Showing papers by "South China University of Technology published in 2012"
TL;DR: This work provides an updated assembly version of the 2008 Asian genome using SOAPdenovo2, a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
Abstract: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
4,284 citations
TL;DR: In this article, the authors showed that PFN can be incorporated into polymer light-emitting devices (PLEDs) to enhance electron injection from high-work-function metals such as aluminium (work function w of 4.3 eV) and gold (w ¼ 5.2 eV).
Abstract: typically based on n-type metal oxides, our device is solutionprocessed at room temperature, enabling easy processibility over a large area. Accordingly, the approach is fully amenable to highthroughput roll-to-roll manufacturing techniques, may be used to fabricate vacuum-deposition-free PSCs of large area, and find practical applications in future mass production. Moreover, our discovery overturns a well-accepted belief (the inferior performance of inverted PSCs) and clearly shows that the characteristics of high performance, improved stability and ease of use can be integrated into a single device, as long as the devices are optimized, both optically and electrically, by means of a meticulously designed device structure. We also anticipate that our findings will catalyse the development of new device structures and may move the efficiency of devices towards the goal of 10% for various material systems. Previously, we reported that PFN can be incorporated into polymer light-emitting devices (PLEDs) to enhance electron injection from high-work-function metals such as aluminium (work function w of 4.3 eV) 22,23 and has thus been used to realize high-efficiency, air-stable PLEDs 24 . Furthermore, we also found that efficient electron injection can be obtained even in the most noble metals with extremely high work functions, such as gold (w ¼ 5.2 eV), by lowering the effective work function (for example lowering w in gold by 1.0 eV), which has previously been ascribed to the formation of a strong interface dipole 25 .
3,651 citations
TL;DR: Thousands of genes with significantly lower diversity in cultivated but not wild rice are identified, which represent candidate regions selected during domestication and should be valuable for breeding and for identifying agronomically important genes in rice.
Abstract: Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.
776 citations
TL;DR: The pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.
646 citations
TL;DR: A comprehensive and fine grained survey on clustering routing protocols proposed in the literature for WSNs, and a novel taxonomy of WSN clustering routed methods based on complete and detailed clustering attributes are presented.
Abstract: The past few years have witnessed increased interest in the potential use of wireless sensor networks (WSNs) in a wide range of applications and it has become a hot research area. Based on network structure, routing protocols in WSNs can be divided into two categories: flat routing and hierarchical or clustering routing. Owing to a variety of advantages, clustering is becoming an active branch of routing technology in WSNs. In this paper, we present a comprehensive and fine grained survey on clustering routing protocols proposed in the literature for WSNs. We outline the advantages and objectives of clustering for WSNs, and develop a novel taxonomy of WSN clustering routing methods based on complete and detailed clustering attributes. In particular, we systematically analyze a few prominent WSN clustering routing protocols and compare these different approaches according to our taxonomy and several significant metrics. Finally, we summarize and conclude the paper with some future directions.
635 citations
TL;DR: In this article, the authors reported that a high power conversion efficiency of 8.4% under AM 1.5G irradiation was achieved for BHJ PSCs with an inverted device structure.
Abstract: Bulk heterojunction (BHJ) polymer solar cells (PSCs) that can be fabricated by solution processing techniques are under intense investigation in both academic institutions and industrial companies because of their potential to enable mass production of flexible and cost-effective alternative to silicon-based solar cells. A combination of novel polymer development, nanoscale morphology control and processing optimization has led to over 8% power conversion efficiencies (PCEs) for BHJ PSCs with a conventional device structure. Attempts to develop PSCs with an inverted device structure as required for achieving high PECs and good stability have, however, met with limited success. Here, we report that a high PCE of 8.4% under AM 1.5G irradiation was achieved for BHJ PSCs with an inverted device structure. This high efficiency was obtained through interfacial engineering of solution-processed electron extraction layer, leading to facilitate electron transport and suppress bimolecular recombination. These results provided an important progress for solution-processed PSCs, and demonstrated that PSCs with an inverted device structure are comparable with PSCs with the conventional device structure.
616 citations
TL;DR: In this paper, the chemical and structural properties of cellulose, lignin, d-xylose, wood meal, and phenolic hydrochars were investigated, and the carbonization mechanism was proposed, and furfural was found to be an important intermediate product during d-Xylose hydrochar production.
