Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity.
ABSTRACT: Identifying the genes and proteins associated with a biological process or disease is a central goal of the biomedical research enterprise. However, relatively few systematic approaches are available that provide objective evaluation of the genes or proteins known to be important to a research topic, and hence researchers often rely on subjective evaluation of domain experts and laborious manual literature review. Computational bibliometric analysis, in conjunction with text mining and data curation, attempts to automate this process and return prioritized proteins in any given research topic. We describe here a method to identify and rank protein-topic relationships by calculating the semantic similarity between a protein and a query term in the biomerical literature while adjusting for the impact and immediacy of associated research articles. We term the calculated metric the weighted copublication distance (WCD) and show that it compares well to related approaches in predicting benchmark protein lists in multiple biological processes. We used WCD to extract prioritized "popular proteins" across multiple cell types, subanatomical regions, and standardized vocabularies containing over 20?000 human disease terms. The collection of protein-disease associations across the resulting human "diseasome" supports data analytical workflows to perform reverse protein-to-disease queries and functional annotation of experimental protein lists. We envision that the described improvement to the popular proteins strategy will be useful for annotating protein lists and guiding method development efforts as well as generating new hypotheses on understudied disease proteins using bibliometric information.
Project description:<h4>Background</h4>Climate change is a problem which is global in nature, and whose effects go across a wide range of disciplines. It is therefore important that this theme is taken into account as part of universities´ teaching and research programs.<h4>Methods</h4>A three-tiered approach was used, consisting of a bibliometric analysis, an online survey and a set of case studies, which allow a profile to be built, as to how a sample of universities from 45 countries handle climate change as part of their teaching programs.<h4>Results</h4>This paper reports on a study which aimed at identifying the extent to which matters related to climate change are addressed within the teaching and research practices at universities, with a focus on the training needs of teaching staff. It consists of a bibliometric analysis, combined with an online worldwide survey aimed at ascertaining the degree of involvement from universities in reducing their own carbon footprint, and the ways they offer training provisions on the topic. This is complemented by a set of 12 case studies from universities round the world, illustrating current trends on how universities handle climate change. Apart from reporting on the outcomes of the study, the paper highlights what some universities are doing to handle climate issues, and discusses the implications of the research.<h4>Conclusions</h4>The paper lists some items via which universities may better educate and train their students on how to handle the many challenges posed by climate change.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1186/s12302-021-00552-5.
Project description:Background:Wearable cardioverter-defibrillators (WCD, LifeVest, ZOLL) can protect from sudden cardiac death bridging a vulnerable period until a decision on implantable cardioverter-defibrillator (ICD) implantation can be reached. WCD is commonly used for 3 months or less. It is unknown, which patients use WCD longer and which patients are most likely to benefit from it. Hypothesis:Extended use of WCD is reasonable in selected cases based on underlying heart disease and overall patient risk profile. Methods:We conducted a systematic and comprehensive research of all published clinical studies on PubMed reporting on the use of the WCD. Only original articles reporting on wear times and time to appropriate shocks were included in our analysis. Results:The search resulted in 127 publications. 14 parameters were reported necessary for inclusion in our analysis. Median wear times ranged from 16 to 394 days. The median wear time was especially long for patients suffering from nonischemic cardiomyopathy (NICM) (range: 50-71 days) and specifically peripartum cardiomyopathy (PPCM) (120 days) and for heart transplant candidates. There was a large variation of appropriate shocks according to indication for WCD use. In contrast to NICM in general, the number of appropriate shocks was particularly high in patients with PPCM (0 in 254 patients and 5 in 49 patients, respectively). The median and maximal time periods to the first appropriate shock were longest in patients with PPCM (median time to the first appropriate shock: 68 days). Conclusions:Prolonged use of WCD is not uncommon in available literature. Patients suffering from NICM and specifically PPCM seem most likely to have longer therapy duration with WCD with success. Careful patient selection for prolonged use may decrease the need for ICD implantation in the future; however, prospective data are needed to confirm this hypothesis.
