Accessible Platform Research Articles

RetroBioCat Database: A Platform for Collaborative Curation and Automated Meta-Analysis of Biocatalysis Data.

Despite the increasing use of biocatalysis for organic synthesis, there are currently no databases that adequately capture synthetic biotransformations. The lack of a biocatalysis database prevents accelerating biocatalyst characterization efforts from being leveraged to quickly identify candidate enzymes for reactions or cascades, slowing their development. The RetroBioCat Database (available at retrobiocat.com) addresses this gap by capturing information on synthetic biotransformations and providing an analysis platform that allows biocatalysis data to be searched and explored through a range of highly interactive data visualization tools. This database makes it simple to explore available enzymes, their substrate scopes, and how characterized enzymes are related to each other and the wider sequence space. Data entry is facilitated through an openly accessible curation platform, featuring automated tools to accelerate the process. The RetroBioCat Database democratizes biocatalysis knowledge and has the potential to accelerate biocatalytic reaction development, making it a valuable resource for the community.

Photoaffinity labelling displacement assay using multiple recombinant protein domains.

The development and optimisation of a photoaffinity labelling (PAL) displacement assay is presented, where a highly efficient PAL probe was used to report on the relative binding affinities of compounds to specific binding sites in multiple recombinant protein domains in tandem. The N- and C-terminal bromodomains of BRD4 were used as example target proteins. A test set of 264 compounds annotated with activity against the bromodomain and extra-terminal domain (BET) family in ChEMBL were used to benchmark the assay. The pIC50 values obtained from the assay correlated well with orthogonal TR‑FRET data, highlighting the potential of this highly accessible PAL biochemical screening platform.

Improving Collection-Based Biodiversity Research in Chile: Digitisation and Implementation of Web Portals

Biodiversity portals are emerging as some of the most powerful tools for scientific research and management based on scientific collections. We discuss the importance of web portals in biodiversity research and highlight the commendable progress made by two digitisation projects in Chile: herbariodigital.cl and the Atlas of Chilean Biodiversity. The aim of herbariodigital.cl and ALA-Chile is to take advantage of technological advances to improve the digitisation of biodiversity data. Using cutting-edge methods, herbariodigital.cl has successfully digitised an extensive collection of plant specimens and associated data from Chilean herbaria (>25,000 specimens), promoting a more accessible and inclusive platform for researchers, educators and decision-makers. Recognising that the complex nature of biodiversity information requires a careful approach to data storage and organisation to ensure efficient exchange across different platforms, we discuss our experience of using the Darwin Core standard (Darwin Core Task Group 2009), a widely accepted data standard in the field of biodiversity informatics. In turn, we discuss the incongruence that arises from adopting different global taxonomic checklists, such as the GBIF taxonomic backbone (GBIF Secretariat 2022) and World Flora Online (WFO 2023), in addition to a localised community catalogue. Using these different taxonomic frameworks is a significant challenge, as discrepancies and inconsistencies can arise, leading to potential under- or over-estimation of biodiversity indicators. By addressing these challenges, we believe that both herbariodigital.cl and ALA-Chile will prove to be invaluable assets for scientific research, educational initiatives, and environmental monitoring and assessment. The comprehensive digitisation of biodiversity information will make it easier for researchers to conduct interdisciplinary studies and formulate evidence-based conservation strategies. In addition, educators will be able to use these web portals to develop interactive teaching materials, fostering a deeper connection between students and the natural world. Stakeholders in both the public and private sectors can also make informed decisions about biodiversity offsetting. In conclusion, we highlight the transformative impact of web portals in the field of biodiversity research. The remarkable progress made by herbariodigital.cl and ALA-Chile in digitising Chile's biodiversity information is opening up unprecedented opportunities for scientific research, education and environmental management. By overcoming the challenges of data standardisation and taxonomic harmonisation, these projects are paving the way for a more comprehensive and collaborative approach to understanding and conserving Chile's biodiversity.

PlantMetSuite: A User-Friendly Web-Based Tool for Metabolomics Analysis and Visualisation.

The advancement of mass spectrometry technologies has revolutionised plant metabolomics research by enabling the acquisition of raw metabolomics data. However, the identification, analysis, and visualisation of these data require specialised tools. Existing solutions lack a dedicated plant-specific metabolite database and pose usability challenges. To address these limitations, we developed PlantMetSuite, a web-based tool for comprehensive metabolomics analysis and visualisation. PlantMetSuite encompasses interactive bioinformatics tools and databases specifically tailored to plant metabolomics data, facilitating upstream-to-downstream analysis in metabolomics and supporting integrative multi-omics investigations. PlantMetSuite can be accessed directly through a user's browser without the need for installation or programming skills. The tool is freely available and will undergo regular updates and expansions to incorporate additional libraries and newly published metabolomics analysis methods. The tool's significance lies in empowering researchers with an accessible and customisable platform for unlocking plant metabolomics insights.

Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria

BackgroundOxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in the case of metagenome analysis. To take the best advantage of long-read sequencing, DNA extraction methods must be able to isolate pure high molecular weight (HMW) DNA from complex metagenomics samples, without introducing any bias. New methods released on the market, and protocols developed at the research level, were specifically designed for this application and need to be assessed.ResultsIn this study, with different bacterial cocktail mixes, analyzed as pure or spiked in a synthetic fecal matrix, we evaluated the performances of 6 DNA extraction methods using various cells lysis and purification techniques, from quick and easy, to more time-consuming and gentle protocols, including a portable method for on-site application. In addition to the comparison of the quality, quantity and purity of the extracted DNA, the performance obtained when doing Nanopore sequencing on a MinION flow cell was also tested. From the obtained results, the Quick-DNA HMW MagBead Kit (Zymo Research) was selected as producing the best yield of pure HMW DNA. Furthermore, this kit allowed an accurate detection, by Nanopore sequencing, of almost all the bacterial species present in a complex mock community.ConclusionAmongst the 6 tested methods, the Quick-DNA HMW MagBead Kit (Zymo Research) was considered as the most suitable for Nanopore sequencing and would be recommended for bacterial metagenomics studies using this technology.

Quantum-dot cellular automata-based design for three-level nanoscale full-subtractor

• A new approach to full-subtractor circuit design is proposed in this research. • The new design is built with XOR and majority gates, making it both efficient on the gate level and abstract. • This structure is created with a significant reduction in the number of cells and the amount of space used. • The QCADesigner-E tool is used for circuit design and verification, as well as for power analysis. Future digital devices and circuits can be frequently designed using quantum-dot cellular automata (QCA). High density and speed are good matches for QCA. As a result, a full subtractor is well suited for this technology. QCA can be utilized to create the full-subtractor at the nanoscale since it is a specific sort of circuit employed in important applications. A subtractor circuit can be created similarly to an adder circuit in electronics. When utilizing the traditional two's complement notation, subtractors are commonly implemented within a binary adder for a low cost by supplying an addition/subtraction selector to the carry-in and inverting the second operand. In this research, we present a new full-subtractor circuit construction. The XOR and majority gates, which work on the Columbic interaction of cells, are utilized for this purpose. QCADesigner-E is used to model and test the proposed structure's functionality. The full-subtractor architecture provides a platform for easier access to the input and output lines. This design is made using the multi-layer crossover approach and 22 QCA-based cells. The number of cells in the suggested structure has been improved by 31 percent, while the occupied area has been improved by 30 percent.

The Facilitators and Barriers to Digital Health for Managing Nutrition in People With Parkinson's Disease and Their Caregivers: A Formative, Qualitative Study

ObjectiveIdentify techniques to assist in designing digital health platforms for nutrition services for people with Parkinson's disease and caregivers to improve their quality of life. DesignSemistructured, dyadic interviews with 20 dyads (20 people with Parkinson's disease and 20 caregivers). SettingHome visits were conducted in the northeast US. ParticipantsPeople with Parkinson's disease and their caregivers were recruited via email, flyers, news articles and announcements at support groups. Phenomenon of InterestIdentification of facilitators and barriers to using digital health platforms to inform future digital nutrition services. AnalysisInterviews were recorded, transcribed and double-coded using a framework analysis method. ResultsReported digital health platforms utilization facilitators were: knowledge acquisition, convenience, intention to use, socializing, enjoyment, and forced adoption. Barriers included: negative feelings toward technology, lack of access or knowledge, disinterest, product design, frustration and functional reliability, and applying health information. Conclusions and ImplicationsAlthough dyads often lack knowledge on both how to use technology and nutrition, they are willing to use digital health platforms to increase their nutrition knowledge if platforms are convenient. Based on the identified facilitators and barriers, the added benefits of access and training nutrition digital health platforms must be clearly communicated to end-users to improve their quality of life.

