There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures ...from fitting these two methods in human cancer can be found online, in the Catalogue Of Somatic Mutations In Cancer (COSMIC) website or a GitHub repository. The two frameworks make differing assumptions regarding independence of base pairs and for that reason may produce different results. Consequently, there is a need to compare and contrast the results of the two methods, but no such tool currently exists. In this paper, we provide a simple and intuitive interface that allows comparisons of pairs of mutational signatures to be easily performed. Cosine similarity measures the extent of signature similarity. To compare mutational signatures of different formats, one signature type (COSMIC or
pmsignature) is converted to the format of the other before the signatures are compared.
iMutSig provides a simple and user-friendly web application allowing researchers to download published mutational signatures of either type and to compare signatures from COSMIC to those from
pmsignature, and vice versa. Furthermore,
iMutSig allows users to input a self-defined mutational signature and examine its similarity to published signatures from both data sources.
iMutSig is accessible
online and source code is available for download from
GitHub.
Digital Twins are becoming fundamental tools to monitor the status of entities, predict their future evolution and simulate alternative scenarios to understand the impact of possible changes for ...planning and design. More recently, Digital Twin solutions have been applied in the context of Smart Cities. Thanks to the large deployment of sensors, together with the increasing amount of information available for municipalities and governmental organizations, it is possible to build wide virtual reproductions of urban environments including structural data and real-time information that can undoubtfully help decision makers to face future challenges in urban development and improve the citizens' quality of life. In this paper, the Snap4City Smart City Digital Twin framework is presented, which can respond to the requirements identified in recent literature and by international forums. The proposed architecture provides an integrated solution for data gathering, indexing, computing, and information distribution, thus realizing a continuously updated digital twin of the urban environment at global and local scales for monitoring operation and planning. It addresses 3D building models, road networks, Internet of Things entities, points of interest, paths, as well as results from analytical processes for traffic density reconstruction, pollutant dispersion, predictions, and what-if analysis for assessing impact of changes, all integrated into a freely accessible interactive 3D web interface, enabling stakeholder and citizen participation to city decision processes. As case study, the digital twin of the city of Florence (Italy) is presented, including what-if analysis. The solution is released on top of the Snap4City platform as open-source and made available through our GitHub repository ( https://github.com/disit ) and as Docker compose.
Knowledge graph technology has distinct advantages in terms of fault diagnosis. In this study, the control rod drive mechanism (CRDM) of the liquid fuel thorium molten salt reactor (TMSR-LF1) was ...taken as the research object, and a fault diagnosis system was proposed based on knowledge graph. The subject–relation–object triples are defined based on CRDM unstructured data, including design specification, operation and maintenance manual, alarm list, and other forms of expert experience. In this study, we constructed a fault event ontology model to label the entity and relationship involved in the corpus of CRDM fault events. A three-layer robustly optimized bidirectional encoder representation from transformers (RBT3) pre-training approach combined with a text convolutional neural network (TextCNN) was introduced to facilitate the application of the constructed CRDM fault diagnosis graph database for fault query. The RBT3-TextCNN model along with the Jieba tool is proposed for extracting entities and recognizing the fault query intent simultaneously. Experiments on the dataset collected from TMSR-LF1 CRDM fault diagnosis unstructured data demonstrate that this model has the potential to improve the effect of intent recognition and entity extraction. Additionally, a fault alarm monitoring module was developed based on WebSocket protocol to deliver detailed information about the appeared fault to the operator automatically. Furthermore, the Bayesian inference method combined with the variable elimination algorithm was proposed to enable the development of a relatively intelligent and reliable fault diagnosis system. Finally, a CRDM fault diagnosis Web interface integrated with graph data visualization was constructed, making the CRDM fault diagnosis process intuitive and effective.
Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production of biofuels and other valuable chemicals. However, the recalcitrance of this material ...in conjunction with its variability and heterogeneity strongly hampers the economic viability and profitability of biofuel production. To complement both academic and industrial experimental research in the field, we designed an advanced web application that encapsulates our in-house developed complex biophysical model of enzymatic plant cell wall degradation. PREDIG (https://predig.cs.hhu.de/) is a user-friendly, free, and fully open-source web application that allows the user to perform in silico experiments. Specifically, it uses a Gillespie algorithm to run stochastic simulations of the enzymatic saccharification of a lignocellulose microfibril, at the mesoscale, in three dimensions. Such simulations can for instance be used to test the action of distinct enzyme cocktails on the substrate. Additionally, PREDIG can fit the model parameters to uploaded experimental time-course data, thereby returning values that are intrinsically difficult to measure experimentally. This gives the user the possibility to learn which factors quantitatively explain the recalcitrance to saccharification of their specific biomass material.
