Social media services make it possible for an increasing number of people to express their opinion publicly. In this context, large amounts of hateful comments are published daily. The PHARM project ...aims at monitoring and modeling hate speech against refugees and migrants in Greece, Italy, and Spain. In this direction, a web interface for the creation and the query of a multi-source database containing hate speech-related content is implemented and evaluated. The selected sources include Twitter, YouTube, and Facebook comments and posts, as well as comments and articles from a selected list of websites. The interface allows users to search in the existing database, scrape social media using keywords, annotate records through a dedicated platform and contribute new content to the database. Furthermore, the functionality for hate speech detection and sentiment analysis of texts is provided, making use of novel methods and machine learning models. The interface can be accessed online with a graphical user interface compatible with modern internet browsers. For the evaluation of the interface, a multifactor questionnaire was formulated, targeting to record the users’ opinions about the web interface and the corresponding functionality.
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•The database, the core engine, and the graphical interface of IrrigaSys are described.•Details on its implementation in an irrigation district in southern Portugal are also given.•The major ...strengths and weaknesses are discussed based a 5-years’ support to farmers.
IrrigaSys is a decision support system (DSS) for irrigation water management based on online, open source tools. The aim of this paper is to describe the structure of IrrigaSys and how it is implementation at the plot scale. The DSS includes remote access to local meteorological stations for weather conditions, a meteorological model for weather forecast, the MOHID-Land model for the computation of the soil water balance and irrigation scheduling, and a database for data repository. Despite its complexity, the data necessary to run IrrigaSys is minimal, and include as mandatory input information on the location of field plots, crop type, sowing and harvest dates, soil texture, irrigation method, and daily/weekly applied irrigation depths. Based on this information, the system automatically downloads the weather data from the meteorological station located closest to the agricultural plot, as well as the weather forecast for the seven incoming days. The soil water balance is then computed from sowing to the present date (updating always the system with newly acquired information) as well as the recommended irrigation schedule for the incoming week. Results are made available via a web interface, a mobile app, a SMS, and email. The IrrigaSys further provides the Normalized Difference Vegetation Index (NDVI) computed from the most recent Sentinel-2 imagery available with a resolution of 10 m. The IrrigaSys was developed in close cooperation with the Water Board from the Sorraia Valley irrigation district, southern Portugal, supporting 103 plots of 30 farmers over the last 5 years. This stakeholder has been fundamental for successfully running the system. This paper further discusses the main strengths and limitations of IrrigaSys, with the latter being naturally associated to difficulties in providing reliable estimates for all field plots based on limited data.
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Background:
Hematologic malignancies, such as acute promyelocytic leukemia (APL) and acute myeloid leukemia (AML), are cancers that start in blood-forming tissues and can affect the blood, bone ...marrow, and lymph nodes. They are often caused by genetic and molecular alterations such as mutations and gene expression changes. Alternative polyadenylation (APA) is a post-transcriptional process that regulates gene expression, and dysregulation of APA contributes to hematological malignancies. RNA-sequencing-based bioinformatic methods can identify APA sites and quantify APA usages as molecular indexes to study APA roles in disease development, diagnosis, and treatment. Unfortunately, APA data pre-processing, analysis, and visualization are time-consuming, inconsistent, and laborious. A comprehensive, user-friendly tool will greatly simplify processes for APA feature screening and mining.
Results:
Here, we present APAview, a web-based platform to explore APA features in hematological cancers and perform APA statistical analysis. APAview server runs on Python3 with a Flask framework and a Jinja2 templating engine. For visualization, APAview client is built on Bootstrap and Plotly. Multimodal data, such as APA quantified by QAPA/DaPars, gene expression data, and clinical information, can be uploaded to APAview and analyzed interactively. Correlation, survival, and differential analyses among user-defined groups can be performed via the web interface. Using APAview, we explored APA features in two hematological cancers, APL and AML. APAview can also be applied to other diseases by uploading different experimental data.
