-by-pixel object segmentation in the images, providing precise information about the pellets to calculate their volume automatically. The results were compared with those obtained using traditional methods, evaluating their conformity with the ISO 4698 standard. In conclusion, this study offers a new approach to measuring the volume of burnt iron ore pellets, providing accurate and reliable results in compliance with safety and environmental preservation standards.

We used the complete set of convex pentagons enabling filing the plane without any overlaps or gaps (including the Marjorie Rice tiles) as generators of Voronoi tessellations. Shannon entropy of the tessellations was calculated. Some of the basic mosaics are flexible and give rise to a diversity of Voronoi tessellations. The Shannon entropy of these tessellations varied in a broad range. Voronoi tessellation, emerging from the basic pentagonal tiling built from hexagons only, was revealed (the Shannon entropy of this tiling is zero). Decagons and hendecagon did not appear in the studied Voronoi diagrams. The most abundant Voronoi tessellations are built from three different kinds of polygons. The most widespread is the combination of pentagons, hexagons and heptagons. The most abundant polygons are pentagons and hexagons. No Voronoi tiling built only of pentagons was registered. Flexible basic pentagonal mosaics give rise to a diversity of Voronoi tessellations, which are characterized by the same symmetry group; however, the coordination number of the vertices is variable. These Voronoi tessellations may be useful for the interpretation of the iso-symmetrical phase transitions.

When discussing the concepts of risk, safety, and security, people have an intuitive understanding of what these concepts mean, and, to a certain level, this understanding is universal. However, when delving into the real meaning of these concepts, one is likely to fall into semantic debates and ontological discussions. In industrial parks, it is important that (risk) managers from dierent companies, belonging to one and the same park, have the same understanding of the concepts of risk, safety, and security. It is even important that all companies in all industrial parks share a common understanding regarding these issues. As such, this paper explores the similarities and dierences behind the perceptions of these concepts, to come to a fundamental understanding of risk, safety, and security, proposing a semantic and ontological ground for safety and security science, based on an etymological and etiological study of the concepts of risk and safety. The foundation has been induced by the semantics used in the ISO 31000 risk management guidance standard. Hence, this article proposes a coherent, standardized set of concepts and definitions with a focus on the notion “objectives” that can be used as an ontological foundation for safety and security science, linking “objectives” with the concepts of safety, security, risk, performance and also failure and success, theoretically allowing for an increasingly more precise understanding and measurement of (un)safety across the whole range of individuals, sectors and organizations, or even society as a whole.

It is established that BCG vaccination results in the development of both a specific immune response to mycobacterial infections and a nonspecific (heterologous) immune response, designated as trained immunity (TRIM), to other pathogens. We hypothesized that local BCG immunization may induce early immune response of bone marrow and spleen innate immunity cells. The early transcriptomic response of various populations of innate immune cells, including monocytes, neutrophils, and natural killer (NK) cells, to BCG vaccination was examined. To this end, C57Bl/6J mice were subcutaneously immunized with 10⁶ CFU of BCG. Three days following BCG administration, the three cell populations were collected from the control and BCG-vaccinated groups by FACS. All cell populations obtained were utilized for the preparation and sequencing of RNA-seq libraries. The analysis of FACS data revealed an increase in the proportion of splenic NK cells and monocytes 3 days post-vaccination. Transcriptomic analysis revealed deregulation of genes associated with regulation of immune response (according to Gene Ontology terms) in NK cells, monocytes, and unsorted bone marrow. Two NK cell-specific immune ligands (Tnfsf14 and S100a8) and two bone marrow-specific immune receptors (C5ar1 and Csf2rb) were identified among differentially expressed genes. No alterations were identified in neutrophils in either the percentage or at the transcriptomic level. Thus, in this study we demonstrated that BCG vaccination provides the early increase in the proportion of murine bone marrow and spleen immune cell populations, as well as the transcriptomic alterations in monocytes, NK cells, and non-sorted bone marrow. This early innate immune response may be beneficial for enhancing TRIM.

Gestational Diabetes Mellitus (GDMs) is worldly wide pregnancy complication. Gestational Diabetes can significantly impact the fetus development. However, the effects of high glucose on embryological development post-fertilization are yet to be researched. Danio rerio embryos are great model to study the embryonic development. In this study, the effects on embryological (morphological and genetic) development were examined in the presence of a high glucose environment that mimic the developing fetus in pregnant women with GMD. Fertilized Zebrafish embryos were treated with normal media and high glucose for 5 days from 3 hours post-fertilization(hpf) to 96hpf respectively as control and experimental groups. Morphological changes are recorded with Microscope images. Hatch rate and heart rate are compared between groups in set up time points. RNA-Seq is performed to examine the gene changes in experimental group. Glucose delayed the zebrafish embryo development by slowing the hatch rate about 24 hours. The brain, heart, and tail started showing morphology smaller in the glucose group compared to the control group at 24 hpf. Heart rate is faster in the glucose group compared to the control group on day 2 and 3 with a statistically significant difference. Among zebrafish whole genome, the significantly changed genes are 556 genes up-regulated and 1118 genes down-regulated respectively in high glucose group. The metabolic and Wnt pathways are altered under high glucose condition. These conditions contribute to significant physiological differences that may provide insight on functionality post-embryological development.

