Literature Search Tools Research Articles

Incorporating Generative AI to Promote Inquiry-Based Learning: Comparing Elicit AI Research Assistant to PubMed and CINAHL Complete

Generative artificial intelligence (GenAI) is transforming education, and faculty can either incorporate GenAI in intentional course design to promote inquiry-based learning (IBL) or resist its use. This study identified an effective strategy to intentionally integrate GenAI in the course design to promote IBL. A descriptive study design was used for graduate nursing students to compare the effectiveness of a GenAI literature search tool, Elicit: The AI Research Assistant, to PubMed and CINAHL. A two-phase framework was utilized to organize complex information and justify a preference. A rubric was designed to promote and assess critical thinking through IBL in educating graduate nursing students on information literacy and structuring a literature search. Discovering a relationship between the search tools, students identified the strengths (pros) and weaknesses (cons) of each tool and determined which tool was more effective in terms of accuracy, relevance and efficiency.

An overview of implementing security and privacy in federated learning

Federated learning has received a great deal of research attention recently,with privacy protection becoming a key factor in the development of artificial intelligence. Federated learning is a special kind of distributed learning framework, which allows multiple users to participate in model training while ensuring that their privacy is not compromised; however, this paradigm is still vulnerable to security and privacy threats from various attackers. This paper focuses on the security and privacy threats related to federated learning. First, we analyse the current research and development status of federated learning through use of the CiteSpace literature search tool. Next, we describe the basic concepts and threat models, and then analyse the security and privacy vulnerabilities within current federated learning architectures. Finally, the directions of development in this area are further discussed in the context of current advanced defence solutions, for which we provide a summary and comparison.

On the Use of Generative AI for Literature Reviews: An Exploration of Tools and Techniques

To carry out a literature review often involves hard and tedious work. There is a tradition of using facilitating tools, that extended to the AI field in 2018 when iris.ai appeared. Today, in the emerging field of Generative AI tools based on Large Language Models, there has been rapid development of new literature search tools and approaches. This study has the aim of exploring this vast array of Generative AI tools, in a literature study where some of the found tools were used to facilitate the selection of relevant publication. Three research questions guided this study: RQ1) "What Generative AI tools can be found in literature?", RQ2) "Which of these tools could be of use in the literature review conducted in this study, and how?", and RQ3) "What are the ethical aspects of using Generative AI tools in literature studies?” The approach has been a scoping review, built around a search that combined the keywords: "AI supported", "AI generated", "AI based" and "Literature review". An initial result set was filtered with inclusion exclusion criteria in a strive for an interesting quality answer to the research questions. However, most publications that passed the filtering lacked any potential to contribute to answer the research questions. The most interesting finding in the first search was a hint about the new feature 'Scopus AI'. A new search with the Scopus AI tool resulted in a small but very relevant set of publications. These publications were analysed in a deductive inductive thematic analysis, and primary sorted into the categories of: 'Generative AI Tools', 'Supportive AI Techniques', and 'Ethical Issues'. Findings indicate that there is a wide variety of tools that can facilitate the skimming process of a literature, and to provide adequate summaries of retrieved publication. However, authors recommendation is to keep the tools on the facilitating support level, and that the main analysis and conclusion should be human conducted. With this, rather traditional approach, researchers will have clearly less ethical issues to consider. Finally, the ethical aspects of Generative AI tools in research ought to be investigated more in detail, in a separate future study.

The Use of Generative AI for Scientific Literature Searches for Systematic Reviews: ChatGPT and Microsoft Bing AI Performance Evaluation.

