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

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

cyjShiny: A cytoscape.js R Shiny Widget for network visualization and analysis.

cyjShiny is an open-source R package that allows users to embed network visualization into Shiny apps and R Markdown documents. cyjShiny (https://github.com/cytoscape/cyjShiny) builds on the cytoscape.js Javascript graph library. Additionally, the package provides helper functions to convert common R data representations (e.g., data.frame) into forms compatible with cytoscape.js.

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

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.

Complete Recovery of Acanthamoeba Motility among Surviving Organisms after Contact Lens Care Disinfection.

Acanthamoeba keratitis is a sight-threatening infection of the cornea which is extremely challenging to treat. Understanding this organism's responses during contact lens contact and disinfection could enhance our understanding of how Acanthamoebae colonize contact lens cases, better inform us on contact lens care solution (CLC) efficacy, and help us better understand the efficacy required of CLC products. To explore this gap in knowledge, we used Acanthamoeba ATCC 30461 and ATCC 50370 trophozoites to examine Acanthamoeba behavior during and after CLC disinfection. Amoebae were added to sterile aluminum flow cells and flow cell solutions were changed to Ringer's solution (control), or one of four CLCs based on biocides (PHMB, PAPB/Polyquad, Polyquad/Aldox, or Polyquad/Alexidine) for 6 h. Each flow cell solution was then changed to axenic culture media (AC6) for 12 h to determine the behavior of amoebae following disinfection. Distance, speed, and displacement were calculated for each organism. As compared to the control of one-quarter Ringer's solution, each CLC significantly impacted Acanthamoeba motility in both the CLC and AC6 conditions. However, the amoebae challenged with the PHMB CLC traveled a significantly greater total distance than with the other three CLCs, indicating differences in effectiveness between biocides. Furthermore, amoebae regaining motility post-disinfection by CLCs were observed to travel considerable distances and thus could be considered dangerous to ocular health. We determined that while all CLCs produced a substantial or complete cessation of movement vs. the control condition during disinfection, those which relied on the Polyquad biocides were the most effective, and that any amoebae which survived disinfection were able to recover motility. Future examinations of these findings should include direct correlations between motility and viability, and how infectivity and motility may be related.

Evaluation of Serratia marcescens Adherence to Contact Lens Materials.

Bacterial keratitis is a risk associated with the use of contact lenses for cosmetic purposes or vision correction. In this in vitro experimental study, we examined the ability of the ocular pathogen Serratia marcescens to adhere to monthly or biweekly replacement contact lenses. We performed quantitative adhesion assays to evaluate the adherence of S. marcescens to seven contact lens materials: comfilcon A, senofilcon A, omafilcon B, fanfilcon A, balafilcon A, senofilcon C, and lehfilcon A. Lehfilcon A is a newly marketed silicon hydrogel contact lens with a surface modification of poly-(2-methacryloyloxyethyl phosphorylcholine) (PMPC). PMPC has previously been demonstrated to be an effective anti-biofouling treatment for numerous surfaces. We observed low S. marcescens adherence to lehfilcon A compared to other materials. We demonstrate the use of the fluorescent dye 5(6)-Carboxytetramethylrhodamine succinimidyl ester to covalently stain live cells prior to material adhesion studies.

Microbial Adherence to Contact Lenses and Pseudomonas aeruginosa as a Model Organism for Microbial Keratitis.

Microbial keratitis (MK), the infection of the cornea, is a devastating disease and the fifth leading cause of blindness and visual impairment around the world. The overwhelming majority of MK cases are linked to contact lens wear combined with factors which promote infection such as corneal abrasion, an immunocompromised state, improper contact lens use, or failing to routinely disinfect lenses after wear. Contact lens-related MK involves the adherence of microorganisms to the contact lens. Therefore, this review discusses the information currently available regarding the disease pathophysiology, the common types of microorganisms causing MK, physical and organic mechanisms of adhesion, material properties which are involved in adhesion, and current antimicrobial strategies. This review also concludes that Pseudomonas aeruginosa is a model organism for the investigation of contact lens microbial adherence due to its prevalence in MK cases, its extremely robust adhesion, antimicrobial-resistant properties, and the severity of the disease it causes.

Reduction of disinfection efficacy of contact lens care products on the global market in the presence of contact lenses and cases.