Background: We investigated the tumor immune response in gastric cancer patients receiving third line nivolumab monotherapy to identify immune-related biomarkers for better patient se-lection. Methods: Nineteen patients (10 males, median age 67 years) who received nivolumab as a third or later line therapy were enrolled. We analyzed the tumor immune response in durable clinical benefit (DCB) and non-DCB patients. Pre-treatment and early-on-treatment tumor transcriptomes were examined, and gene expression profiles, immunograms, and T cell receptor (TCR) repertoire were analyzed. Results: DCB was observed in 15.8% of patients, with comparable secondary endpoints (ORR, OS, PFS) to previous trials. Individual immunograms showed no significant changes before and ear-ly-on-treatment, nor consistent alterations among DCB cases. The intratumoral immune response was suppressed by previous treatments in most third or later line nivolumab recipients. TCR repertoire analysis revealed newly emerged clonotypes in on-treatment tumors, but clonal re-placement did not impact efficacy. High T cells/Tregs ratios and a low UV radiation response gene signature were linked to DCB and treatment response. Conclusions: This study emphasizes the tumor immune response's importance in nivolumab ef-ficacy for gastric cancer. High T cells/Tregs ratios and specific gene expression signatures show promise as potential biomarkers for treatment response. Larger cohort validation is crucial to optimize immune checkpoint inhibitors in gastric cancer treatment.

Single-cell RNA sequencing (scRNA-seq) technology has significantly advanced our understanding of the diversity of cells and how this diversity is implicated in diseases. Yet, translating these findings across various scRNA-seq datasets poses challenges due to technical variability and dataset-specific biases. To overcome this, we present a novel approach that employs both an LLM-based framework and explainable machine learning to facilitate generalization across single-cell datasets and identify gene signatures to capture disease-driven transcriptional changes. Our approach uses scBERT, which harnesses shared transcriptomic features among cell types to establish consistent cell-type annotations across multiple scRNA-seq datasets. Additionally, we employ a symbolic regression algorithm to pinpoint highly relevant yet minimally redundant models and features for inferring a cell type’s disease state based on its transcriptomic profile. We ascertain the versatility of these cell-specific gene signatures across datasets, showcasing their resilience as molecular markers to pinpoint and characterize disease-associated cell types. Validation is carried out using four publicly available scRNA-seq datasets from both healthy individuals and those suffering from ulcerative colitis (UC). This demonstrates our approach’s efficacy in bridging disparities specific to different datasets, fostering comparative analyses. Notably, the simplicity and symbolic nature of the retrieved gene signatures facilitate their interpretability, allowing us to elucidate underlying molecular disease mechanisms using these models.

The achievement of reproductive competence in male mammals is dependent on the testis. Goat testis’ development and spermatogenesis involve physiological events with high complexity. In the current work, 6 testes were respectively collected from immature, sexually mature and physically mature Qianbei Ma goats (1, 6 and 12 months old, respectively). RNA-Seq was carried out to reveal changes in testis mRNA expression levels in Qianbei Ma goats at various developmental stages, and gene expression profiling at different ages was established. Totally 18 libraries were established for screening genes and pathways associated with testis development and spermatogenic processes. Totally 9,724 upregulated and 4,153 downregulated genes were identified between immature (I) and sexually mature (S) testes; 7 upregulated and 3 downregulated genes were detected between sexually mature (S) and physically mature (P) testes, and approximately 4% of genes were alternately spliced between the I and S groups. Selected genes were verified by qRT-PCR, in agreement with sequencing data indicating their reliability. Those genes have critical functions in various developmental stages of goat testicular development and spermatogenesis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out to evaluate differentially expressed genes (DEGs). GO analysis suggested DEGs were involved in “reproduction process”, “channel activity” and “cell periphery part” between I and S, and in “ion transport process”, “channel activity” and “transporter complex part” between S and P. KEGG analysis indicated that pathways such as “glycerolipid metabolism”, “steroid hormone biosynthesis” and “MAPK signaling pathway” may be involved in testis development and spermatogenesis. Genes including IGF1, TGFB1, TGFBR1 and EGFR may regulate the development of the testis from immature to sexually mature, which may be key candidate genes for the development of goat testis. These findings provide novel insights into goat testicular development and spermatogenesis.

