Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Automatic mental processes, automatic actions and behaviours in game transfer phenomena: an empirical self-report study using online forum data

Previous studies have demonstrated that the playing of videogames can have both intended and unintended effects. The purpose of this study was to investigate the influence of videogames on players’ mental processes and behaviours in day-to-day settings. A total of 1,023 self-reports from 762 gamers collected from online videogame forums were classified, quantified, described and explained. The data include automatic thoughts, sensations and impulses, automatic mental replays of the game in real life, and voluntary/involuntary behaviours with videogame content. Many gamers reported that they had responded – at least sometimes – to real life stimuli as if they were still playing videogames. This included overreactions, avoidances, and involuntary movements of limbs. These experiences lasted relatively short periods of time but in a minority of players were recurrent. The gamers' experiences appeared to be enhanced by virtual embodiment, repetitive manipulation of game controls, and their gaming habits. However, similar phenomena may also occur when doing other non-gaming activities. The implications of these game transfer experiences are discussed

Smartphone tool to collect repeated 24 h dietary recall data in Nepal

Objective To outline the development of a smartphone-based tool to collect thrice-repeated 24 h dietary recall data in rural Nepal, and to describe energy intakes, common errors and researchers' experiences using the tool. Design We designed a novel tool to collect multi-pass 24 h dietary recalls in rural Nepal by combining the use of a CommCare questionnaire on smartphones, a paper form, a QR (quick response)-coded list of foods and a photographic atlas of portion sizes. Twenty interviewers collected dietary data on three non-consecutive days per respondent, with three respondents per household. Intakes were converted into nutrients using databases on nutritional composition of foods, recipes and portion sizes. Setting Dhanusha and Mahottari districts, Nepal. Subjects Pregnant women, their mothers-in-law and male household heads. Energy intakes assessed in 150 households; data corrections and our experiences reported from 805 households and 6765 individual recalls. Results Dietary intake estimates gave plausible values, with male household heads appearing to have higher energy intakes (median (25th-75th centile): 12 079 (9293-14 108) kJ/d) than female members (8979 (7234-11 042) kJ/d for pregnant women). Manual editing of data was required when interviewers mistook portions for food codes and for coding items not on the food list. Smartphones enabled quick monitoring of data and interviewer performance, but we initially faced technical challenges with CommCare forms crashing. Conclusions With sufficient time dedicated to development and pre-testing, this novel smartphone-based tool provides a useful method to collect data. Future work is needed to further validate this tool and adapt it for other contexts

Clinical Implication of Targeting of Cancer Stem Cells

The existence of cancer stem cells (CSCs) is receiving increasing interest particularly due to its potential ability to enter clinical routine. Rapid advances in the CSC field have provided evidence for the development of more reliable anticancer therapies in the future. CSCs typically only constitute a small fraction of the total tumor burden; however, they harbor self-renewal capacity and appear to be relatively resistant to conventional therapies. Recent therapeutic approaches aim to eliminate or differentiate CSCs or to disrupt the niches in which they reside. Better understanding of the biological characteristics of CSCs as well as improved preclinical and clinical trials targeting CSCs may revolutionize the treatment of many cancers. Copyright (c) 2012 S. Karger AG, Base

Participatory Women's Groups with Cash Transfers Can Increase Dietary Diversity and Micronutrient Adequacy during Pregnancy, whereas Women's Groups with Food Transfers Can Increase Equity in Intrahousehold Energy Allocation

Background: There is scarce evidence on the impacts of food transfers, cash transfers, or women's groups on food sharing, dietary intakes, or nutrition during pregnancy, when nutritional needs are elevated. // Objective: This study measured the effects of 3 pregnancy-focused nutrition interventions on intrahousehold food allocation, dietary adequacy, and maternal nutritional status in Nepal. // Methods: Interventions tested in a cluster-randomized controlled trial (ISRCTN 75964374) were “Participatory Learning and Action” (PLA) monthly women's groups, PLA with transfers of 10 kg fortified flour (“Super Cereal”), and PLA plus transfers of 750 Nepalese rupees (∼US$7.5) to pregnant women. Control clusters received usual government services. Primary outcomes were Relative Dietary Energy Adequacy Ratios (RDEARs) between pregnant women and male household heads and pregnant women and their mothers-in-law. Diets were measured by repeated 24-h dietary recalls. // Results: Relative to control, RDEARs between pregnant women and their mothers-in-law were 12% higher in the PLA plus food arm (log-RDEAR coefficient = 0.12; 95% CI: 0.02, 0.21; P = 0.014), but 10% lower in the PLA-only arm between pregnant women and male household heads (−0.11; 95% CI: −0.19, −0.02; P = 0.020). In all interventions, pregnant women's energy intakes did not improve, but odds of pregnant women consuming iron-folate supplements were 2.5–4.6 times higher, odds of pregnant women consuming more animal-source foods than the household head were 1.7–2.4 times higher, and midupper arm circumference was higher relative to control. Dietary diversity was 0.4 food groups higher in the PLA plus cash arm than in the control arm. // Conclusions: All interventions improved maternal diets and nutritional status in pregnancy. PLA women's groups with food transfers increased equity in energy allocation, whereas PLA with cash improved dietary diversity. PLA alone improved diets, but effects were mixed. Scale-up of these interventions in marginalized populations is a policy option, but researchers should find ways to increase adherence to interventions. This trial was registered at www.controlled-trials.com as ISRCTN 75964374