A large language model is a type of artificial intelligence (AI) model that opens up great possibilities for health care practice, research, and education, although scholars have emphasized the need to proactively address the issue of unvalidated and inaccurate information regarding its use. One of the best-known large language models is ChatGPT (OpenAI). It is believed to be of great help to medical research, as it facilitates more efficient data set analysis, code generation, and literature review, allowing researchers to focus on experimental design as well as drug discovery and development. This study aims to explore the potential of ChatGPT as a real-time literature search tool for systematic reviews and clinical decision support systems, to enhance their efficiency and accuracy in health care settings. The search results of a published systematic review by human experts on the treatment of Peyronie disease were selected as a benchmark, and the literature search formula of the study was applied to ChatGPT and Microsoft Bing AI as a comparison to human researchers. Peyronie disease typically presents with discomfort, curvature, or deformity of the penis in association with palpable plaques and erectile dysfunction. To evaluate the quality of individual studies derived from AI answers, we created a structured rating system based on bibliographic information related to the publications. We classified its answers into 4 grades if the title existed: A, B, C, and F. No grade was given for a fake title or no answer. From ChatGPT, 7 (0.5%) out of 1287 identified studies were directly relevant, whereas Bing AI resulted in 19 (40%) relevant studies out of 48, compared to the human benchmark of 24 studies. In the qualitative evaluation, ChatGPT had 7 grade A, 18 grade B, 167 grade C, and 211 grade F studies, and Bing AI had 19 grade A and 28 grade C studies. This is the first study to compare AI and conventional human systematic review methods as a real-time literature collection tool for evidence-based medicine. The results suggest that the use of ChatGPT as a tool for real-time evidence generation is not yet accurate and feasible. Therefore, researchers should be cautious about using such AI. The limitations of this study using the generative pre-trained transformer model are that the search for research topics was not diverse and that it did not prevent the hallucination of generative AI. However, this study will serve as a standard for future studies by providing an index to verify the reliability and consistency of generative AI from a user's point of view. If the reliability and consistency of AI literature search services are verified, then the use of these technologies will help medical research greatly.

Describing diversity of real world data sources in pharmacoepidemiologic studies: The DIVERSE scoping review.

Real-world evidence (RWE) is increasingly used for medical regulatory decisions, yet concerns persist regarding its reproducibility and hence validity. This study addresses reproducibility challenges associated with diversity across real-world data sources (RWDS) repurposed for secondary use in pharmacoepidemiologic studies. Our aims were to identify, describe and characterize practices, recommendations and tools for collecting and reporting diversity across RWDSs, and explore how leveraging diversity could improve the quality of evidence. In a preliminary phase, keywords for a literature search and selection tool were designed using a set of documents considered to be key by the coauthors. Next, a systematic search was conducted up to December 2021. The resulting documents were screened based on titles and abstracts, then based on full texts using the selection tool. Selected documents were reviewed to extract information on topics related to collecting and reporting RWDS diversity. A content analysis of the topics identified explicit and latent themes. Across the 91 selected documents, 12 topics were identified: 9 dimensions used to describe RWDS (organization accessing the data source, data originator, prompt, inclusion of population, content, data dictionary, time span, healthcare system and culture, and data quality), tools to summarize such dimensions, challenges, and opportunities arising from diversity. Thirty-six themes were identified within the dimensions. Opportunities arising from data diversity included multiple imputation and standardization. The dimensions identified across a large number of publications lay the foundation for formal guidance on reporting diversity of data sources to facilitate interpretation and enhance replicability and validity of RWE.

Questionnaire-based exposome-wide association studies for common diseases in the Personalized Environment and Genes Study.

The exposome collectively refers to all exposures, beginning in utero and continuing throughout life, and comprises not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The exposome interacts with individual genetic and epigenetic characteristics to affect human health and disease, but large-scale studies that characterize the exposome and its relationships with human disease are limited. To address this gap, we used extensive questionnaire data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS, n = 9, 429) to evaluate exposure associations in relation to common diseases. We performed an exposome-wide association study (ExWAS) to examine single exposure models and their associations with 11 common complex diseases, namely allergic rhinitis, asthma, bone loss, fibroids, high cholesterol, hypertension, iron-deficient anemia, ovarian cysts, lower GI polyps, migraines, and type 2 diabetes. Across diseases, we found associations with lifestyle factors and socioeconomic status as well as asbestos, various dust types, biohazardous material, and textile-related exposures. We also found disease-specific associations such as fishing with lead weights and migraines. To differentiate between a replicated result and a novel finding, we used an AI-based literature search and database tool that allowed us to examine the current literature. We found both replicated findings, especially for lifestyle factors such as sleep and smoking across diseases, and novel findings, especially for occupational exposures and multiple diseases.

