Academic Users Research Articles

GVAF: generalized, flexible filtering software for annotated variant files.

In the rapidly advancing field of genomics, many tools have been developed to interpret genetic variants using next-generation sequencing (NGS) data. However, these tools often produce annotated variant files in different formats, which require specific software or programming skills to filter and analyze. To provide a filtering tool that can be used with diverse variant annotation tools without requiring specific software or programming skills. We developed Germline Variant Annotation and Filtering (GVAF), a command-line software tool that can handle annotated variant files in any table-shaped format. GVAF offers powerful filtering operations without the need for additional software or programming expertise. Built on the Java framework and bash scripts, it provides extensive features, including flexible filtering rules, recognition of genotype-related fields from variant call format (VCF) files, and customizable result generation. GVAF also integrates easily into existing data analysis pipelines. Compared to other tools, GVAF offers a broader range of functionalities, making it more flexible and intuitive for managing annotated variant files. This GVAF software and online manual is publicly available at https://www.sysbiolab.org/gvaf for academic users and is designed to streamline the variant interpretation process, aiding researchers in producing meaningful results.

AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function.

The rapid expansion of biological sequence databases due to high-throughput genomic and proteomic sequencing methods has left a considerable number of identified protein sequences with unclear or incomplete functional annotations. Domains of unknown function (DUFs) are protein domains that lack functional annotations but are present in numerous proteins. To address the challenge of finding functional annotations for DUFs, we have developed a computational method that efficiently identifies and annotates these enigmatic protein domains by utilizing the position-specific iterative basic local alignment search tool (PSI-BLAST) and data mining techniques. Our pipeline identifies putative potential functionalities of DUFs, thereby decreasing the gap between known sequences and functions. The tool can also take user input sequences to annotate. We executed our pipeline on 5111 unique DUF sequences obtained from Pfam, resulting in putative annotations for 2007 of these. These annotations were subsequently incorporated into a comprehensive database and interfaced with a web-based server named "AnnoDUF". AnnoDUF is freely accessible to both academic and industrial users, via the World Wide Web at the link http://bts.ibab.ac.in/annoduf.php. All scripts used in this study are uploaded to the GitHub repository, and these can be accessed from https://github.com/BioToolSuite/AnnoDUF.

Towards achieving a sustainable academic library: Users' awareness and perceptions in a developing country

This study aims to ascertain how academic library users perceive the conversion of their library into a sustainable one and how aware they are of library sustainability. A structured questionnaire was utilized to collect data from users of a central public university library in Bangladesh using a quantitative approach. Results revealed that though the majority of users were aware of the sustainable library concept, they did not believe their library was sustainable. However, they expressed a desire to learn more and actively participate in eco-friendly activities at the library. The majority of users believed that the library would have an eco-friendly and healthy indoor and outdoor environment if such a renovation were to occur. Technological obstacles were the major barriers to such transformation identified by the users. Finally, the study provides recommendations for addressing the issues raised and promoting a long-term, user-friendly atmosphere for academic libraries in Bangladesh.

In the realm of the databases: how academic users navigate the e-resourciverse

In the realm of the databases: how academic users navigate the e-resourciverse

A method of identifying domain-specific academic user information needs based on academic Q&A communities

PurposeTo address the shortcomings of existing academic user information needs identification methods, such as low efficiency and high subjectivity, this study aims to propose an automated method of identifying online academic user information needs.Design/methodology/approachThis study’s method consists of two main parts: the first is the automatic classification of academic user information needs based on the bidirectional encoder representations from transformers (BERT) model. The second is the key content extraction of academic user information needs based on the improved MDERank key phrase extraction (KPE) algorithm. Finally, the applicability and effectiveness of the method are verified by an example of identifying the information needs of academic users in the field of materials science.FindingsExperimental results show that the BERT-based information needs classification model achieved the highest weighted average F1 score of 91.61%. The improved MDERank KPE algorithm achieves the highest F1 score of 61%. The empirical analysis results reveal that the information needs of the categories “methods,” “experimental phenomena” and “experimental materials” are relatively high in the materials science field.Originality/valueThis study provides a solution for automated identification of academic user information needs. It helps online academic resource platforms to better understand their users’ information needs, which in turn facilitates the platform’s academic resource organization and services.