Web site usability is a critical metric for assessing the quality of a firm's Web presence. A measure of usability must not only provide a global rating for a specific Web site, ideally it should ...also illuminate specific strengths and weaknesses associated with site design. In this paper, we describe a heuristic evaluation procedure for examining the usability of Web sites. The procedure utilizes a comprehensive set of usability guidelines developed by Microsoft.
We present the categories and subcategories comprising these guidelines, and 7discuss the development of an instrument that operationalizes the measurement of usability. The proposed instrument was tested in a heuristic evaluation study where 1,475 users rated multiple Web sites from four different industry sectors: airlines, online bookstores, automobile manufacturers, and car rental agencies. To enhance the external validity of the study, users were asked to assume the role of a consumer or an investor when assessing usability. Empirical results suggest that the evaluation procedure, the instrument, as well as the usability metric exhibit good properties. Implications of the findings for researchers, for Web site designers, and for heuristic evaluation methods in usability testing are offered.
The diffuse nature of nonpoint source (NPS) pollution as well as that of the effectiveness of best management practices (BMP) to control NPS pollution necessitates BMP evaluation at the field scale. ...In this study, a web interface was developed for application of the Agricultural Policy Environmental eXtender (APEX) model at the field scale. The interface contains background databases for field location, soil, agricultural management and climate across the contiguous United States. Users can specify properties to run the model for an individual field and compare the results under various land management and conservation practice choices. A case study was conducted to demonstrate the capability of the web interface for simulating various land management scenarios. This tool can help provide on-site information for NPS pollution management related policies and serve as a communication tool among scientists, engineers, and stakeholders.
•An efficient web-interface for the APEX model was developed.•Databases for model inputs and management operations can be systematically prepared.•Multiple modeling outputs can be visibly demonstrated through the interface.•Evaluation of hydrologic and water quality processes can be conducted efficiently.
Information and communication technology plays essential role for people’s day-to-day business activities. People receive most of their knowledge by processing, recording and transferring necessary ...information through surfing Internet websites. Internet as an essential part of information technology (IT) has grown remarkably. Nowadays, there have been significant amount of efforts in Iran for developing e-commerce. This paper studies the effects of environmental internet features on internet purchase intention. The study divides internet environment into demographic and technologic parts and, for studying each of them, many features are investigated such as internet connection speed, connectivity model, web browser, type of payments, user’s income, user’s education, user’s gender, frequency of online usage per week and users’ goal for using internet. Using Logistic regression technique, the study has determined a meaningful effects of income, education, connection type, browser and goal on consumers’ behavior.
Abstract
Background
Literature about SARS-CoV-2 widely discusses the effects of variations that have spread in the past 3 years. Such information is dispersed in the texts of several research ...articles, hindering the possibility of practically integrating it with related datasets (e.g., millions of SARS-CoV-2 sequences available to the community). We aim to fill this gap, by mining literature abstracts to extract—for each variant/mutation—its related effects (in epidemiological, immunological, clinical, or viral kinetics terms) with labeled higher/lower levels in relation to the nonmutated virus.
Results
The proposed framework comprises (i) the provisioning of abstracts from a COVID-19–related big data corpus (CORD-19) and (ii) the identification of mutation/variant effects in abstracts using a GPT2-based prediction model. The above techniques enable the prediction of mutations/variants with their effects and levels in 2 distinct scenarios: (i) the batch annotation of the most relevant CORD-19 abstracts and (ii) the on-demand annotation of any user-selected CORD-19 abstract through the CoVEffect web application (http://gmql.eu/coveffect), which assists expert users with semiautomated data labeling. On the interface, users can inspect the predictions and correct them; user inputs can then extend the training dataset used by the prediction model. Our prototype model was trained through a carefully designed process, using a minimal and highly diversified pool of samples.
Conclusions
The CoVEffect interface serves for the assisted annotation of abstracts, allowing the download of curated datasets for further use in data integration or analysis pipelines. The overall framework can be adapted to resolve similar unstructured-to-structured text translation tasks, which are typical of biomedical domains.
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