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  1. Article ; Online: Comparative Evaluation of Pseudomonas aeruginosa Adhesion to a Poly-(2-Methacryloyloxyethyl Phosphorylcholine)-Modified Silicone Hydrogel Contact Lens

    Valerie Harris / Reed Pifer / Paul Shannon / Monica Crary

    Vision, Vol 7, Iss 27, p

    2023  Volume 27

    Abstract: Pseudomonas aeruginosa is the most common causative agent associated with microbial keratitis. During contact lens wear, pathogens may be introduced into the ocular environment, which might cause adverse events. Lehfilcon A is a recently developed ... ...

    Abstract Pseudomonas aeruginosa is the most common causative agent associated with microbial keratitis. During contact lens wear, pathogens may be introduced into the ocular environment, which might cause adverse events. Lehfilcon A is a recently developed contact lens with a water gradient surface composed of polymeric 2-methacryloyloxyethyl phosphorylcholine (MPC). MPC is re-ported to impart anti-biofouling properties onto modified substrates. Therefore, in this in vitro experimental study, we tested the capability of lehfilcon A to resist adhesion by P. aeruginosa . Quantitative bacterial adhesion assays using five strains of P. aeruginosa were conducted to compare the adherence properties of lehfilcon A to five currently marketed silicone hydrogel (SiHy) contact lenses (comfilcon A, fanfilcon A, senofilcon A, senofilcon C, and samfilcon A). Compared to lehfilcon A, we observed 26.7 ± 8.8 times ( p = 0.0028) more P. aeruginosa binding to comfilcon A, 30.0 ± 10.8 times ( p = 0.0038) more binding to fanfilcon A, 18.2 ± 6.2 times ( p = 0.0034) more binding to senofilcon A, 13.6 ± 3.9 times ( p = 0.0019) more binding to senofilcon C, and 29.5 ± 11.8 times ( p = 0.0057) more binding to samfilcon A. These results demonstrate that, for various strains of P. aeruginosa , lehfilcon A reduces bacterial adhesion compared to other contact lens materials.
    Keywords Pseudomonas aeruginosa ; keratitis ; ocular infection ; contact lenses ; medical device ; 2-methacryloyloxyethyl phosphorylcholine ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Evaluating Alternate Methods of Determining the Antimicrobial Efficacy of Contact Lens Care Products against Acanthamoeba Trophozoites

    Allison Campolo / Paul Shannon / Monica Crary

    Pathogens, Vol 10, Iss 2, p

    2021  Volume 126

    Abstract: Acanthamoeba keratitis (AK) is a serious ocular infection caused by a ubiquitous free-living amoeba, Acanthamoeba . This infection often results in extensive corneal damage and blindness, and is notoriously difficult to cure. While Acanthamoeba is an ... ...

    Abstract Acanthamoeba keratitis (AK) is a serious ocular infection caused by a ubiquitous free-living amoeba, Acanthamoeba . This infection often results in extensive corneal damage and blindness, and is notoriously difficult to cure. While Acanthamoeba is an abundant organism, AK is most associated with contact lens hygiene noncompliance and inadequate contact lens care (CLC) disinfection regimens. Thus, accurate and timely antimicrobial efficacy testing of CLC solutions is paramount. Published methods for antimicrobial efficacy testing of Acanthamoeba trophozoites requires 14 days for results. Presently, alternate and/or rapid methods for evaluating CLC products rarely demonstrate equivalent results compared to commonly-reported methods. Propidium iodide is a cellular stain that can only bind to cells with damaged outer membranes. We evaluated propidium iodide staining as an alternative method for determining the relative antimicrobial efficacy of 11 different CLC products against Acanthamoeba trophozoites. Following exposure to a CLC product, the fluorescence intensity of propidium iodide in an Acanthamoeba population demonstrated a strong correlation to the log reduction determined by established, growth-based Acanthamoeba testing used to evaluate the antimicrobial efficacy of CLC products. Thus, propidium iodide was found to be an effective rapid tool for determining cell death in Acanthamoeba trophozoites following exposure to CLC solutions.
    Keywords Acanthamoeba ; contact lens care ; propidium iodide ; antimicrobial efficacy ; Medicine ; R
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Variables Affecting the Recovery of Acanthamoeba Trophozoites

    Monica J. Crary / Rhonda Walters / Paul Shannon / Manal M. Gabriel

    Pathogens, Vol 10, Iss 2, p

    2021  Volume 221

    Abstract: While the results of Acanthamoeba testing have been extensively published, laboratories conducting such testing are left to develop their own methods in the absence of a standardized methodology. The wide disparity of methods has resulted in equally ... ...

