To address the need for systematic investigation of the phenome enabled by ever-growing genotype and phenotype data, we describe our step-by-step software implementation of a graph-embedded topic model, including data preprocessing, graph learning, topic inference, and phenotype prediction. As a demonstration, we use simulated data that mimic the UK Biobank data as in our original study. We will demonstrate topic analysis to discover disease comorbidities and computational phenotyping via the inferred topic mixture for each subject. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).1.

Due 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.

Massive hemorrhage remains a major cause of potentially preventable deaths. Better control of bleeding could improve survival rates by 10%-20%. Transfusion intervention concepts have been formulated in order to minimize acute traumatic coagulopathy. These interventions still have not been standardized and vary among medical centers.

Annotation of a set of genes is often accomplished through comparison to a library of labelled gene sets such as biological processes or canonical pathways. However, this approach might fail if the employed libraries are not up to date with the latest research, don't capture relevant biological themes or are curated at a different level of granularity than is required to appropriately analyze the input gene set. At the same time, the vast biomedical literature offers an unstructured repository of the latest research findings that can be tapped to provide thematic sub-groupings for any input gene set.

Fear of falling (FoF) is a major challenge for the quality of life among older adults. Despite extensive work in previous scoping and systematic reviews on separate domains of FoF and interventions related to FoF, very little attention has been devoted to a comprehensive scoping review mapping the range and scope of this burgeoning area of study, with only a few exceptions. This scoping review aims to provide an overarching review mapping FoF research by identifying main topics, gaps in the literature and potential opportunities for bridging different strains of research on FoF. Such a comprehensive scoping review will allow the subsequent creation of an interdisciplinary theoretical and empirical framework, which may help push forward policy and practice innovations for people living with FoF.

Bibliometric analysis is a research method used in library and information science to evaluate research performance. It applies quantitative and statistical analyses to describe patterns observed in a set of publications and can help identify previous, current, and future research trends or focus. To better guide our institutional strategic plan in cancer population science, we conducted bibliometric analysis on publications of investigators currently funded by either Division of Cancer Preventions (DCP) or Division of Cancer Control and Population Science (DCCPS) at National Cancer Institute. We applied two topic modeling techniques: author topic modeling (AT) and dynamic topic modeling (DTM). Our initial results show that AT can address reasonably the issues related to investigators' research interests, research topic distributions and popularities. In compensation, DTM can address the evolving trend of each topic by displaying the proportion changes of key words, which is consistent with the changes of MeSH headings.

The gut microbiota is composed of a large number of different bacteria, that play a key role in the construction of a metabolic signaling network. Deepening the link between metabolic pathways of the gut microbiota and human health, it seems increasingly essential to evolutionarily define the principal technologies applied in the field and their future trends. We use a topic analysis tool, Latent Dirichlet Allocation, to extract themes as a probabilistic distribution of latent topics from literature dataset. We also use the Prophet neural network prediction tool to predict future trend of this area of study. A total of 1,271 abstracts (from 2006 to 2020) were retrieved from MEDLINE with the query on "gut microbiota" and "metabolic pathway." Our study found 10 topics covering current research types: dietary health, inflammation and liver cancer, fatty and diabetes, microbiota community, hepatic metabolism, metabolomics-based approach and SFCAs, allergic and immune disorders, gut dysbiosis, obesity, brain reaction, and cardiovascular disease. The analysis indicates that, with the rapid development of gut microbiota research, the metabolomics-based approach and SCFAs (topic 6) and dietary health (topic 1) have more studies being reported in the last 15 years. We also conclude from the data that, three other topics could be heavily focused in the future: metabolomics-based approach and SCFAs (topic 6), obesity (topic 8) and brain reaction and cardiovascular disease (topic 10), to unravel microbial affecting human health.