Clinical practice guidelines for cardiovascular disease: how is depression addressed? Protocol for a systematic review

IntroductionDepression frequently affects patients with cardiovascular disease (CVD). When these conditions co-occur, outcomes such as quality of life and life expectancy worsen. In everyday practice, this specific and prevalent disease-disease...

Clinical Practice Guidelines on Palliative Sedation Around the World: A Systematic Review.

Objective: The principal aim of this study was to identify, systematically and transparently, clinical practice guidelines (CPGs) on palliative sedation from around the world. Methods: A systematic search was performed using 5 databases, grey literature search tools, citation tracking, and contact with palliative care experts across the world. Current CPGs accredited by an international, national, or regional authority, published in English, German, French, or Italian, were subjected to content analysis. Results: In total, 35 CPGs from 14 countries and 1 international CPG were included in the analysis. The CPGs had diverse formal characteristics. Their thematic scope was difficult to analyze and compare because of differences in the terms and definitions of palliative sedation in those texts. We identified 3 main situations: (1) CPGs with a fully explicit thematic scope; (2) CPGs with a partially explicit thematic scope; and (3) CPGs without an explicit thematic scope. Several CPGs explicitly stated what forms of sedation were excluded from the text. However, this presentation was often confusing. Conclusion: Our review provides several pieces of information that could guide international reflections in this field, and be used to develop or update CPGs at all levels. Efforts should be made to clarify the thematic scope of each CPG on palliative sedation, in order to generate an understanding of the forms of this therapy addressed in the text.

Tree of Science with Scopus: A Shiny Application

Tree of Science (ToS) is a scientific literature search tool that produces a small, selected list of citations from a larger pool of citations. Initially developed for searches in the Web of Science, this paper shows how to use it with bibliographic data from Scopus. This new Shiny web application analyzes data from Scopus. It processes a dataset from a Scopus search and creates three reports. The first one shows a descriptive analysis, the second one presents the Tree of Science of the search, and the third one presents a clustering analysis of the three main subtopics. The application is accessible from this link: https://coreofscience.shinyapps.io/scientometrics/.

Tree of Science with Scopus: A Shiny Application

Tree of Science (ToS) is a scientific literature search tool that produces a small, selected list of citations from a larger pool of citations. Initially developed for searches in the Web of Science, this paper shows how to use it with bibliographic data from Scopus. This new Shiny web application analyzes data from Scopus. It processes a dataset from a Scopus search and creates three reports. The first one shows a descriptive analysis, the second one presents the Tree of Science of the search, and the third one presents a clustering analysis of the three main subtopics. The application is accessible from this link: https://coreofscience.shinyapps.io/scientometrics/.

Adversarial Training Methods for Deep Learning: A Systematic Review

Deep neural networks are exposed to the risk of adversarial attacks via the fast gradient sign method (FGSM), projected gradient descent (PGD) attacks, and other attack algorithms. Adversarial training is one of the methods used to defend against the threat of adversarial attacks. It is a training schema that utilizes an alternative objective function to provide model generalization for both adversarial data and clean data. In this systematic review, we focus particularly on adversarial training as a method of improving the defensive capacities and robustness of machine learning models. Specifically, we focus on adversarial sample accessibility through adversarial sample generation methods. The purpose of this systematic review is to survey state-of-the-art adversarial training and robust optimization methods to identify the research gaps within this field of applications. The literature search was conducted using Engineering Village (Engineering Village is an engineering literature search tool, which provides access to 14 engineering literature and patent databases), where we collected 238 related papers. The papers were filtered according to defined inclusion and exclusion criteria, and information was extracted from these papers according to a defined strategy. A total of 78 papers published between 2016 and 2021 were selected. Data were extracted and categorized using a defined strategy, and bar plots and comparison tables were used to show the data distribution. The findings of this review indicate that there are limitations to adversarial training methods and robust optimization. The most common problems are related to data generalization and overfitting.

