Thurstonian Scaling of Compositional Questionnaire Data

To prevent response biases, personality questionnaires may use comparative response formats. These include forced choice, where respondents choose among a number of items, and quantitative comparisons, where respondents indicate the extent to which items are preferred to each other. The present article extends Thurstonian modeling of binary choice data (Brown & Maydeu-Olivares, 2011a) to “proportion-of-total” (compositional) formats. Following Aitchison (1982), compositional item data are transformed into log-ratios, conceptualized as differences of latent item utilities. The mean and covariance structure of the log-ratios is modelled using Confirmatory Factor Analysis (CFA), where the item utilities are first-order factors, and personal attributes measured by a questionnaire are second-order factors. A simulation study with two sample sizes, N=300 and N=1000, shows that the method provides very good recovery of true parameters and near-nominal rejection rates. The approach is illustrated with empirical data from N=317 students, comparing model parameters obtained with compositional and Likert scale versions of a Big Five measure. The results show that the proposed model successfully captures the latent structures and person scores on the measured traits

Agreeing on meaning: a fundamental sharing of health information

Topic: A preliminary study on the reproducibility of results when mapping terms from an existing terminology to SNOMED CT post-coordinated expressions is described. Background: Implementing SNOMED CT requires a strategy for migrating existing systems and data that currently use other terminologies as well as ensuring that SNOMED CT contains suitable content that covers the domain. Mapping terms from these terminologies to SNOMED CT is one element of such a strategy. Snapper is a tool designed to assist in this complex task and enable the creation of quality mappings. Methods: Ten terms from the ANZICS diagnosis codes were selected to be mapped according to specified guidelines. The resulting mapping expressions were compared with each other and discussions were conducted with the mapping participants to determine issues they encountered during the process. Results: Consistency was easily achievable with mapping to single concepts, but was more difficult when mapping to post-coordinated expressions. The difficulties were traced to a lack of specificity in the supplied guidelines resulting in uncertainty in structuring the representation of compound concepts

Neutron stars and strange stars in the chiral SU(3) quark mean field model

We investigate the equations of state for pure neutron matter and strange hadronic matter in $\beta$-equilibrium, including $\Lambda$, $\Sigma$ and $\Xi$ hyperons. The masses and radii of pure neutron stars and strange hadronic stars are obtained. For a pure neutron star, the maximum mass is about $1.8 M_{\mathrm{sun}}$, while for a strange hadronic star, the maximum mass is around $1.45 M_{\mathrm{sun}}$. The typical radii of pure neutron stars and strange hadronic stars are about 11.0-12.3 km and 10.7-11.7 km, respectively.Comment: 18 pages, 7 figure

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

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

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