Text mining

With a society increasingly demanding alternative protein food sources, new strategies for evaluating protein safety issues, such as allergenic potential, are needed. Large-scale and systemic studies on allergenic proteins are hindered by the limited and non-harmonized clinical information available for these substances in dedicated databases. A missing key information is that representing the symptomatology of the allergens, especially given in terms of standard vocabularies, that would allow connecting with other biomedical resources to carry out different studies related to human health...

This study evaluates the performance of two major artificial intelligence-based tools (ChatGPT-4 and Google Bard) in debunking sleep-related myths. More in detail, the present research assessed 20 sleep misconceptions using a 5-point Likert scale for falseness and public health significance, comparing responses of artificial intelligence tools with expert opinions. The results indicated that Google Bard correctly identified 19 out of 20 statements as false (95.0% accuracy), not differing from ChatGPT-4 (85...

Antibiotic-resistance Acinetobacter baumannii is a very important nosocomial pathogen worldwide. Thousands of studies have been conducted about this pathogen. However, there has not been any attempt to use all this information to highlight the research trends concerning this pathogen. Here we use unsupervised learning and natural language processing (NLP), two areas of Artificial Intelligence, to analyse the most extensive database of articles created (5,500+ articles, from 851 different journals, published over 3 decades)...

Short texts generated by individuals in online environments can provide social and behavioral scientists with rich insights into these individuals' internal states. Trained manual coders can reliably interpret expressions of such internal states in text. However, manual coding imposes restrictions on the number of texts that can be analyzed, limiting our ability to extract insights from large-scale textual data. We evaluate the performance of several automatic text analysis methods in approximating trained human coders' evaluations across four coding tasks encompassing expressions of motives, norms, emotions, and stances...

INTRODUCTION: At the beginning of the COVID-19 pandemic, the UK's Scientific Committee issued extreme social distancing measures, termed 'shielding', aimed at a subpopulation deemed extremely clinically vulnerable to infection. National guidance for risk stratification was based on patients' age, comorbidities and immunosuppressive therapies, including biologics that are not captured in primary care records. This process required considerable clinician time to manually review outpatient letters...

Space medicine is a vital discipline with often time-intensive and costly projects and constrained opportunities for studying various elements such as space missions, astronauts, and simulated environments. Moreover, private interests gain increasing influence in this discipline. In scientific disciplines with these features, transparent and rigorous methods are essential. Here, we undertook an evaluation of transparency indicators in publications within the field of space medicine. A meta-epidemiological assessment of PubMed Central Open Access (PMC OA) eligible articles within the field of space medicine was performed for prevalence of code sharing, data sharing, pre-registration, conflicts of interest, and funding...

The year 2023 marked a significant surge in the exploration of applying large language model (LLM) chatbots, notably ChatGPT, across various disciplines. We surveyed the applications of ChatGPT in various sectors of bioinformatics and biomedical informatics throughout the year, covering omics, genetics, biomedical text mining, drug discovery, biomedical image understanding, bioinformatics programming, and bioinformatics education. Our survey delineates the current strengths and limitations of this chatbot in bioinformatics and offers insights into potential avenues for future development...

OBJECTIVE: Designing a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. This study proposes an approach based on knowledge graph embeddings and semantics-driven inductive inference for generating such recommendations. METHOD: The proposed recommendation methodology is based on neural embeddings trained on first-of-its-kind knowledge graph constructed from clinical trials data...

INTRODUCTION: The field of vestibular science, encompassing the study of the vestibular system and associated disorders, has experienced notable growth and evolving trends over the past five decades. Here, we explore the changing landscape in vestibular science, focusing on epidemiology, peripheral pathologies, diagnosis methods, treatment, and technological advancements. METHODS: Publication data was obtained from the US National Center for Biotechnology Information (NCBI) PubMed database...

Topic modeling aims to discover latent themes in collections of text documents. It has various applications across fields such as sociology, opinion analysis, and media studies. In such areas, it is essential to have easily interpretable, diverse, and coherent topics. An efficient topic modeling technique should accurately identify flat and hierarchical topics, especially useful in disciplines where topics can be logically arranged into a tree format. In this paper, we propose Community Topic, a novel algorithm that exploits word co-occurrence networks to mine communities and produces topics...

