Development of a novel 3D simulation modelling system for distributed manufacturing

This paper describes a novel 3D simulation modelling system for supporting our distributed machine design and control paradigm with respect to simulating and emulating machine behaviour on the Internet. The system has been designed and implemented using Java2D and Java3D. An easy assembly concept of drag-and-drop assembly has been realised and implemented by the introduction of new connection features (unified interface assembly features) between two assembly components (modules). The system comprises a hierarchical geometric modeller, a behavioural editor, and two assemblers. During modelling, designers can combine basic modelling primitives with general extrusions and integrate CAD geometric models into simulation models. Each simulation component (module) model can be visualised and animated in VRML browsers. It is reusable. This makes machine design re-configurable and flexible. A case study example is given to support our conclusions

Assessing alignment-based taxonomic classification of ancient microbial DNA

The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.Raphael Eisenhofer and Laura Susan Weyric

A framework of web-based conceptual design

A web-based conceptual design prototype system is presented. The system consists of four parts which interpret on-line sketches as 2D and 3D geometry, extract 3D hierarchical configurations, allow editing of component behaviours, and produce VRML-based behavioural simulations for design verification and web-based application. In the first part, on-line freehand sketched input is interpreted as 2D and 3D geometry, which geometrically represents conceptual design. The system then infers 3D configuration by analysing 3D modelling history. The configuration is described by a parent–child hierarchical relationship and relative positions between two geometric components. The positioning information is computed with respect to the VRML97 specification. In order to verify the conceptual design of a product, the behaviours can be specified interactively on different components. Finally, the system creates VRML97 formatted files for behavioural simulation and collaborative design application over the Internet. The paper gives examples of web-based applications. This work forms a part of a research project into the design and establishing of modular machines for automation manufacture. A consortium of leading automotive companies is collaborating on the research project

Correction of Dropped Frames in High-resolution Push-broom Hyperspectral Images for Cultural Heritage

Dropped frames can occur in line-scan cameras, which result in non-uniform spatial sampling of the scene. A dropped frame occurs when data from an image sensor is not successfully recorded. When mosaicking multiple line-scan images, such as in high-resolution imaging, this can cause misalignment. Much previous work to identify dropped frames in video prioritises fast computation over high accuracy, whereas in heritage imaging, high accuracy is often preferred over short computation time. Two approaches to identify the position of dropped frames are presented, both using the A* search algorithm to correct dropped frames. One method aligns overlapping sections of push-broom images and the other aligns the push-broom image to a lower resolution reference image. The two methods are compared across a range of test images, and the method aligning overlapping sections is shown to perform better than the method using a reference image under most circumstances. The overlap method was applied to hyperspectral images acquired of La Ghirlandata, an 1873 oil on canvas painting by D. G. Rossetti, enabling a high-resolution hyperspectral image mosaic to be produced. The resulting composite image is 10,875 $\times$ 14,697 pixels each with 500 spectral bands from 400–2,500 nm. This corresponds to a spatial resolution of 80 \,\mathrm{\upmu }\mathrm{m} and a spectral resolution of 3–6 nm

The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

A high-affinity antibody against the CSP N-terminal domain lacks Plasmodium falciparum inhibitory activity

Malaria is a global health concern and research efforts are ongoing to develop a superior vaccine to RTS,S/AS01. To guide immunogen design, we seek a comprehensive understanding of the protective humoral response against Plasmodium falciparum circumsporozoite protein (PfCSP). In contrast to the well-studied responses to the repeat region and the C-terminus, the antibody response against the N-terminal domain of PfCSP (N-CSP) remains obscure. Here, we characterized the molecular recognition and functional efficacy of the N-CSP-specific monoclonal antibody 5D5. The crystal structure at 1.85 Åresolution revealed that 5D5 binds an α-helical epitope in N-CSP with high affinity through extensive shape and charge complementarity, and the unusual utilization of an N-linked glycan. Nevertheless, functional studies indicated low 5D5 binding to live Pf sporozoites, and lack of sporozoite inhibition in vitro and in mosquitoes. Overall, our data on low recognition and inhibition of sporozoites do not support the inclusion of the 5D5 epitope into the next generation of CSP-based vaccines.Summary Statement The Plasmodium falciparum sporozoite surface protein, PfCSP, is an attractive vaccine target, but the antibody response against the CSP N-terminal domain has remained understudied. Here, to guide immunogen design, Thai et al. provide insights into the binding motif and functional efficacy of the N-terminal domain-specific monoclonal antibody, 5D5

Contamination in low microbial biomass microbiome studies: issues and recommendations

Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.Raphael Eisenhofer, Jeremiah J. Minich, Clarisse Marotz, Alan Cooper, Rob Knight, and Laura S. Weyric