Ethical challenges in palliative sedation of adults: protocol for a systematic review of current clinical practice guidelines

IntroductionThis study aims to identify the full spectrum of ethical challenges of all forms of palliative sedation for adults as presented in current clinical practice guidelines (CPGs) and to determine...

Gamification and e-learning for young learners: A systematic literature review, bibliometric analysis, and future research agenda

• A bibliometric study and a systematic review revealed the growth of the new concept and the emerging trends of gamification and e-learning for young learners. • The bibliometric analysis incorporated a systematic, transparent, and reproducible assessment. • Google scholar was chosen as the main academic literature search tool. • The study uses the TCCM framework to systematically review the literature and to identify any under-researched areas. • We provide a future research agenda based on the theory, characteristics, context, and methodology. Over the last few years, gamification has sparked significant interest in both industry and academia. However, the focus of the debate has been mostly on game studies and human-computer interaction (HCI). Even though games are increasingly being supplied as services to customers, few academic works have linked game studies to the service or marketing literature ( Dikcius and Urbonavicius, 2020 ; Dukembay and Zhaksylyk, 2019 ). This paper presents an examination of the emerging trends of gamification and e-learning for young learners. The first section presents a text-based cluster bibliometric analysis based on 222 qualified articles published between 2015 and 2020. We conducted this analysis to identify the most prominent themes in the literature through cluster identification via the VOS viewer software. As the themes were found to be interlinked, the second section presents a systematic literature review based on a bibliometric analysis performed using the PRISMA method on 32 qualified articles. The findings highlighted the four major future research themes of personalization, game elements, learner styles, and learner engagement. Finally, we provide a future research agenda based on the theory, characteristics, context, and methodology (TCCM) framework. Our findings offer key insights aimed at enabling actors in education policy making and gamification-based software companies and agencies to identify the gamification techniques best suited for e-learning.

A Method for a Literature Search on Microbiota and Obesity for PhD Biomedical Research Using the Web of Science (WoS) and the Tree of Science (ToS)

In this article, the process and results of a literature search using a new proposed scientific literature search tool (ToS: Tree of Science) aimed at partially overcoming the need to search in different databases was used. In its present form, ToS needs, as input, a previous search in the Web of Science (WoS), and by means of all references used in the articles found in the WoS search, it selects the more significant items, classifying them into three categories: root, trunk and leaves. In our example, from an initial total sum of 164 hits found in WoS, ToS provided 90 items. The following fields of these two results were put together in an Excel sheet for elimination of repetitions and further consideration: title, authors, source, year of publication and DOI (Digital Object Identifier). Then, the titles of the articles were read and graded by the three authors (a senior researcher, a junior researcher, and a PhD student) as 0 (of no interest for the topic), 1 (of possible interest) or 2 (of interest). The marks were added up and those with a score > 3 (56) were selected for the abstracts to be read by the PhD student to establish a final student’s own selection (SoS) of articles for initiating the review of the literature on her topic of interest.

Properties of Acrylic Resin For CAD/CAM: A Systematic Review and Meta-Analysis of In Vitro Studies.

This systematic review and meta-analysis of in vitro studies compared the prepolymerized acrylic resin used for CAD/CAM complete denture manufacturing versus the heat-polymerized acrylic resin for conventional complete dentures in terms of surface roughness, wettability, hardness and flexural strength. An electronic search was performed in the PubMed, Embase, LILACS and Web of Science databases, without language or date restrictions. Gray literature and manual search tools were also used. The systematic review was carried out by two researchers independently, following the inclusion criteria: in vitro studies testing the CAD/CAM acrylic resin with a control group of heat-polymerized acrylic resin which compared at least one of the four material properties above. The meta-analysis was performed separately for each property, using a random effect model. Of the 914 studies found by means of search strategies, 698 were selected for the systematic review. After applying the eligibility criteria, only 17 articles were selected for the qualitative analysis in the systematic review; among these, 14 were included in the quantitative meta-analysis. The CAD/CAM prepolymerized acrylic resin in blocks had similar properties when compared to heat-polymerized acrylic resin in almost all outcome measures, with the exception of a statistically significant reduction in surface roughness. Based on the findings of this systematic review and meta-analysis, equally satisfactory results can be expected from dental prosthesis manufactured by the CAD/CAM system when compared to conventional ones, with the additional potential of reducing the pigmentation and attached microorganisms due to the reduced surface roughness of the prepolymerized resin.

