Inter-Laboratory Reproducibility of Inducible HIV-1 Reservoir Quantification by TILDA

Substantial efforts to eliminate or reduce latent HIV-1 reservoirs are underway in clinical trials and have created a critical demand for sensitive, accurate, and reproducible tools to evaluate the efficacy of these strategies. Alternative reservoir quantification assays have been developed to circumvent limitations of the quantitative viral outgrowth assay. One such assay is tat/rev induced limiting dilution assay (TILDA), which measures the frequency of CD4+ T cells harboring inducible latent HIV-1 provirus. We modified pre-amplification reagents and conditions (TILDA v2.0) to improve assay execution and first internally validated assay performance using CD4+ T cells obtained from cART-suppressed HIV-1-infected individuals. Detection of tat/rev multiply spliced RNA was not altered by modifying pre-amplification conditions, confirming the robustness of the assay, and supporting the technique’s amenability to limited modifications to ensure better implementation for routine use in clinical studies of latent HIV-1 reservoirs. Furthermore, we cross-validated results of TILDA v2.0 and the original assay performed in two separate laboratories using samples from 15 HIV-1-infected individuals. TILDA and TILDA v2.0 showed a strong correlation (Lin’s Concordance Correlation Coefficient = 0.86). The low inter-laboratory variability between TILDAs performed at different institutes further supports use of TILDA for reservoir quantitation in multi-center interventional HIV-1 Cure trials

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Background: 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods: We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings: Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding: EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health

A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites

Contains fulltext : 154712.PDF (publisher's version ) (Open Access)The identification of translation initiation sites (TISs) constitutes an important aspect of sequence-based genome analysis. An erroneous TIS annotation can impair the identification of regulatory elements and N-terminal signal peptides, and also may flaw the determination of descent, for any particular gene. We have formulated a reference-free method to score the TIS annotation quality. The method is based on a comparison of the observed and expected distribution of all TISs in a particular genome given prior gene-calling. We have assessed the TIS annotations for all available NCBI RefSeq microbial genomes and found that approximately 87% is of appropriate quality, whereas 13% needs substantial improvement. We have analyzed a number of factors that could affect TIS annotation quality such as GC-content, taxonomy, the fraction of genes with a Shine-Dalgarno sequence and the year of publication. The analysis showed that only the first factor has a clear effect. We have then formulated a straightforward Principle Component Analysis-based TIS identification strategy to self-organize and score potential TISs. The strategy is independent of reference data and a priori calculations. A representative set of 277 genomes was subjected to the analysis and we found a clear increase in TIS annotation quality for the genomes with a low quality score. The PCA-based annotation was also compared with annotation with the current tool of reference, Prodigal. The comparison for the model genome of Escherichia coli K12 showed that both methods supplement each other and that prediction agreement can be used as an indicator of a correct TIS annotation. Importantly, the data suggest that the addition of a PCA-based strategy to a Prodigal prediction can be used to 'flag' TIS annotations for re-evaluation and in addition can be used to evaluate a given annotation in case a Prodigal annotation is lacking

MGcV: the microbial genomic context viewer for comparative genome analysis

Contains fulltext : 117085.pdf (publisher's version ) (Open Access)BACKGROUND: Conserved gene context is used in many types of comparative genome analyses. It is used to provide leads on gene function, to guide the discovery of regulatory sequences, but also to aid in the reconstruction of metabolic networks. We present the Microbial Genomic context Viewer (MGcV), an interactive, web-based application tailored to strengthen the practice of manual comparative genome context analysis for bacteria. RESULTS: MGcV is a versatile, easy-to-use tool that renders a visualization of the genomic context of any set of selected genes, genes within a phylogenetic tree, genomic segments, or regulatory elements. It is tailored to facilitate laborious tasks such as the interactive annotation of gene function, the discovery of regulatory elements, or the sequence-based reconstruction of gene regulatory networks. We illustrate that MGcV can be used in gene function annotation by visually integrating information on prokaryotic genes, like their annotation as available from NCBI with other annotation data such as Pfam domains, sub-cellular location predictions and gene-sequence characteristics such as GC content. We also illustrate the usefulness of the interactive features that allow the graphical selection of genes to facilitate data gathering (e.g. upstream regions, ID's or annotation), in the analysis and reconstruction of transcription regulation. Moreover, putative regulatory elements and their corresponding scores or data from RNA-seq and microarray experiments can be uploaded, visualized and interpreted in (ranked-) comparative context maps. The ranked maps allow the interpretation of predicted regulatory elements and experimental data in light of each other. CONCLUSION: MGcV advances the manual comparative analysis of genes and regulatory elements by providing fast and flexible integration of gene related data combined with straightforward data retrieval. MGcV is available at http://mgcv.cmbi.ru.nl