Knowledge Sharing as a Central Idea of Open Science and NDT 4.0

NDT 4.0 has become a buzz word in the world of NDT in recent years. At the same time, terms like open science, open access or open peer review cross our ways regularly and define present and future concepts to advance knowledge sharing in society. This article brings the concept of open science and NDT 4.0 together. While knowledge sharing as part of artificial intelligence and the internet of things are often in focus when talking about Industry 4.0 or NDT 4.0, this paper draws on the importance of knowledge sharing between humans as a substantial aspect of Industry 4.0, and more specifically NDT 4.0. Knowledge sharing between humans has especially become relevant with the introduction of the internet and the world wide web (www), but its importance cannot be disregarded in times where everybody is talking about technical developments, machine learning and artificial intelligence. On the contrary, sharing knowledge openly between humans remains central to advancing todays developments and innovation. The NDT community has had the benefit to share, create and exchange knowledge at an early stage of the internet through a unique platform that was established in 1996; NDT.net. After reviewing the concepts of open science and NDT 4.0, this paper illustrates how the NDT community has had the benefit of knowledge sharing since the early days of the internet through the establishment of NDT.net. This open access platform has been playing and continues to play a central role in advancing ideas of open science and NDT 4.0.

PENGEMBANGAN JURNAL ILMIAH ONLINE PADA SEKOLAN TINGGI TEOLOGIA BETHEL MEDAN

This community service aims to document the process of developing an online scientific journal as an effort to expand the impact of academic knowledge from Bethel College of Theology (STT) in Medan. Through a collaborative approach, this research involved faculty members and administrative staff in developing an effective and accessible online scientific journal platform. The development process included needs analysis, interface design, technical development, and pilot testing and evaluation. The outcome of this service was the launch of a scientific journal platform that facilitates publication, peer-review, and knowledge exchange digitally. It is hoped that this initiative will enrich the quality of research and scientific understanding among students, lecturers, as well as the academic community, while making a sustainable contribution to the development of knowledge in the field of theology and religion.

Racial and sex differences in tumor genomics in urothelial carcinoma

PurposeDifferences in bladder cancer outcomes have been demonstrated by sex and race/ethnicity, with studies showing a higher burden of adverse outcomes among women and racially minoritized populations. Despite these epidemiologic differences, populations with disproportionally adverse outcomes are often underrepresented in genomic cohorts. This exclusion impacts the accuracy and generalizability of genomic studies in bladder cancer and has the potential to widen disparities by sex and/or race/ethnicity. Basic ProceduresWe analyzed pooled somatic mutational data from publicly available cohorts in the cBioPortal open access platform. FindingsA total of 796 unique patients were identified. Average age for the cohort was 67 years (range: 25–98 years), 188 (24%) were female, and the majority were White (n = 423, 85% among those who report race). Median total mutation count was 91 (IQR: 20, 202) per patient. We used multivariable logistic regression to independently evaluate the association between race/sex and mutation status in each of 122 genes of interest, identified from TCGA, adjusting for age and bladder cancer invasive status. In adjusted analyses, male sex was associated with increased risk of mutation in ARID1A, CHD6, and NCOR1 compared with female sex. White race was associated with increased risk of mutation in ARID1A, EP300, PIK3CA, and TP53 and decreased risk of mutation in HRAS compared with non-White race. ConclusionsThese differences highlight the importance of enriching cohorts for female and non-White patients in genomic studies and clinical trials, especially as we test the use of molecular biomarkers to personalize care for patients with bladder cancer.

Design and fabrication of biomass densification machine for teaching and research purposes

In developing nations, research output is limited due to factors like unreliable power supply and inadequate laboratory equipment. The high cost of purchasing completed laboratory equipment and the unavailability of accessories for imported equipment further contribute to this issue. A biomass densification machine was designed and constructed to address these challenges for teaching and research purposes. The machine was tested at five different compaction pressures (100, 200, 300, 400, and 500 kPa) using gelatinized cassava starch as a binder. The physical and mechanical characteristics of the produced fuel briquettes were investigated following ASTM standards and procedures reported in the literature. The results show that the physical and mechanical properties of the fuel briquettes increase with compaction pressure. The compressive strength, durability, and water resistance of the briquettes varied between 55 and 101 kN·m−2, 89–99%, and 20–120 min, respectively, while the compressed and relaxed densities range from 0.780 to 1.220 g·cm−3 and 0.670 to 0.990 g·cm−3, respectively. The machine performed satisfactorily because the briquettes’ characteristics were found to meet the specified ISO Standard (17225). The development of this machine will enable academic institutions, researchers, and students to harness the potential of biomass through the densification process without the challenges posed by imported equipment. The creation of the machine will also facilitate students’ hands-on learning. By providing an easily accessible and reliable platform, academic and research institutions can integrate biomass solid fuel production experiments into their curricula, fostering a thorough understanding of renewable energy solutions and supporting sustainable practices. Therefore, it can be recommended for teaching and research in developing nations. Incorporating an electronic component, such as a digital pressure gauge and electric hydraulic jack, is recommended for future research to enhance the performance.

