10th Student Council Symposium of the International-Society-for-Computational-Biology (ISCB) held in conjunction with the 22nd Annual Meeting of Intelligent Systems for Molecular Biology (ISMB)
JUL 11, 2014
[Xie, Yinlong] S China Univ Technol, Sch Biosci & Bioengn, Guangzhou 510006, Guangdong, Peoples R China.^[Xie, Yinlong;Wu, Gengxiong;Tang, Jingbo;Luo, Ruibang;Liu, Shanlin;Huang, Weihua;He, Guangzhu;Gu, Shengchang;Li, Shengkang;Zhou, Xin;Xu, Xun;Wong, Gane Ka-Shu;Wang, Jun] BGI Shenzhen, Shenzhen 518083, Peoples R China.^[Xie, Yinlong;Luo, Ruibang;Lam, Tak-Wah] Univ Hong Kong, HKU BGI Bioinformat Algorithms & Core Technol Res, Hong Kong, Hong Kong, Peoples R China.^[Xie, Yinlong;Luo, Ruibang;Lam, Tak-Wah] Univ Hong Kong, Dept Comp Sci, Pokfulam, Hong Kong, Peoples R China.^[Tang, Jingbo] Cent S Univ, XiangYa Sch Med, Inst Biomed Engn, Changsha 410008, Hunan, Peoples R China.^[Luo, Ruibang] BGI Shenzhen, BGI Tech, Shenzhen 518083, Peoples R China.^[Patterson, Jordan;Wong, Gane Ka-Shu] Univ Alberta, Dept Med, Edmonton, AB T6G 2E1, Canada.^[Gu, Shengchang] Chinese Acad Sci, Shenzhen Inst Adv Technol, Shenzhen 518055, Peoples R China.^[Wong, Gane Ka-Shu] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada.^[Wang, Jun] Univ Copenhagen, Novo Nordisk Fdn, Ctr Basic Metab Res, DK-2200 Copenhagen, Denmark.^[Wang, Jun] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark.^[Wang, Jun] King Abdulaziz Univ, Princess Al Jawhara Ctr Excellence Res Hereditary, Jeddah 21589, Saudi Arabia.
Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. Contact:firstname.lastname@example.org or email@example.com Supplementary information:Supplementary data are available at Bioinformatics online.
Bauxite residue (Red mud) is produced in alumina plants by the Bayer process in which Al-containing minerals are dissolved in hot NaOH. The global residue inventory reached an estimated 3.5 billion tons in 2014, increasing by approximately 120 million tons per annum. The appropriate management of bauxite residue is becoming a global environmental concern following increased awareness of the need for environmental protection. Establishment of a vegetation cover is the most promising way forward for the management of bauxite residue, although its physical and chemical properties can limit plant growth due to high alkalinity and salinity, low hydraulic conductivity, trace element toxicity (Al and Fe), and deficiencies in organic matter and nutrition concentrations. This paper discusses the various revegetation and rehabilitation strategies. Studies of the rehabilitation of bauxite residues have mainly focused on two approaches, amelioration of the surface layer and screening of tolerant plants and soil microorganisms. Amendment with gypsum can reduce the high alkalinity and salinity, promote soil aggregation, and increase the hydraulic conductivity of bauxite residues. Organic matter can provide a source of plant nutrients, form stable complexes with metal cations, promote hydraulic conductivity, stabilize soil structure, and provide an energy source for soil organisms. Tolerant plants and microorganisms such as halophytes and alkaliphilic microbes show the greatest potential to ameliorate bauxite residues. However, during restoration or as a result of natural vegetation establishment, soil formation becomes a critical issue and an improved understanding of the various pedogenic processes are required, and future direction should focus on this area.
Halloysite nanotubes (HNTs) showed natural nanotubular structures with similar chemical composition to kaolin. This paper reviewed the exciting applications of HNTs due to their abundantly deposit, nanoscale lumens, high length-to-diameter ratios, and relatively low surface hydroxyl group density. HNTs have been used as ideal templates for conveniently immobilizing nanoparticles, which could enable the construction of designed nanoarchitectures that are extremely attractive as supports for heterogeneous catalysts and for use in the fuel cells and related technologies that exploited the inherent 'smallness' and hollow characteristics of the nanoparticles. The recent developments in this area by exploring the various techniques with which HNTs could be functionalized with metal nanoparticles, and the diverse applications of the resulting materials overviewed in detail. The corresponding interfacial characteristics of the nanocomposites were emphasized. (C) 2015 Elsevier B.V. All rights reserved.
