Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Time-Lapse Imaging of the Dynamics of CNS Glial-Axonal Interactions In Vitro and Ex Vivo

Myelination is an exquisite and dynamic example of heterologous cell-cell interaction, which consists of the concentric wrapping of multiple layers of oligodendrocyte membrane around neuronal axons. Understanding the mechanism by which oligodendrocytes ensheath axons may bring us closer to designing strategies to promote remyelination in demyelinating diseases. The main aim of this study was to follow glial-axonal interactions over time both in vitro and ex vivo to visualize the various stages of myelination.We took two approaches to follow myelination over time: i) time-lapse imaging of mixed CNS myelinating cultures generated from mouse spinal cord to which exogenous GFP-labelled murine cells were added, and ii) ex vivo imaging of the spinal cord of shiverer (Mbp mutant) mice, transplanted with GFP-labelled murine neurospheres. We demonstrate that oligodendrocyte-axonal interactions are dynamic events with continuous retraction and extension of oligodendroglial processes. Using cytoplasmic and membrane-GFP labelled cells to examine different components of the myelin-like sheath, we provide evidence from time-lapse fluorescence microscopy and confocal microscopy that the oligodendrocytes' cytoplasm-filled processes initially spiral around the axon in a corkscrew-like manner. This is followed subsequently by focal expansion of the corkscrew process to form short cuffs, which then extend longitudinally along the axons. We predict from this model that these spiral cuffs must extend over each other first before extending to form internodes of myelin.These experiments show the feasibility of visualizing the dynamics of glial-axonal interaction during myelination over time. Moreover, these approaches complement each other with the in vitro approach allowing visualization of an entire internodal length of myelin and the ex vivo approach validating the in vitro data

Investigating a training supporting shared decision making (IT'S SDM 2011): study protocol for a randomized controlled trial

<p/> <p>Background</p> <p>Shared Decision Making (SDM) is regarded as the best practice model for the communicative challenge of decision making about treatment or diagnostic options. However, randomized controlled trials focusing the effectiveness of SDM trainings are rare and existing measures of SDM are increasingly challenged by the latest research findings. This study will 1) evaluate a new physicians' communication training regarding patient involvement in terms of SDM, 2) validate SDM_MASS, a new compound measure of SDM, and 3) evaluate the effects of SDM on the perceived quality of the decision process and on the elaboration of the decision.</p> <p>Methods</p> <p>In a multi-center randomized controlled trial with a waiting control group, 40 physicians from 7 medical fields are enrolled. Each physician contributes a sequence of four medical consultations including a diagnostic or treatment decision.</p> <p>The intervention consists of two condensed video-based individual coaching sessions (15min.) supported by a manual and a DVD. The interventions alternate with three measurement points plus follow up (6 months).</p> <p>Realized patient involvement is measured using the coefficient SDM_MASSdrawn from the Multifocal Approach to the Sharing in SDM (MAPPIN'SDM) which includes objective involvement, involvement as perceived by the patient, and the doctor-patient concordance regarding their judges of the involvement. For validation purposes, all three components of SDM_MASSare supplemented by similar measures, the OPTION observer scale, the Shared Decision Making Questionnaire (SDM-Q) and the dyadic application of the Decisional Conflict Scale (DCS). Training effects are analyzed using t-tests. Spearman correlation coefficients are used to determine convergent validities, the influence of involvement (SDM_MASS) on the perceived decision quality (DCS) and on the elaboration of the decision. The latter is operationalised by the ELAB coefficient from the UP24 (Uncertainty Profile, 24 items version).</p> <p>Discussion</p> <p>Due to the rigorous blinded randomized controlled design, the current trial promises valid and reliable results. On the one hand, we expect this condensed time-saving training to be adopted in clinical routine more likely than previous trainings. On the other hand, the exhaustivity of the MAPPIN'SDM measurement system qualifies it as a reference measure for simpler instruments and to deepen understanding of decision-making processes.</p> <p>Trial registration</p> <p>Current Controlled Trials <a href="http://www.controlled-trials.com/ISRCTN78716079">ISRCTN78716079</a></p

The developmental pattern of stimulus and response interference in a color-object Stroop task: an ERP study

