144 research outputs found
Exploring Image Virality in Google Plus
Reactions to posts in an online social network show different dynamics
depending on several textual features of the corresponding content. Do similar
dynamics exist when images are posted? Exploiting a novel dataset of posts,
gathered from the most popular Google+ users, we try to give an answer to such
a question. We describe several virality phenomena that emerge when taking into
account visual characteristics of images (such as orientation, mean saturation,
etc.). We also provide hypotheses and potential explanations for the dynamics
behind them, and include cases for which common-sense expectations do not hold
true in our experiments.Comment: 8 pages, 8 figures. IEEE/ASE SocialCom 201
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality
2openInternationalMetagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.openAlbanese, Davide; Donati, ClaudioAlbanese, D.; Donati, C
Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.
Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes
Integrating gene expression profiling and clinical data
AbstractWe propose a combination of machine learning techniques to integrate predictive profiling from gene expression with clinical and epidemiological data. Starting from BioDCV, a complete software setup for predictive classification and feature ranking without selection bias, we apply semisupervised profiling for detecting outliers and deriving informative subtypes of patients. During the profiling process, sampletracking curves are extracted, and then clustered according to a distance derived from dynamic time warping. Sampletracking allows also the identification of outlier cases, whose removal is shown to improve predictive accuracy and stability of derived gene profiles. Here we propose to employ clinical features to validate the semisupervising procedure. The procedure is demonstrated in the analysis of a liver cancer dataset of 213 samples described by 1993 genes and by pathological features
Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state
<p>Abstract</p> <p>Background</p> <p>The endemic seagrass <it>Posidonia oceanica </it>(L.) Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on <it>Posidonia </it>meadows has been tested. Quantification of a putative stress indicator, <it>i.e</it>. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples.</p> <p>Results</p> <p>The overall expression pattern from <it>Posidonia </it>rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by p<it>I </it>and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples.</p> <p>Conclusion</p> <p><it>Posidonia </it>showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor <it>Posidonia </it>meadows health state.</p
Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy
Erwinia amylovora is a Gram-negative bacterium that colonizes a wide variety of plant species causing recurrent local outbreaks of fire blight in crops of the Rosaceae family. Recent genomic surveys have documented the limited genomic diversity of this species, possibly related to a recent evolutionary bottleneck and a strong correlation between geography and phylogenetic structure of the species. Despite its economic importance, little is known about the genetic variability of co-circulating strains during local outbreaks. Here, we report the genome sequences of 82 isolates of E. amylovora, collected from different host plants in a period of 16 years in Trentino, a small region in the Northeastern Italian Alps that has been characterized by recurrent outbreaks of fire blight in apple orchards. While the genome isolated before 2018 are closely related to other strains already present in Europe, we found a novel subclade composed only by isolates that were sampled starting from 2018 and demonstrate that the endemic population of this pathogen can be composed by mixture of strain
Aesthetic Dentistry, How You Say and How You See: A 500-People Survey on Digital Preview and Color Perception
Purpose: Digital technologies have improved ways to perform aesthetic dentistry in the last few years. The aims of this survey were to investigate the most preferred way to preview the result of an aesthetic dental rehabilitation among a population of dental professionals and laypeople and to compare aesthetic standards of the general population and dentists in terms of the color of teeth for aesthetic dental rehabilitations. Patients and Methods: A questionnaire was sent to the subjects (dentists and laypeople) during a 1-year period and, together with their demographic data, different ways to preview the result of an aesthetic rehabilitation were submitted, such as digital smile design, dental wax-up and oral explanation. Furthermore, an additional section of the questionnaire inves-tigated the most suitable color for an aesthetic rehabilitation based on the colors of the VITA Scale. Results were statistically analyzed (with Chi-square of independence and Mann\u2013 Whitney U-test) highlighting differences of answers based on age groups, educational attainment, gender, and belonging or not to the dental field. Results: Findings showed that digital smile design (digital preview) is a high-appreciated method for previewing and communicating with patients both by dental professionals and laypeople. Furthermore, lighter colors were found to be more valued by laypeople and significant differences were highlighted between the two populations assessed. Conclusion: It seems to be viable to use digital preview for dentists and laypeople to improve previewing and communicating ways. It might be advisable to better motivate patients in recognizing aesthetical features and to raise their awareness in preferring more mimetic aesthetic results. Great opportunities are opened up by digital smile design in teaching, learning, and routine practic
Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
We introduce a novel implementation in ANSI C of the MINE family of
algorithms for computing maximal information-based measures of dependence
between two variables in large datasets, with the aim of a low memory footprint
and ease of integration within bioinformatics pipelines. We provide the
libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave
and C++. The C solution reduces the large memory requirement of the original
Java implementation, has good upscaling properties, and offers a native
parallelization for the R interface. Low memory requirements are demonstrated
on the MINE benchmarks as well as on large (n=1340) microarray and Illumina
GAII RNA-seq transcriptomics datasets.
Availability and Implementation: Source code and binaries are freely
available for download under GPL3 licence at http://minepy.sourceforge.net for
minepy and through the CRAN repository http://cran.r-project.org for the R
package minerva. All software is multiplatform (MS Windows, Linux and OSX).Comment: Bioinformatics 2012, in pres
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