Design and simulation of district heating networks: A review of modeling approaches and tools

District heating (DH) systems have been identified as an important component in efforts to mitigate greenhouse gas emissions and achieve climate targets in the near future. Software tools for analyzing these systems use different modeling approaches, making it challenging for practitioners to choose the most suitable tool based on specific use case requirements. This paper systematically reviews available DH network modeling and simulation tools, comparing their modeling approaches, application scope, and functional capabilities. An online survey was conducted among DH tool developers and experts to assess the technical evaluation criteria for these tools. First, the basic concepts and principles of DH networks modeling are discussed. Moreover, it provides an overview of DH network mathematical models, and discusses various numerical methods used for simulation and analysis, while highlighting potential areas for further research and tools development. The aim of this paper is to support academic and industrial users in selecting appropriate modeling approaches, tools, and libraries.

Biopharmaceutical beamline TLS 15A1 for macromolecular crystallography at the National Synchrotron Radiation Research Center

AbstractSynchrotron protein crystallography (PX) remains an indispensable tool for uncovering the atomic structures of biomolecules. TLS 15A1, operated by the protein diffraction group of NSRRC, has been accessible to both academic and industrial users since January 2013. This beamline is energy‐tunable within a range between 5.6 and 15.5 keV, which is suitable for phasing experiments. Over the past 11 years, TLS 15A1 has supported 657 projects and facilitated 1523 experiments across 41,656 h of beamtime. This article describes the beamline layout, studies of factors influencing data quality, and significant scientific contributions.

Effect of Induction and Blade Elasticity Modelling on Wind Turbine Rotor Performance Predictions

This study investigates the impact of blade induction modelling on the accuracy of wind turbine rotor aeroelastic predictions. It extends the capabilities of AEOLIAN (AErOeLastic sImulAtioN), a Fluid Structure Interaction (FSI) solver based on Blade Element Momentum Theory (BEMT) coupled with a Lumped Mass approach to represent the blade structure. Herein, AEOLIAN’s analytical wake induction engineering model is replaced with the outcomes of a physically-consistent three-dimensional Free-Vortex Wake (FVW) formulation initially employed in AeroROTOR. This versatile aeroelastic simulation tool is implemented within the framework of MATLAB Simulink/Simscape-Multibody©, a modular environment suitable for industry analysts, researchers, and academic users focusing on wind turbine aero-servo-elastic applications. Furthermore, it serves to lay the groundwork for the development of advanced control laws for multi-megawatt rotors, fostering innovation in the design and optimization of the next-generation wind turbines. The presented analyses focus on predicting the aeroelastic behavior of the bottom-fixed NREL 5MW rotor in uniform axial flow over the operating range, complemented by more detailed investigations at the rated condition undergoing inflow with/without wind misalignment (yaw). The study on key performance parameters is conducted by comparing with the higher-fidelity data from available Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD) coupled with CFD.

Suitable forestry machines for mechanical fuel load reduction and salvage recovery: a short review

Forest fires are one of the most severe incidents that can destroy large areas of forest lands and cause substantial damages to the nearby residential areas and farmlands. Human efforts to reduce the likelihood of starting forest fires include prescribed burning, mechanical fuel load reduction and livestock grazing. Following natural disasters in forest areas, a salvage recovery operation is usually conducted that may cause some environmental impacts. This article aimed to review the literatures to provide a summary of different types of machines and working methods that have been studied in different countries. The review results showed that the most common method for mechanical fuel load reduction was mechanised cut-to-length using a harvester and a forwarder. This method has been widely applied in Canada, USA, Europe, and Oceania. In some countries (e.g. Australia and USA) the whole tree method is also applied for mechanical fuel load reduction. This method was often conducted using feller-bunchers, grapple skidders and chippers/grinders. The majority of mechanical fuel load reduction projects produced the extra fibre which could be used for bioenergy purposes. The number of salvage recovery studies was limited compared with studies on mechanical fuel load reduction. Salvage recovery operations applied a cut-to-length and whole tree harvesting methods. Windthrown trees were extracted to the roadside using heavy size forwarders or grapple skidders in flat/moderate terrains while tower yarders were applied in steep terrains. Detailed information on work productivity is described in this article which can be of use to the academic and industrial users. 