    Abstract While the results of Acanthamoeba testing have been extensively published, laboratories conducting such testing are left to develop their own methods in the absence of a standardized methodology. The wide disparity of methods has resulted in equally inconsistent reported results for contact lens care (CLC) products. This study’s objective was to determine the source of these discrepancies by evaluating basic Acanthamoeba biology and their impact on antimicrobial efficacy testing, including the ability of a recovery method to stimulate a single trophozoite to proliferate. Antimicrobial efficacy testing was conducted using well-published Acanthamoeba strains, storage conditions, and growth-based recovery methods. To identify variables that influence results, test solutions with low Acanthamoeba disinfection rates were utilized to prevent differences from being masked by high log reductions. In addition, single-cell proliferation assays were executed to understand the growth requirements to stimulate trophozoite propagation in two recovery methods. These studies indicated that both nutrient density (>10 6 CFU) and the length of plate incubation (at least 14 days) could significantly influence the accurate recovery of trophozoites. Together, this study emphasizes the need to understand how Acanthamoeba trophozoites biology can impact test methods to create divergent results.
    Keywords Acanthamoeba ; contact lens care ; efficacy testing ; trophozoites ; Medicine ; R
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Correction

    Ravi Madduri / Kyle Chard / Mike D'Arcy / Segun C Jung / Alexis Rodriguez / Dinanath Sulakhe / Eric Deutsch / Cory Funk / Ben Heavner / Matthew Richards / Paul Shannon / Gustavo Glusman / Nathan Price / Carl Kesselman / Ian Foster

    PLoS ONE, Vol 18, Iss 11, p e

    Reproducible big data science: A case study in continuous FAIRness.

    2023  Volume 0294883

    Abstract: This corrects the article DOI:10.1371/journal.pone.0213013.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pone.0213013.].
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Antimicrobial Efficacy of Contact Lens Solutions Assessed by ISO Standards

    Cindy McAnally / Rhonda Walters / Allison Campolo / Valerie Harris / Jamie King / Megan Thomas / Manal M Gabriel / Paul Shannon / Monica Crary

    Microorganisms, Vol 9, Iss 2173, p

    2021  Volume 2173

    Abstract: Microbial keratitis (MK) is an eye infection caused by opportunistic bacteria or fungi, which may lead to sight-threatening corneal ulcers. These microorganisms can be introduced to the eye via improper contact lens usage or hygiene, or ineffective ... ...

    Abstract Microbial keratitis (MK) is an eye infection caused by opportunistic bacteria or fungi, which may lead to sight-threatening corneal ulcers. These microorganisms can be introduced to the eye via improper contact lens usage or hygiene, or ineffective multipurpose solutions (MPSs) to disinfect daily wear contact lenses. Thus, the patient’s choice and use of these MPSs is a known risk factor for the development of MK. It is then critical to determine the efficacy of popular MPSs against ubiquitous ocular microorganisms. Therefore, we compare the efficacy of nine major MPSs on the global market against four different microorganism species, and with four different common contact lenses. In accordance with International Standards Organization protocol 14729 and 18259, the microorganisms were inoculated into each MPS with and without contact lenses, and held for the manufacturer’s disinfection time, 24 h, and 7 days after challenge with Serratia marcescens or Fusarium spp. Plates were incubated for 2–7 days and plate counts were conducted to determine the number of surviving microorganisms. The majority of MPSs demonstrated significantly higher disinfection efficacies without contact lenses. Broadly, among the microorganisms tested, the OPTI-FREE products (Puremoist, Express, and Replenish) maintained the highest disinfection efficacies at the manufacturer’s stated disinfection time when paired with any contact lens, compared with other MPSs. These were followed closely by RevitaLens and renu Advanced. MPSs containing dual biocides polyquaternium-1 and myristamidopropyl dimethylamine possessed the highest disinfection efficacy against multiple ocular pathogens.
    Keywords microbial keratitis ; serratia ; fusarium ; contact lens ; multipurpose disinfecting solution ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: CyREST

    Keiichiro Ono / Tanja Muetze / Georgi Kolishovski / Paul Shannon / Barry Demchak

    F1000Research, Vol

    Turbocharging Cytoscape Access for External Tools via a RESTful API [v1; ref status: indexed, http://f1000r.es/5ly]

    2015  Volume 4

    Abstract: As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and ... ...

    Abstract As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.
    Keywords Bioinformatics ; Medicine ; R ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2015-08-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Reproducible big data science

    Ravi Madduri / Kyle Chard / Mike D'Arcy / Segun C Jung / Alexis Rodriguez / Dinanath Sulakhe / Eric Deutsch / Cory Funk / Ben Heavner / Matthew Richards / Paul Shannon / Gustavo Glusman / Nathan Price / Carl Kesselman / Ian Foster

    PLoS ONE, Vol 14, Iss 4, p e

    A case study in continuous FAIRness.

