Diversity in Psychological Research Activities: Quantitative Approach With Topic Modeling.
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ABSTRACT:
SUBMITTER: Otsuka S
PROVIDER: S-EPMC8716499 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDue to scientific and technical advancements in the field, published hypertension research has developed substantially during the last decade. Given the amount of scientific material published in this field, identifying the relevant information is difficult. We used topic modeling, which is a strong approach for extracting useful information from enormous amounts of unstructured text.ObjectiveThis study aims to use a machine learning algorithm to uncover hidden topics and subtopics from 100 years of peer-reviewed hypertension publications and identify temporal trends.MethodsThe titles and abstracts of hypertension papers indexed in PubMed were examined. We used the latent Dirichlet allocation model to select 20 primary subjects and then ran a trend analysis to see how popular they were over time.ResultsWe gathered 581,750 hypertension-related research articles from 1900 to 2018 and divided them into 20 topics. These topics were broadly categorized as preclinical, epidemiology, complications, and therapy studies. Topic 2 (evidence review) and topic 19 (major cardiovascular events) are the key (hot topics). Most of the cardiopulmonary disease subtopics show little variation over time, and only make a small contribution in terms of proportions. The majority of the articles (414,206/581,750; 71.2%) had a negative valency, followed by positive (119, 841/581,750; 20.6%) and neutral valency (47,704/581,750; 8.2%). Between 1980 and 2000, negative sentiment articles fell somewhat, while positive and neutral sentiment articles climbed substantially.ConclusionsThe number of publications has been increasing exponentially over the period. Most of the uncovered topics can be grouped into four categories (ie, preclinical, epidemiology, complications, and treatment-related studies).
| S-EPMC9161044 | biostudies-literature
Project description:Diatoms are fundamental carbon sources in a wide range of aquatic food webs and have the potential for wide application in addressing environmental change. Understanding the evolution of topics in diatom research will provide a clear and needed guide to strengthen research on diatoms. However, such an overview remains unavailable. In this study, we used Latent Dirichlet Allocation (LDA), a generative model, to identify topics and determine their trends (i.e., cold and hot topics) by analyzing the abstracts of 19,000 publications from the Web of Science that were related to diatoms during 1991-2018. A total of 116 topics were identified from a Bayesian model selection. The hot topics (diversity, environmental indicator, climate change, land use, and water quality) that were identified by LDA indicated that diatoms are increasingly used as indicators to assess water quality and identify modern climate change impacts due to intensive anthropogenic activities. In terms of cold topics (growth rate, culture growth, cell life history, copepod feeding, grazing by microzooplankton, zooplankton predation, and primary productivity) and hot topics (spatial-temporal distribution, morphology, molecular identification, gene expression, and review), we determined that basic studies on diatoms have decreased and that studies tend to be more comprehensive. This study notes that future directions in diatom research will be closely associated with the application of diatoms in environmental management and climate change to cope with environmental challenges, and more comprehensive issues related to diatoms should be considered.
| S-EPMC6722707 | biostudies-literature
Project description:Disease ecology is a rapidly growing subdiscipline, and mammals and their parasites feature prominently in both historical and more recent research efforts. Nevertheless, the diversity of topics explored, and those not well explored, has not been systematically assessed. We conducted a systematic review of the published scientific literature in disease ecology of mammals and subjected the collection of original and review articles identified to a topic modeling approach, which is based on the words used in the published texts and their contexts (i.e., the frequency and strength of their semantic relationships with one another). In addition to concept maps identifying the most prominent research themes, we identified eight (not mutually exclusive) subcategories of studies, including experimental, theoretical, comparative, behavioral, immunological-microbiological, biogeographic-macroecological, vector-focused (e.g., mosquitoes), and disturbance-focused. The most prominent themes arising in review papers included the ecology of zoonotic diseases transmitted from non-human mammals, comparisons of pathogen prevalence between mammalian species, and pathogen discovery-disease surveillance studies, particularly of marine mammals and bats. For the original articles, the most prominent themes included ecology of rodent-transmitted viral and bacterial diseases and the population biology of zoonotic hosts. Most studies used comparative or descriptive approaches to investigate mammal-pathogen-disease relationships at a local scale, focusing on vector-borne diseases. Experimental, modeling, immunological, and behavioral approaches were strikingly underrepresented. Topics of strong conceptual importance, but that are underrepresented in the current literature, include: 1) the effects of the population density of mammalian hosts, and manipulations of density, on pathogen transmission; 2) macroecological studies that quantify effects of mammalian host species on parasite abundance and prevalence; and 3) effects of climate change on physiological and behavioral processes relevant to mammal-parasite interactions.
