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Abstract/Introduction: Inter-organ communication is a vital process to maintain physiologic homeostasis, and its dysregulation contributes to many human diseases. Beginning with the discovery of insulin over a century ago, characterization of molecules responsible for signal between tissues has required careful and elegant experimentation where these observations have been integral to deciphering physiology and disease. Given that circulating bioactive factors are stable in serum, occur naturally, and are easily assayed from blood, they present obvious focal molecules for therapeutic intervention and biomarker development. For example, physiologic dissection of the actions of soluble proteins such as proprotein convertase subtilisin/kexin type 9 (PCSK9) and glucagon-like peptide 1 (GLP1) have yielded among the most promising therapeutics to treat cardiovascular disease and obesity, respectively1–4. A major obstacle in the characterization of such soluble factors is that defining their tissues and pathways of action requires extensive experimental testing in cells and animal models. Recently, studies have shown that secreted proteins mediating inter-tissue signaling could be identified by “brute-force” surveys of all genes within RNA-sequencing measures across tissues within a population5–9. Expanding on this intuition, we reasoned that parallel strategies could be used to understand how individual genes mediate signaling across metabolic tissues through correlative analyses of gene variation between individuals. Thus, comparison of quantitative levels of gene expression relationships between organs in a population could aid in understanding cross-organ signaling. Here, we surveyed gene-gene correlation structure across 18 metabolic tissues in 310 human individuals and 7 tissues in 103 diverse strains of mice fed a normal chow or HFHS diet. Variation of genes such asFGF21, ADIPOQ, GCGandIL6showed enrichments which recapitulate experimental observations. Further, similar analyses were applied to explore both within-tissue signaling mechanisms (liverPCSK9) as well as genes encoding enzymes producing metabolites (adiposePNPLA2), where inter-individual correlation structure aligned with known roles for these critical metabolic pathways. Examination of sex hormone receptor correlations in mice highlighted the difference of tissue-specific variation in relationships with metabolic traits. We refer to this resource asGene-DerivedCorrelationsAcrossTissues (GD-CAT) where all tools and data are built into a web portal enabling users to perform these analyses without a single line of code (gdcat.org). This resource enables querying of any gene in any tissue to find correlated patterns of genes, cell types, pathways and network architectures across metabolic organs.

Plants, being sessile organisms, are exposed to a diverse range of environmental challenge. Over time, they have evolved various mechanisms to withstand these harsh conditions, often acquiring functional redundancy in genes with similar sequence. This genetic redundancy, while advantageous for the plant's adaptability, poses challenges in functional genomics research. To address this issue, we developed CAFRI-Arabidopsis (https://cafri.khu.ac.kr/arabidopsis/), a web resource designed to intuitively explore functional redundancy in Arabidopsis, a model plant that has significantly contributed to understanding the morphological and physiological traits. Our tool combines transcriptome data with Pfam-based phylogenetic data across 33 tissues/organs to visualize and quantify functional redundancy. Its effectiveness has been validated through a comprehensive literature review. User-friendly in design, CAFRI-Arabidopsis allows users to quickly generate results by inputting the desired locus. We anticipate that this tool will be invaluable in uncovering new insights in plant developmental and physiological studies that have been previously obscured due to functional redundancy. [ABSTRACT FROM AUTHOR]

This resource description explores a web-assisted learning and teaching approach for Tamil facilitated by the Penn Language Center. Tamil is an ancient language spoken predominantly in the Indian state of Tamil Nadu and Sri Lanka. The language has significant cultural and linguistic relevance. However, due to limited resources and geographical constraints, access to high-quality Tamil language instruction has often been challenging for learners outside Tamil-speaking regions. To address these challenges, the Penn Language Center developed the WALTT program, which integrates web-based technologies into Tamil language learning and teaching. This web resource description aims to examine the structure of the syllabi in detail. Overall, this resource description aims to decode the presence of web-assisted learning resources in the field of Tamil language education, as well as provide valuable resources for the broader community of web-assisted language learning and teaching practitioners and beginners of the language. [ABSTRACT FROM AUTHOR]

