Children's Interface Design for Searching and Browsing

Elementary-age children are among the largest user groups of computers and the Internet, so it is important to design searching and browsing interfaces to support them. However, many interfaces for children do not consider their skills and preferences. Children can perform simple, single item searches, and are also capable of conducting Boolean searches involving multiple search criteria. However, they have difficulty creating Boolean searches using hierarchical structures found in many interfaces. These interfaces often employ a sequential presentation of the category structure, where only one branch or facet at a time can be explored. This combination of structure and presentation keeps the screen from becoming cluttered, but requires a lot of navigation to explore categories in different areas and an understanding of potentially abstract high-level categories. Based on previous research with adults, I believed that a simultaneous presentation of a flat category structure, where users could explore multiple, single-layer categories simultaneously, would better facilitate searching and browsing for children. This method reduces the amount of navigation and removes abstract categories. However, it introduces more visual clutter and sometimes the need for paging or scrolling. My research investigated these tradeoffs in two studies comparing searching and browsing in two interfaces with children in first, third, and fifth grade. Children did free browsing tasks, searched for a single item, and searched for two items to create conjunctive Boolean queries. The results indicate that a flat, simultaneous interface was significantly faster, easier, likeable, and preferred to a hierarchical, sequential interface for the Boolean search tasks. The simultaneous interface also allowed children to create significantly more conjunctive Boolean searches of multiple items while browsing than the sequential interface. These results suggest design guidelines for others who create children's interfaces, and inform design changes in the interfaces used in the International Children's Digital Library

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.

BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq. RESULTS: Our optimized bioinformatics pipeline for PacBio sequence analysis was able to achieve an error rate of 0.007% on the Staphylococcus aureus full-length 16S rRNA gene. Capillary sequencing of the full-length bacterial 16S rRNA gene from the pool of 50 colonies from stool identified 40 bacterial species of which up to 80% could be identified by PacBio full-length bacterial 16S rRNA gene sequencing. Analysis of the human vaginal microbiome using the bacterial 16S rRNA V1V2 gene region on MiSeq generated 129 operational taxonomic units (OTUs) from which 70 species could be identified. For the PacBio, 36,000 sequences from over 58,000 raw reads could be assigned to a barcode, and the in silico selected bacterial 16S rRNA V1V2 gene region generated 154 OTUs grouped into 63 species, of which 62% were shared with the MiSeq dataset. The PacBio full-length bacterial 16S rRNA gene datasets generated 261 OTUs, which were grouped into 52 species, of which 54% were shared with the MiSeq dataset. Alpha diversity index reported a higher diversity in the MiSeq dataset. CONCLUSION: The PacBio sequencing error rate is now in the same range of the previously widely used Roche 454 sequencing platform and current MiSeq platform. Species-level microbiome analysis revealed some inconsistencies between the full-length bacterial 16S rRNA gene capillary sequencing and PacBio sequencing

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

Acknowledgements The Rowett Institute of Nutrition and Health (University of Aberdeen) receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS). POS is a PhD student supported by the Scottish Government (RESAS) and the Science Foundation Ireland, through a centre award to the APC Microbiome Institute, Cork, Ireland. Data Summary The high-quality draft genomes generated in this work were deposited at the European Nucleotide Archive under the following accession numbers: 1. Eubacterium rectale T1-815; CVRQ01000001–CVRQ0100 0090: http://www.ebi.ac.uk/ena/data/view/PRJEB9320 2. Roseburia faecis M72/1; CVRR01000001–CVRR010001 01: http://www.ebi.ac.uk/ena/data/view/PRJEB9321 3. Roseburia inulinivorans L1-83; CVRS01000001–CVRS0 100 0151: http://www.ebi.ac.uk/ena/data/view/PRJEB9322Peer reviewedPublisher PD