Assessment of the E3C corpus for the recognition of disorders in clinical texts

Abstract Disorder named entity recognition (DNER) is a fundamental task of biomedical natural language processing, which has attracted plenty of attention. This task consists in extracting named entities of disorders such as diseases, symptoms, and pathological functions from unstructured text. The European Clinical Case Corpus (E3C) is a freely available multilingual corpus (English, French, Italian, Spanish, and Basque) of semantically annotated clinical case texts. The entities of type disorder in the clinical cases are annotated at both mention and concept level. At mention -level, the annotation identifies the entity text spans, for example, abdominal pain. At concept level, the entity text spans are associated with their concept identifiers in Unified Medical Language System, for example, C0000737. This corpus can be exploited as a benchmark for training and assessing information extraction systems. Within the context of the present work, multiple experiments have been conducted in order to test the appropriateness of the mention-level annotation of the E3C corpus for training DNER models. In these experiments, traditional machine learning models like conditional random fields and more recent multilingual pre-trained models based on deep learning were compared with standard baselines. With regard to the multilingual pre-trained models, they were fine-tuned (i) on each language of the corpus to test per-language performance, (ii) on all languages to test multilingual learning, and (iii) on all languages except the target language to test cross-lingual transfer learning. Results show the appropriateness of the E3C corpus for training a system capable of mining disorder entities from clinical case texts. Researchers can use these results as the baselines for this corpus to compare their own models. The implemented models have been made available through the European Language Grid platform for quick and easy access.

Snow cover persistence as a useful predictor of alpine plant distributions

AbstractAimSnow cover persistence (SCP) has significant effects on plants in high‐elevation ecosystems. It determines the length of the growing season, provides insulation against low temperatures and influences water availability, thereby shaping the vegetation mosaic. Despite its importance, SCP is rarely used in plant species distribution modelling. In this study, we examine whether incorporating SCP in plant species distribution models (SDMs) improves their predictive power. We investigate the link between species' ecology and SDM improvements by the addition of various SCP predictors.LocationWestern Swiss Alps.Taxon206 alpine flowering plants (angiosperms).MethodsWe produced three maps of landsat satellite‐based SCP indices over an entire mountain region, one of them using an online open access platform allowing quick and easy replication and used them as a predictor in plant SDMs alongside commonly used predictors. We tested whether this improved the predictive performance of plant SDMs.ResultsAll three SCP indices improved the overall SDM predictive accuracy, but the overall improvement was potentially limited by their correlation with other climatic predictors. Alpine plant species known for their dependence on snow benefited more from the additional snow information.Main ConclusionsSCP should be used for predicting at least the distribution of alpine, snow‐related plant species. Given that adding snow cover improves SDMs and that snow duration decreases as climate warms, future predictions of alpine plant distributions should account for both snow predictor and associated snow change scenarios.

The Digital Transformation of Instructional Materials. Views and Practices of Teachers, Families and Editors

The purpose of this article is to present the design and main findings of a three-year study analyzing the transition from printed to digital educational materials for primary education in Spain. Special attention has been given to the metamorphosis of didactic materials in the context of the digital society. The research focused on two issues: (a) the opinion of educational agents regarding digital educational material, and (b) the use made of digital educational materials in schools and classrooms. Two different but complementary studies were designed and carried out. The first explored the perspectives or subjectivities of educational agents—teachers, material creators and families. The second was a multi-case study involving several schools and analyzing the educational use of materials by teachers. Our findings indicate that the dissemination of digital educational materials is carried out through both paid commercial platforms and public access platforms promoted by educational administrations and that an expository teaching model underlies most online teaching materials. Educational agents have high expectations and a positive predisposition towards digital resources. Likewise, it has been found that teachers make functional and hybrid didactic adaptations of digital resources. Finally, it is suggested that the study’s approach and methodology have potential for extrapolation to other national contexts.

Food Access Support Technology (FAST): a Centralized City-Wide Platform for Rapid Response to Food Insecurity.

Food access for patients remains a critical need for health systems to address given varying resource availability and inefficient coordination among health and food services. Develop and evaluate the Food Access Support Technology (FAST), a centralized digital platform for food access that pairs health systems with food and delivery community-based organizations (CBOs). Two health systems, 12 food partners, and 2 delivery partners in Philadelphia, PA. Using FAST, referrers can post requests for food delivery on recipients' behalf, which are reviewed and claimed by eligible CBOs that can prepare food boxes for delivery to people's homes. Between March 2021 and July 2022, FAST received 364 requests, representing 207 food insecure households in 51 postal codes. The platform facilitated the completion of 258 (70.9%) requests, with a median completion time of 5 (IQR 0-7) days and a median of only 1.5days (IQR 0-5) for requests marked "urgent." Qualitative interviews with FAST end-users endorsed the usability of the FAST platform and its effectiveness in facilitating resource-sharing between partners. Our findings suggest that centralized platforms can address household food insecurity by (1) streamlining partnerships between health systems and CBOs for food delivery and (2) facilitating the real-time coordination of resources among CBOs.