<p>Abstract</p> <p>Background</p> <p>Several studies have shown that Stroop interference is stronger in children than in adults. However, in a standard Stroop paradigm, stimulus interference and response interference are confounded. The purpose of the present study was to determine whether interference at the stimulus level and the response level are subject to distinct maturational patterns across childhood. Three groups of children (6–7 year-olds, 8–9 year-olds, and 10–12 year-olds) and a group of adults performed a manual Color-Object Stroop designed to disentangle stimulus interference and response interference. This was accomplished by comparing three trial types. In congruent (C) trials there was no interference. In stimulus incongruent (SI) trials there was only stimulus interference. In response incongruent (RI) trials there was stimulus interference and response interference. Stimulus interference and response interference were measured by a comparison of SI with C, and RI with SI trials, respectively. Event-related potentials (ERPs) were measured to study the temporal dynamics of these processes of interference.</p> <p>Results</p> <p>There was no behavioral evidence for stimulus interference in any of the groups, but in 6–7 year-old children ERPs in the SI condition in comparison with the C condition showed an occipital P1-reduction (80–140 ms) and a widely distributed amplitude enhancement of a negative component followed by an amplitude reduction of a positive component (400–560 ms). For response interference, all groups showed a comparable reaction time (RT) delay, but children made more errors than adults. ERPs in the RI condition in comparison with the SI condition showed an amplitude reduction of a positive component over lateral parietal (-occipital) sites in 10–12 year-olds and adults (300–540 ms), and a widely distributed amplitude enhancement of a positive component in all age groups (680–960 ms). The size of the enhancement correlated positively with the RT response interference effect.</p> <p>Conclusion</p> <p>Although processes of stimulus interference control as measured with the color-object Stroop task seem to reach mature levels relatively early in childhood (6–7 years), development of response interference control appears to continue into late adolescence as 10–12 year-olds were still more susceptible to errors of response interference than adults.</p

Retos de gestión intercultural en las actividades de internacionalización de microempresas de Medellín

El objetivo de este trabajo es analizar retos de gestión intercultural en las actividades de internacionalizaciónde microempresas de Medellín, Colombia. Para tales efectos, se recogió información de 5 microempresas delsector servicios por medio de cuestionarios electrónicos, los cuales fueron posteriormente estudiados usandouna metamatriz parcialmente ordenada siguiendo el método analítico-sintético. El trabajo se diferencia deotros que se enfocan en habilidades empresariales para la supervivencia, porque se centra en explorar competenciasavanzadas relacionadas con el crecimiento y la rentabilidad, esto es: gestión intercultural en la gerenciainternacional. Se postulan 11 retos que describen las capacidades que la microempresa de servicios deMedellín debe construir para que sus actividades de internacionalización sean más efectivas

Computational Models of Classical Conditioning guest editors’ introduction

In the present special issue, the performance of current computational models of classical conditioning was evaluated under three requirements: (1) Models were to be tested against a list of previously agreed-upon phenomena; (2) the parameters were fixed across simulations; and (3) the simulations used to test the models had to be made available. These requirements resulted in three major products: (a) a list of fundamental classical-conditioning results for which there is a consensus about their reliability; (b) the necessary information to evaluate each of the models on the basis of its ordinal successes in accounting for the experimental data; and (c) a repository of computational models ready to generate simulations. We believe that the contents of this issue represent the 2012 state of the art in computational modeling of classical conditioning and provide a way to find promising avenues for future model development

Regeneration of myelin sheaths of normal length and thickness in the zebrafish CNS correlates with growth of axons in caliber

Demyelination is observed in numerous diseases of the central nervous system, including multiple sclerosis (MS). However, the endogenous regenerative process of remyelination can replace myelin lost in disease, and in various animal models. Unfortunately, the process of remyelination often fails, particularly with ageing. Even when remyelination occurs, it is characterised by the regeneration of myelin sheaths that are abnormally thin and short. This imperfect remyelination is likely to have implications for the restoration of normal circuit function and possibly the optimal metabolic support of axons. Here we describe a larval zebrafish model of demyelination and remyelination. We employ a drug-inducible cell ablation system with which we can consistently ablate 2/3rds of oligodendrocytes in the larval zebrafish spinal cord. This leads to a concomitant demyelination of 2/3rds of axons in the spinal cord, and an innate immune response over the same time period. We find restoration of the normal number of oligodendrocytes and robust remyelination approximately two weeks after induction of cell ablation, whereby myelinated axon number is restored to control levels. Remarkably, we find that myelin sheaths of normal length and thickness are regenerated during this time. Interestingly, we find that axons grow significantly in caliber during this period of remyelination. This suggests the possibility that the active growth of axons may stimulate the regeneration of myelin sheaths of normal dimensions