Much of the host antiviral response is mediated through changes to host gene expression levels. Likewise, viruses induce changes to host gene expression levels in order to promote the viral life cycle and evade the host immune system. However, there is no resource that specifically collects human gene expression levels pre- and post-virus infection. Further, public gene expression repositories do not contain enough specialized metadata to easily find relevant experiments. Here, we present the Virus Expression Database (VExD), a freely available website and database, that collects human gene expression datasets in response to viral infection. VExD contains ~8,000 uniformly processed samples obtained from 289 studies examining 51 distinct human viruses. We show that the VExD processing pipeline captures known antiviral responses in the form of interferon-stimulated genes. We further show that the datasets collected in VExD can be used to quickly identify supporting data for experiments performed in human cells or model organisms. VExD is freely available at https://vexd.cchmc.org/. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus. [ABSTRACT FROM AUTHOR]

Goal. To develop a system for monitoring WEB sites based on the research of methods and software tools that are used to raise the position of the site in search engines and increase the visitor rating with the help of SEO optimization. Methodology. The development of the system was based on theoretical and experimental research, which is used to analyze services and programs for promoting the site to the top positions of search engines, professional analysis of parameters, re-engagement of customers and monitoring of sites on the Internet. Results. As a result of the study of site monitoring systems, services and software AddWeb, Google Analytics, Web Position Gold were developed and analyzed. Based on the analysis, certain shortcomings were identified, which prevent a more accurate analysis of the resource. Taking this into account, a monitoring system called "WebMonit" was developed in the form of a website. This system uses a complex method of performance analysis and testing of site accessibility parameters on the Internet, and the developed software modules - scripts make it possible to output results for analysis and resolution of problem detection/This system checks resource elements that are important for search engine optimization. They include, in particular, tags, selection of keywords for which the resource is planned to be promoted, usability, ranking, semantic core of the site, content, user-friendly interface. If these elements are optimized, it is possible to display the resource in the TOP in search engines and the Internet. Scientific novelty. The proposed original solution in the form of a monitoring system that provides the opportunity to display not only the statistics of the site's working condition, but also to find problems and provide advice on their elimination to improve SEO optimization and expansion of functionality in the decisions made. Practical significance. There are many tools for promoting a site on the Internet, each of which is effective in a specific aspect. The work gives comparative characteristics of the use of tools for site promotion, identified advantages and disadvantages of existing systems and developed a monitoring system called "WebMonit" in the form of a website that will improve site monitoring, and developed software modules - scripts will improve site promotion. [ABSTRACT FROM AUTHOR]

The methodology for analyzing the structure of a web resource using an object model, which is based on the description of the page in HTML and using style sheets, has been proposed. The object of research is a web resource page, the model of which is depicted as a DOM tree. Data on the structural elements of the tree are supplemented with information about the styles of the design of the pages. To determine the similarity of pages, it is proposed to apply a criterion that takes into account the structural and stylistic similarity of pages with the corresponding coefficients. To compare page models with each other, the method of aligning trees will be used. Editing distance is used as a metric, and renaming operations, deleting, and adding a tree node is used as editing operations. To determine the similarity in styles, the Jaccard metric is used. To cluster web pages, the k-means method with a cosine distance measure is applied. Intracluster analysis is carried out using a modification of the Zhang-Shasha algorithm. The proposed approach is implemented in the form of an algorithm and software using Python programming language and related libraries. The computational experiment was performed to analyze the structure of individual websites existing on the Internet, as well as to group pages from different web resources. The structure of the formed clusters was analyzed, the RMS similarity of elements in the middle of the clusters was calculated. To assess the quality of the developed approach for the tasks under consideration, expert partitioning was built, the values of accuracy and completeness metrics were calculated. The results of the analysis of the structure of the web resource can be used to improve the structure of the components of the web resource, to understand the navigation of users on the site, to reengineer the web resource. [ABSTRACT FROM AUTHOR]

This research draws from the communicative problem of the unfamiliarity of people with deafness and the rest of the population with the learning, mastery and use of sign language. Given this situation, people with deafness are presented with a platform based on accessibility. The platform is also intended for hearing people and even for non-deaf people. There are 1,253 adaptable interactive objects registered through videos, braille lines and screen readers. The study methodology was developed under the design-based research model, which validates the construction of the design in the context where it is to become usable. Pressman's methodology for software engineering was employed for developing the EnSenias platform. As a qualitative evaluation method, focus groups with potential users validated the process by applying content analysis to their complements and by completing quantitative analyses, resulting in the categories 'general validation of the platform', 'validation of the platform to learn' and 'to teach'. There are no digital online resources, as far as we know, created from the model employed on this occasion neither for its context nor its language, and EnSenias has shown itself as a paradigmatic example of its necessity. [ABSTRACT FROM AUTHOR]

Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like 'metabolic process' and 'cellular process', molecular functions like 'binding' and 'catalytic activities' and cellular components like 'cell', 'cell part' and 'membrane part'. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.

