Search results for "scala"

HPG pore: an efficient and scalable framework for nanopore sequencing data.

2016

The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable. Here we present HPG Pore, a toolkit for …

S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light

2017

The availability and amount of sequenced genomes have been rapidly growing in recent years because of the adoption of next-generation sequencing (NGS) technologies that enable high-throughput short-read generation at highly competitive cost. Since this trend is expected to continue in the foreseeable future, the design and implementation of efficient and scalable NGS bioinformatics algorithms are important to research and industrial applications. In this paper, we introduce S-Aligner–a highly scalable read mapper designed for the Sunway Taihu Light supercomputer and its fourth-generationShenWei many-core architecture (SW26010). S-Aligner employs a combination of optimization techniques to o…

Management of febrile neutropenia in the perspective of antimicrobial de-escalation and discontinuation.

2019

Introduction: Infections are among the most frequent complications in patients with hematological and oncological diseases. They might be classified as fever of unknown origin and microbiologically or clinically documented infections. Optimal duration of antimicrobial treatment is still unclear in these patients.Areas covered: We provide an overview on the management of febrile neutropenia in the perspective of antimicrobial de-escalation and discontinuation.Expert opinion: Patients with febrile high-risk neutropenia should be treated empirically with an anti-pseudomonal agent such as piperacillin/tazobactam. Several clinical studies support the assumption that the primary antibiotic regime…

A phase I dose-escalation of trifluridine/tipiracil in combination with oxaliplatin in metastatic colorectal cancer.

2017

TPS3626 Background: Trifluridine/tipiracil, also known as TAS‐102, is a combination of an antineoplastic thymidine‐based nucleoside analogue (trifluridine) and a thymidine phosphorylase inhibitor (tipiracil hydrochloride). The antitumor activity of combined trifluridine/tipiracil and oxaliplatin has been studied in gastrointestinal tumor xenografts, including a 5‐FU resistant subline, using a nude mouse model. This study demonstrated increased antitumor activity for the combination compared to trifluridine/tipiracil or oxaliplatin alone (p < 0.001) (Nukatsuka et al., Anticancer Res 2015). These data support the rationale for clinical use of the combination. We describe a phase 1, intern…

A phase I study of nintedanib combined with cisplatin/gemcitabine as first-line therapy for advanced squamous non-small cell lung cancer (LUME-Lung 3)

2018

Abstract Background There are limited treatment options for squamous non-small cell lung cancer (sqNSCLC) and prognosis remains poor. The safety and pharmacokinetics (PK) of nintedanib, a triple angiokinase inhibitor, plus cisplatin/gemcitabine as first-line treatment for advanced sqNSCLC patients, were evaluated. Materials and methods A phase I, dose-escalation study administering drugs in a 21-day cycle: cisplatin (75 mg/m2, Day 1), gemcitabine (1250 mg/m2, Days 1 and 8) and nintedanib (Days 2–7, 9–21) were given for 4–6 cycles, followed by monotherapy until disease progression or adverse events (AEs). Two nintedanib doses were tested, 150 mg twice daily (bid) and 200 mg bid, to determine…

Stochastic sampling effects favor manual over digital contact tracing.

2020

Isolation of symptomatic individuals, tracing and testing of their nonsymptomatic contacts are fundamental strategies for mitigating the current COVID-19 pandemic. The breaking of contagion chains relies on two complementary strategies: manual reconstruction of contacts based on interviews and a digital (app-based) privacy-preserving contact tracing. We compare their effectiveness using model parameters tailored to describe SARS-CoV-2 diffusion within the activity-driven model, a general empirically validated framework for network dynamics. We show that, even for equal probability of tracing a contact, manual tracing robustly performs better than the digital protocol, also taking into accou…

2016

The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 alig…

Correlation between work impairment, scores of rhinitis severity and asthma using the MASK-air ® App

2020

Background: In allergic rhinitis, a relevant outcome providing information on the effectiveness of interventions is needed. In MASK-air (Mobile Airways Sentinel Network), a visual analogue scale (VAS) for work is used as a relevant outcome. This study aimed to assess the performance of the work VAS work by comparing VAS work with other VAS measurements and symptom-medication scores obtained concurrently. Methods: All consecutive MASK-air users in 23 countries from 1 June 2016 to 31 October 2018 were included (14 189 users; 205 904 days). Geolocalized users self-assessed daily symptom control using the touchscreen functionality on their smart phone to click on VAS scores (ranging from 0 to 1…

GSaaS: A Service to Cloudify and Schedule GPUs

2018

Cloud technology is an attractive infrastructure solution that provides customers with an almost unlimited on-demand computational capacity using a pay-per-use approach, and allows data centers to increase their energy and economic savings by adopting a virtualized resource sharing model. However, resources such as graphics processing units (GPUs), have not been fully adapted to this model. Although, general-purpose computing on graphics processing units (GPGPU) is becoming more and more popular, cloud providers lack of flexibility to manage accelerators, because of the extended use of peripheral component interconnect (PCI) passthrough techniques to attach GPUs to virtual machines (VMs). F…

parSRA: A framework for the parallel execution of short read aligners on compute clusters

2018

The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework to accelerate the execution of existing short read aligners on distributed-memory systems. parSRA can be used to parallelize a variety of short read alignment tools installed in the system without any modification to their source code. We show that our framework provides good scalability on a compute cluster for accelerating the popular BWA-MEM and Bowtie2 aligners. On average, it is able to accelerate sequence alignments on 16 64-core nodes (in total, 1024 cores) with speedup of 10.48 …