Clinical trials are crucial for the advancement of treatment and knowledge within the medical community. Although the ClinicalTrials.gov initiative has resulted in a rich source of information for clinical trial research, only a handful of analytic studies have been carried out to understand this valuable data source. Analysis of this database provides insight for emerging trends of clinical research. In this study, we propose to use network analysis to understand infectious disease clinical trial research. Our goal is to understand two important issues related to the clinical trials: (1) the concentrations and characteristics of infectious disease clinical trial research, and (2) recommendation of clinical trials to a sponsor (or an investigator). The first issue helps summarize clinical trial research related to a particular disease(s), and the second issue helps match clinical trial sponsors and investigators for information recommendation. By using 4228 clinical trials as the test bed, our study investigates 4864 sponsors and 1879 research areas characterized by Medical Subject Heading (MeSH) keywords. We use a network to characterize infectious disease clinical trials, and design a new community-topic-based link prediction approach to predict sponsors' interests. Our design relies on network modeling of both clinical trial sponsors and keywords. For sponsors, we extract communities with each community consisting of sponsors with coherent interests. For keywords, we extract topics with each topic containing semantic consistent keywords. The communities and topics are combined for accurate clinical trial recommendation. This transformative study concludes that using network analysis can tremendously help the understanding of clinical trial research for effective summarization, characterization, and prediction.

The COVID-19 outbreak was designated a global pandemic on March 11, 2020. The relationship between vaping and contracting COVID-19 is unclear, and information on the internet is conflicting. There is some scientific evidence that vaping cannabidiol (CBD), an active ingredient in cannabis that is obtained from the hemp plant, or other substances is associated with more severe manifestations of COVID-19. However, there is also inaccurate information that vaping can aid COVID-19 treatment, as well as expert opinion that CBD, possibly administered through vaping, can mitigate COVID-19 symptoms. Thus, it is necessary to study the spread of inaccurate information to better understand how to promote scientific knowledge and curb inaccurate information, which is critical to the health of vapers. Inaccurate information about vaping and COVID-19 may affect COVID-19 treatment outcomes.

Fear of falling (FoF) is a major concern among older adults and is associated with negative outcomes, such as decreased quality of life and increased risk of falls. Despite several systematic reviews conducted on various specific domains of FoF and its related interventions, the research area has only been minimally covered by scoping reviews, and a comprehensive scoping review mapping the range and scope of the research area is still lacking. This review aims to provide such a comprehensive investigation of the existing literature and identify main topics, gaps in the literature, and potential opportunities for bridging different strains of research. Using the PRISMA-ScR guidelines, we searched the Cochrane Database of Systematic Reviews, CINAHL, Embase, MEDLINE, PsycInfo, Scopus, and Web of Science databases. Following the screening process, 969 titles and abstracts were chosen for the review. Pre-processing steps included stop word removal, stemming, and term frequency-inverse document frequency vectorization. Using the Non-negative Matrix Factorization algorithm, we identified seven main topics and created a conceptual mapping of FoF research. The analysis also revealed that most studies focused on physical health-related factors, particularly balance and gait, with less attention paid to cognitive, psychological, social, and environmental factors. Moreover, more research could be done on demographic factors beyond gender and age with an interdisciplinary collaboration with social sciences. The review highlights the need for more nuanced and comprehensive understanding of FoF and calls for more research on less studied areas.

This descriptive study analyzed 1849 international and 212 Korean studies to explore the main topics of nursing research on accidental falls. We extracted only nouns from each abstract, and four topics were identified through topic modeling, which were divided into aspects of fall prevention and its consequences. "Fall prevention program and scale" is popular among studies on the validity of fall risk assessment tools and the development of exercise and education programs. "Nursing strategy for fall prevention" is common in studies on nurse education programs and practice guidelines to improve the quality of patient safety care. "Hospitalization by fall injury" is used in studies about delayed discharge, increased costs, and deaths of subjects with fall risk factors hospitalized at medical institutions due to fall-related injuries. "Long-term care facility falls" is popular in studies about interventions to prevent fall injuries that occur in conjunction with dementia in long-term care facilities. It is necessary to establish a system and policy for fall prevention in Korean medical institutions. This study confirms the trends in domestic and international fall-related research, suggesting the need for studies to address insufficient fall-related policies and systems and translational research to be applied in clinical trials.

Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure.