Rose (Rosa spp.), especially R. hybrida, is one of the most popular ornamental plants in the world and the third largest cut flower crop in Taiwan. Rose mosaic disease (RMD), showing mosaic, line patterns and ringspots on leaves, is a common rose disease caused by complex infection of various viruses. Due to pests and diseases, the rose planting area in Taiwan has been decreasing since 2008; however, no rose virus disease has been reported in the past five decades. In the spring of 2020, rose samples showing RMD-like symptoms were observed at an organic farm in Chiayi, central Taiwan. The virome in the farm was analyzed by RNA-seq. Rose genomic sequences were filtered from the obtained reads. The remaining reads were de novo assembled to generate 294 contigs, 50 of which were annotated as viral sequences corresponding to 10 viruses. Through reverse transcription-polymerase chain reaction validation, a total of seven viruses were detected, including six known rose viruses, namely apple mosaic virus, prunus necrotic ringspot virus, rose partitivirus, apple stem grooving virus, rose spring dwarf-associated virus and rose cryptic virus 1, and a novel ilarvirus. After completing the whole genome sequencing and sequence analysis, the unknown ilarvirus was demonstrated as a new species, tentatively named rose ilarvirus 2. This is the first report of the rose viruses in Taiwan.

The objective of this study was to identify key transcription factors involved in lipid metabolism and immune response related to the differentially expressed genes (DEG) from the liver samples of 35 pig model for metabolic diseases fed diets containing either 1.5 or 3.0% soybean oil (SOY1.5 or SOY3.0). A total of 281 DEG between SOY1.5 and SOY3.0 diets (log2fold-change ≥ 1 or ≤ −1; FDR-corrected p-value < 0.1) were identified, in which 129 were down-regulated and 152 were up-regulated in SOY1.5 group. The functional annotation analysis detected transcription factors linked to lipid homeostasis and immune response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key transcription factors related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive the food technology and science.

Background: Jerusalem artichoke (Helianthus tuberosus L.) is tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, the plant physiology, biochemistry and gene transcription are likely to undergo large changes. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h, 6 h, 12 h, 24 h and 48 h, with 150,129 unigenes and 9023 DEGs (Differentially Expressed Genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among the groups convergence. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belongs to PYL (abscisic acid receptor PYR / PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (Genes such as jasmonate ZIM-domain gene) and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qPCR of 12 randomly selected genes confirmed the accuracy of RNA-seq. Conclusions: Under the impact of high salinity (300mM) environment, Jerusalem artichoke in the seedling stage was difficult to survive for a long time, and the phenotype was severe in the short term. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern.

A definitive transcriptome atlas for the non-coding expressed elements of pathogenic mycobacteria does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g. Mycobacterium tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasising the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non- coding transcriptome with experiments that can help refine and confirm these predictions.

Single cell RNA-seq (scRNA-seq) profiles conceal temporal and spatial tissue developmental information. De novo reconstruction of single cell temporal trajectory has been fairly addressed, but reverse engineering single cell 3D spatial tissue localization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here we show that a new algorithm - named D-CE - for coalescent embedding of single cell transcriptomic networks can address this open problem. We rely merely on the spatial information encoded in the expression patterns of developmental signal transcription factor (DST) genes, and we find that D-CE of cell-cell association DST-transcriptomic networks reliably reconstructs the Geo-seq or single cell samples’ 3D spatial tissue distribution. Comparison to the novoSpaRC and CSOmap (recent and only available de novo 3D spatial reconstruction methods) on 16 datasets and 681 reconstructions, reveals a significantly distinctive superior performance of D-CE.

Geckos demonstrate a remarkable variability in sex determination systems, but our limited knowledge prohibits accurate conclusions on the evolution of sex determination in this group. Eyelid geckos (Eublepharidae) are of particular interest, as they encompass species with both environmental and genotypic sex determination. We identified for the first time the X-specific gene content in the Yucatán banded gecko, Coleonyx elegans, possessing X1X1X2X2/X1X2Y multiple sex chromosomes by comparative genome coverage analysis between sexes. The X-specific gene content of Coleonyx elegans was revealed to be partially homologous to genomic regions linked to the chicken autosomes 1, 6 and 11. A qPCR-based test was applied to validate a subset of X-specific genes by comparing the difference in gene copy numbers between sexes, and to explore the homology of sex chromosomes across 11 eublepharid, two phyllodactylid and one sphaerodactylid species. Homologous sex chromosomes are shared between Coleonyx elegans and Coleonyx mitratus, two species diverged approximately 34 million years ago, but not with other tested species. As far as we know, the X-specific gene content of Coleonyx elegans / Coleonyx mitratus was never involved in the sex chromosomes of other gecko lineages, indicating that the sex chromosomes in this clade of eublepharid geckos evolved independently.