Recent developments in antimicrobial and antifouling coatings to reduce or prevent contamination and cross-contamination of food contact surfaces by bacteria.

Illness as the result of ingesting bacterially contaminated foodstuffs represents a significant annual loss of human quality of life and economic impact globally. Significant research investment has recently been made in developing new materials that can be used to construct food contacting tools and surfaces that might minimize the risk of cross-contamination of bacteria from one food item to another. This is done to mitigate the spread of bacterial contamination and resultant foodborne illness. Internet-based literature search tools such as Web of Science, Google Scholar, and Scopus were utilized to investigate publishing trends within the last 10 years related to the development of antimicrobial and antifouling surfaces with potential use in food processing applications. Technologies investigated were categorized into four major groups: antimicrobial agent-releasing coatings, contact-based antimicrobial coatings, superhydrophobic antifouling coatings, and repulsion-based antifouling coatings. The advantages for each group and technical challenges remaining before wide-scale implementation were compared. A diverse array of emerging antimicrobial and antifouling technologies were identified, designed to suit a wide range of food contact applications. Although each poses distinct and promising advantages, significant further research investment will likely be required to reliably produce effective materials economically and safely enough to equip large-scale operations such as farms, food processing facilities, and kitchens.

A new literature search model for multi data objective programming

Aiming at the problem that the current literature search algorithms only provide literature clues and original texts, which can not realize the analysis and evaluation, it is the formal comparison and cannot compare the actual contents of new papers and existing literatures; the objective programming target algorithm is introduced to calculate the “copy ratio” of the substantive content by minimizing the deviation between the objective function and the target value; small sample verification is carried out It is feasible and can open up a new idea for the upgrading of literature search tools.

Genomics of human aggression: current state of genome-wide studies and an automated systematic review tool.

There are substantial differences, or variation, between humans in aggression, with its molecular genetic basis mostly unknown. This review summarizes knowledge on the genetic contribution to variation in aggression with the following three foci: (1) a comprehensive overview of reviews on the genetics of human aggression, (2) a systematic review of genome-wide association studies (GWASs), and (3) an automated tool for the selection of literature based on supervised machine learning. The phenotype definition 'aggression' (or 'aggressive behaviour', or 'aggression-related traits') included anger, antisocial behaviour, conduct disorder, and oppositional defiant disorder. The literature search was performed in multiple databases, manually and using a novel automated selection tool, resulting in 18 reviews and 17 GWASs of aggression. Heritability estimates of aggression in children and adults are around 50%, with relatively small fluctuations around this estimate. In 17 GWASs, 817 variants were reported as suggestive (P ≤ 1.0E), including 10 significant associations (P ≤ 5.0E). Nominal associations (P ≤ 1E) were found in gene-based tests for genes involved in immune, endocrine, and nervous systems. Associations were not replicated across GWASs. A complete list of variants and their position in genes and chromosomes are available online. The automated literature search tool produced literature not found by regular search strategies. Aggression in humans is heritable, but its genetic basis remains to be uncovered. No sufficiently large GWASs have been carried out yet. With increases in sample size, we expect aggression to behave like other complex human traits for which GWAS has been successful.

