Identification of a broad-spectrum high-affinity peptide ligand for the purification of spike proteins.

Since the outbreak of coronavirus disease 2019, the global demand for vaccines has increased rapidly to prevent infection and protect high-risk populations. However, identifying viral mutations poses an additional challenge for chromatographic purification of vaccines and subunit vaccines. In this study, a new affinity peptide model, X1VX2GLNX3WX4RYSK, was established, and a library of 612 peptides was generated for ligand screening. Based on a multistep strategy of ligand screening, 18 candidate peptides were obtained. The top ranking peptide, LP14 (YVYGLNIWLRYSK), and two other representative peptides, LP02 and LP06, with lower rankings were compared via molecular dynamics simulation. The results revealed that peptide binding to the receptor binding domain (RBD) was driven by hydrophobic interactions and the key residues involved in the binding were identified. Surface plasmon resonance analysis further confirmed that LP14 had the highest affinity for the wild RBD (Kd=0.520 µmol/L), and viral mutation had little influence on the affinity of LP14, demonstrating its great potential as a broad-spectrum ligand for RBD purification. Finally, chromatographic performance of LP14-coupled gel-packed column verified that both wild and omicron RBDs could be purified and were eluted by 0.1 mol/L Gly-HCl buffer (pH 3.0). This research identified a broad-spectrum peptide for RBD purification based on rational design and demonstrated its potential application in the purification of RBDs from complex feedstock.

The p38 MAPK/snail signaling axis participates in cadmium-induced lung cancer cell migration and invasiveness.

To determine that p38 MAPK activation contributes to the migration and invasion of lung cancer cells caused by cadmium (Cd). A549 lung cancer cell migration and invasion were assessed using a transwell plate system, and the role of p38 was determined by knocking down p38 activity with two different inhibitors of p38. The activity of p38 was measured by western blot analysis using phospho-specific p38 antibodies and normalized to blots using antibodies directed to total p38 proteins. Snail transcripts were measured using qRT-PCR. The inhibition of p38 blocked Cd-induced migration and invasion, which correlated with an increased activation of p38 as a function of dose and time. Furthermore, Cd-induced activation of p38 MAPK controlled the increase of snail mRNA expression. The p38 MAPK/snail signaling axis was involved in Cd-induced lung cancer cell migration and invasion.

Development of a Natural Language Processing System to Identify Clinical Documentation of Electronic Cigarette Use.

Electronic Nicotine Delivery Systems (ENDS) use has increased substantially in the United States since 2010. To date, there is limited evidence regarding the nature and extent of ENDS documentation in the clinical note. In this work we investigate the effectiveness of different approaches to identify a patient's documented ENDS use. We report on the development and validation of a natural language processing system to identify patients with explicit documentation of ENDS using a large national cohort of patients at the United States Department of Veterans Affairs.

Determining the prevalence of cannabis, tobacco, and vaping device mentions in online communities using natural language processing.

INTRODUCTION: The relationship between cannabis, tobacco, and vaping devices is both rapidly changing and poorly understood, with consumers rapidly shifting between use of all three product types. Given this dynamic and evolving landscape, there is an urgent need to monitor and better understand co-use, dual-use, and transition patterns between these products. This study describes work that utilizes social media - in this case, Reddit - in conjunction with automated Natural Language Processing (NLP) methods to better understand cannabis, tobacco, and vaping device product usage patterns. METHODS: We collected Reddit data from the period 2013-2018, sourced from eight popular, high-volume Reddit communities (subreddits) related to the three product categories. We then manually annotated (coded) a set of 2640 Reddit posts and trained a machine learning-based NLP algorithm to automatically identify and disambiguate between cannabis or tobacco mentions (both smoking and vaping) in Reddit posts. This classifier was then applied to all data derived from the eight subreddits, 767,788 posts in total. RESULTS: The NLP algorithm achieved an overall moderate performance (overall F-score of 0.77). When applied to our large corpus of Reddit posts, we discovered that over 10% of posts in the smoking cessation subreddit r/stopsmoking were classified as referring to vaping nicotine, and that only 2% of posts from the subreddits r/electronic_cigarette and r/vaping were classified as referring to smoking (tobacco) cessation. CONCLUSIONS: This study presents the results of applying an NLP algorithm designed to identify and distinguish between cannabis and tobacco mentions (both smoking and vaping) in Reddit posts, hence contributing to our currently limited understanding of co-use, dual-use, and transition patterns between these products.

Examining Cannabis, Tobacco, and Vaping Discourse on Reddit: An Exploratory Approach Using Natural Language Processing.