FL-Online: An x-ray crystallographic web-server for atomic-scale structure analysis of biomolecule

Abstract FL-Online (http://fanlab.ac.cn) is an out-of-box modern web service featuring a user-friendly interface and simplified parameters, providing academic users with access to a series of online programs for biomolecular crystallography, including SAPI-online, OASIS-online, C-IPCAS-online and a series of upcoming software releases. Meanwhile, it is a highly scalable and maintainable web application framework that provides a powerful and flexible solution for academic web development needs. All the codes are open-source under MIT licenses in GitHub.

Cartographic Resources for Equitable University–Community Interaction in Slum Areas

Cartographic resources play a crucial role in facilitating communication across various sectors, including research projects focused on low-income communities. Despite this, some researchers still adhere to colonialist and exploitative approaches. This study aims to promote equitable university–community interaction though cartographic resources, aid academic and vulnerable community users in choosing a better platform for their work, and provide insights to developers for improving the platforms to better serve the user profiles of community members. To achieve this, we examined the use of cartographic resources in five projects within low-income communities (commonly referred to as favelas or so-called “slums”) in three Brazilian cities, all guided by equitable principles. The study unfolds in four stages: (i) data collection from documents and interviews; (ii) systematization into seven analytical categories—cartographic resources, data, personnel, processes, equipment, general objectives, and specific objectives; (iii) analysis of eight cartographic resources; and (iv) a critical examination of the outcomes. The synthesis of the collected information identified 65 characteristics/demands, with 17 common to all projects, including vector feature creation, thematic map design, printed map usage, and satellite imagery. We also identified 53 geographic information system (GIS) functionalities required for the projects, predominantly related to vector data generation and editing. The outcomes demonstrate the benefits of project methodologies, contributing to a decolonial university–community praxis. Additionally, they underscore the potential of digital cartographic resources, functioning not solely as data collection tools but also as powerful instruments that empower slum residents to advocate for improvements and foster local development.

Designing an Academic Website User Interface Using the Design Thinking Method

As an educational institution, Telkom University Surabaya (TUS) has academic-related information media that applies to students in the form of academic websites. However, the presentation and management of information regarding academic business processes through the official TUS academic website still has several obstacles. The website has not been managed in a structured manner and is able to provide an easy-to-use experience for users in accessing information. Therefore, this study aims to improve the business process of the TUS academic website to be more informative, structured, and have a modern and user-friendly user interface (UI / UX) design. The research method used is based on a user-centered design approach using design thinking. Design Thinking is a method with an iterative approach that identifies problems and needs of users, with the aim of creating designs that can understand and provide innovative solutions for users. The final result of this research is to create an interface that is easy to understand, responsive, and reflects the characteristics of Telkom University Surabaya (TUS).

Gameful interaction: How principles of game design can be applied to enhance user experiences in non-game applications

In the era of digital transformation, the integration of game design and interaction design has become an important trend, and its scope of application has gone beyond purely entertaining applications. This thesis investigates the principles of gamified interaction with a focus on how game design elements can be utilized to enhance the user experience in non-game applications. The research objective of this thesis is to investigate the effectiveness and limitations of gamification design in a variety of contexts when incorporating it into educational, business, health, and other types of applications. The study employs a mixed research methodology, which includes analysis and comparison of the literature, as well as a specific case study of the Chinese fitness app "Keep" to demonstrate real-world applications. The data for this study came from existing academic papers, app analysis, user feedback and design evaluation. This thesis finds that gamified interactions have a significant impact on user engagement and motivation, providing valuable insights for designers to create more engaging digital environments.

Conceptualisation of Open Educational Resources, Audiovisual Resources and Electronic Information Resources: A Literature-based Study of Selected Academic Libraries in Ebonyi State Nigeria

Teaching, learning and research at every level of the education system cannot be successful without appropriate resources. Adequate, quality resources are not readily available, especially in resource-constrained countries like Nigeria. These resources come in various formats (physically and/or electronically). Audiovisual resources (AVRs), electronic information resources (EIRs) and open educational resources (OERs) are examples of teaching and learning materials that could be procured by educational institutions and accessed by students and other members of the academic community. The instrument for data collection was a literature review directed to the librarians of the selected university libraries. The educational resources—in terms of availability and usage—were presented in tables comparatively. Findings show that each of the three university libraries has certain types of AVR, EIR and OER, which are available for students’ use. Strategies for the effective use of these educational resources in Nigeria’s academic libraries were discussed. It is recommended that adequate learning facilities, other than books, be provided by the government or private individual owners of the academic libraries in Ebonyi State, Nigeria. There is also a need for academic librarians and users to keep themselves abreast of the skills necessary for the appropriate use of educational resources (subscription or free-based) in the institutions where they are available.