BACKGROUND: Despite the life-threatening nature of sepsis, little is known about the emotional experiences of patients and their families during sepsis events. We conducted a sentiment analysis pertaining to sepsis incidents involving patients and families, leveraging textual data retrieved from a publicly available blog post disseminated by the Centers for Disease Control and Prevention (CDC). OBJECTIVE: This investigation involved a sentiment analysis of patient- and family-related sepsis events, leveraging text responses sourced from a publicly accessible blog post disseminated by the CDC...

BACKGROUND: Due to limited numbers of palliative care specialists and/or resources, accessing palliative care remains limited in many low and middle-income countries. Data science methods, such as rule-based algorithms and text mining, have potential to improve palliative care by facilitating analysis of electronic healthcare records. This study aimed to develop and evaluate a rule-based algorithm for identifying cancer patients who may benefit from palliative care based on the Thai version of the Supportive and Palliative Care Indicators for a Low-Income Setting (SPICT-LIS) criteria...

AIM: It is essential for health researchers to have a systematic understanding of third-party variables that influence both the exposure and outcome under investigation, as shown by a directed acyclic graph (DAG). The traditional construction of DAGs through literature review and expert knowledge often needs to be more systematic and consistent, leading to potential biases. We try to introduce an automatic approach to building network linking variables of interest. METHODS: Large-scale text mining from medical literature was utilized to construct a conceptual network based on the Semantic MEDLINE Database (SemMedDB)...

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium...

BACKGROUND: The study of disease progression relies on clinical data, including text data, and extracting valuable features from text data has been a research hot spot. With the rise of large language models (LLMs), semantic-based extraction pipelines are gaining acceptance in clinical research. However, the security and feature hallucination issues of LLMs require further attention. OBJECTIVE: This study aimed to introduce a novel modular LLM pipeline, which could semantically extract features from textual patient admission records...

BACKGROUND: The COVID-19 pandemic has caused significant disruptions to everyday life and has had social, political, and financial consequences that will persist for years. Several initiatives with intensive use of technology were quickly developed in this scenario. However, technologies that enhance epidemiological surveillance in contexts with low testing capacity and healthcare resources are scarce. Therefore, this study aims to address this gap by developing a data science model that uses routinely generated healthcare encounter records to detect possible new outbreaks early in real-time...

INTRODUCTION: Qualitative information in the form of written reflection reports is vital for evaluating students' progress in education. As a pilot study, we used text mining, which analyzes qualitative information with quantitative features, to investigate how rehabilitation students' goals change during their first year at university. METHODS: We recruited 109 first-year students (66 physical therapy and 43 occupational therapy students) enrolled in a university rehabilitation course...

Public opinion will significantly affect investor decision-making and stock prices, which ultimately has an impact on the long-term development of the new energy industry. This paper mainly aims to delve in the impact of public opinion on the efficacy of financial risk early warning effect and try to establish an enhanced financial risk early warning model for the new energy list companies. To achieve this, we collect the financial data and public evaluation texts of 185 new energy listed companies, converting the text into emotional indicators which are combined with financial indicators to build a financial risk early warning model for new energy listed companies...

In the realm of open innovation, users have emerged as a significant external source of innovation that enterprises cannot afford to overlook. Implemented ideas play a pivotal role in driving the iterative innovation of products within enterprises. However, the existing literature still lacks an exploration of specific impact mechanisms on contributions in idea implementation. This study presents a model that delineates the impact of user personality traits on idea implementation contributions, drawing upon theories such as personality trait theory, user engagement perspective, and trait activation theory...

Myasthenia gravis (MG) is a rare, autoimmune, antibody-mediated, neuromuscular disease. This study analyzed digital conversations about MG to explore unprovoked perspectives. Advanced search, data extraction, and artificial intelligence-powered algorithms were used to harvest, mine, and structure public domain digital conversations about MG from US Internet Protocol addresses (August 2021 to August 2022). Thematic analyses examined topics, mindsets, and sentiments/key drivers via natural language processing and text analytics...