| S-EPMC6533029 | biostudies-literature
Project description:Probabilistic topic models, have been widely deployed for various applications such as learning disease or tissue subtypes. Yet, learning the parameters of such models is usually an ill-posed problem and may result in losing valuable information about disease severity. A common approach is to add a discriminative loss term to the generative model's loss in order to learn a representation that is also predictive of disease severity. However, finding a balance between these two losses is not straightforward. We propose an alternative way in this paper. We develop a framework which allows for incorporating external covariates into the generative model's approximate posterior. These covariates can have more discriminative power for disease severity compared to the representation that we extract from the posterior distribution. For instance, they can be features extracted from a neural network which predicts disease severity from CT images. Effectively, we enforce the generative model's approximate posterior to reside in the subspace of these discriminative covariates. We illustrate our method's application on a large-scale lung CT study of Chronic Obstructive Pulmonary Disease (COPD), a highly heterogeneous disease. We aim at identifying tissue subtypes by using a variant of topic model as a generative model. We quantitatively evaluate the predictive performance of the inferred subtypes and demonstrate that our method outperforms or performs on par with some reasonable baselines. We also show that some of the discovered subtypes are correlated with genetic measurements, suggesting that the identified subtypes may characterize the disease's underlying etiology.
| S-EPMC8797254 | biostudies-literature
Project description:BACKGROUND:High Content Screening (HCS) has become an important tool for toxicity assessment, partly due to its advantage of handling multiple measurements simultaneously. This approach has provided insight and contributed to the understanding of systems biology at cellular level. To fully realize this potential, the simultaneously measured multiple endpoints from a live cell should be considered in a probabilistic relationship to assess the cell's condition to response stress from a treatment, which poses a great challenge to extract hidden knowledge and relationships from these measurements. METHOD:In this work, we applied a text mining method of Latent Dirichlet Allocation (LDA) to analyze cellular endpoints from in vitro HCS assays and related to the findings to in vivo histopathological observations. We measured multiple HCS assay endpoints for 122 drugs. Since LDA requires the data to be represented in document-term format, we first converted the continuous value of the measurements to the word frequency that can processed by the text mining tool. For each of the drugs, we generated a document for each of the 4 time points. Thus, we ended with 488 documents (drug-hour) each having different values for the 10 endpoints which are treated as words. We extracted three topics using LDA and examined these to identify diagnostic topics for 45 common drugs located in vivo experiments from the Japanese Toxicogenomics Project (TGP) observing their necrosis findings at 6 and 24 hours after treatment. RESULTS:We found that assay endpoints assigned to particular topics were in concordance with the histopathology observed. Drugs showing necrosis at 6 hour were linked to severe damage events such as Steatosis, DNA Fragmentation, Mitochondrial Potential, and Lysosome Mass. DNA Damage and Apoptosis were associated with drugs causing necrosis at 24 hours, suggesting an interplay of the two pathways in these drugs. Drugs with no sign of necrosis we related to the Cell Loss and Nuclear Size assays, which is suggestive of hepatocyte regeneration. CONCLUSIONS:The evidence from this study suggests that topic modeling with LDA can enable us to interpret relationships of endpoints of in vitro assays along with an in vivo histological finding, necrosis. Effectiveness of this approach may add substantially to our understanding of systems biology.
| S-EPMC3851019 | biostudies-literature
Project description:Newspapers are very important for a society as they inform citizens about the events around them and how they can impact their life. Their importance becomes more crucial and indispensable in the times of health crisis such as the current COVID-19 pandemic. Since the starting of this pandemic newspapers are providing rich information to the public about various issues such as the discovery of a new strain of coronavirus, lockdown and other restrictions, government policies, and information related to the vaccine development for the same. In this scenario, analysis of emergent and widely reported topics/themes/issues and associated sentiments from various countries can help us better understand the COVID-19 pandemic. In our research, the database of more than 100,000 COVID-19 news headlines and articles were analyzed using top2vec (for topic modeling) and RoBERTa (for sentiment classification and analysis). Our topic modeling results highlighted that education, economy, US, and sports are some of the most common and widely reported themes across UK, India, Japan, South Korea. Further, our sentiment classification model achieved 90% validation accuracy and the analysis showed that the worst affected country, i.e. the UK (in our dataset) also has the highest percentage of negative sentiment.