'We Should Not Be Quiet but We Should Talk': Qualitative Accounts of Community-Based Communication of HIV Pre-Exposure Prophylaxis.

Community leaders play an important role in the acceptance of public health services, but little is known about their willingness to facilitate HIV pre-exposure prophylaxis (PrEP) roll-out in Eswatini. We conducted in-depth interviews (n = 25) with purposefully selected male and female community leaders in Eswatini. We analysed our data inductively using a thematic analysis approach. Community leaders feel they are important communicators of culturally appropriate PrEP messaging. Our participants described a complex social space within their communities influenced by religion, tradition, values, and HIV stigma. Community leaders use their position to provide leverage for unique, effective, and easily accessible messages and platforms to reach the community in a manner that ensures trust, relatability, familiarity, and shared faith. Community leaders feel that they are trusted and see trust manifesting in the conversations they are able to engage in, and have a reach that extends beyond formal health services. Existing PrEP programming should embed community leader participation in PrEP programming and engage the trust, knowledge, and potential of community leaders to support PrEP uptake and acceptance.

Electronic Tender Advertisement System on Operational Performance of Small & Medium Enterprises in Kenya

The aim of the study was to evaluate how the electronic tender advertisement system affects the the operational performance of SMEs in Kenya. Schumpeter’s theory of entrepreneurship has been applied to ground the study. A descriptive study design was adopted. The target population for the study included 2500 SMEs operating in Murang’a County. The Yamane sample formula was used to determine a sample size of 189 SMEs. Drop and pick method was used in administering questionnaires with a response of 88%. The data collected was cleaned before being processed by use of SPSS version 23. Multiple regression analysis was used to test the hypotheses. R2 of 0.671 postulated that 67.1% of the operational performance of SMEs can be attributed to e-tender advertisement. It was concluded that there is a significant effect between E-tender advertisement and SMEs' operational performance. The study recommended that for easier visibility on upcoming tender contracts, firms should opt advertising tender on the most visited or accessible media platform

The AGILE 4.0 Project: MBSE to Support Cyber‐Physical Collaborative Aircraft Development

AbstractThis paper presents the main output of the EU‐funded H2020 AGILE 4.0 project: the AGILE 4.0 MBSE‐MDAO Development Framework. The framework aims at connecting upstream Model‐Based Systems Engineering (MBSE) activities to downstream Multidisciplinary Design Analysis and Optimization (MDAO) activities, applied to the development of complex aeronautical systems. Upstream activities include the definition of stakeholders, needs, semantic requirements, and modeling the system architecture design space. Downstream activities include defining, implementing, and executing cross‐organizational and collaborative MDAO workflows to support system synthesis. The development framework is implemented in an Operational Collaborative Environment (OCE), a web‐based platform for project data and modeling tool access. A business jet family design application case demonstrates the use of the development framework and OCE.

HEalth And Dementia outcomes following Traumatic Brain Injury (HEAD-TBI): protocol for a retrospective cohort study

BackgroundIt is estimated that by 2050 the global incidence of dementia will have exceeded 152 million. At present, there are no effective therapies for dementia, with a focus in research...

An Accessible Serious Game-Based Platform for Process Learning of People with Intellectual Disabilities

This research presents the “LudoMinga” platform based on serious games designed to facilitate the learning process of people with intellectual disabilities. The platform is focused on providing an inclusive and accessible learning environment. Serious Games combines educational content with video game mechanics, and the platform aims to enhance the learning experience and promote active participation. Through an iterative development process, including user feedback and evaluations, the platform was developed using the iPlus methodology to align with the specific requirements of the target audience. Preliminary user test results indicate positive results in terms of user engagement, learning, and satisfaction. This accessible platform based on serious games promises to improve educational opportunities and outcomes for people with intellectual disabilities, ultimately fostering their personal and cognitive development. The success of the “LudoMinga” platform lies in the combination of interactive games, personalized support, and accessibility features, ultimately creating an engaging and effective learning environment. Continued advances in this area have the potential to unlock barriers for people with intellectual disabilities, fostering their growth, independence, and active participation in society.