Background: DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B and HER2-positive Breast Cancer (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). Methods: To decipher its function, DSCAM-AS1 expression was measured by qRT-PCR in tissue samples from 93 BC patients in addition to a meta-analysis of 30 gene expression datasets, together with the evaluation of its association with clinical data. By computational analyses of our RNA-Seq in MCF-7 cells, we investigated the DSCAM-AS1 knock-down effects at both gene and isoform levels. Results: We confirmed DSCAM-AS1 overexpression in high grade Luminal A, B and HER2+ BCs and found a significant correlation with disease relapse. 908 genes were regulated by DSCAM-AS1-silencing, primarily involved in cell cycle and inflammatory response. Noteworthy, the analysis of alternative splicing and isoform regulation revealed 2,085 splicing events regulated by DSCAM-AS1, enriched in differential polyadenylation sites and 3’UTR shortening events. Finally, the DSCAM-AS1-interacting splicing factor hnRNPL was predicted as the most enriched RBP for exon skipping and 3’UTR events. Conclusion: The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is one of many severe diseases that threaten bread wheat (Triticum aestivum L.) yield and quality worldwide. The discovery and deployment of powdery mildew resistance genes (Pm) can prevent this disease epidemic in wheat. In a previous study, we transferred the powdery mildew resistance gene Pm57 from Aegilops searsii into common wheat and cytogenetically mapped the gene in a chromosome region with the fraction length (FL) 0.75-0.87, which represents 12% of 2Ss#1 segment on the long arm of chromosome 2Ss#1. In this study, we performed RNA-Seq on three infected and mock-infected wheat-Ae. searsii 2Ss#1 introgression lines with Bgt-isolates inoculation at 0, 12, 24, and 48 hours after inoculation. Then we designed 79 molecular markers based on transcriptome sequences and physically mapped them to Ae. searsii chromosome 2Ss#1- in seven intervals. We used these markers to identify 46 wheat-Ae. searsii 2Ss#1 recombinants induced by ph1b, a deletion mutant of pairing homoelogous (Ph) genes. Analysis of the 46 ph1b-induced 2Ss#1L recombinants with different Bgt-responses using 28 2Ss#1L-specific molecular markers in the interval FL0.72-0.87 where Pm57 is located, and the flanking intervals, we physically mapped Pm57 gene on the long arm of 2Ss#1 in a 5.13 Mb genomic region, which was flanked by markers X67593 (773.72 Mb) and X62492 (778.85 Mb). By comparative synteny analysis of the corresponding region on chromosome 2B in Chinese spring (T. aestivum L.) with other model species we identified ten genes that are putative plant defense-related (R) genes which includes six coiled-coil nucleotide-binding site-leucine-rich repeat (CNL), three nucleotide-binding site-leucine-rich repeat (NL) and a leucine-rich receptor-like repeat (RLP) encoding proteins. This study will lay a foundation for further cloning of Pm57, and benefit the understanding of interactions between resistance genes of wheat and powdery mildew pathogens.

Experimental studies and numerical analyses were conducted to estimate the laminar flame speeds of butyl ether, n-octane, iso-octane, and 1-octene at temperatures of 373 and 443 K and pressures ranging from 0.03 to 0.3 MPa in a constant-volume combustion chamber. Iso-octane had the slowest laminar flame speed whereas butyl ether had the highest. The LLNL model for large hydrocarbons and the Cai model for butyl ether were combined to describe the chemical kinetic mechanism for the test fuels. The simulation data calculated with the constructed model agree with the experimental data. The discrepancies in the laminar flame speeds of the four fuels were clarified from the perspectives of thermodynamics, diffusion, and chemical kinetics. The results reveal that the thermodynamics and chemical kinetics were dominant. Butyl ether had the highest laminar flame speed. This was attributed to it having the highest adiabatic flame temperature and a higher concentration of H and OH radicals, which have a high reactivity in a flame. Iso-octane produces the highest concentration of CH3, which inhibits flame propagation, so that it had the slowest laminar flame speed.