The description of resources and their relationships is an essential task on the web. Generally, the web users do not share the same interests and viewpoints. Each user wants that the web provides data and information according to their interests and specialty. The existing query languages, which allow querying data on the web, cannot take into consideration the viewpoint of the user. We propose introducing the viewpoint in the description of the resources. The Resource Description Framework (RDF) represents a common framework to share data and describe resources. In this study, we aim at introducing the notion of the viewpoint in the RDF. Therefore, we propose a View-Point Resource Description Framework (VP-RDF) as an extension of RDF by adding new elements. The existing query languages (e.g., SPARQL) can query the VP-RDF graphs and provide the user with data and information according to their interests and specialty. Therefore, VP-RDF can be useful in intelligent systems on the web.

Subclinical mastitis (SCM) in buffalo is one of the most challenging paradoxes for the dairy sector with very significant milk production losses and poses an imminent danger to milch animal's milk-producing ability. We present here the genome-wide methylation specific to SCM in water buffalo and its consequential effect on the gene expression landscape for the first time. Whole-genome DNA methylation profiles from peripheral blood lymphocytes and gene expression profiles from milk somatic cells of healthy and SCM cases were catalogued from the MeDIP-Seq and RNA-Seq data. The average methylation in healthy buffaloes was found to be higher than that in the SCM-infected buffaloes. DNA methylation was abundant in the intergenic region followed by the intronic region in both healthy control and SCM groups. A total of 3,950 differentially methylated regions (DMRs) were identified and annotated to 370 differentially methylated genes (DMGs), most of which were enriched in the promoter region. Several important pathways were activated due to hypomethylation and belonged to the Staphylococcus aureus infection, Th17 cell differentiation, and antigen processing and presentation pathways along with others of defense responses. DNA methylome was compared with transcriptome to understand the regulatory role of DNA methylation on gene expression specific to SCM in buffaloes. A total of 4,778 significant differentially expressed genes (DEGs) were extracted in response to SCM, out of which 67 DMGs were also found to be differentially expressed, suggesting that during SCM, DNA methylation could be one of the epigenetic regulatory mechanisms of gene expression. Genes like CSF2RB, LOC102408349, C3 and PZP like, and CPAMD8 were found to be downregulated in our study, which are known to be involved in the immune response to SCM. Association of DNA methylation with transposable elements, miRNAs, and lncRNAs was also studied. The present study reports a buffalo SCM web resource (BSCM2TDb) available at http://webtom.cabgrid.res.in/BSCM2TDb that catalogues all the mastitis-related information of the analyses results of this study in a single place. This will be of immense use to buffalo researchers to understand the host–pathogen interaction involving SCM, which is required in endeavors of mastitis control and management. [ABSTRACT FROM AUTHOR]

