Search results for "NEXT-GENERATION"
showing 10 items of 80 documents
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
2021
Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among…
Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing
2016
ABSTRACT Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, …
AP5Z1/SPG4 8 frequency in autosomal recessive and sporadic spastic paraplegia
2014
Hereditary spastic paraplegias (HSP) constitute a rare and highly heterogeneous group of neurodegenerative disorders, defined clinically by progressive lower limb spasticity and pyramidal weakness. Autosomal recessive HSP as well as sporadic cases present a significant diagnostic challenge. Mutations in AP5Z1, a gene playing a role in intracellular membrane trafficking, have been recently reported to be associated with spastic paraplegia type 48 (SPG48). Our objective was to determine the relative frequency and clinical relevance of AP5Z1 mutations in a large cohort of 127 HSP patients. We applied a targeted next-generation sequencing approach to analyze all coding exons of the AP5Z1 gene. …
Next-Generation Sequencing in Clinical Practice
2019
Abstract During the past few decades, Sanger sequencing represented the “gold standard” technique. In order to better define the mutational status of several genes at the same time, next-generation sequencing methodologies have been introduced in the molecular laboratory workflow. In the era of personalized medicine, this technological improvement plays a key role in the comprehensive molecular characterization of cancer patients in order to get a “tile” target therapy. For different cancer patients, different target therapies are available and different genes serve as clinical it relevant biomarkers. This chapter reviews the principal features of these novel technologies and their applicat…
Lightweight BWT Construction for Very Large String Collections
2011
A modern DNA sequencing machine can generate a billion or more sequence fragments in a matter of days. The many uses of the BWT in compression and indexing are well known, but the computational demands of creating the BWT of datasets this large have prevented its applications from being widely explored in this context. We address this obstacle by presenting two algorithms capable of computing the BWT of very large string collections. The algorithms are lightweight in that the first needs O(m log m) bits of memory to process m strings and the memory requirements of the second are constant with respect to m. We evaluate our algorithms on collections of up to 1 billion strings and compare thei…
Lightweight algorithms for constructing and inverting the BWT of string collections
2013
Recent progress in the field of \{DNA\} sequencing motivates us to consider the problem of computing the Burrows‚ÄìWheeler transform (BWT) of a collection of strings. A human genome sequencing experiment might yield a billion or more sequences, each 100 characters in length. Such a dataset can now be generated in just a few days on a single sequencing machine. Many algorithms and data structures for compression and indexing of text have the \{BWT\} at their heart, and it would be of great interest to explore their applications to sequence collections such as these. However, computing the \{BWT\} for 100 billion characters or more of data remains a computational challenge. In this work we ad…
Media Delivery to Remote Renderers Controlled by the Mobile Phone
2009
In today's content delivery solutions, service delivery and control are still tightly coupled, a service typically being delivered to the same device that controls the session. We present a solution that was designed with the goal to decouple service control and delivery. Using our approach, multimedia streaming services can be delivered to off-the-shelf DLNA devices in visited networks. The service provider receives information about the remote media player and access environment via a mobile phone. Proximity technologies (e.g. barcodes, NFC) of the control device are used for the exchange of required credentials. This paper describes a typical scenario and our prototype implementation.
A global service level guarantee in NGN networks
2010
In this paper, we propose an end-to-end service level negotiation protocol which enables a global service offer covering quality of service (QoS) and security while taking into account user's mobility in this offer. This protocol provides all the domains involved in the transport of a various offered services with a negotiation capability to achieve an agreement on a service level. This paper shows also results of measurements evaluating the performances of the considered negotiation protocol and security impact on QoS.
An Integrated Multi-service Software Simulation Platform: SIMPSONS Architecture
2005
This paper describes SIMPSONS (SIp and MPls Simulations On NS-2), which is a software platform for simulating multiple network scenarios, such as Telephony Over IP (TOIP), and multi-services networks extending the functionalities of Network Simulator NS-2. The innovative aspects of SIMPSONS is the complete integration of control protocols and traffic engineering mechanisms inside the same simulation tool. In fact, next generation networks must meet basically two fundamental requirements: support of Quality of Service (QoS) and Traffic Engineering (TE) functionalities. SIMPSONS is able to simulate DiffServ, MPLS, OSPF and SIP and their interaction in everything TOIP scenario. So with this po…
Transport service for session initiation protocol in SIP-T scenarios
2005
The traditional telephone service has undergone deep changes in the years concerning the techniques of commutation and signaling. Today, public switched telecom networks (PSTNs) and private integrated services networks (PINSs) are strongly directed to adopt IP-based backbone. If it is possible to transfer the voice on packet switching network, in such reliable way, using voice over IP (VoIP) techniques, there is not still a valid alternative to the signaling systems, reliable and unfailing, like signaling system n.7 (SST). Session initiation protocol (SIP) seems to be the best candidate. SIP is an application layer signaling protocol and the problem remains still opened for what it concerns…