Distribution of Pathogenic Variants in Von Willebrand Disease Type 2A in the American Population: Results from a National Clinical Reference Laboratory

Introductionvon Willebrand disease (VWD) is a common inherited bleeding disorder with a reported incidence ranging from 0.01% to 1%. VWD is classified as quantitative (types 1 and 3) and qualitative (type 2) defects in von Willebrand factor (VWF). Classical VWD type 2A, the most common qualitative defect of VWD, is characterized by decreased VWF-dependent platelet adhesion and a selective deficiency of high molecular weight VWF multimers. The majority of type 2A VWD is inherited in an autosomal dominant fashion. This subtype is caused by missense variants acting through a variety of mechanisms including defects in multimer assembly or an intrinsically increased sensitivity to cleavage by ADAMTS-13. The majority of pathogenic mutations are located in exon 28, predominantly affecting the A2 domain. Missense mutations have also been reported in the D3 and A1 domains (exons 22 and 25-28). Less common missense mutations include those responsible for dimerization (CK domain, exon 52) and multimerization defects (D2 domain, exons 11-17). Our objective was to determine the genomic distribution of mutations underlying type 2A VWD in patients referred to a USA-based clinical reference laboratory.MethodsIn a clinical reference laboratory, BloodCenter of Wisconsin, VWF gene sequence analysis results from January 2009 to July 2018 were reviewed. Molecular testing was performed by polymerase chain reaction (PCR) amplification and bi-directional Sanger sequencing or capture-based enrichment and next-generation sequencing (NGS). Complete coding region and splice junction of VWF gene was compared to the reference sequence (NM_00552.3). Variant interpretation was performed according to American College of Medical Genetics (ACMG) standards and guidelines by utilizing genome databases, population frequency data, variant specific literature search and predictive computational tools. Variant interpretation was reviewed by a team comprising of genetic counselors, molecular experts and experts in coagulation disorders correlating these findings with the patient's clinical phenotype provided.ResultsPathogenic variants were identified in 46 cases received. Of these, 56.5 % (26 of 46) were in exon 28 of the VWF gene.(Figure 1) 21.7% of mutations (10 out of 46) were identified in exon 26, 4.3% were identified in exon 25 (2 of 46) and 6.5% (3 out of 46) were identified in exon 52 of VWF gene. The remaining 10.7% were identified in exons 6,11,12,22 and 27 (1 each). The distribution of these mutations according to VWF domains was also studied. 39% of these mutations were found in the A2 domain, 30.4% were identified in the D3 domain, and 13% were found in the A1 domain. A small number of these mutations were identified in the D1 domain (1/46), D2 domain (2/46) and CK domain (2/46). Phenotypic information was available for most patients evaluated.ConclusionsIn a predominantly Caucasian population with others of mixed ethnicities, the distribution of VWD type 2A mutations was studied in patients evaluated in a clinical reference laboratory. Most mutations were identified in VWF Exon 28 and in the A2 domain. Next generation sequencing platform enables sequencing of large amounts of DNA in parallel thereby allowing all VWF exons to be evaluated at one time. However, in smaller laboratories, without access to a NGS platform, initial evaluation of the VWF Exon 28 for evaluation of VWD type 2A variants is a cost effective measure. Subsequently, sequencing of other less implicated exons may be performed utilizing a reflexive algorithm. Genetic testing can be very useful in diagnosis of type 2 variants, where mutations in specific regions correspond to the defect in VWF function. [Display omitted] DisclosuresFriedman:Shire: Membership on an entity's Board of Directors or advisory committees; CSL Behring: Membership on an entity's Board of Directors or advisory committees.

Use of acronyms in anaesthetic and associated investigations: appropriate or unnecessary? - the UOAIAAAIAOU Study.

We examined the prevalence of novel acronyms in the titles of anaesthetic and related studies and the response of anaesthetists to them. We separately analysed trainee-led research projects in the UK supported by the Research and Audit Federation of Trainees (RAFT), and a 10-year cohort of papers identified using the PubMed literature search tool. We also conducted a survey of 20 anaesthetists within our institution regarding the utility and impact of titles containing acronyms, and their recall of the associated topics. Finally, we developed a scoring system for acronym accuracy and complexity, the ORigin of AcroNym letterinG Used Term AppropriateNess (ORANGUTAN) score, and measured the progression of acronym usage over the 10-year period studied. Our results show that while acronyms themselves are sometimes considered memorable, they do not aid recall of topics and are, in general, not considered helpful. There has been an increase in the prevalence of acronymic titles over 10years, and in the complexity of acronyms used, suggesting that there is currently a selective pressure favouring the use of acronyms even if they are of limited benefit.