Project description:<h4>Objective</h4>The study quantitatively investigated the related research progress in pharmaceutical sciences/pharmacy education from a bibliometric angle and provided feasible suggestions to facilitate the development of pharmaceutical sciences/pharmacy postgraduate education.<h4>Methods</h4>Bibliometric analysis was conducted using the database of Web of Science Core Collection. The literature published in 1985-2021 was screened and selected. The overall profile description, citation analysis, and research hotspot mining were performed using the citation report of Clarivate Analytics, bibliometrics online platform, and VOSviewer software. The bibliometric results and profiles were plotted and illustrated.<h4>Results</h4>The bibliometric analysis of 485 papers of interest showed that the research frontier was continuously expanding; especially the institutions from the USA were the main contributors. The numbers of citing papers have been ascending, and a considerable part of citations were from the areas other than the education research. Mining results showed that the in-school and residency education of pharmacy postgraduates was a research hotspot, as well as interprofessional training and new education styles for Coronavirus Disease 2019 (COVID-19) therapy were the emerging trends in the field.<h4>Conclusion</h4>Through the analysis of the studies, it was found that encouraging relevant research programs, establishing financial supports, and launching specified publication sources could be helpful to boost the development of pharmaceutical sciences/pharmacy postgraduate education. Besides, the results suggested that this was a less discussed topic and was worthy for the investigators to pay more attention to such an issue.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s12247-021-09611-z.
Project description:This article surveys topic distributions of the academic literature that employs the terms bibliometrics, scientometrics, and informetrics. This exploration allows informing on the adoption of those terms and publication patterns of the authors acknowledging their work to be part of bibliometric research. We retrieved 20,268 articles related to bibliometrics and applied methodologies that exploit various features of the dataset to surface different topic representations. Across them, we observe major trends including discussions on theory, regional publication patterns, databases, and tools. There is a great increase in the application of bibliometrics as science mapping and decision-making tools in management, public health, sustainability, and medical fields. It is also observed that the term bibliometrics has reached an overall generality, while the terms scientometrics and informetrics may be more accurate in representing the core of bibliometric research as understood by the information and library science field. This article contributes by providing multiple snapshots of a field that has grown too quickly beyond the confines of library science.
Project description:Emotions are considered a fundamental aspect of sport scenarios, and within sports, consumer behavior is a very popular area of research in the sport management field. Thus, in recent years, there has been a growing interest for sport managers regarding the role that emotions play in sport consumer behavior. Thus, the aim of this paper is to provide an overview of the academic research on emotions in the sport management field using two techniques: a bibliometric performance analysis and a graphic mapping of the references in this field. This analysis focuses on authors, journals, papers, institutions and countries. Bibliometric indicators including the h-index measure, productivity and the number of citations were used to perform the performance analysis. Then, VOSviewer software was used to perform co-citation, bibliographic coupling and co-occurrence of keyword analysis (mapping analysis). The results of both types of analysis are consistent, with the United States being the most influential country in emotions in sport management research because the main authors and institutions in this research field belong to this country. The overall results indicate that the literature on this research topic has grown significantly in recent years in all scientific disciplines; however, the research topic is incipient, and therefore, the number of articles is still limited. Thus, this research presents the key aspects in the topic of emotions in sport management that could be helpful for researchers and policy makers in the field of sport management to make future decisions.
Project description:Cohort studies collect, generate and distribute data over long periods of time – often over the lifecourse of their participants. It is common for these studies to host a list of publications (which can number many thousands) on their website to demonstrate the impact of the study and facilitate the search of existing research to which the study data has contributed. The ability to search and explore these publication lists varies greatly between studies. We believe a lack of rich search and exploration functionality of study publications is a barrier to entry for new or prospective users of a study’s data, since it may be difficult to find and evaluate previous work in a given area. These lists of publications are also typically manually curated, resulting in a lack of rich metadata to analyse, making bibliometric analysis difficult. We present here a software pipeline that aggregates metadata from a variety of third-party providers to power a web based search and exploration tool for lists of publications. Alongside core publication metadata (i.e. author lists, keywords etc.), we include geocoding of first authors and citation counts in our pipeline. This allows a characterisation of a study as a whole based on common locations of authors, frequency of keywords, citation profile etc. This enriched publications metadata can be useful for generating study impact metrics and web-based graphics for public dissemination. In addition, the pipeline produces a research data set for bibliometric analysis or social studies of science. We use a previously published list of publications from a cohort study as an exemplar input data set to show the output and utility of the pipeline here.