The findings of the marketing analysis academic library’s services

The author accomplished the marketing analysis of academic library services as the case study of Cherepovets State University Library, a flagship university of Vologda Region. She characterizes the status of library services, strengths and weaknesses, opportunities and threats, challenges and expectations of modern library users. The novelty of the article lies in the use of marketing analysis tools and the results obtained. The practical value of library services for users is revealed. With four criteria, namely demographic, geographic, psychographic and behavioral, the target user of university library services is characterized in detail. The author applies the research methods of analysis, comparison, observation, Google survey, in-depth interview, and empathy mapping. Four levels of university library services aree analyzed based on the “service pyramid”. The quantitative findings of marketing research are provided. The author demonstrates that despite most students prefer electronic communications, they do not ignore the hybrid, online and offline, mode of interaction with the library. She also shows that modern academic library users are emotionally neutral towards the library services. Recommendations are offered for the further development of academic library services.

FROM ACADEMIA TO ANECDOTES: ASSESSING THE QUALITY OF ULCERATIVE COLITIS CONTENT ON YOUTUBE

Abstract INTRODUCTION This study examines the varying impact of YouTube videos on Ulcerative Colitis (UC) from academic and private institutions. While academic channels offer evidence-based, scientifically vetted information, private sources may lack rigorous scrutiny and sometimes prioritize commercial or anecdotal content. With YouTube's massive user base, the absence of an editorial process can result in misinformation. This content quality and credibility discrepancy can significantly affect patient education and treatment outcomes for UC. METHODS We conducted a search on YouTube using the keywords "Ulcerative Colitis" and "UC IBD" to identify relevant videos. Exclusions were made for videos that were not in English, irrelevant, or lacked audio. We documented various video attributes such as views, likes, dislikes, comments, and the nature of the source (academic or private). The videos were then classified as reliable or unreliable based on the scientific accuracy of their content. We employed DISCERN, Global Quality Score (GQS), and the Patient Education Materials Assessment Tool (PEMAT) to evaluate video quality. The consistency among seven investigators in applying DISCERN, GQS, and PEMAT was measured using intraclass correlation. RESULTS We reviewed 21 YouTube videos that appeared in the search results, of which 11 (52.3%) were academic and 10 (47.6%) were private. Academic videos received higher DISCERN scores than private ones (317.5 vs. 23.64 5.07, p=0.018). The Global Quality Score was also higher for academic videos (3.9 vs. 2.2, p< 0.01), as was the PEMAT score (4.1 vs. 2.7, p= 0.022). Furthermore, academic videos were found to have a positive correlation with the number of likes (OR: 0.75, P< 0.001), subscribers (OR:0.68, P< 0.0001), and views (OR:1.52, P< 0.001). CONCLUSION Our study reveals significant quality discrepancies in YouTube videos on Ulcerative Colitis. Academic sources consistently outperformed private ones in accuracy and reliability, as indicated by higher DISCERN, Global Quality Score, and PEMAT ratings. The data also showed a positive correlation between academic sources and user engagement metrics like likes, subscribers, and views. These findings highlight the necessity of directing patients to academically-backed information to minimize the risk of misinformation.

Application of Technology Acceptance Model and Delone and McLean IS Success Model to Measure Information System Design for Academic Activities in Higher Education Institution

The purpose of this study is to investigate the variables that may affect how well the academic information system performs. Quantitative approaches are employed in this study. The basic random sampling technique was used in this study to get samples from the community of academic information system users. There were 100 samples used in this investigation. The Technology Acceptance Model (TAM) and the Delone & Mclean model are used in this study. In this study, questionnaires were distributed as part of the data collection process. The SmartPLS was used in this study's inferential statistical analysis. According to the analysis results, introducing elements that have the biggest impact namely, perceived ease of use and service quality should be prioritized in order to improve helpdesk services in academic information systems. This involves establishing a report ticket function to resolve user complaints and offer updates on problem resolution, as well as optimizing academic information system for mobile displays to promote simple access to various academic information system -related demands. Perceived ease of use on perceived usefulness (path coefficient value: 0.79); service quality on perceived ease of use (path coefficient value: 0.79); user satisfaction on net benefits (path coefficient value: 0.74); and system quality on net benefits (path coefficient value: 0.03), are the variables that have the biggest influence in this research.