Among the livestock species, buffalo remained as an integral part of the Indian rural economy. With the advent of genome sequencing technologies, it became possible to sequence the whole genome of ...Murrah buffalo. Also, significant amount of information on different genomic elements of buffalo is available at National Centre for Biotechnology Information (NCBI). However, the positions of these elements on the genome are not fully known. In addition, the 3D structures of buffalo proteins are not available and also there exist no browser to visualize important genic elements on buffalo genome. Hence, a study was taken up to develop a web-based information system having information on genomic elements, protein 3-D structures and genome browser. Initially, information on nucleotide and protein sequences were retrieved from NCBI and parsed suitably. Later, the protein structures were predicted, validated, refined and stabilized in silico. An Information System on Buffalo Genome (ISBG) with 3-tier architecture was developed containing the sequence and structural information. ISBG contains complete coding sequences (CDS), Mitochondrial DNAs, 1k upstream regions and Untranslated Regions (UTRs) of buffalo genome. The buffalo genes were also mapped onto the genome. The results revealed that maximum number of genes were found distributed on chromosome 4 followed by chromosome 18, which can also be visualized from the developed genome browser. ISBG can be accessed at http://cabgrid.res.in:8080/bgis. The proposed information system helps animal breeders and biotechnologist in animal improvement.
Arrays provide a cost-effective platform for the analysis of human DNA methylation. ShinyÉPICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA ...methylation arrays (450 k and EPIC), from the user's own computer or from a server. This tool covers the analysis entirely, from the raw data input to the final list of differentially methylated positions or regions. Here, we describe the steps of the analysis, the different parameters available, and useful information to understand and select the best options in each step.
This paper introduces details of a new hybrid beam system connected to a reinforced concrete (RC) column. The hybrid beam system is a wide-flange steel beam embedded in RC beams on both ends without ...any shear connectors. The wide-flange steel beam does not penetrate through the beam-column joint, which reduces the fabrication cost compared to the typical steel beam-RC column hybrid system. A total of 10 hybrid beam specimens were designed with a slab-web interface. Four specimens were used to examine the shear sliding capacity at the slab-web interface, and an equivalent coefficient of friction at the interface, together with a method to evaluate the shear sliding capacity, was proposed. The remaining six specimens were used to examine the flexural capacity and plastic deformation capacity of the hybrid beam, and shear-friction reinforcement details required for ductile flexural behavior were proposed. Keywords: coefficient of friction; concrete-to-concrete interface; concrete-to-steel interface; flexural capacity; hybrid beam; shear-friction capacity; shear-friction reinforcement; slab-web interface.
Today, we are living in the realm of Internet of Things (IoT) where simple objects are embedded with the capabilities to understand and operate in its surroundings for offering distinct services to ...the users. These objects are shipped with their user interfaces that facilitate user to perform administrative activities on the devices using a web browser linked to the device's server. Cross-Site Scripting (XSS) is the most prevalent web application's vulnerability, exploited by an attacker to compromise the embedded devices. This research work is focused towards the development of an approach to defend against XSS attack to safeguard embedded devices deployed in intelligent IoT system. It performs identification through comparing injected strings with the blacklisted attack vectors and mitigates its harmful effects by implementing filtering method in an optimized fashion. It is a fog-enabled approach that operates locally to identify the compromised device within the IoT network. We demonstrate attack exploitation on two smart devices including digital IP Camera and wireless router and then tested the performance of our proposed approach on them. The experimental results highlight the efficacy of the approach as it attains an accuracy of 0.9 and above, on both the tested platforms.
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This study developed a computational tool with a graphical interface and a web-service that allows the identification of phage regions through homology search and gene clustering. It uses G+C content ...variation evaluation and tRNA prediction sites as evidence to reinforce the presence of prophages in indeterminate regions. Also, it performs the functional characterization of the prophages regions through data integration of biological databases. The performance of PhageWeb was compared to other available tools (PHASTER, Prophinder, and PhiSpy) using Sensitivity (Sn) and Positive Predictive Value (PPV) tests. As a reference for the tests, more than 80 manually annotated genomes were used. In the PhageWeb analysis, the Sn index was 86.1% and the PPV was approximately 87%, while the second best tool presented Sn and PPV values of 83.3 and 86.5%, respectively. These numbers allowed us to observe a greater precision in the regions identified by PhageWeb while compared to other prediction tools submitted to the same tests. Additionally, PhageWeb was much faster than the other computational alternatives, decreasing the processing time to approximately one-ninth of the time required by the second best software. PhageWeb is freely available at http://computationalbiology.ufpa.br/phageweb.
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