There is currently an exponential growth in the electric vehicle market, which will require an increase in the electrical grid capacity to meet the demand of charging. If, on the one hand, the introduction of energy generation from renewable sources can be used to meet that requirement, the intermittent nature of some of these sources poses challenges to the required real time equilibrium between generation and consumption. The impossibility of controlling generation from some of these sources leads to the attempt of controlling and manage the consumption of electricity, according with the levels of generation. In this context, the emergence of smart grids has introduced mechanisms that guarantee a balance between consumption and generation of electricity. One of these mechanisms is the smart charging of electric vehicles. Effective smart charging relies on communication between the supply equipment and the electric vehicle, en-abling the adjustment of the energy transfer according with the generation levels. Thus, there is a necessity for a standardised system that guarantees this communication. In this context, the ISO 15118 standard, allows high level communication mechanisms, much beyond the basic control solutions offered by the IEC 61851-1 specification. In this context, this paper presents the development of a charge emulation system, based on the ISO 15118 communication protocol and discusses its application for demand response purposes.

The building blocks of a scientific facility based on particle beams comprise magnets and electro-magnetic devices. The design of an overall accelerator usually imposes a demanding accuracy on their exact position and orientation. Their non-geometrical functional features are frequently either not clearly defined – what is the « magnetic axis » of a magnet –, or not explicitly used along their lifecycle. Improving the process to establish and use these functional features would contribute to meeting demanding challenges. The European Spallation Source (ESS) is aiming at providing a powerful proton linear accelerator and a target system to produce pulsed neutrons. The challenging complex design and integration yielded to introducing a tool for all stakeholders along the lifecycle: the "situation features", as defined in ISO GPS (Geometrical Product Specifications) standards. This paper deals with the beyond-mechanics non-geometrical use cases and generalizes the use of the association operation to theoretically exact features. The examples of the functional specification, fiducialization (measure of the real features with respect to external marks) and installation phases of quadrupole magnets is developed. Perspectives of generic use are highlighted.

The objective of the present report is the dissemination of information acquired during the application of ISO 6579-1:2017 for the isolation of Salmonella spp. from swine samples. ISO 6579-1:2017 is the officially recommended by the EU protocol for the isolation of Salmonella spp., aiming in the harmonization of effective successful control of Salmonella infection in food producing animals. Successful control of animal salmonellosis is highly dependent on the sensitivity of the biochemical methods reliably detecting the presence of the pathogen in various stages of food production. Application of ISO 6579-1:2017 resulted in the isolation of twelve Salmonella spp. and eighteen other members of the family of Enterobacteriaceae biochemically and antigenically resembling salmonellae. The findings necessitated in the depth evaluation of the culture media xylose-lysine-desoxycholate agar (XLD), Salmonella-Shigella Agar (SS), Brilliant Green Agar (BGA), Salmonella Chromogenic Agar (SCA), Triple Sugar Iron (TSI) and modified semi-solid Rappaport–Vassiliadis (MSRV) agar. The evaluation showed that these culture selective media differed significantly in their performance regarding the isolation of Salmonella from swine samples. It was concluded that the presence of atypical Salmonella strains negatively affects the prevalence of Salmonella, thus the identification of carrier pigs, eventually affecting the efficiency of control programs. Thus, doubtful results require additional biochemical testing for confirming the accuracy of such universally recommended isolation methods.

Although traditional automotive development has mainly focused on functional safety, as the number of automotive hacking cases has increased due to the growing Internet connectivity of automotive control systems, security is also becoming more important. Accordingly, various international organizations are preparing cybersecurity regulations or standards to ensure security in automotive development by emphasizing the concept of security-by-design(i.e. security engineering) which emphasizes trustworthiness from the beginning of development. The problem, however, is that no specific methodology has been suggested. In this paper, we propose a specific security-by-design methodology for automotive development based on Secure System Development Life Cycle (secure SDLC) standards and evidence-based standards. Our methodology could be easily used in the actual field as it is more general and detailed than existing secure SDLC standards and research. Also, since it satisfies all requirements of United Nations Economic Commission for Europe (UNECE) regulation, automobile manufacturers could respond to the upcoming cybersecurity regulation with our methodology.

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragment repeats within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue or stage-specific. We analysed the ALDH gene's expression patterns under six stress types, namely salt, chilling, waterlogged, powdery mildew, fusarium wilt, and gummy stem blight. The results showed differential expression of MELO3C024328 and MELO3C004430 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Cotton seeds as the main by-product of cotton are not only an important raw material for edible oil and feed but also a source of biofuel. The quality of cotton seeds directly affects cotton planting and is closely related to the yield and fiber quality. However, the molecular mechanism governing cotton seed size remains largely unexplored. This study investigates the regulatory mechanisms of cotton seed size by focusing on two cotton genotypes, N10 and N12, which exhibit notable phenotypic variations across multiple environments. Developing seeds were sampled at various stages (5, 20, 30, and 35 DAP) and subjected to RNA-seq. The temporal pattern clustering and WGCNA on differentially expressed genes identified 413 candidate genes, including these related to sugar metabolism that were significantly enriched in transcriptional regulation. A genetic transformation experiment indicated that the overexpression of the GhUXS5 gene encoding UDP-glucuronate decarboxylase 5 significantly increased seed size, suggesting an important role of GhUXS5 in regulating cotton seed size. This discovery provides crucial insights into the molecular mechanisms controlling cotton seed size, helping to unravel the complex regulatory network and offering new strategies and targets for cotton breeding to enhance the economic value of cotton seeds and overall cotton yield.