OBJECTIVE: Sight-threatening infections can be caused by pathogenic micro-organisms colonising the cornea, leading to microbial keratitis (MK). These micro-organisms can be introduced to the eye via improper contact lens use and care. MK can also result from ineffective contact lens care solutions (CLCs), even if the patient is following best practice guidelines. Therefore, it is critical to understand the differences between the effectiveness of popular CLCs on the global market. METHODS AND ANALYSIS: Following the International Standards Organisation standards 14 729 and 18259, bacteria (Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus), fungi (Candida albicans, Fusarium strains) and Acanthamoeba strains were inoculated into each CLC with and without contact lenses, and held for the manufacturer's stated disinfection time. Plate counts were conducted to determine the number of surviving micro-organisms. RESULTS: All CLCs examined met the primary log reduction criteria during stand-alone testing for Pseudomonas, Staphylococcus, Candida and Fusarium. renu Multiplus, All Clean Soft, and Kombilösung Super did not meet the primary criteria when challenged with Serratia. Only OPTI-FREE Express exceeded 4 log reduction for both strains of Acanthamoeba tested. We noted a substantial reduction in disinfection efficacy when CLCs were challenged with Fusarium in the presence of lenses and cases versus stand-alone testing. OPTI-FREE Express demonstrated significantly less net log reduction loss than the other four CLCs tested. CONCLUSION: Of the popular CLCs on the global market, the product which relies on dual biocides polyquaternium-1 and myristamidopropyl dimethylamine demonstrated the highest disinfection efficacy in microbial disinfection challenges in the absence and presence of contact lenses.

Differential Antimicrobial Efficacy of Preservative-Free Contact Lens Disinfection Systems against Common Ocular Pathogens.

Microbial keratitis is a devastating disease that can cause eye damage and blindness and can be the result of infections by several common ocular pathogens. Importantly, some of these pathogens, such as Acanthamoeba, are particularly unsusceptible to biocides in common contact lens care solutions. Therefore, the disinfection efficacy of preservative-free (PF) disinfection systems against bacteria, fungi, and Acanthamoeba trophozoites and cysts should be assessed as products with the most potential to be efficacious against resistant organisms. PF disinfection systems were analyzed for antimicrobial efficacy. These were the one-step (hydrogen peroxide-based) Clear Care and Clear Care Plus systems and the two-step (povidone-iodine-based) Cleadew system. Stand-alone challenges using bacteria, fungi, and Acanthamoeba were prepared according to the International Standards Organization method 14729. These same challenges were also conducted in the presence of the following contact lenses: Boston RGP, Acuvue Oasys, Biofinity, Ultra, and 2-week PremiO. All challenges were performed at the manufacturer's recommended disinfection time. All preservative-free disinfection systems demonstrated similarly high rates of antimicrobial efficacy when challenged with bacteria or fungi, with or without lenses. However, both Clear Care and Clear Care Plus demonstrated significantly greater disinfection efficacy against Acanthamoeba trophozoites and cysts, with and without lenses (P < 0.05). Cleadew efficacy was impacted by the addition of contact lenses, whereas Clear Care/Clear Care Plus maintained similar efficacies in the absence or presence of lenses. While both hydrogen peroxide and povidone-iodine are highly effective against bacteria and fungi, hydrogen peroxide maintains significantly greater disinfection capabilities than povidone-iodine against all forms of Acanthamoeba. IMPORTANCE Understanding the most efficacious products will allow clinicians to best communicate to patients and consumers the safest products on the market to reduce adverse events, including microbial keratitis, during contact lens use.

Acanthamoeba spp. aggregate and encyst on contact lens material increasing resistance to disinfection.

Introduction: Acanthamoeba keratitis is often caused when Acanthamoeba contaminate contact lenses and infect the cornea. Acanthamoeba is pervasive in the environment as a motile, foraging trophozoite or biocide-resistant and persistent cyst. As contact lens contamination is a potential first step in infection, we studied Acanthamoeba's behavior and interactions on different contact lens materials. We hypothesized that contact lenses may induce aggregation, which is a precursor to encystment, and that aggregated encystment would be more difficult to disinfect than motile trophozoites. Methods: Six clinically and/or scientifically relevant strains of Acanthamoeba (ATCC 30010, ATCC 30461, ATCC 50370, ATCC 50702, ATCC 50703, and ATCC PRA-115) were investigated on seven different common silicone hydrogel contact lenses, and a no-lens control, for aggregation and encystment for 72 h. Cell count and size were used to determine aggregation, and fluorescent staining was used to understand encystment. RNA seq was performed to describe the genome of Acanthamoeba which was individually motile or aggregated on different lens materials. Disinfection efficacy using three common multi-purpose solutions was calculated to describe the potential disinfection resistance of trophozoites, individual cysts, or spheroids. Results: Acanthamoeba trophozoites of all strains examined demonstrated significantly more aggregation on specific contact lens materials than others, or the no-lens control. Fluorescent staining demonstrated encystment in as little as 4 hours on contact lens materials, which is substantially faster than previously reported in natural or laboratory settings. Gene expression profiles corroborated encystment, with significantly differentially expressed pathways involving actin arrangement and membrane complexes. High disinfection resistance of cysts and spheroids with multi-purpose solutions was observed. Discussion: Aggregation/encystment is a protective mechanism which may enable Acanthamoeba to be more disinfection resistant than individual trophozoites. This study demonstrates that some contact lens materials promote Acanthamoeba aggregation and encystment, and Acanthamoeba spheroids obstruct multi-purpose solutions from disinfecting Acanthamoeba.