Project description:Recently, substantial studies have increased around the topic of the tai chi fall-prevention field. Few studies, however, have revealed the current progress and hotspots under a bibliometric analysis. Therefore, the present study aimed to conduct Citespace, a significant application for bibliometric analysis, to carry out the situation and trend in this field. This study has identified the core countries are the United States, China, Australia, and England, which are also the origins of the core institutions. Besides this, we also have found two large research groups led by Li and Sherrington. Moreover, the result has revealed that <i>J Aging Phys Act</i> and <i>J Am Geriatr Soc</i> are the primary journals. Geriatrics and gerontology, sport sciences, rehabilitation, and gerontology are the leading categories. Furthermore, one of the more important findings to come out in this study are that "elderly", "Parkinson's disease", "vestibular rehabilitation", "frail patient", and "community fall prevention" are the research hotspots. "Women", "proprioception", "cognitive impairment", "dementia", "osteoarthritis", and "stroke" are the potential research trend in the future. These findings suggest that the tai chi fall-prevention field has a broad research prospect. Although several questions remain uncertain currently, it is worthy for scholars to do further study.
Project description:The US scientific workforce is primarily composed of White men. Studies have demonstrated the systemic barriers preventing women and other minoritized populations from gaining entry to science; few, however, have taken an intersectional perspective and examined the consequences of these inequalities on scientific knowledge. We provide a large-scale bibliometric analysis of the relationship between intersectional identities, topics, and scientific impact. We find homophily between identities and topic, suggesting a relationship between diversity in the scientific workforce and expansion of the knowledge base. However, topic selection comes at a cost to minoritized individuals for whom we observe both between- and within-topic citation disadvantages. To enhance the robustness of science, research organizations should provide adequate resources to historically underfunded research areas while simultaneously providing access for minoritized individuals into high-prestige networks and topics.
Project description:<h4>Background</h4>Kidney transplantation (KT) has become common in the treatment of end-stage renal disease. However, to date, there have been no bibliometric analyses of KT research to identify the most influential articles. The purpose of this research is to identify and characterize the 100 most cited articles that focus on KT and to clarify the trends in the accomplishments in this field.<h4>Methods</h4>We searched the Thomson Reuters Web of Science citation indexing database and used keyword mapping of VOSviewer. The top 100 most cited manuscripts were analyzed based on their titles, authors, institutions, countries of origin, years of publication, and topics.<h4>Results</h4>The New England Journal of Medicine has published the most manuscripts on kidney transplantation (n = 26) and is the most cited journal (n = 15,642). The United States has the highest number of publications (n = 61). Kashika is the corresponding author with the most published papers (n = 5; 2892 citations). The most common topics of publication are immunosuppressant (n = 34), clinical outcome (n = 26), and pathology (n = 22). Keywords related to immunosuppressant are the most common in keyword mapping with VOSviewer.<h4>Conclusions</h4>This bibliometric analysis of KT research provides the research characteristics and publication trends of this topic. In KT research, immunosuppressants and post-transplant clinical outcomes have been important topics.
Project description:BACKGROUND:Psychological distress is common in patients with cardiovascular disease and negatively impacts outcome. HYPOTHESIS:Psychological distress is high in acute high risk cardiac patients eligible for a WCD, and associated with low quality of life. Distress is aggravated by WCD. METHODS:Consecutive patients eligible for a WCD were included in the prospective, multicenter "Cologne Registry of External Defibrillator" registry. Quality of life (Short Form-12), depressive symptoms (Beck-Depression Inventory II) and anxiety (State Trait Anxiety Inventory) were assessed at enrollment and 6-weeks, and associations with WCD prescription were analyzed. RESULTS:123 patients (mean [SD] age 59 [± 14] years, 75% male) were included, 85 (69%) of whom received a WCD. At enrollment 21% showed clinically significant depressive symptoms and 52% anxiety symptoms, respectively. At 6 weeks, depressive and anxious symptoms significantly decreased to 7% and 25%, respectively. Depressive symptoms at enrollment and changes at 6 weeks showed significant associations with health-related quality of life, whereas anxious symptoms did not. There was a trend for better improvement of depression scores in patients with WCD (mean [SD] change in score points: -4.1 [6.1] vs -1.8 [3.9]; p = 0.09), whereas change of the anxiousness score was not different (-4.6 [9.5]) vs -3.7 [9.1], p = 0.68). CONCLUSION:In patients eligible for a WCD, depressive and anxiety symptoms were initially common and depressive symptoms showed a strong association with reduced health-related quality of life contributing to their clinical relevance. WCD recipients showed at least similar improvement of depression and anxiety at 6 weeks when compared to non recipients.