Streptococcus agalactiae is a highly contagious Gram- positive bacterium that causes mastitis, has a high infectivity for mammary epithelial cells, and is challenging to treat. However, the molecular interactions between it and mammary epithelial cells remains poorly understood. This study analyzed differential gene expression in mammary epithelial cells with varying levels of S. agalactiae infection using UID- Dual Seq and bioinformatics tools. This study identified 211 differentially expressed mRNAs (DEmRNAs) and 452 differentially expressed lncRNAs (DElncRNAs) in host cells, primarily enriched in anti-inflammatory responses, immune responses, and cancer-related processes. Additionally, 854 pathogen differentially expressed mRNAs (pDEmRNAs) were identified, mainly enriched in protein metabolism, gene expression, and biosynthesis processes. Mammary epithelial cells activate pathways, such as the ERK1/2 pathway to produce, to produce reactive oxygen species (ROS) to eliminate bacteria. However, the bacteria disrupt the host's innate immune mechanisms by interfering with the alternative splicing processes of mammary epithelial cells. Specifically, the bacterial genes of tsf, prfB, and infC can interfere with lncRNAs targeting RUNX1 and BCL2L11 in mammary epithelial cells, affecting the alternative splicing of target genes and altering normal molecular regulation.

With the rapid development of gene therapy technology in recent years, its abuse as a method of sports doping in athletic has become a concern. However, there is still room for improvement in gene doping testing methods, and a robust animal model needs to be developed. Therefore, the purposes of this study were to establish a model of gene doping using recombinant adeno-associated virus vector-9 including the human erythropoietin gene (rAAV9-hEPO), and to establish a relevant testing method. First, it was attempted to establish the model using rAAV9-hEPO on mice. The results showed a significant increase in erythrocyte volume accompanied by an increase in spleen weight, confirming the validity of the model. Next, we attempted to detect proof of gene doping by targeting DNA and RNA. Direct proof of gene doping was detected using a TaqMan-qPCR assay with certain primers/probes. In addition, some indirect proof was identified in RNAs through the combination of a TB Green qPCR assay with RNA sequencing. Taken together, these results could provide the foundation for an effective test for gene doping in human athletes in the future.

The addition of 50% vitreous humor to the media bathing lens explants results in the induction of both fiber cell differentiation and a significant immune/inflammatory response. Although Fgfr loss blocks differentiation in lens epithelial explants, this loss is partially rescued by deleting Pten. To investigate the functions of the Fgfrs and Pten during lens fiber cell differentiation, we utilized a lens epithelial explant system and conducted RNA sequencing on vitreous humor-exposed explants lacking Fgfrs, or Pten or both Fgfrs and Pten. We found that Fgfr loss impairs both vitreous-induced differentiation and inflammation while the additional loss of Pten restores these responses. Furthermore, transcriptomic analysis suggested that PDGFR-signaling in FGFR-deficient explants is required to mediate the rescue of vitreous-induced fiber differentiation in explants lacking both Fgfrs and Pten. The blockage of β-crystallin induction in explants lacking both Fgfrs and Pten in the presence of a PDGFR-inhibitor supports this hypothesis. Our findings demonstrate that a wide array of genes associated with fiber cell differentiation are downstream of FGFR-signaling and that the vitreous-induced immune responses also depend on FGFR-signaling. Our data also demonstrates that many of the vitreous-induced gene expression changes Fgfr-deficient explants are rescued in explants lacking both Fgfrs and Pten.