Subclinical mastitis (SCM) in buffalo is one of the most challenging paradoxes for the dairy sector with very significant milk production losses and poses an imminent danger to milch animal’s milk-producing ability. We present here the genome-wide methylation specific to SCM in water buffalo and its consequential effect on the gene expression landscape for the first time. Whole-genome DNA methylation profiles from peripheral blood lymphocytes and gene expression profiles from milk somatic cells of healthy and SCM cases were catalogued from the MeDIP-Seq and RNA-Seq data. The average methylation in healthy buffaloes was found to be higher than that in the SCM-infected buffaloes. DNA methylation was abundant in the intergenic region followed by the intronic region in both healthy control and SCM groups. A total of 3,950 differentially methylated regions (DMRs) were identified and annotated to 370 differentially methylated genes (DMGs), most of which were enriched in the promoter region. Several important pathways were activated due to hypomethylation and belonged to the Staphylococcus aureus infection, Th17 cell differentiation, and antigen processing and presentation pathways along with others of defense responses. DNA methylome was compared with transcriptome to understand the regulatory role of DNA methylation on gene expression specific to SCM in buffaloes. A total of 4,778 significant differentially expressed genes (DEGs) were extracted in response to SCM, out of which 67 DMGs were also found to be differentially expressed, suggesting that during SCM, DNA methylation could be one of the epigenetic regulatory mechanisms of gene expression. Genes like CSF2RB, LOC102408349, C3 and PZP like, and CPAMD8 were found to be downregulated in our study, which are known to be involved in the immune response to SCM. Association of DNA methylation with transposable elements, miRNAs, and lncRNAs was also studied. The present study reports a buffalo SCM web resource (BSCM2TDb) available at http://webtom.cabgrid.res.in/BSCM2TDb that catalogues all the mastitis-related information of the analyses results of this study in a single place. This will be of immense use to buffalo researchers to understand the host–pathogen interaction involving SCM, which is required in endeavors of mastitis control and management.

Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet.

This work is devoted to the development of the web resource, which automates the search for information about higher education institutions and admission to them. The object of the study are institutions of higher education and specialization, which can be obtained by applicants. The task of design is to develop a server part of a web resource that interacts with the database. After researching the main problems of the subject area, analysis of analogues and the choice of means of implementation, a database and functionality of the website were developed. MySQL with a web application for its administration Phpmyadmin was chosen as the database management system. To implement the interface, the language of hypertext markup HTML, cascading tables of CSS styles were chosen and the Bootstrap framework, which uses modern developments in the field of HTML and CSS.. PHP programming language and JavaScript scripting language were chosen for writing functions. The scientific significance of the development lies in the storage of all necessary information on higher education institutions in Odessa, Ukraine on a single information resource. As a result of the work, a web resource with a map of the entrant of Odessa was created, which meets all the requirements for storage and structuring of information. This website is supported by all modern browsers, which makes it accessible to all Internet users. [ABSTRACT FROM AUTHOR]

Wound‐induced hair follicle neogenesis (WIHN) has been an important model to study hair follicle regeneration during wound repair. However, the cellular and molecular components of the dermis that make large wounds more regenerative are not fully understood. Here, we compare and contrast recently published scRNA‐seq data of small scarring wounds to wounds that regenerate in hope to elucidate the role of fibroblasts lineages in WIHN. Our analysis revealed an over‐representation of the newly identified upper wound fibroblasts in regenerative wound conditions, which express the retinoic acid binding protein Crabp1. This regenerative cell type shares a similar gene signature to the murine papillary fibroblast lineage, which are necessary to support hair follicle morphogenesis and homeostasis. RNA velocity analysis comparing scarring and regenerating wounds revealed the divergent trajectories towards upper and lower wound fibroblasts and that the upper populations were closely associated with the specialized dermal papilla. We also provide analyses and explanation reconciling the inconsistency between the histological lineage tracing and the scRNA‐seq data from recent reports investigating large wounds. Finally, we performed a computational test to map the spatial location of upper wound fibroblasts in large wounds which revealed that upper peripheral fibroblasts might harbour equivalent regenerative competence as those in the centre. Overall, our scRNA‐seq reanalysis combining multiple samples suggests that upper wound fibroblasts are required for hair follicle regeneration and that papillary fibroblasts may migrate from the wound periphery to the centre during wound re‐epithelialization. Moreover, data from this publication are made available on our searchable web resource: https://skinregeneration.org/. [ABSTRACT FROM AUTHOR]

Pathogenic microorganism analysis based on next-generation sequencing technology is an important tool for clinical diagnosis, public health surveillance, and outbreak investigation. However, scientific researchers without the relevant background lack the time, training, or infrastructure to use large data sets or install and use command line tools. Therefore, the bioinformatic team at the Chinese Center for Disease Control and Prevention developed the Microbial Data Analysis Cloud Platform (MDACP) as a safe, professional, and efficient pathogen genetic data analysis platform for rapid microbial data mining, such as for candidate pathogen detection, genome typing, and traceability. MDACP is a web service system based on the Docker platform and can be used for data analysis on various operating systems. The platform focuses on pathogen analysis and continuously develops new analysis processes according to the analysis needs of the users. This platform has a friendly user interface and is easy to operate, allowing users to submit data through data pages or graphical clients, flexibly control parameters according to data conditions, and analyze data in parallel with multiple tasks. Researchers can quickly carry out bioinformatic analyses without coding work, promote follow-up research and information mining of projects, and improve the utilization of big data in the field of disease control. MDACP enables research personnel to conduct data analysis and management and assists clinicians and disease control personnel with mining information, such as pathogen identification, classification, and traceability.

