66 research outputs found
Measuring the diversity of the human microbiota with targeted next-generation sequencing
No full textThe human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq
White matter and task-switching in young adults: A Diffusion Tensor Imaging study
No full textThe capacity to flexibly switch between different task rules has been previously associated with distributed fronto-parietal networks, predominantly in the left hemisphere for phasic switching sub-processes, and in the right hemisphere for more tonic aspects of task-switching, such as rule maintenance and management. It is thus likely that the white matter (WM) connectivity between these regions is critical in sustaining the flexibility required by task-switching. This study examined the relationship between WM microstructure in young adults and task-switching performance in different paradigms: classical shape-color, spatial and grammatical tasks. The main results showed an association between WM integrity in anterior portions of the corpus callosum (genu and body) and a sustained measure of task-switching performance. In particular, a higher fractional anisotropy and a lower radial diffusivity in these WM regions were associated with smaller mixing costs both in the spatial task-switching paradigm and in the shape-color one, as confirmed by a conjunction analysis. No association was found with behavioral measures obtained in the grammatical task-switching paradigm. The switch costs, a measure of phasic switching processes, were not correlated with WM microstructure in any task. This study shows that a more efficient inter-hemispheric connectivity within the frontal lobes favors sustained task-switching processes, especially with task contexts embedding non-verbal components
The neural substrate of spatial memory stabilization depends on the distribution of the training sessions
No full textDistributed training is known to lead to more robust memory formation as compared to training experiences with short intervals. Although this phenomenon, termed distributed practice effect, ubiquitous over a wide variety of tasks and organisms, has long been known by psychologists, its neurobiological underpinning is still poorly understood. Using the striatum as a model system here we tested the hypothesis that the ability of distributed training to optimize memory might depend upon the recruitment of different neural substrates compared to those engaged by massed training. First, by contrasting the medial and the lateral domains of the dorsal striatum after massed and distributed training we demonstrated that neuronal activity, as assessed using c-Fos expression, is differentially affected by the training protocol in the two striatal subregions. Next, by blocking the AMPA receptors before recall we provide evidence to support a selective role of the medial and the lateral striatum in the storage of information acquired respectively by massed and distributed training. Finally, we found that optogenetic stimulation of the dorsolateral striatum during massed training enables the formation of an enduring memory similarly to what is observed with distributed learning. Overall, these findings identify a possible mechanism for the distributed practice effect, a still poorly understood aspect of learning
Study of PMMA materials for a digital optical module
No full textThis work illustrates the material characterization to realize of a prototypal polymeric cover of a Digital Optical Module for the Hyper-Kamiokande neutrino experiment. The cover was made of a high transmittance poly-methyl methacrylate (PMMA), used as a glass substitute. The main objective of the present research is to investigate the structural and optical properties of PMMA, evaluating the respect of the project specification
Diversity indices and normalization approaches in microbiome studies
No full textThis thesis explores human microbiota, by investigating how to consistently measure biodiversity, both within and between different body sites, and how to correctly compare and normalize samples. In this work we propose a new method, called zero imputation, that tries to account for data sparsity; it proves to outperform common normalization approaches in recovering true data richness and relative abundances. We also develop a microbiome data simulator, useful to test all the methods reviewedopenEmbargo per motivi editorial
Compressed Sensing: a new paradigm for Rapid MR Imaging
No full textLa teoria del Compressed Sensing si propone di risolvere il problema della ricostruzione di una immagine da un campionamento in frequenza incompleto, sfruttando la proprietà di sparsità di molte immagini. Le immagini da risonanza magnetica (MR) offrono un campo di applicazione a questa teoria, con possibili significativi miglioramenti in termini di tempi di acquisizione e qualità dell'immagineope
Diversity indices and normalization approaches in microbiome studies
No full textThis thesis explores human microbiota, by investigating how to consistently measure biodiversity, both within and between different body sites, and how to correctly compare and normalize samples. In this work we propose a new method, called zero imputation, that tries to account for data sparsity; it proves to outperform common normalization approaches in recovering true data richness and relative abundances. We also develop a microbiome data simulator, useful to test all the methods reviewe
Compressed Sensing: a new paradigm for Rapid MR Imaging
No full textLa teoria del Compressed Sensing si propone di risolvere il problema della ricostruzione di una immagine da un campionamento in frequenza incompleto, sfruttando la proprietà di sparsità di molte immagini. Le immagini da risonanza magnetica (MR) offrono un campo di applicazione a questa teoria, con possibili significativi miglioramenti in termini di tempi di acquisizione e qualità dell'immagin
Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota
No full textEffect of sterilization on the canine vagina microbiota: a pilot study
No full textBackground: Surgical sterilization is the most effective method of contraception for dogs. It also prevents pyometra and reduces the risk of mammary tumour development. However, this procedure also has negative effects, such as urinary incontinence. Steroid hormone deprivation following gonadectomy could also affect canine vaginal mucosa conditions and the microbial community colonizing the vaginal tract. This hypothesis was tested by comparing the vaginal cytology and microbial community of two groups of bitches, including 11 in anoestrus and 10 sterilized bitches (post-pubertal sterilization in the last 4 years). Bacteria were identified through metataxonomic analysis, amplifying the V3-V4 regions of 16S rRNA gene, and culturing methods.
Results: Vaginal mucosa cytology was suggestive of dystrophic conditions in sterilized bitches, whereas a typical anoestrus pattern with parabasal and intermediate cells was appreciable in anoestrous animals. Metataxonomic analysis revealed large inter-individual variability. Salmonella, Mycoplasma and Staphylococcus were present in moderate quantities in almost all the samples in both groups. Mollicutes (class level) and Tenericutes (phylum level) were commonly present in moderate quantities in anoestrus samples, whereas these microbes were present at high levels in a single sample from the sterilized group. Based on culturing, a higher number of different species were isolated from the anoestrous bitches, and Mycoplasma canis was exclusively identified in an anoestrous bitch. Staphylococcus spp. was the most frequently isolated genus in both groups, followed by Streptococcus spp., and, among gram-negative bacteria, Escherichia spp. and Haemophilus spp. A comparison of the numbers of the most frequently isolated genera of bacteria from vaginal cultures of bitches revealed that Pasteurella and Proteus were the most frequently identified in sterilized animals based on metataxonomic analysis (p-value = 0.0497 and 0.0382, respectively), whereas Streptococcus was significantly and most frequently isolated from anoestrous bitches using culture methods (p value = 0.0436).
Conclusions: In this preliminary investigation, no global patterns of the vaginal bacteria community were noted that characterized the condition of the bitches; however, cytology suggested local modifications. Sterilization after puberty caused minimal alterations in the vaginal microbial community of bitches within 4 years after surgery
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