BASE: a practical de novo assembler for large genomes using long NGS reads

© 2016 The Author(s). Background: De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more efficient assembler like SOAPdenovo2. Yet SOAPdenovo2, based on de Bruijn graph, fails to take full advantage of longer NGS reads (say, 150 bp to 250 bp from Illumina HiSeq and MiSeq). Assemblers that are based on string graphs (e.g., SGA), though less popular and also very slow, are more favorable for longer reads. Methods: This paper shows a new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs. Results: Experiments on two bacteria and four human datasets shows the advantage of BASE in both contig quality and speed in dealing with longer reads. In the experiment on bacteria, two datasets with read length of 100 bp and 250 bp were used. Especially for the 250 bp dataset, BASE gives much better quality than SOAPdenovo2 and SGA and is simlilar to SPAdes. Regarding speed, BASE is consistently a few times faster than SPAdes and SGA, but still slower than SOAPdenovo2. BASE and Soapdenov2 are further compared using human datasets with read length 100 bp, 150 bp and 250 bp. BASE shows a higher N50 for all datasets, while the improvement becomes more significant when read length reaches 250 bp. Besides, BASE is more-meory efficent than SOAPdenovo2 when sequencing data with error rate. Conclusions: BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.published_or_final_versio

An intelligent system for trading signal of cryptocurrency based on market tweets sentiments

The purpose of this study is to examine the efficacy of an online stock trading platform in enhancing the financial literacy of those with limited financial knowledge. To this end, an intelligent system is proposed which utilizes social media sentiment analysis, price tracker systems, and machine learning techniques to generate cryptocurrency trading signals. The system includes a live price visu�alization component for displaying cryptocurrency price data and a prediction function that provides both short-term and long-term trading signals based on the sentiment score of the previous day’s cryptocurrency tweets. Additionally, a method for refining the sentiment model result is outlined. The results illustrate that it is feasible to incorporate the Tweets sentiment of cryptocurrencies into the system for generating reliable trading signals

EDN1 Lys198Asn is Associated with Diabetic Retinopathy in Type 2 Diabetes

Purpose: We tested the hypothesis that genetic variants in vasoactive and angiogenic factors regulating the retina vasculature contribute to the development of diabetic retinopathy (DR). Methods: A case-control study was performed to study the genetic association between DR and polymorphic variants of EDN1 (Lys198Asn), LTA (IVS1–80C>A, IVS1–206G>C, IVS1–252>G), eNOS (Glu298Asp), and ITGA2 (BgI II) in a Chinese population with type 2 diabetes mellitus. A well defined population with type 2 diabetes, consisting of 127 controls and 216 DR patients, was recruited. Results: A higher frequency of the Asn/Asn genotype of EDN1 was found in individuals with at least 10 years of diabetes and no retinopathy (controls) compared with DR patients with any duration of diabetes (DR: 2.3%; control: 11.0%; p=0.0002). The Asn allele was also more frequent in controls than DR patients (DR: 16.4%; control: 29.5%; p=0.007). Multiple logistic regression analysis showed that the Asn/Asn genotype was the factor most significantly associated with reduced risk of DR (odds ratio=0.19; 95% CI: 0.07-0.53; p=0.002) and with late onset of diabetes (Asn/Asn: 59 years; Lys/Lys + Lys/Asn: 53 years; p=0.02). Moreover, the Lys/Lys genotype was more common among patients with nonproliferative (75.7%) than proliferative DR (56.9%; p=0.008). The distributions of Lys198Asn alleles in hypertension did not differ from normotensive subjects. No associations between DR and polymorphisms of LTA, eNOS, or ITGA2 were detected, and there were no detectable gene-gene or gene-environmental interactions among the polymorphisms.Conclusions The Asn/Asn genotype of EDN1 was associated with a reduced risk of DR and with delayed onset of type 2 diabetes

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Examining consumers’ adoption of wearable healthcare technology: The role of health attributes

With the advancement of information technology, wearable healthcare technology has emerged as one of the promising technologies to improve the wellbeing of individuals. However, the adoption of wearable healthcare technology has lagged when compared to other well-established durable technology products, such as smartphones and tablets, because of the inadequate knowledge of the antecedents of adoption intention. The aim of this paper is to address an identified gap in the literature by empirically testing a theoretical model for examining the impact of consumers’ health beliefs, health information accuracy, and the privacy protection of wearable healthcare technology on perceived usefulness. Importantly, this study also examines the influences of perceived usefulness, consumer innovativeness, and reference group influence on the adoption intention of wearable healthcare technology. The model seeks to enhance understanding of the influential factors in adopting wearable healthcare technology. Finally, suggestions for future research for the empirical investigation of the model are provided

Implementation of the compulsory universal testing scheme in Hong Kong: Mathematical simulations of a household-based pooling approach

This study aims to propose a pooling approach to simulate the compulsory universal RT-PCR test in Hong Kong and explore the feasibility of implementing the pooling method on a household basis. The mathematical model is initially verified, and then the simulation is performed under different prevalence rates and pooled sizes. The simulated population is based in Hong Kong. The simulation included 10,000,000 swab samples, with a representative distribution of populations in Hong Kong. The samples were grouped into a batch size of 20. If the entire batch is positive, then the group is further divided into an identical group size of 10 for re-testing. Different combinations of mini-group sizes were also investigated. The proposed pooling method was extended to a household basis. A representative from each household is required to perform the RT-PCR test. Results of the simulation replications, indicate a significant reduction (p < 0.001) of 83.62, 64.18, and 48.46% in the testing volume for prevalence rate 1, 3, and 5%, respectively. Combined with the household-based pooling approach, the total number of RT-PCR is 437,304, 956,133, and 1,375,795 for prevalence rates 1, 3, and 5%, respectively. The household-based pooling strategy showed efficiency when the prevalence rates in the population were low. This pooling strategy can rapidly screen people in high-risk groups for COVID-19 infections and quarantine those who test positive, even when time and resources for testing are limited

A Gramaticalização do Verbo Ir e a Variação de Formas para Expressar o Futuro do Presente: uma Fotografia Capixaba

Esta pesquisa verifica o estágio do processo de gramaticalização do verbo IR, que tem assumido a função de auxiliar em construções perifrásticas para expressar tempo. Para isso, investiga-se a variação entre as formas sintética e perifrástica com IR para expressão do futuro do presente. Temos por hipótese que a forma perifrástica já atinge todos os gêneros das duas modalidades da língua, uma vez que já se especializou para codificar tempo. São examinados dois gêneros, tomando-os como prototípicos do continuun oral/escrito: entrevistas com informantes universitários e editoriais de jornal. Partindo de uma orientação teórica Funcionalista, num quadro mais geral, concebe-se a língua como flexível ao uso, passível de influências cognitivas, sociais e também individuais, embora haja nela forças que atuam no sentido de regularizar a estrutura. Seguindo algumas pesquisas que têm se mostrado frutíferas, o modelo funcionalista estará em diálogo com outro modelo que procura dar conta da heterogeneidade estruturada da língua e de seus processos de mudança: a Teoria Variacionista. Num quadro mais específico, os fundamentos que orientam a pesquisa são os da Gramaticalização. Os dados extraídos dos gêneros selecionados serão submetidos ao programa computacional GOLDVARB 2001 e, em seguida, interpretados à luz das teorias lingüísticas que fundamentam esta pesquisa

Effects of physical activity on functional health of older adults: a systematic review

Reviews on the relationships between functional health and physical activity of general older adults have been well documented in literature. However, specific age range of older adults, in particular, older adults of 75 years or above, is currently under-examined. A systematic review was conducted to investigate the effects of physical activity on functional health older adults aged 75 years or above. The reviewed articles cover a variety range of functional health outcomes, including balance, muscle conditioning, joint range of motion, quadriceps strength, reaction time, gait speed, health-related quality of life, back and knee pain, muscle mass, and walking ability. In general, interventions of the reviewed articles had favourable effects on function health of older adults. While physical activity has been identified as an important determinant of functional health, the ways to engage in and accumulate sufficient daily physical activity warrant investigation. It is also important to explore interventions which enhance daily, self-driven physical activity of elderly, as normally supervised physical activity bears higher costs

Handgrip strength assessment at baseline in addition to bone parameters could potentially predict the risk of curve progression in adolescent idiopathic scoliosis

IntroductionAdolescent idiopathic scoliosis (AIS) is characterized by deranged bone and muscle qualities, which are important prognostic factors for curve progression. This retrospective case–control study aims to investigate whether the baseline muscle parameters, in addition to the bone parameters, could predict curve progression in AIS.MethodsThe study included a cohort of 126 female patients diagnosed with AIS who were between the ages of 12 and 14 years old at their initial clinical visit. These patients were longitudinally followed up every 6 months (average 4.08 years) until they reached skeletal maturity. The records of these patients were thoroughly reviewed as part of the study. The participants were categorized into two sub-groups: the progressive AIS group (increase in Cobb angle of ≥6°) and the stable AIS group (increase in Cobb angle <6°). Clinical and radiological assessments were conducted on each group.ResultsCobb angle increase of ≥6° was observed in 44 AIS patients (34.9%) prior to skeletal maturity. A progressive AIS was associated with decreased skeletal maturity and weight, lower trunk lean mass (5.7%, p = 0.027) and arm lean mass (8.9%, p < 0.050), weaker dominant handgrip strength (8.8%, p = 0.027), deranged cortical compartment [lower volumetric bone mineral density (vBMD) by 6.5%, p = 0.002], and lower bone mechanical properties [stiffness and estimated failure load lowered by 13.2% (p = 0.005) and 12.5% (p = 0.004)]. The best cut-off threshold of maximum dominant handgrip strength is 19.75 kg for distinguishing progressive AIS from stable AIS (75% sensitivity and 52.4% specificity, p = 0.011).DiscussionPatients with progressive AIS had poorer muscle and bone parameters than patients with stable AIS. The implementation of a cut-off threshold in the baseline dominant handgrip strength could potentially be used as an additional predictor, in addition to bone parameters, for identifying individuals with AIS who are at higher risk of experiencing curve progression