Search results for "speed"
showing 10 items of 876 documents
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 …
CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm
2015
Clustering of molecular systems according to their three-dimensional structure is an important step in many bioinformatics workflows. In applications such as docking or structure prediction, many algorithms initially generate large numbers of candidate poses (or decoys), which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates can easily range from thousands to millions, performing the clustering on standard central processing units (CPUs) is highly time consuming. In this paper, we analyse and evaluate different approaches to parallelize the nearest neighbour chain algorithm to perform hierarc…
Prognosis of Pain and Physical Functioning in Patients With Knee Osteoarthritis: A Systematic Review and Meta-Analysis
2016
Objective To systematically summarize the literature on the course of pain in patients with knee osteoarthritis (OA), prognostic factors that predict deterioration of pain, the course of physical functioning, and prognostic factors that predict deterioration of physical functioning in persons with knee OA. Methods A search was conducted in PubMed, CINAHL, Embase, Psych-INFO, and SPORTDiscus up to January 2014. A meta-analysis and a qualitative data synthesis were performed. Results Of the 58 studies included, 39 were of high quality. High heterogeneity across studies (I(2) >90%) and within study populations (reflected by large SDs of change scores) was found. Therefore, the course of pain a…
Type of surgery is associated with pain and walking difficulties among older people with previous hip fracture
2015
Aim The aim was to assess the level of lower body pain among people with previous femoral neck fracture, and whether the type of surgery was associated with pain and physical function a mean of 2 years after surgery. Methods The study included 115 community-dwelling older adults aged 60 years and older with previous femoral neck fracture, and 31 reference subjects without previous lower limb injuries. A total of 30 patients had internal fixation surgery, 70 had hemiarthroplasty and 15 had total hip replacement. All patients had surgery in the same hospital and received typical inpatient rehabilitation. From 1.6 months to 7.5 years after the fracture, the patients underwent examination inclu…
Mechanical Plantar Foot Stimulation in Parkinson′s Disease: A Scoping Review
2020
Background: Parkinson′s disease (PD) is the second most prevalent neurodegenerative disease in older individuals. Neurorehabilitation-based interventions such as those improving gait are crucial for a holistic approach and to limit falls. Several studies have recently shown that mechanical plantar foot stimulation is a beneficial intervention for improving gait impairment in PD patients. The objective of this scoping review is to evaluate the beneficial effects of this stimulation on gait parameters, and to analyse protocols of foot stimulation and other effects in non-motor symptoms. Relevant articles were searched in the Medline database using Pubmed and Scopus, using the primary search t…
Nordic walking influence on biomechanical parameters: a systematic review
2020
INTRODUCTION Nordic walking (NW) as a form of physical activity has been shown to have benefits in various domains, but little is known about the effect of NW on more specific biomechanical parameters. The purpose is to determine the impact of NW on the following parameters: walking speed/distance, muscle activation, spatiotemporal parameters, kinematics and ground reaction force. EVIDENCE ACQUISITION A literature search was carried out in different databases from October 2008 to October 2018. This review was conducted and reported in accordance with the PRISMA statement. Finally, 42 studies with a median PEDro Score of 5.5/10 were included. EVIDENCE SYNTHESIS The included studies reported …
Association of Barriers, Fear of Falling and Fatigue with Objectively Measured Physical Activity and Sedentary Behavior in Chronic Stroke.
2021
Understanding the fostering factors of physical activity (PA) and sedentary behavior (SB) in post-stroke chronic survivors is critical to address preventive and health interventions. This cross-sectional study aimed to analyze the association of barriers to PA, fear of falling and severity of fatigue encountered by stroke chronic survivors with device-measured PA and SB. Ambulatory community-dwelling post-stroke subjects (≥six months from stroke onset) were evaluated and answered the Barriers to Physical Activity after Stroke Scale (BAPAS), Short Falls Efficacy Scale-International (Short FES-I) and Fatigue Severity Scale (FSS). SB and PA were measured with an Actigraph GT3X+ accelerometer f…
Responsiveness and Minimal Clinically Important Difference of the Five Times Sit-to-Stand Test in Patients with Stroke
2021
This study aimed to analyze the responsiveness of the 5STS test among stroke patients and to estimate the MCIDs (minimal clinically important differences) for different severity levels of community ambulation and stages of recovery. The 5STS and comparator instruments (gait speed and Functional Ambulatory Category (FAC)) were evaluated at baseline. These measures were repeated at 4 (Stage 1) and 8 weeks (Stage 2), together with the Global Rating of Change (GROC). The MCIDs were calculated with two anchor-based methods using the GROC as the external criterion. Responsiveness to change for the 5STS was estimated analyzing the correlation with changes in the two comparator instruments and thei…
Suggestions for revised scoring of the Tower of Hanoi test
2000
Detailed time and error analyses of the Tower of Hanoi (TOH) test was performed using four repeated assessments of eight children (ages 9-12 years), who had perceptual and problem solving deficits. The time before each move was measured. In addition to the traditionally counted time scores, new, relative time scores were computed in order to separate the planning time from the general reaction speed. New error scores were defined and sum scores of serious errors (perserative moves, illegal moves, and wrong results) and mild errors (self-corrected moves, almost performed moves, and interrupted trials) were computed. The relative planning time correlated positively with the achieved score, a…
Automatic Identification System data - potential resource for marine vessels drift studies in the Baltic Sea
2020
Automatic Identification System (AIS) has been employed for increasing the safety at the sea. Nowadays general information about the marine traffic can be tracked in operational mode using www.marinetraffic.com web portal. Additional information can be purchased for commercial and research purposes. Our study highlights a possibility to study the drift using an additional information available at www.marinetraffic.com - selected data on vessel position during its status “not under command”, which corresponds to the drifting vessels. Trajectories of the drift from AIS have been compared with mathematically modeled point-wise drifter paths. Copernicus Marine Environmental Monitoring Service's…