Over the past decade, hundreds of genome-wide association studies (GWAS) have implicated genetic variants in various diseases, including cancer. However, only a few of these variants have been functionally characterized to date, mainly because the majority of the variants reside in non-coding regions of the human genome with unknown function. A comprehensive functional annotation of the candidate variants is thus necessary to fill the gap between the correlative findings of GWAS and the development of therapeutic strategies. By integrating large-scale multi-omics datasets such as the Cancer Genome Atlas (TCGA) and the Encyclopedia of DNA Elements (ENCODE), we performed multivariate linear regression analysis of expression quantitative trait loci, sequence permutation test of transcription factor binding perturbation, and modeling of three-dimensional chromatin interactions to analyze the potential molecular functions of 2,813 single nucleotide variants in 93 genomic loci associated with estrogen receptor-positive breast cancer. To facilitate rapid progress in functional genomics of breast cancer, we have created “Analysis of Breast Cancer GWAS” (ABC-GWAS), an interactive database of functional annotation of estrogen receptor-positive breast cancer GWAS variants. Our resource includes expression quantitative trait loci, long-range chromatin interaction predictions, and transcription factor binding motif analyses to prioritize putative target genes, causal variants, and transcription factors. An embedded genome browser also facilitates convenient visualization of the GWAS loci in genomic and epigenomic context. ABC-GWAS provides an interactive visual summary of comprehensive functional characterization of estrogen receptor-positive breast cancer variants. The web resource will be useful to both computational and experimental biologists who wish to generate and test their hypotheses regarding the genetic susceptibility, etiology, and carcinogenesis of breast cancer. ABC-GWAS can also be used as a user-friendly educational resource for teaching functional genomics. ABC-GWAS is available at http://education.knoweng.org/abc-gwas/.

The subject of the article's research is the model and technology of information support for the medical diagnostic and treatment center (MDTC). The goal is to reduce costs and the time to organize the work a medical diagnostic and treatment center by applying and developed models and an information system. The following problems were solved in the paper: to conduct an analytical review of existing integrated medical information systems; to develop a model for the functioning of the MDTC; to develop software for the subsystem of information support for the MDTC functioning, including the local drug formulary. Methods of the theory of algorithms, automaton models and technologies for software applications development were used to solve these problems. The following results were obtained. Existing medical systems that allow automating the business processes of medical institutions are analyzed, their advantages and disadvantages are designated. The functional subsystems of the MDTC that automate the functions of the departments of a medical institution are designated. Automation models and expressions of the algebra of relationships have been obtained for the main departments of the MDTC, that allow to present in a formalized form the process of a medical institution functioning. The model of the functioning of the MDTC is formed on the basis of the theory of automate and an expression of the algebra of relations is obtained that describes in a formalized form the work of the medical center. The structure of the software system for information support of the MDTC is proposed. The navigation system of the web-resource of MDTC was developed. A use-case diagram was developed showing the functionality of the main categories of users. Conclusions: the information support of the MDTC will reduce the time for patient care due to the organized sequence of actions of department staff and reduce the risk of errors in diagnosis due to mathematical and statistical processing of the results of the diagnostics. A drug formulary was developed, which allows the patient to receive recommendations on the use of drugs based on the entered search parameters.