Urothelial cancer (UC) includes carcinomas of the bladder, ureters, and renal pelvis. New treatments and biomarkers of UC emerged in this decade. To identify the key information in a vast amount of literature can be challenging. In this study, we use text mining to explore UC publications to identify important information that may lead to new research directions.

Many countries around the world are currently threatened by the COVID-19 pandemic, and nurses are facing increasing responsibilities and work demands related to infection control. To establish a developmental strategy for infection control, it is important to analyze, understand, or visualize the accumulated data gathered from research in the field of nursing.

Social media dedicated to health are increasingly used by patients and health professionals. They are rich textual resources with content generated through free exchange between patients. We are proposing a method to tackle the problem of retrieving clinically relevant information from such social media in order to analyze the quality of life of patients with breast cancer.

There is a rapidly growing body of literature on the topic of hip arthroscopic surgery.

The microbiome is a complex micro-ecosystem that provides the host with pathogen defense, food metabolism, and other vital processes. Alterations of the microbiome (dysbiosis) have been linked with a number of diseases such as cancers, multiple sclerosis (MS), Alzheimer's disease, etc. Generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria (enriched or depleted in one group). However, simply providing a singular species of bacteria to an individual lacking that species for health improvement has not been as successful as fecal matter transplant (FMT) therapy. Interestingly, FMT therapy transfers the entire gut microbiome of a healthy (or mixture of) individual to an individual with a disease. FMTs do, however, have limited success, possibly due to concerns that not all bacteria in the community may be responsible for the healthy phenotype. Therefore, it is important to identify the community of microorganisms linked to the health as well as the disease state of the host. Here we applied topic modeling, a natural language processing tool, to assess latent interactions occurring among microbes; thus, providing a representation of the community of bacteria relevant to healthy vs. disease state. Specifically, we utilized our previously published data that studied the gut microbiome of patients with relapsing-remitting MS (RRMS), a neurodegenerative autoimmune disease that has been linked to a variety of factors, including a dysbiotic gut microbiome. With topic modeling we identified communities of bacteria associated with RRMS, including genera previously discovered, but also other taxa that would have been overlooked simply with differential abundance testing. Our work shows that topic modeling can be a useful tool for analyzing the microbiome in dysbiosis and that it could be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.

Research on perennial staple crops has increased in the past ten years due to their potential to improve ecosystem services in agricultural systems. However, multiple past breeding efforts as well as research on traditional ratoon systems mean there is already a broad body of literature on perennial crops. In this review, we compare the development of research on perennial staple crops, including wheat, rice, rye, sorghum, and pigeon pea. We utilized the advanced search capabilities of Web of Science, Scopus, ScienceDirect, and Agricola to gather a library of 914 articles published from 1930 to the present. We analyzed the metadata in the entire library and in collections of literature on each crop to understand trends in research and publishing. In addition, we applied topic modeling to the article abstracts, a type of text analysis that identifies frequently co-occurring terms and latent topics. We found: 1.) Research on perennials is increasing overall, but individual crops have each seen periods of heightened interest and research activity; 2.) Specialist journals play an important role in supporting early research efforts. Research often begins within communities of specialists or breeders for the individual crop before transitioning to a more general scientific audience; 3.) Existing perennial agricultural systems and their domesticated crop material, such as ratoon rice systems, can provide a useful foundation for breeding efforts, accelerating the development of truly perennial crops and farming systems; 4.) Primary research is lacking for crops that are produced on a smaller scale globally, such as pigeon pea and sorghum, and on the ecosystem service benefits of perennial agricultural systems.

Healthcare professionals (HCP) perform various needle procedures that can be distressing and painful for children and adults. Even though many strategies have been proven effective in reducing distress and pain, topical anesthetic use before needle procedures is uncommon. However, there are limited studies in the existing literature comparing specifically liposomal lidocaine and tetracaine hydrochloride topical creams.

In recent years, the number of scientific publications on artificial intelligence (AI), primarily on machine learning, with respect to neurosurgery, has increased. The aim of the study was to conduct a systematic literature review and identify the main areas of AI applications in neurosurgery.