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Inflammatory responses of the intestinal epithelial barrier in patients with Crohn's disease (CD), a chronic inflammatory bowel disease (IBD), are associated with gut microbial alterations. At a community level, there is scarce mechanistic evidence on the effects of gut microbial alterations on host mucosal barrier responses. We used a computational microbe-host interaction prediction framework based on network diffusion and systems biology to integrate publicly available paired gut microbial and intestinal gene expression datasets. The ileal signaling network potentially modulated by the microbiota was enriched with immune-related pathways such as those associated with IL-4, IL-2, IL-13, NFkB, and toll-like receptors. We identified bacterial proteins eliciting post-translational modifications on host receptors, resulting in the de-repression of pro-inflammatory cytokines via critical hub proteins such as NFkB. The signaling networks were over-represented with CD associated genes and CD drug targets. Using datasets generated from our validation cohorts, we confirmed some of the results., Competing Interests: BV reports financial support for research from 10.13039/100004319Pfizer; lecture fees from 10.13039/100006483Abbvie, 10.13039/501100003122Ferring, 10.13039/100005570Takeda Pharmaceuticals, 10.13039/100005205Janssen, and R Biopharm; consultancy fees from Janssen and Sandoz. JS reports lecture fees from Abbvie, Takeda, Janssen, and 10.13039/100010886Nestle Health Sciences. MF reports financial support for: research from AbbVie, 10.13039/100000042Amgen, Biogen, Janssen, Pfizer, Takeda; consultancy from Abbvie, Boehringer-Ingelheim, Lilly, MSD, Pfizer,Sandoz,Takeda, and Thermo Fisher; speaking from Abbvie, Amgen, Biogen, Boehringer-Ingelheim, Falk, Ferring, Janssen, Lamepro, MSD, Mylan, Pfizer, Sandoz, Takeda, and Truvion Healthcare. GM received financial support for research from DSM Nutritional Products, Karyopharm Therapeutics, and Janssen. SV reports financial support for: research from MSD, AbbVie, Takeda, Pfizer, J&J; lectures from MSD, AbbVie, Takeda, Ferring, Centocor, Hospira,Pfizer, J&J, Genentech/Roche; consultancy fromMSD,AbbVie,Takeda,Ferring, Centocor, Hospira,Pfizer, J&J,Genentech/Roche,Celgene, Mundipharma, Celltrion, Second Genome, Prometheus, Shire, Prodigest, Gilead, Galapagos., (© 2022 The Authors.)

Abstract: The purpose of this multisite, randomized, pretest/posttest quasi-experimental study was to compare student nurse competency, learning retention, and perceived student support after exposure to a deliberate practice debriefing versus standardized debriefing. Fifty undergraduate students participated in the complex response to rescue simulation. The intervention group had significantly higher total mean and three subscale scores on the competency tool than the comparison group, although differences in learning retention and student support were not significant. This study provides preliminary support for the effectiveness of deliberate practice debriefing to enhance students' mastery of skills and behaviors in complex simulations., Competing Interests: The authors have declared no conflict of interest., (Copyright © 2020 National League for Nursing.)

The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a context specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis., Competing Interests: The authors have declared that no competing interests exist.

Microbiome-host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe-host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions-as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn's disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.

The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior over time. Furthermore, they can suggest new directions to deal with influenza. This work presents triplet entropy analysis as a potential phylodynamic tool to quantify nucleotide organization of viral sequences. The application of this measure to segments of hemagglutinin (HA) and neuraminidase (NA) of H1N1 and H3N2 virus subtypes has shown some variability effects along timeline, inferring about virus evolution. Sequences were divided by year and compared for virus subtype (H1N1 and H3N2). The nonparametric Mann-Whitney test was used for comparison between groups. Results show that differentiation in entropy precedes differentiation in GC content for both groups. Considering the HA fragment, both triplet entropy as well as GC concentration show intersection in 2009, year of the recent pandemic. Some conclusions about possible flu evolutionary lines were drawn., (© 2013 Elsevier B.V. All rights reserved.)