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Many algorithms have been proposed that create a path for a robot in an environment with obstacles. Most methods are aimed at finding a solution. However, for many applications, the path must be of a good quality as well. That is, a path should be short and should keep some amount of minimum clearance to the obstacles. Traveling along such a path reduces the chances of collisions due to the difficulty of measuring and controlling the precise position of the robot. This paper reports a new technique, called Partial shortcut, which decreases the path length. While current methods have difficulties in removing all redundant motions, the technique efficiently removes these motions by interpolating one degree of freedom at a time. Two algorithms are also studied that increase the clearance along paths. The first one is fast but can only deal with rigid, translating bodies. The second algorithm is slower but can handle a broader range of robots, includin

Reachability Analysis of Sampling Based Planners

The last decade, sampling based planners like the Probabilistic Roadmap Method have proved to be successful in solving complex motion planning problems. We give a reachability based analysis for these planners which leads to a better understanding of the success of the approach and enhancements of the techniques suggested. This also enables us to study the effect of using new local planners

Sampling and Node Adding in Probabilistic Roadmap Planners

many different researchers. This has led to a large number of variants of the approach, each with its own merits. It is difficult to compare the different techniques because they were tested on different types of scenes, using different underlying libraries, implemented by different people on different machines. In this paper we provide a comparative study of a number of these techniques, all implemented in a single system and run on the same test scenes and on the same computer. In particular we compare collision checking techniques, sampling techniques, and node adding techniques. The results were surprising in the sense that techniques often performed differently than claimed by the designers. The study also showed how difficult it is to evaluate the quality of the techniques. The results should help future users of the probabilistic roadmap planning approach in deciding which technique is suitable for their situation

Creating small roadmaps for solving motion planning problems

Abstract — In robot motion planning, many algorithms have been proposed that create a roadmap from which a path for a moving object can be extracted. These algorithms generally do not give guarantees on the quality of the roadmap, i.e. they do not promise that a path will always be found in the roadmap if one exists in the world. Furthermore, such roadmaps often become very large which can cause memory problems and high query times. We present a new efficient algorithm that creates small roadmaps for two- and three-dimensional problems. The algorithm ensures that a path is always found (if one exists) at a given resolution. These claims are verified on a broad range of environments. The results also give insight in the structure of covering roadmaps. Keywords—motion planning, small roadmaps, PRM I

Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.

Contains fulltext : 119522.pdf (publisher's version ) (Open Access)Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expression profiles of the transcriptional units (TUs) were compared. The TUs that displayed correlated expression were used to identify putative cis-regulatory elements by searching the upstream regions of the TUs for conserved motifs. Predicted motifs were extended and refined by searching for motifs in the upstream regions of additional TUs with correlated expression. In this way, cis-acting elements were identified for 41 regulons consisting of at least four TUs (correlation > 0.7). This set of regulons included the known regulons of CtsR and LexA, but also several novel ones encompassing genes with coherent biological functions. Visualization of the regulons and their connections revealed a highly interconnected regulatory network. This network contains several subnetworks that encompass genes of correlated biological function, such as sugar and energy metabolism, nitrogen metabolism and stress response.01 mei 201

R.: Flexible path planning using corridor maps

Abstract. Path planning is a central problem in virtual environments and games. When computer-controlled characters move around in virtual worlds they have to plan their paths to desired locations. These paths must avoid collisions with the environment and with other moving characters. Also a chosen path must be natural, meaning that it is the kind of path a real human being could take. The algorithms for planning such paths must be able to handle hundreds of characters in real-time and must be flexible. The Corridor Map Method (cmm) was recently introduced as a flexible path planning method in interactive virtual environments and games. The method is fast and flexible and the resulting paths are reasonable. However, the paths tend to take unnatural turns when characters get close to other characters or small obstacles. In this paper we will improve on the cmm by decoupling collision avoidance with the environment and local steering behavior. The result is a method that keeps the advantages of the cmm but has much more natural steering. Also the method allows for more flexibility in the desired routes of the characters.