Pathogenic microorganism analysis based on next-generation sequencing technology is an important tool for clinical diagnosis, public health surveillance, and outbreak investigation. However, scientific researchers without the relevant background lack the time, training, or infrastructure to use large data sets or install and use command line tools. Therefore, the bioinformatic team at the Chinese Center for Disease Control and Prevention developed the Microbial Data Analysis Cloud Platform (MDACP) as a safe, professional, and efficient pathogen genetic data analysis platform for rapid microbial data mining, such as for candidate pathogen detection, genome typing, and traceability. MDACP is a web service system based on the Docker platform and can be used for data analysis on various operating systems. The platform focuses on pathogen analysis and continuously develops new analysis processes according to the analysis needs of the users. This platform has a friendly user interface and is easy to operate, allowing users to submit data through data pages or graphical clients, flexibly control parameters according to data conditions, and analyze data in parallel with multiple tasks. Researchers can quickly carry out bioinformatic analyses without coding work, promote follow-up research and information mining of projects, and improve the utilization of big data in the field of disease control. MDACP enables research personnel to conduct data analysis and management and assists clinicians and disease control personnel with mining information, such as pathogen identification, classification, and traceability. [ABSTRACT FROM AUTHOR]

Over the past decade, hundreds of genome-wide association studies (GWAS) have implicated genetic variants in various diseases, including cancer. However, only a few of these variants have been functionally characterized to date, mainly because the majority of the variants reside in non-coding regions of the human genome with unknown function. A comprehensive functional annotation of the candidate variants is thus necessary to fill the gap between the correlative findings of GWAS and the development of therapeutic strategies. By integrating large-scale multi-omics datasets such as the Cancer Genome Atlas (TCGA) and the Encyclopedia of DNA Elements (ENCODE), we performed multivariate linear regression analysis of expression quantitative trait loci, sequence permutation test of transcription factor binding perturbation, and modeling of three-dimensional chromatin interactions to analyze the potential molecular functions of 2,813 single nucleotide variants in 93 genomic loci associated with estrogen receptor-positive breast cancer. To facilitate rapid progress in functional genomics of breast cancer, we have created "Analysis of Breast Cancer GWAS" (ABC-GWAS), an interactive database of functional annotation of estrogen receptor-positive breast cancer GWAS variants. Our resource includes expression quantitative trait loci, long-range chromatin interaction predictions, and transcription factor binding motif analyses to prioritize putative target genes, causal variants, and transcription factors. An embedded genome browser also facilitates convenient visualization of the GWAS loci in genomic and epigenomic context. ABC-GWAS provides an interactive visual summary of comprehensive functional characterization of estrogen receptor-positive breast cancer variants. The web resource will be useful to both computational and experimental biologists who wish to generate and test their hypotheses regarding the genetic susceptibility, etiology, and carcinogenesis of breast cancer. ABC-GWAS can also be used as a user-friendly educational resource for teaching functional genomics. ABC-GWAS is available at http://education.knoweng.org/abc-gwas/. [ABSTRACT FROM AUTHOR]

The problem of incorrect and outdated interpretation of the library activity, as well as its positioning in the modern world, is considered. Compiled information model of the future of software, that is the goal and the means by which the system can operate for achieving this goal and that is demanding these features, so they can be used. According to the results of the research, in order to systematize the modern view of the library, it was decided to implement the Library 3.0 standard, which, in turn, is responsible for modernizing the form of library services using such technologies as semantic network, cloud services, mobile devices, in the scientific- technical library. Library 3.0 is the standard that is responsible for the electronic systematization of services that ensure the life of the academic library through communication between departments and the user. At the moment, this is the most exciting achievement in the research and development of higher education libraries, as the standard presented emphasizes context, not just the means of providing information services. A thorough analysis was carried out on the basis of existing methodologies and approaches to create the conceptual model of the project, basic principles and principles of software development, auxiliary parameters and tools for achieving the desired result, analytical data. A web resource was developed to present the Library of Science and Technology ONAHT on Library 3.0 principles, taking into account the latest Web 2.0 capabilities. [ABSTRACT FROM AUTHOR]

For far too many years we have been unable to fulfill re- quests for a current biographical reference on African American Kentuckians. In response, two librarians, Reinette Jones and Rob Aken, created Notable Kentucky African Americans , a continuously updated online reference source that is tailored to the profiles of African Americans in and from Kentucky. [ABSTRACT FROM AUTHOR]