Conservation with moving meshes over orography

Adaptive meshes have the potential to improve the accuracy and efficiency of atmospheric modelling by increasing resolution where it is most needed. Mesh re-distribution, or r-adaptivity, adapts by moving the mesh without changing the connectivity. This avoids some of the challenges with h-adaptivity (adding and removing points): the solution does not need to be mapped between meshes, which can be expensive and introduces errors, and there are no load balancing problems on parallel computers. A long standing problem with both forms of adaptivity has been changes in volume of the domain as resolution changes at an uneven boundary. We propose a solution which achieves exact local conservation and maintains a uniform scalar field while the mesh changes volume as it moves over orography. This is achieved by introducing a volume correction parameter which tracks the cell volumes without using expensive conservative mapping. A finite volume solution of the advection equation over orography on moving meshes is described and results are presented demonstrating improved accuracy for cost using moving meshes. Exact local conservation and maintenance of uniform scalar fields is demonstrated and the correct mesh volume is preserved. We use optimal transport to generate meshes which are guaranteed not to tangle and are equidistributed with respect to a monitor function. This leads to a Monge-Ampère equation which is solved with a Newton solver. The superiority of the Newton solver over other techniques is demonstrated in the appendix. However the Newton solver is only efficient if it is applied to the left hand side of the Monge-Ampère equation with fixed point iterations for the right hand side

Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5

Molecular Technology and Informatics for Personalised Medicine and Healt

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability

Accessing elite nurses for research: reflections on the theoretical and practical issues of telephone interviewing

Elite groups are interesting as they frequently are powerful (in terms of position, knowledge and influence) and enjoy considerable authority. It is important, therefore, to involve them in research concerned with understanding social contexts and processes. This is particularly pertinent in healthcare, where considerable strategic development and change are features of everyday practice that may be guided or perceived as being guided, by elites. This paper evolved from a study investigating the availability and role of nurses whose remit involved leading nursing research and development within acute NHS Trusts in two health regions in Southern England. The study design included telephone interviews with Directors of Nursing Services during which time the researchers engaged in a reflective analysis of their experiences of conducting research with an `elite' group. Important issues identified were the role of gatekeepers, engagement with elites and the use of the telephone interview method in this context. The paper examines these issues and makes a case for involving executive nurses in further research. The paper also offers strategies to help researchers design and implement telephone interview studies successfully to maximise access to the views and experiences of `hard to reach groups', such as elites, while minimising the associated disruption

Mesh adaptation on the sphere using optimal transport and the numerical solution of a Monge-Ampère type equation

An equation of Monge-Ampère type has, for the first time, been solved numerically on the surface of the sphere in order to generate optimally transported (OT) meshes, equidistributed with respect to a monitor function. Optimal transport generates meshes that keep the same connectivity as the original mesh, making them suitable for r-adaptive simulations, in which the equations of motion can be solved in a moving frame of reference in order to avoid mapping the solution between old and new meshes and to avoid load balancing problems on parallel computers. The semi-implicit solution of the Monge-Ampère type equation involves a new linearisation of the Hessian term, and exponential maps are used to map from old to new meshes on the sphere. The determinant of the Hessian is evaluated as the change in volume between old and new mesh cells, rather than using numerical approximations to the gradients. OT meshes are generated to compare with centroidal Voronoi tesselations on the sphere and are found to have advantages and disadvantages; OT equidistribution is more accurate, the number of iterations to convergence is independent of the mesh size, face skewness is reduced and the connectivity does not change. However anisotropy is higher and the OT meshes are non-orthogonal. It is shown that optimal transport on the sphere leads to meshes that do not tangle. However, tangling can be introduced by numerical errors in calculating the gradient of the mesh potential. Methods for alleviating this problem are explored. Finally, OT meshes are generated using observed precipitation as a monitor function, in order to demonstrate the potential power of the technique

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping.

Funder: Royal SocietyHuman health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.Sir Henry Dale Fellowship jointly funded by Wellcome Trust and Royal Society [206245/Z/17/Z]. Rosetrees Trust [A2194]. Wellcome Trust [098051]

A human gut bacterial genome and culture collection for improved metagenomic analyses

Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota