Search results for "Databases"
showing 10 items of 937 documents
On algebraic supergroups, coadjoint orbits and their deformations
2004
In this paper we study algebraic supergroups and their coadjoint orbits as affine algebraic supervarieties. We find an algebraic deformation quantization of them that can be related to the fuzzy spaces of non-commutative geometry.
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing.
2013
Background DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components. Results Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (c…
Predicting disease outbreaks: evaluating measles infection with Wikipedia Trends.
2019
The primary aim of this study was to evaluate the temporal correlation between Wikitrends and conventional surveillance data generated for measles infection reported by bulletin of Istituto Superiore di Sanità (ISS). The reported cases of measles were selected from July 2015 to October 2018. Wikipedia Trends was used to assess how many times a specific page was read by users, data were extracted as daily data and aggregated on a weekly and monthly basis. The following data were extracted: number of views by users from 1 July 2015 to 31 October 2018 of the Morbillo, Vaccinazione del Morbillo, Vaccinazione MPR and Macchie di Koplik pages (Measles, Measles Vaccination, MPR Vaccination and Kopl…
New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast
2019
Caretta caretta is the most common sea turtle species in the Mediterranean Sea. The species is threatened by anthropomorphic activity that causes thousands of deaths and hundreds of strandings along the Mediterranean coast. Stranded turtles are often cared for in rehabilitation centres until they recover or die. The objective of this study was to characterize the gut microbiome of nine sea turtles stranded along the Sicilian coast of the Mediterranean Sea using high-throughput sequencing analysis targeting V3–V4 regions of the bacterial 16S rRNA gene. Stool samples were collected from eight specimens hosted in the recovery centre after a few days of hospitalization (under 7) and from one ho…
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic net…
2020
The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the…
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
2013
Background The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases. Results We present CUDASW++ 3.0, a fast Smith-Waterman protein database search algorithm, which couples CPU and GPU SIMD instructions and carries out concurrent CPU and GPU computations. For the CPU computation, this algorithm employs SSE-based vector execution units as accelerators. For the GPU computation, we have investigated for the first time a GPU …
Applying Support Vector Machines for Gene Ontology based gene function prediction.
2004
Abstract Background The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions. Results We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general perform…
A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data
2008
Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster Sum-of-S…
Bayesian network based pathway analysis of microarray data
2011
Forty-one recent cases of invasive zygomycosis from a global clinical registry.
2009
Background Invasive zygomycosis accounts for a significant proportion of all invasive fungal diseases (IFD), but clinical data on the clinical course and treatment response are limited. Patients and methods Fungiscope-A Global Rare Fungal Infection Registry is an international university-based case registry that collects data of patients with rare IFD, using a web-based electronic case form at www.fungiscope.net. Results Forty-one patients with invasive zygomycosis from central Europe and Asia were registered. The most common underlying conditions were malignancies (n = 26; 63.4%), diabetes mellitus (n = 7; 17.1%) and solid organ transplantation (n = 4; 9.8%). Diagnosis was made by culture …