| S-EPMC8545217 | biostudies-literature
Project description:ObjectivesThis study aimed to explore the health inequality discourse in the Korean press by analyzing newspaper articles using a relatively new content analysis technique.MethodsThis study used the search term "health inequality" to collect articles containing that term that were published between 2000 and 2018. The collected articles went through pre-processing and topic modeling, and the contents and temporal trends of the extracted topics were analyzed.ResultsA total of 1038 articles were identified, and 5 topics were extracted. As the number of studies on health inequality has increased over the past 2 decades, so too has the number of news articles regarding health inequality. The extracted topics were public health policies, social inequalities in health, inequality as a social problem, healthcare policies, and regional health gaps. The total number of occurrences of each topic increased every year, and the trend observed for each theme was influenced by events related to its contents, such as elections. Finally, the frequency of appearance of each topic differed depending on the type of news source.ConclusionsThe results of this study can be used as preliminary data for future attempts to address health inequality in Korea. To make addressing health inequality part of the public agenda, the media's perspective and discourse regarding health inequality should be monitored to facilitate further strategic action.
| S-EPMC6893224 | biostudies-literature
Project description:IntroductionThe utilization of social media presents a promising avenue for the prevention and management of diabetes. To effectively cater to the diabetes-related knowledge, support, and intervention needs of the community, it is imperative to attain a deeper understanding of the extent and content of discussions pertaining to this health issue. This study aims to assess and compare various topic modeling techniques to determine the most effective model for identifying the core themes in diabetes-related tweets, the sources responsible for disseminating this information, the reach of these themes, and the influential individuals within the Twitter community in India.MethodsTwitter messages from India, dated between 7 November 2022 and 28 February 2023, were collected using the Twitter API. The unsupervised machine learning topic models, namely, Latent Dirichlet Allocation (LDA), non-negative matrix factorization (NMF), BERTopic, and Top2Vec, were compared, and the best-performing model was used to identify common diabetes-related topics. Influential users were identified through social network analysis.ResultsThe NMF model outperformed the LDA model, whereas BERTopic performed better than Top2Vec. Diabetes-related conversations revolved around eight topics, namely, promotion, management, drug and personal story, consequences, risk factors and research, raising awareness and providing support, diet, and opinion and lifestyle changes. The influential nodes identified were mainly health professionals and healthcare organizations.DiscussionThe study identified important topics of discussion along with health professionals and healthcare organizations involved in sharing diabetes-related information with the public. Collaborations among influential healthcare organizations, health professionals, and the government can foster awareness and prevent noncommunicable diseases.
| S-EPMC10895681 | biostudies-literature
Project description:Previous studies have used a query-based approach to search and gather scientific literature. Instead, the current study focused on domain-specific journals in the field of eating disorders. A total of 8651 documents (since 1981 to 2020), from which 7899 had an abstract, were retrieved from: International Journal of Eating Disorders (n = 4185, 48.38%), Eating and Weight Disorders (n = 1540, 17.80%), European Eating Disorders Review (n = 1461, 16.88%), Eating Disorders (n = 1072, 12.39%), and Journal of Eating Disorders (n = 393, 4.54%). To analyze these data, diverse methodologies were employed: bibliometrics (to identify top cited documents), network analysis (to identify the most representative scholars and collaboration networks), and topic modeling (to retrieve major topics using text mining, natural language processing, and machine learning algorithms). The results showed that the most cited documents were related to instruments used for the screening and evaluation of eating disorders, followed by review articles related to the epidemiology, course and outcome of eating disorders. Network analysis identified well-known scholars in the field, as well as their collaboration networks. Finally, topic modeling identified 10 major topics whereas a time series analysis of these topics identified relevant historical shifts. This study discusses the results in terms of future opportunities in the field of eating disorders.
| S-EPMC9754234 | biostudies-literature
Project description:We present TopicFlow, a computational framework for flow cytometry data analysis of patient blood samples for the identification of functional and dynamic topics in circulating T cell population. This framework applies a Latent Dirichlet Allocation (LDA) model, adapting the concept of topic modeling in text mining to flow cytometry. To demonstrate the utility of our method, we conducted an analysis of ∼17 million T cells collected from 138 peripheral blood samples in 51 patients with melanoma undergoing treatment with immune checkpoint inhibitors (ICIs). Our study highlights three latent dynamic topics identified by LDA: a T cell exhaustion topic that independently recapitulates the previously identified LAG-3+ immunotype associated with ICI resistance, a naive topic and its association with immune-related toxicity, and a T cell activation topic that emerges upon ICI treatment. Our approach can be broadly applied to mine high-parameter flow cytometry data for insights into mechanisms of treatment response and toxicity.
| S-EPMC10475788 | biostudies-literature