Search results for " SEARCH"
showing 10 items of 654 documents
Secure and Privacy Preserving Pattern Matching in Distributed Cloud-based Data Storage
2019
Given two strings: pattern $p$ of length $m$ and text $t$ of length $n$ . The string matching problem is to find all (or some) occurrences of the pattern $p$ in the text $t$ . We introduce a new simple data structure, called index arrays, and design fast privacy-preserving matching algorithm for string matching. The motivation behind introducing index arrays is determined by the need for pattern matching on distributed cloud-based datasets with semi-trusted cloud providers. It is intended to use encrypted index arrays both to improve performance and protect confidentiality and privacy of user data.
Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS
2016
Interaction between genes has become a major topic in quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Due to the number of tests required for an exhaustive search in genome-wide association studies (GWAS), a large amount of computational power is required. In this paper, we present a hybrid architecture consisting of tightly interconnected CPUs, GPUs and FPGAs and a fine-tuned software suite to outperform other implementations in pairwise interaction analysis while consuming less than 300Watts and fitting into a standard desktop computer case.
Genetic susceptibility to angiotensin-converting enzyme-inhibitor induced angioedema: A systematic review and evaluation of methodological approaches.
2019
Angiotensin-converting enzyme (ACE) converts angiotensin I to angiotensin II which causes vasoconstriction. ACE inhibitors reduce blood pressure by inhibiting ACE. A well-known adverse drug reaction to ACE inhibitors is ACE inhibitor-induced angioedema (ACEi-AE). Angioedema is a swelling of skin and mucosa, which can be fatal if the airway is compromised. We have performed a systematic review of the evidence suggesting that genetic polymorphisms are associated with ACEi-AE and evaluated the methodological approaches of the included studies. The Cochrane Database of Systematic Reviews, Google Scholar, and PubMed were searched. Studies investigating the association between genetic markers and…
Efficient Algorithms for Sequence Analysis with Entropic Profiles
2017
Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to study the under-/over-representation of subwords, by also providing information about the scale of conserved DNA regions. Here, we focus on the algorithmic aspects related to entropic profiles. In particular, we propose linear time algorithms for their computation that rely on suffix-based data structures, more specifically on the truncated suffix tree (TST) and on the enhanced suffix array (ESA). We performed an extensive experimental campaign …
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
Feasibility of sample size calculation for RNA-seq studies
2017
Sample size calculation is a crucial step in study design but is not yet fully established for RNA sequencing (RNA-seq) analyses. To evaluate feasibility and provide guidance, we evaluated RNA-seq sample size tools identified from a systematic search. The focus was on whether real pilot data would be needed for reliable results and on identifying tools that would perform well in scenarios with different levels of biological heterogeneity and fold changes (FCs) between conditions. We used simulations based on real data for tool evaluation. In all settings, the six evaluated tools provided widely different answers, which were strongly affected by FC. Although all tools failed for small FCs, s…
MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs.
2016
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions …
Update of the therapeutic planning of irrigation and intracanal medication in root canal treatment. A literature review
2019
Background The success of endodontic treatment derives from the complete elimination of microorganisms capable of causing an intraradicular or extraradicular infection. To achieve a more effective eradication of these microorganisms, endodontic instrumentation must always be implemented with abundant irrigation, which has to achieve chemical, mechanical and biological effects. The irrigators most used today are NaOCl, CHX and EDTA, released into the ducts through different techniques such as syringe, manual agitation, positive or negative apical pressure, sonic or ultrasonic activation, PIPS and PDT. The objective of this review is to update the different irrigating solutions and intracanal…
Exploring the neural correlates of the reversed letter effect: Evidence from left and right parietal patients.
2019
To investigate the hemispheric lateralization of attentional processes during visual search tasks depending on the stimulus material embedding the target, twelve patients with unilateral left (n = 7) or right (n = 5) parietal lesions and 20 age and education matched healthy controls (HC) were recruited. We used a visual search task for a uniquely tilted oblique bar embedded in an object shape 'N' or in its mirror reversal 'И'. The accuracy and the averaged reaction times (RTs) in each stimulus type ('N' or 'И') were analysed.\ud \ud HC presented significantly longer RTs when the target bar was embedded in 'N' among its mirror reversed 'И' (p < .05). This “reversed letter effect” was also…
Extended Flight Bouts Require Disinhibition from GABAergic Mushroom Body Neurons
2019
Summary Insect flight is a complex behavior that requires the integration of multiple sensory inputs with flight motor output. Although previous genetic studies identified central brain monoaminergic neurons that modulate Drosophila flight, neuro-modulatory circuits underlying sustained flight bouts remain unexplored. Certain classes of dopaminergic and octopaminergic neurons that project to the mushroom body, a higher integrating center in the insect brain, are known to modify neuronal output based on contextual cues and thereby organismal behavior. This study focuses on how monoaminergic modulation of mushroom body GABAergic output neurons (MBONs) regulates the duration of flight bouts. O…