Gramm, M. | Search bioRxiv

bioRxiv2020

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

Literature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on words from abstracts and/or other text. SimText can be used for (i) data generation: text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis of data using unsupervised learning techniques and visualization in a Shiny web application.Availability and Implementation We developed SimText as an open-source R software and integrated it into Galaxy, an online data analysis platform. A command line version of the toolset is available for download from GitHub at https://github.com/mgramm1/simtext.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2019

Altered Relationship between Soluble TREM2 and Inflammatory Markers in Young Adults with Down Syndrome

Individuals with Down syndrome (DS) develop Alzheimers disease (AD) - related neuropathology, characterized by amyloid plaques with amyloid {beta} (A{beta}) and neurofibrillary tangles with tau accumulation more frequently and at an earlier age than their neurotypical counterparts. Peripheral inflammation and the innate immune response are elevated in DS. Triggering receptor expressed in myeloid cells 2 (TREM2) genetic variants are risk factors for AD and other neurodegenerative diseases. A soluble cleavage product of TREM2 (sTREM2) has been described as elevated in AD cerebrospinal fluid and positively correlates with A{beta} and cognitive decline. There is relatively little information about TREM2 in DS. The objective of this study was to examine the relationship between sTREM2 and inflammatory markers in DS, prior to the development of dementia symptoms. Since TREM2 plays a role in the innate immune response and has been associated with dementia, the hypothesis of this exploratory study was that young adults with DS pre-dementia (n=15, mean age 29.5 years) would exhibit a different relationship between sTREM2 and inflammatory markers in plasma, compared to neurotypical, age-matched controls (n=16, mean age 29.6 years). Indeed, young adults with DS had significantly elevated plasma sTREM2 and inflammatory markers. In addition, in young adults with DS, sTREM2 correlated positively with 24 of the measured cytokines, while there were no significant correlations in the control group. Hierarchical clustering of sTREM2 and cytokine concentrations also differed between the group with DS and controls, supporting the hypothesis that its function is altered in people with DS pre-dementia. This exploratory study provides a basis for future studies investigating the relationship between TREM2 and the broader immune response pre-dementia.

neuroscience↗