The aim of the research. The aim of the research is to analyze objects of the marketing Internet environment, systematize and classify elements of the communication process. Research results. The article presents analysis of the main problems of marketing online communications classification. Some of them are as follows: traditional scientific and methodological approaches disregard Internet as a media resource; development of software technology and technical means of product promotion via the Internet occurs on practice prior to theoretic and methodological basis, which requires considerable time; new means and technologies of communicative impact on the target audience. Different approaches to classification of marketing online communications were analyzed. Along with traditional tools of marketing online communications (Internet Advertising, Online PR, sales promotion, direct marketing) the researchers define interactive sales, searching optimization and virtual communities, e-mail advertising, electronic bulletin boards (BBS), context (searching) advertising, media (banner) advertising, rich media, lead generation, websites sponsorship, targeting, search engine marketing (SEM), social networking optimization, social media marketing, viral internet marketing, direct Internet marketing etc. The authors defined the place of marketing online communications in the company’s communication system and proposed their own approach to their classification. The system of marketing online communications was proposed to be considered as a complex of traditional instruments that differ in means and technologies of influence: Internet advertising (media, banner, contextual, background, video, static, etc.); Public Relations (PR) («good works» on behalf of the organization or individual manager’s PR, promotional YouTube videos, etc.); sales promotions (discounts while on-line orders, discount coupons, bonuses, volume discounts, etc.); personal sales (online sales, personal communication via chats or Skype and Viber, on-line sales consultation); direct marketing (mailing list, social networks personal pages appeal etc.). Communicative Internet technologies were meant to be communication software techniques of creation of communicative messages, informational resources support and transmitting this information to target consumers on the Internet. Internet communications tools were offered to be viewed as materialized online means used to transmit communicative information to the consumer by means of Internet technologies. More over, a website was proposed to be considered as the only means of communication on the Internet, but the information (communicative message) can be presented online in various forms, hence the need to distinguish various means of Internet communications occurs: electronic media, banners, portals, Rich media, blogs, forums search engines, message boards, e-mail, articles, video blocks, files, cookies, personal pages, virtual communities and so on. Conclusions and further research. Effective use of tools of marketing online communication complex is plausible only regarding their features, understanding the technology of their impact on the target consumer – an Internet user. Such internet environment offers great opportunities for successful operation in various business (B2B and B2C). Results can form the basis of methodological approaches to selection and assessment of the effectiveness of marketing online communications, and also selection of appropriate strategies since traditional scientific and methodological approaches disregard Internet as a media resource

KnowPulse (https://knowpulse.usask.ca) is a breeder-focused web portal for pulse breeders and geneticists. With a focus on diversity data, KnowPulse provides information on genetic markers, sequence variants, phenotypic traits and germplasm for chickpea, common bean, field pea, faba bean, and lentil. Genotypic data is accessible through the genotype matrix tool, displayed as a marker-by-germplasm table of genotype calls specific to germplasm chosen by the researcher. It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data. These plots are accessible through trait, germplasm, and experiment pages, as well as through a single page search tool. KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations. KnowPulse is constantly evolving with data and tools added as they become available. Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.

The social web interactions have extended the sharing and the growth of web resources on the web. The collaborative web services (folksonomies) enable users to assign their freely chosen keywords (tags) to describe web resources. The advent of folksonomy has evolved the role of web users from consumers to contributors of information. Thus, users attribute their descriptive tags to annotate, organize and classify web resources of interests. Folksonomy became popular with the emergence of collaborative tagging. It offers a practical classification of web resources via the attributed tags. Nonetheless, the freely chosen tags weaken the semantic description of web resources. Folksonomy can give rise to a poor classification system based on ambiguous and inconsistent tags. Therefore, it is essential to pertinently describe the semantic of web resources to enhance their classification, findability and discoverability. The proposed approach represents a combined semantic enrichment strategy that explores collaborative tagging towards describing each web resource using different types of descriptive metadata, namely relevant folksonomy tags, content-based main keywords and matching ontology terms. The experimental evaluation has shown relevant results attesting the efficiency of our proposal. The alignment of social tagging with the ontology will not only enhances the classification of web resources but also constructs their semantic clustering. This emergent semantic will establish new challenges to improve the context-aware recommender systems of web resources in different real-world applications (healthcare, social education and cultural heritage). [ABSTRACT FROM AUTHOR]