Trichothecene mycotoxin T-2 toxin is an important environmental pollutant and poses a global threat to human and animal health. T-2 toxin could induce nephrotoxicity, however, the precise molecular mechanism remains unclear. In this study, the mice were intraperitoneally administrated with a single dose of 2 mg/kg T-2 toxin. The kidney function and ultrastructural observation were also assessed and found T-2 toxin exposure could cause kidney damage. Transmission electron microscopy showed a significant swelling and vacuolization of the mitochondria of renal cell. A total of 1122, 58, and 391 differential expression genes (DEGs) that were predominantly expressed in kidney tissues at 1 d, 3 d, and 7 d after T-2 toxin exposure, respectively. Early transcriptomic changes at 1 d after exposure were down-regulation of DEGs involved in the cell cycle, p53 signaling pathway, and cellular senescence, while up-regulation of DEGs referred to the ribosome pathway. The temporal variations in gene expression pattern in T-2 toxin exposure in mice kidney were presented and cellular metabolism was disturbed at the exposure recovery period with 7 d. In conclusion, this study, for the first time, provided a comprehensive comparative transcriptomic analysis of gene regulation in T-2 toxin exposure-induced nephrotoxicity at different temporal periods and explored the nephrotoxicity mechanism of T-2 toxin at the mRNA level.

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and secondary meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperm class are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom, and determined the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.

Because rice is native to tropical and subtropical regions, it is generally more sensitive to cold stress compared to other cereals. Low temperature stress has become one of the most important conditions that affects the growth, development, and yield of rice. Plant NAC (NAM, ATAF1/2, and CUC) transcription factors are known to play significant regulatory roles in the stress response. In our research, we found that OsNAC050 (LOC_Os03g60080） is mainly expressed in leaves, and low temperature can further up-regulate its expression. OsNAC050 mutants created using CRISPR-Cas9 gene editing technology showed significantly enhanced tolerance to low temperature treatment. Detection of enzyme activities related to the redox pathway also showed that the mutants had stronger viability under low temperature stress. Comparative transcriptome analysis showed that photosynthesis and soluble sugar metabolism were significantly affected in the osnac050 mutant lines, suggesting that OsNAC050 may participate in the above molecular pathways in the response to low temperature stress. The results will enhance our understanding of molecular mechanisms underlying the responses to cold stress in rice and can provide new strategies for engineering cold-tolerance in high-yielding rice varieties.

The emergence of drug resistant pathogenic bacteria is increasingly challenging conventional antibiotics. Plant derived flavonoids are considered as potential alternatives to antibiotics due to their antimicrobial properties. However, the mechanisms by which flavonoids modulate pathogenic microorganisms’ growth are not fully understood. In our previous studies we found that Rutin, a kind of flavonoids showed inhibition against Klebsiella pneumoniae strains. In order to better understand its inhibitory mechanism on strain growth, we used both Rutin and Luteolin as treatments to incubate K. pneumoniae ATCC700603 strain. After incubation for 4 hours, the homogenous and differential effects of two different flavonoids on the growth of K. pneumoniae were evaluated. The integrated metabolomic and transcriptomic analysis was performed. The expression levels of 5,483 genes and the contents of 882 metabolites were measured. The differentially expressed genes (DEGs) and metabolites (DEMs) were screened and analyzed. The correlation between DEGs and DEMs were also studied. Our results showed that Rutin could inhibit the strain growth by changing metabolic pathways and ABC transporters pathways. Our study also revealed FU841_RS17580 and FU841_RS19145 as functional genes that played vital roles in the strain growth.

Systems genetics is key for integrating a large number of variants associated with diseases. Vitamin K (VK) is one of the scarcely studied conditions in lieu of ascertaining either the differentially expressed genes (DEGs) or variants in an individual subpopulation of diseased phenotypes associated with VK, viz. myocardial infarction, renal failure, prostate cancer, thrombosis, thrombocytopenia, coagulation related diseases to name a few. In this work, we have screened characteristic DEGs common to three VK-related diseases, viz. myocardial infarction, renal failure and prostate cancer and asked whether or not any DEGs in addition to pathogenic variants are common to these conditions. We attempt to bridge the gap in finding characteristic biomarkers and discuss the role of long noncoding RNAs (lncRNAs) in the biogenesis of VK deficiencies.

Single-cell RNA sequencing data facilitates investigation of cell heterogeneity and subpopulations as well as differentially abundant states however modern single-cell RNA sequencing datasets are growing in size and complexity requiring advances in the bioinformatic methods that analyze them. Many methods exist for each step of analysis including read alignment, normalization, quality control, batch effect correction, imputation and dimensionality reduction. With so many options to choose from at each step of the analysis, benchmarking and a synthesis of the literature on the methods available is necessary to inform biological researchers on the most optimal workflow for their data. Here, recent key methods of analysis are highlighted with a focus on methods that facilitate identification of cell subpopulations and differentially abundant cell states. With a constantly expanding toolset for each step in single-cell RNA sequencing dataset analysis, biological researchers should stay informed to utilize the most applicable methods for their own analyses.