Differential Antimicrobial Efficacy of Multipurpose Solutions against Acanthamoeba Trophozoites.

SIGNIFICANCE: This investigation examines the effectiveness of several common contact lens solutions in the disinfection of Acanthamoeba, which causes a serious eye infection most often resulting from dysfunctional or improper use of contact lens products. PURPOSE: Acanthamoeba keratitis is an eye infection caused by a free-living amoeba, which can lead to extensive corneal damage and frequently blindness. Acanthamoeba keratitis is linked with contact lens use combined with noncompliance with contact lens care cleaning regimens. The patient's choice and use of multipurpose solutions (MPSs) continue to be a risk factor for Acanthamoeba keratitis. Thus, it is critical that the Acanthamoeba disinfection efficacy of the popular MPSs be determined. Here we compare the efficacy of seven major MPSs on the global market. METHODS: Using standard methods of Acanthamoeba disinfection and quantification, Acanthamoeba ATCC 30461, 30868, 50370, and 50676 trophozoites were inoculated into each MPS and held for the manufacturer's recommended disinfection time. Acanthamoeba recovery plates were incubated for 14 days, after which positive wells were identified and cell concentrations determined using the 50% endpoint method. RESULTS: Members of the OPTI-FREE products (Express, Replenish, and Puremoist [Alcon, Fort Worth, TX]) demonstrated significantly higher percentages of antimicrobial activity compared with the renu Advanced Formula (Bausch + Lomb, Rochester, NY), Biotrue (Bausch + Lomb), Acuvue RevitaLens (Johnson & Johnson, Santa Ana, CA), and Lite products (Cooper Vision, Scottsville, NY) for four of the trophozoite strains tested. CONCLUSIONS: Many of the popular MPS biocides maintain little or no antimicrobial activity against Acanthamoeba trophozoites, and the number of biocides in an MPS does not necessarily indicate its antimicrobial activity.

Antimicrobial Efficacy of Contact Lens Solutions Assessed by ISO Standards.

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.

Variables Affecting the Recovery of Acanthamoeba Trophozoites.

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 (>106 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.

Evaluating Alternate Methods of Determining the Antimicrobial Efficacy of Contact Lens Care Products against Acanthamoeba Trophozoites.

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.

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis.

Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.

Integrative network modeling reveals mechanisms underlying T cell exhaustion.

Failure to clear antigens causes CD8+ T cells to become increasingly hypo-functional, a state known as exhaustion. We combined manually extracted information from published literature with gene expression data from diverse model systems to infer a set of molecular regulatory interactions that underpin exhaustion. Topological analysis and simulation modeling of the network suggests CD8+ T cells undergo 2 major transitions in state following stimulation. The time cells spend in the earlier pro-memory/proliferative (PP) state is a fixed and inherent property of the network structure. Transition to the second state is necessary for exhaustion. Combining insights from network topology analysis and simulation modeling, we predict the extent to which each node in our network drives cells towards an exhausted state. We demonstrate the utility of our approach by experimentally testing the prediction that drug-induced interference with EZH2 function increases the proportion of pro-memory/proliferative cells in the early days post-activation.

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

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.

Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate.

Hematopoiesis provides an accessible system for studying the principles underlying cell-fate decisions in stem cells. Proposed models of hematopoiesis suggest that quantitative changes in lineage-specific transcription factors (LS-TFs) underlie cell-fate decisions. However, evidence for such models is lacking as TF levels are typically measured via RNA expression rather than by analyzing temporal changes in protein abundance. Here, we used single-cell mass cytometry and absolute quantification by mass spectrometry to capture the temporal dynamics of TF protein expression in individual cells during human erythropoiesis. We found that LS-TFs from alternate lineages are co-expressed, as proteins, in individual early progenitor cells and quantitative changes of LS-TFs occur gradually rather than abruptly to direct cell-fate decisions. Importantly, upregulation of a megakaryocytic TF in early progenitors is sufficient to deviate cells from an erythroid to a megakaryocyte trajectory, showing that quantitative changes in protein abundance of LS-TFs in progenitors can determine alternate cell fates.

Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.

Transcriptional regulatory changes in the developing and adult brain are prominent features of brain diseases, but the involvement of specific transcription factors (TFs) remains poorly understood. We integrated brain-specific DNase footprinting and TF-gene co-expression to reconstruct a transcriptional regulatory network (TRN) model for the human brain. We identified key regulator TFs whose predicted target genes were enriched for differentially expressed genes in the prefrontal cortex of individuals with psychiatric and neurodegenerative diseases. Many of these TFs were further implicated in the same diseases through disruption of their binding sites by disease-associated SNPs and associations of TF loci with disease risk. Using primary human neural stem cells, we validated network predictions that link the TF POU3F2 to schizophrenia and bipolar disorder via both cis- and trans-acting mechanisms. Our models of brain-specific TF binding sites and target genes provide a resource for network analysis of brain diseases.