Mesial temporal lobe epilepsy (MTLE) is a particularly devastating form of human epilepsy with significant incidence of medical intractability. MicroRNAs (miRs) are small, noncoding RNAs that regulate the posttranscriptional expression of protein-coding mRNAs, which may have key roles in the pathogenesis of MTLE development. To study the dynamic expression patterns of brain-specific miR-124 and miR-134 and inflammation-related miR-132 and miR-21, we performed qPCR on the hippocampi of immature rats at 25 days of age. Expressions were monitored in the three stages of MTEL and in the control hippocampal tissues corresponding to the same timeframes. A similar expression method was applied to hippocampi obtained from children with MTLE and normal controls. The expression patterns of miR-124 and miR-134 nearly showed the same dynamics in the three stages of MTLE development. On the other hand, miR-132 and miR-21 showed significant upregulation in acute and chronic stages, while in the latent stage, miR-132 was upregulated and miR-21 was downregulated. The four miRs were upregulated in hippocampal tissues obtained from children with MTLE. The significant upregulation of miR-124 and miR-134 in the seizure-related stages and children suggested that both can be potential targets for anticonvulsant drugs in the epileptic developing brains, while the different expression patterns of miR-132 and miR-21 may suggest different functions in MTLE pathogenesis.
[Wang, Jian-qiang; Yu, Su-min; Wang, Jing] Cent S Univ, Sch Business, Changsha 410083, Hunan, Peoples R China.;[Li, Lin] Hunan Univ, Sch Business, Changsha 410082, Hunan, Peoples R China.
[Wang, Jian-qiang] Cent S Univ, Sch Business, Changsha 410083, Hunan, Peoples R China.
IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) held as part of IEEE World Congress on Computational Intelligence (IEEE WCCI)
JUL 24-29, 2016
[Yu, Su-min;Wang, Jing;Wang, Jian-qiang] Cent S Univ, Sch Business, Changsha 410083, Hunan, Peoples R China.^[Li, Lin] Hunan Univ, Sch Business, Changsha 410082, Hunan, Peoples R China.
Linguistic distribution assessments;Multi-criteria decision-making;Online reviews;Hotel selection
The effect of online reviews on resulting decisions attracted the interests of merchants and researchers in different fields. According to existing studies, the decisions of tourists are highly likely modified after browsing online reviews from other travelers on a tourism website. The manner in which online reviews on tourism websites are utilized to select hotels and support tourists is a noteworthy research problem. Online reviews of a hotel are provided by various tourists with respect to different criteria; thus, each tourist is regarded as a decision-maker. In this instance, the problem of hotel selection is based on online reviews in a tourism website and is expressed as a multi-criteria decision-making problem. In this study, a mathematical model was designed to select appropriate hotels on websites. First, a new comparison method for linguistic distribution assessments was proposed based on linguistic scale functions. Second, a novel distance measurement between linguistic distribution assessments with different numbers of linguistic terms was defined with an adjustable parameter. Third, a model for calculating weights and a mathematical model were constructed according to the idea of prioritized aggregation operator and distance measurement. Finally, a case study of TripAdvisor.com was conducted to select suitable hotels using online reviews of hotels. Data analysis was completed to prove the viability of the designed model.
SiC particle reinforced pure aluminum composites were fabricated using a powder metallurgy method.The effect of the volume fraction of the SiC particles on the mechanical properties of the composites was studied by both model simulation and experiment.The results indicate that the yield strength and tensile strength increase,but the elongation decreases with the increase in the volume fraction of the SiC particles.Both the modified shear lag model and the multi-scale model predicted yield strength and normalized elongation show similar evolution trends with the experimental data.However,the modified shear lag model underestimates the yield strength due to the ignorance of the strengthening mechanisms caused by grain refinement and dislocations interaction by the introduction of the SiC particles,and the multi-scale model overestimates the normalized elongation due to the ignorance of the pores distributed in the matrix.