    2019  Volume 0213013

    Abstract: Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, ...

    Abstract Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and reusable forms, and harness fast networks and powerful cloud computers to process data rapidly, all without sacrificing usability or reproducibility-thus ensuring that big data are not hard-to-(re)use data. We evaluate our approach via a user study, and show that 91% of participants were able to replicate a complex analysis involving considerable data volumes.
    Keywords Medicine ; R ; Science ; Q
    Subject code 306
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Wrangling phosphoproteomic data to elucidate cancer signaling pathways.

    Mark L Grimes / Wan-Jui Lee / Laurens van der Maaten / Paul Shannon

    PLoS ONE, Vol 8, Iss 1, p e

    2013  Volume 52884

    Abstract: The interpretation of biological data sets is essential for generating hypotheses that guide research, yet modern methods of global analysis challenge our ability to discern meaningful patterns and then convey results in a way that can be easily ... ...

    Abstract The interpretation of biological data sets is essential for generating hypotheses that guide research, yet modern methods of global analysis challenge our ability to discern meaningful patterns and then convey results in a way that can be easily appreciated. Proteomic data is especially challenging because mass spectrometry detectors often miss peptides in complex samples, resulting in sparsely populated data sets. Using the R programming language and techniques from the field of pattern recognition, we have devised methods to resolve and evaluate clusters of proteins related by their pattern of expression in different samples in proteomic data sets. We examined tyrosine phosphoproteomic data from lung cancer samples. We calculated dissimilarities between the proteins based on Pearson or Spearman correlations and on Euclidean distances, whilst dealing with large amounts of missing data. The dissimilarities were then used as feature vectors in clustering and visualization algorithms. The quality of the clusterings and visualizations were evaluated internally based on the primary data and externally based on gene ontology and protein interaction networks. The results show that t-distributed stochastic neighbor embedding (t-SNE) followed by minimum spanning tree methods groups sparse proteomic data into meaningful clusters more effectively than other methods such as k-means and classical multidimensional scaling. Furthermore, our results show that using a combination of Spearman correlation and Euclidean distance as a dissimilarity representation increases the resolution of clusters. Our analyses show that many clusters contain one or more tyrosine kinases and include known effectors as well as proteins with no known interactions. Visualizing these clusters as networks elucidated previously unknown tyrosine kinase signal transduction pathways that drive cancer. Our approach can be applied to other data types, and can be easily adopted because open source software packages are employed.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book: Design presentation

    Paul, Shannon

    (CPL bibliography ; no. 298)

    1993  

    Author's details Shannon Paul
    Series title CPL bibliography ; no. 298
    Language English
    Size 41 S
    Publisher Council of Planning Librarians
    Publishing place Knoxville, Tenn
    Document type Book
    Note Includes index
    ISBN 0866022988 ; 9780866022989
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  10. Article: Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

    Bonneau, Richard / Eric W Deutsch / Leroy Hood / Nitin S Baliga / Paul Shannon

    Genome biology. 2004 July, v. 5, no. 8

    2004  

    Abstract: BACKGROUND: Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of ... ...

    Abstract BACKGROUND: Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function. RESULTS: We have used Rosetta de novo structure prediction to predict three-dimensional structures for 1,185 proteins and protein domains (<150 residues in length) found in Halobacterium NRC-1, a widely studied halophilic archaeon. Predicted structures were searched against the Protein Data Bank to identify fold similarities and extrapolate putative functions. They were analyzed in the context of a predicted association network composed of several sources of functional associations such as: predicted protein interactions, predicted operons, phylogenetic profile similarity and domain fusion. To illustrate this approach, we highlight three cases where our combined procedure has provided novel insights into our understanding of chemotaxis, possible prophage remnants in Halobacterium NRC-1 and archaeal transcriptional regulators. CONCLUSIONS: Simultaneous analysis of the association network, coordinated mRNA level changes in microarray experiments and genome-wide structure prediction has allowed us to glean significant biological insights into the roles of several Halobacterium NRC-1 proteins of previously unknown function, and significantly reduce the number of proteins encoded in the genome of this haloarchaeon for which no annotation is available.
    Keywords chemotaxis ; databases ; gene expression ; Halobacterium ; messenger RNA ; microarray technology ; operon ; phylogeny ; prediction ; protein synthesis ; transcription factors
    Language English
    Dates of publication 2004-07
    Size p. 856.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2004-5-8-r52
    Database NAL-Catalogue (AGRICOLA)

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