Microglia activation causes neuroinflammation, which is a hallmark of neurodegenerative disorders, brain injury, and aging. Ladostigil, a bifunctional reagent with antioxidant and anti-inflammatory properties, reduced microglial activation and enhanced brain functioning in elderly rats. In this study, we studied SH-SY5Y, a human neuroblastoma cell line, and tested viability in the presence of hydrogen peroxide and Sin1 (3-morpholinosydnonimine), which generates reactive oxygen and nitrogen species (ROS/RNS). Both stressors caused significant apoptosis and necrotic cell death that was attenuated by ladostigil. Our results from RNA-seq experiments show that long non-coding RNAs (lncRNAs) account for 30% of all transcripts in SH-SY5Y cells treated with Sin1 for 24 hours. Altogether, we identify 94 differently expressed lncRNAs in the presence of Sin1, including MALAT1, a highly expressed lncRNA with anti-inflammatory and anti-apoptotic functions. Additional activities of Sin-1 upregulated lncRNAs include redox homeostasis (e.g., MIAT, GABPB1-AS1), energy metabolism (HAND2-AS1), and neurodegeneration (e.g., MIAT, GABPB1-AS1, NEAT1). Four lncRNAs implicated as enhancers were significantly upregulated in cells exposed to Sin1 and ladostigil. Finally, we show that H2O2 and Sin1 increased the expression of DJ-1, a redox sensor and modulator of Nrf2 (nuclear factor erythroid 2–related factor 2). Nrf2 (NFE2L2 gene) is a major transcription factor regulating antioxidant genes. In the presence of ladostigil, DJ-1 expression is restored to its baseline. The mechanisms governing SH-SY5Y cell survival and homeostasis are highlighted by the beneficial role of ladostigil in the crosstalk involving Nrf2, antioxidant transcription factor DJ-1, and lncRNAs. Stress-dependent induction of lncRNAs represents an underappreciated regulatory level that contributes to cellular homeostasis and the capacity of SH-SY5Y to cope with oxidative stress.

Intratumoral heterogeneity associates with more aggressive disease progression and worse patient outcomes. Understanding the reasons enabling the emergence of such heterogeneity remains incomplete, which restricts our ability to manage it from a therapeutic perspective. Technological advancements such as high-throughput molecular imaging, single-cell omics and spatial transcriptomics now allow recording the patterns of spatiotemporal heterogeneity in a longitudinal manner, thus offering insights into the multi-scale dynamics of its evolution. Here, we review latest technological trends and biological insights from molecular diagnostics as well as spatial transcriptomics, both of which have witnessed a burgeoning growth in recent past in terms of mapping heterogeneity within tumor cell types as well as stromal constitution. We also discuss ongoing challenges, indicating possible ways to integrate insights across these methods to have a systems-level spatiotemporal map of heterogeneity in each tumor, and a more systematic investigation of implications of heterogeneity for the patient outcomes.

Prostate cancer (Pca) is a highly heterogeneous disease and the second more common tumor in males. Molecular and genetic profiles have been used to identify subtypes and guide therapeutic intervention. However, roughly 26% of primary Pca are driven by unknown molecular lesions. We use Principal Component Analysis (PCA) and custom RNAseq-data normalization to identify a gene expression signature which segregates primary PRAD from normal tissues. This Core-Expression Signature (PRAD-CES) includes 33 genes and accounts for 39% of data complexity along the PC1-cancer axis. The PRAD-CES is populated by protein-coding (AMACR, TP63, HPN) and RNA-genes (PCA3, ARLN1) sparsely found in previous studies, validated/predicted biomarkers (HOXC6, TDRD1, DLX1), and/or cancer drivers (PCA3, ARLN1, PCAT-14). Of note, the PRAD-CES also comprises six over-expressed LncRNAs without previous Pca association, four of them potentially modulating driver’s genes TMPRSS2, PRUNE2 and AMACR. Overall, our PCA capture 57% of data complexity within PC1-3. GO enrichment and correlation analysis involving major clinical features (i.e., Gleason Score, AR Score, TMPRSS2-ERG fusion and Tumor Cellularity) suggest that PC2 and PC3 gene signatures might describe more aggressive and inflammation-prone transitional forms of PRAD. Of note, surfaced genes may entail novel prognostic biomarkers and molecular alterations to intervene. Particularly, our work uncovered RNA genes with appealing implications on Pca biology and progression.

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

As a major infectious disease in chickens, Newcastle disease causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 dpi after infection at day21 with a lentogenic Newcastle disease virus in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV challenged and nonchallenged groups, 526 differentially expressed genes (DEGs) (FDR < 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, IPA analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis and angiogenesis. Upregulation of Interferon Induced Protein with Tetratricopeptide Repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK Signaling Antagonist 1 (SPRY1), a DEG in the current study is located in a significant QTL associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.