Background: Perceptions of tobacco, cannabis, and electronic nicotine delivery systems (ENDS) are continually evolving in the United States. Exploring these characteristics through user generated text sources may provide novel insights into product use behavior that are challenging to identify using survey-based methods. The objective of this study was to compare the topics frequently discussed among Reddit members in cannabis, tobacco, and ENDS-specific subreddits. Methods: We collected 643,070 posts on the social media site Reddit between January 2013 and December 2018. We developed and validated an annotation scheme, achieving a high level of agreement among annotators. We then manually coded a subset of 2,630 posts for their content with relation to experiences and use of the three products of interest, and further developed word cloud representations of the words contained in these posts. Finally, we applied Latent Dirichlet Allocation (LDA) topic modeling to the 643,070 posts to identify emerging themes related to cannabis, tobacco, and ENDS products being discussed on Reddit. Results: Our manual annotation process yielded 2,148 (81.6%) posts that contained a mention(s) of either cannabis, tobacco, or ENDS with 1,537 (71.5%) of these posts mentioning cannabis, 421 (19.5%) mentioning ENDS, and 264 (12.2%) mentioning tobacco. In cannabis-specific subreddits, personal experiences with cannabis, cannabis legislation, health effects of cannabis use, methods and forms of cannabis, and the cultivation of cannabis were commonly discussed topics. The discussion in tobacco-specific subreddits often focused on the discussion of brands and types of combustible tobacco, as well as smoking cessation experiences and advice. In ENDS-specific subreddits, topics often included ENDS accessories and parts, flavors and nicotine solutions, procurement of ENDS, and the use of ENDS for smoking cessation. Conclusion: Our findings highlight the posting and participation patterns of Reddit members in cannabis, tobacco, and ENDS-specific subreddits and provide novel insights into aspects of personal use regarding these products. These findings complement epidemiologic study designs and highlight the potential of using specific subreddits to explore personal experiences with cannabis, ENDS, and tobacco products.

Investigating the Attitudes of Adolescents and Young Adults Towards JUUL: Computational Study Using Twitter Data.

BACKGROUND: Increases in electronic nicotine delivery system (ENDS) use among high school students from 2017 to 2019 appear to be associated with the increasing popularity of the ENDS device JUUL. OBJECTIVE: We employed a content analysis approach in conjunction with natural language processing methods using Twitter data to understand salient themes regarding JUUL use on Twitter, sentiment towards JUUL, and underage JUUL use. METHODS: Between July 2018 and August 2019, 11,556 unique tweets containing a JUUL-related keyword were collected. We manually annotated 4000 tweets for JUUL-related themes of use and sentiment. We used 3 machine learning algorithms to classify positive and negative JUUL sentiments as well as underage JUUL mentions. RESULTS: Of the annotated tweets, 78.80% (3152/4000) contained a specific mention of JUUL. Only 1.43% (45/3152) of tweets mentioned using JUUL as a method of smoking cessation, and only 6.85% (216/3152) of tweets mentioned the potential health effects of JUUL use. Of the machine learning methods used, the random forest classifier was the best performing algorithm among all 3 classification tasks (ie, positive sentiment, negative sentiment, and underage JUUL mentions). CONCLUSIONS: Our findings suggest that a vast majority of Twitter users are not using JUUL to aid in smoking cessation nor do they mention the potential health benefits or detriments of JUUL use. Using machine learning algorithms to identify tweets containing underage JUUL mentions can support the timely surveillance of JUUL habits and opinions, further assisting youth-targeted public health intervention strategies.

Recent Advances in Using Natural Language Processing to Address Public Health Research Questions Using Social Media and ConsumerGenerated Data.

OBJECTIVE: We present a narrative review of recent work on the utilisation of Natural Language Processing (NLP) for the analysis of social media (including online health communities) specifically for public health applications. METHODS: We conducted a literature review of NLP research that utilised social media or online consumer-generated text for public health applications, focussing on the years 2016 to 2018. Papers were identified in several ways, including PubMed searches and the inspection of recent conference proceedings from the Association of Computational Linguistics (ACL), the Conference on Human Factors in Computing Systems (CHI), and the International AAAI (Association for the Advancement of Artificial Intelligence) Conference on Web and Social Media (ICWSM). Popular data sources included Twitter, Reddit, various online health communities, and Facebook. RESULTS: In the recent past, communicable diseases (e.g., influenza, dengue) have been the focus of much social media-based NLP health research. However, mental health and substance use and abuse (including the use of tobacco, alcohol, marijuana, and opioids) have been the subject of an increasing volume of research in the 2016 - 2018 period. Associated with this trend, the use of lexicon-based methods remains popular given the availability of psychologically validated lexical resources suitable for mental health and substance abuse research. Finally, we found that in the period under review "modern" machine learning methods (i.e. deep neural-network-based methods), while increasing in popularity, remain less widely used than "classical" machine learning methods.