PhyreRisk is an open-access, publicly accessible web application for interactively bridging genomic, proteomic and structural data facilitating the mapping of human variants onto protein structures. A major advance over other tools for sequence-structure variant mapping is that PhyreRisk provides information on 20,214 human canonical proteins and an additional 22,271 alternative protein sequences (isoforms). Specifically, PhyreRisk provides structural coverage (partial or complete) for 70% (14,035 of 20,214 canonical proteins) of the human proteome, by storing 18,874 experimental structures and 84,818 pre-built models of canonical proteins and their isoforms generated using our in house Phyre2. PhyreRisk reports 55,732 experimentally, multi-validated protein interactions from IntAct and 24,260 experimental structures of protein complexes. Another major feature of PhyreRisk is that, rather than presenting a limited set of precomputed variant-structure mapping of known genetic variants, it allows the user to explore novel variants using, as input, genomic coordinates formats (Ensembl, VCF, reference SNP ID and HGVS notations) and Human Build GRCh37 and GRCh38. PhyreRisk also supports mapping variants using amino acid coordinates and searching for genes or proteins of interest. PhyreRisk is designed to empower researchers to translate genetic data into protein structural information, thereby providing a more comprehensive appreciation of the functional impact of variants. PhyreRisk is freely available at http://phyrerisk.bc.ic.ac.uk Unlabelled Image • PhyreRisk is a web application that facilitates mapping of human variants onto protein structures. • PDB and predicted structures are provided for both canonical and isoform proteins. • Genetic variants can be mapped from genomic and proteomic coordinates. • PhyreRisk provides total or partial coverage for 70% of human proteins. [ABSTRACT FROM AUTHOR]

The purpose of the research is to analyze the information resources of the Internet and their division into the categories to ensure further use in the study of phenomena of historical and cultural sphere. The methods of the research are based on the application of general scientific and special methods of cognition, in particular, analysis and synthesis, historical-comparative, retrospective, comparative, terminological analysis and analytical monitoring of global information services. The scientific novelty of the paper lies in the analysis of the Internet information resources for the documentation of historical and historical-cultural processes in Ukraine and in the world. It has made it possible to state that the Internet, as a new information environment, where the main directions of development of domestic resources are being worked out, should become a modern source base for the researchers in the humanitarian field. Conclusions. As a result of the study, it has been proved that the Internet has become a real informational environment for studying the phenomena of cultural history. It has been emphasized that the state of resources from national history and cultural history requires serious analysis and should become a full-value source for scientists. Information resources of the Internet are a convenient environment for representing and generating relevant documents. It has been proved that it is the most convenient to consider the whole complex of information resources not only depending on the form of presentation of historical material on the Internet, but also from the stage of research. With each stage of the research (collection of information on the topic, working with sources and literature, analysis of materials and testing of results), the types of resources involved have been correlated. It has been revealed that among the documentation services, Wikipedia plays a key role today. The influence and significance of Wikipedia on social processes in the field of history and cultural history have been evaluated in the paper. The emphasis has been placed on the fact that archival resources on the Internet are gaining special importance today, and especially their forms such as databases with a search engine, electronic directories of various genres and types - guides, fund and subject directories, etc., and digital images of documents. [ABSTRACT FROM AUTHOR]

Mathematical models of the efficiency dynamics of information web resources are considered in this paper. The application of interval discrete models in the form of difference equations is substantiated and the approach to estimation of the model parameters is proposed. The proposed approach is based on the artificial bee colony algorithm (ABCA). A number of experimental studies have been carried out based on data on the functioning of web resources related to environmental monitoring services. The indicator of an information web resource user’s activity has been investigated. Three cases of model building in the form of difference equations as interval discrete models (IDM) have been considered. They vary in the general kind of expression. As a result of the computational experiments, it is shown that the adequacy of a model depends on the expression of the difference equation. In the case of its incorrect choice, the proposed method of parameters’ identification may be ineffective. The obtained interval discrete model in the difference equation form, which describes the efficiency of a web resource, makes it possible to optimize business processes in an organization that uses this web resource, as well as optimally allocate organizational resources and the workload of employees of the administrative service center. Based on the conducted experiments, the efficiency of the proposed model’s application is confirmed.

The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) – a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.