Unconstraining Evaluative Conditioning Research by Using the Reverse Correlation Task

In the evaluative conditioning effect, pairing neutral stimuli (conditioned stimuli) with valenced stimuli (unconditioned stimuli) changes the evaluation of the former. We examined this effect with a reverse correlation task that assesses how participants visually remember the conditioned stimuli. Importantly, this measure (1) does not require participants to evaluate stimuli and (2) allows them to capture multiple trait attributions. In a pre-registered experiment with US Prolific Academic users, we observed an evaluative conditioning effect in both an evaluation task and a reverse correlation task. Moreover, the effect in the reverse correlation task went beyond mere changes in valence. Our work opens new empirical and theoretical challenges for future conditioning research.

FRAGSITE2: A structure and fragment-based approach for virtual ligand screening.

Protein function annotation and drug discovery often involve finding small molecule binders. In the early stages of drug discovery, virtual ligand screening (VLS) is frequently applied to identify possible hits before experimental testing. While our recent ligand homology modeling (LHM)-machine learning VLS method FRAGSITE outperformed approaches that combined traditional docking to generate protein-ligand poses and deep learning scoring functions to rank ligands, a more robust approach that could identify a more diverse set of binding ligands is needed. Here, we describe FRAGSITE2 that shows significant improvement on protein targets lacking known small molecule binders and no confident LHM identified template ligands when benchmarked on two commonly used VLS datasets: For both the DUD-E set and DEKOIS2.0 set and ligands having a Tanimoto coefficient (TC) < 0.7 to the template ligands, the 1% enrichment factor (EF1% ) of FRAGSITE2 is significantly better than those for FINDSITEcomb2.0 , an earlier LHM algorithm. For the DUD-E set, FRAGSITE2 also shows better ROC enrichment factor and AUPR (area under the precision-recall curve) than the deep learning DenseFS scoring function. Comparison with the RF-score-VS on the 76 target subset of DEKOIS2.0 and a TC < 0.99 to training DUD-E ligands, FRAGSITE2 has double the EF1% . Its boosted tree regression method provides for more robust performance than a deep learning multiple layer perceptron method. When compared with the pretrained language model for protein target features, FRAGSITE2 also shows much better performance. Thus, FRAGSITE2 is a promising approach that can discover novel hits for protein targets. FRAGSITE2's web service is freely available to academic users at http://sites.gatech.edu/cssb/FRAGSITE2.

Best practice: setting up and operating a mid-sized cryo-EM facility

Ever since the resolution revolution in 2013, cryo-electron microscopy (cryo-EM) has become a powerful methodology in structural biology that is especially suited to study the structure of large flexible molecular complexes. Since then, the need of setting up state-of-the-art cryo-EM facilities around the world has increased tremendously. Access to high-end cryo-EM instrumentation is however expensive and requires expertise. The establishment of large cryo-EM centers worldwide, many of which provide academic users free access for both data collection and user training, has been possible with the support of government agencies across the globe. In addition, many universities, and private institutions like the Van Andel Institute (VAI) have made significant investments to establish their own cryo-EM core facilities, ensuring on-site access to their researchers. This paper aims to serve as a blueprint for establishing a new mid-sized cryo-EM facility, as it provides key information based on our experience at VAI and discusses strategies used to optimize routine operation towards high performance and efficiency for single-particle cryo-EM. Information regarding initial planning, selection of equipment as well as the development of IT solutions that were required to improve data collection and analysis are included. In addition, we present an account of the most common issues affecting operation as well as the needs for maintenance over a 6-year period, which can help interested parties to estimate the long-term costs of running this type of facility. Lastly, a brief discussion on the pros and cons of establishing the facility is also included.