The parallel development of ODD and CD symptoms from early childhood to adolescence

This study examined the developmental relations between symptoms of oppositional defiant disorder (ODD) and conduct disorder (CD) from early childhood to adolescence. Specifically we tested, according to parent-reported problems, whether symptoms of ODD precede the development of CD symptoms, whether ODD and CD symptoms are reciprocally associated across time, or whether ODD and CD symptoms develop parallel to each other across time. Participants were a community-based sample (at time 1: N = 485, 48% boys) assessed biannually five times from age 4 to 6 until age 12-14. The findings suggested that, with control for stability effects, baseline SES, and symptoms of attention deficit hyperactivity disorder, ODD and CD symptoms develop parallel to each other. No gender differences were obtained. We conclude that without the initial presence of CD symptoms, ODD symptoms are not developmental precursors to CD symptoms

A Comparison of Different Approaches to Unravel the Latent Structure within Metabolic Syndrome

Background: Exploratory factor analysis is a commonly used statistical technique in metabolic syndrome research to uncover latent structure amongst metabolic variables. The application of factor analysis requires methodological decisions that reflect the hypothesis of the metabolic syndrome construct. These decisions often raise the complexity of the interpretation from the output. We propose two alternative techniques developed from cluster analysis which can achieve a clinically relevant structure, whilst maintaining intuitive advantages of clustering methodology. Methods: Two advanced techniques of clustering in the VARCLUS and matroid methods are discussed and implemented on a metabolic syndrome data set to analyze the structure of ten metabolic risk factors. The subjects were selected from the normative aging study based in Boston, Massachusetts. The sample included a total of 847 men aged between 21 and 81 years who provided complete data on selected risk factors during the period 1987 to 1991. Results: Four core components were identified by the clustering methods. These are labelled obesity, lipids, insulin resistance and blood pressure. The exploratory factor analysis with oblique rotation suggested an overlap of the loadings identified on the insulin resistance and obesity factors. The VARCLUS and matroid analyses separated these components and were able to demonstrate associations between individual risk factors. Conclusions: An oblique rotation can be selected to reflect the clinical concept of a single underlying syndrome, howeve

The impact of the social environment on children's mental health in a prosperous city: an analysis with data from the city of Munich

BACKGROUND: Children with a low socioeconomic position are more affected by mental difficulties as compared to children with a higher socioeconomic position. This paper explores whether this socioeconomic pattern persists in the prosperous German city of Munich which features high quality of life and coverage of children mental health specialists that lies well above the national average and is among the highest in Europe. METHODS: 1,265 parents of preschool children participated in a cross-sectional health survey. They were given a self-administered questionnaire (including socioeconomic variables) and the 'Strengths and Difficulties Questionnaire (SDQ)', a well-established method to identify mental difficulties among children and adolescents. Prevalence estimates for the 'SDQ-Total Difficulties Score' were calculated, with a special focus on differences by parental (resp. household) socioeconomic position. The association between parental education, household income, single parenthood, nationality, and parental working status on one hand, and their children's mental health on the other, was explored using multivariable logistic regression models. The coverage of mental health specialists per 100,000 children aged 14 or younger in the city of Munich was also calculated. RESULTS: In Munich, the distribution of mental health difficulties among children follows the same socioeconomic pattern as described previously at the national level, but the overall prevalence is about 30% lower. Comparing different indicators of socioeconomic position, low parental education and household income are the strongest independent variables associated with mental difficulties among children (OR = 2.7; CI = 1.6 - 4.4 and OR = 2.8; CI = 1.4 - 5.6, respectively). CONCLUSIONS: Socioeconomic differences in the prevalence of childhood mental difficulties are very stable. Even in a city such as Munich, which is characterized by high quality of life, high availability of mental health specialists, and low overall prevalence of these mental difficulties, they are about as pronounced as in Germany as a whole. It can be concluded that the effect of several characteristics of socioeconomic position 'overrules' the effect of a health promoting regional environment

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

<p>Abstract</p> <p>Background</p> <p>An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays.</p> <p>Results</p> <p>Pyrosequencing reads (126174 reads, 1045 unique sequences) represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae) than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus <it>Prevotella</it>), Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age.</p> <p>Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93) probes per individual sample.</p> <p>A caries-free oral status significantly associated with the higher signal of the probes targeting <it>Porphyromonas catoniae </it>and <it>Neisseria flavescens</it>.</p> <p>Conclusions</p> <p>The potential role of <it>P. catoniae </it>and <it>N. flavescens </it>as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.</p