Abstract: Hydrothermal carbonization of cellulose, lignin, d-xylose (substitute for hemicellulose), and wood meal (WM) was experimentally conducted between 225 and 265 °C, and the chemical and structural properties of the hydrochars were investigated. The hydrochar yield is between 45 and 60%, and the yield trend of the feedstock is lignin > WM > cellulose > d-xylose. The hydrochars seem stable below 300 °C, and aromatic structure is formed in all of these hydrochars. The C content, C recovery, energy recovery, ratio of C/O, and ratio of C/H in all of these hydrochars are among 63–75%, 80–87%, 78–89%, 2.3–4.1, and 12–15, respectively. The higher heating value (HHV) of the hydrochars is among 24–30 MJ/kg, with an increase of 45–91% compared with the corresponding feedstock. The carbonization mechanism is proposed, and furfural is found to be an important intermediate product during d-xylose hydrochar production, while lignin hydrothermal carbonization products are made of polyaromatic hydrochar and phenolic hydrocha...
548 citations
TL;DR: A new live-cell-permeable, fluorescent light-up probe is designed and synthesized for real-time cell apoptosis imaging that provides a new opportunity to screen enzyme inhibitors and evaluate the apoptosis-associated drug efficacy.
Abstract: Real-time monitoring of cell apoptosis could provide valuable insights into early detection of therapy efficiency and evaluation of disease progression. In this work, we designed and synthesized a new live-cell-permeable, fluorescent light-up probe for real-time cell apoptosis imaging. The probe is comprised of a hydrophilic caspase-specific Asp-Glu-Val-Asp (DEVD) peptide and a hydrophobic tetraphenylethene (TPE) unit, a typical fluorogen with aggregation-induced emission characteristics. In aqueous solution, the probe is almost nonfluorescent but displays significant fluorescence enhancement in response to caspase-3/-7, which are activated in the apoptotic process and able to cleave the DEVD moieties. This fluorescence “turn-on” response is ascribed to aggregation of cleaved hydrophobic TPE residues, which restricts the intramolecular rotations of TPE phenyl rings and populates the radiative decay channels. The light-up nature of the probe allows real-time monitoring of caspase-3/-7 activities both in so...
516 citations
TL;DR: This article investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents and found that hypermutability is a property of ASD genes and may also include nucleotide substitution hot spots.
505 citations
TL;DR: In this paper, a dynamic polymer hydrogel with an environmental adaptive self-healing ability and dual responsive sol-gel transitions was prepared by combining acylhydrazone and disulfide bonds together in the same system.
Abstract: Dynamic polymer hydrogels with an environmental adaptive self-healing ability and dual responsive sol–gel transitions were prepared by combining acylhydrazone and disulfide bonds together in the same system. The hydrogel can automatically repair damage to it under both acidic (pH 3 and 6) and basic (pH 9) conditions through acylhydrazone exchange or disulfide exchange reactions. However, the hydrogel is not self-healable at pH 7 because both bonds are kinetically locked, whereas the hydrogel gains self-healing ability by accelerating acylhydrazone exchange with the help of catalytic aniline. All of the self-healing processes are demonstrated to be effective without an external stimulus at room temperature in air. The hydrogel also displays unique reversible sol–gel transitions in response to both pH (HCl/triethylamine) and redox (DTT/H2O2) triggers.
486 citations
TL;DR: A brief overview of the recent development of push-pull conjugated polymers and their application in solar cells is provided in this paper, where the relationships between the materials' chemical structures and properties, such as absorption spectra, energy levels, mobilities and photovoltaic behaviors, are also discussed.
Abstract: Bulk-heterojunction polymer solar cells have emerged as an attractive type of cost-effective solar energy–electrical power transforming device. Recently, great progress in the development of new photo-harvesting materials and device optimizations have been achieved in this field, resulting in the significant improvement of the power conversion efficiencies of polymer solar cells from around 1% to higher than 8.0%. The rational design and fine tailoring of the molecular structures of donor polymers significantly contributed to these prominent advances. Among all kinds of donor polymers, push–pull conjugated polymers, which consist of alternating electron-rich and electron-deficient units have been most extensively developed and have dominated the library of donor materials for polymer solar cells, because their intrinsic optical and electronic properties can be readily tuned to the desired situation by controlling the intramolecular charge transfer from donor unit to acceptor unit. This review provides a brief overview of the recent development of push–pull conjugated polymers and their application in solar cells. The relationships between the materials' chemical structures and properties, such as absorption spectra, energy levels, mobilities and photovoltaic behaviors, were also discussed.
TL;DR: This work focuses on developing simple and efficient methods to construct new carbon-carbon and carbon-heteroatom bonds with O(2) as the oxidant and/or reactant and proposes several mechanistic scenarios that describe the in situ generation of different intermediates and discuss the plausible reaction pathways.
Abstract: Oxidation reactions are central components of organic chemistry, and modern organic synthesis increasingly requires selective and mild oxidation methods. Although researchers have developed new organic oxidation methods in recent years, the chemistry community faces continuing challenges to use “green” reagents and maximize atom economy. Undoubtedly, with its low cost and lack of environmentally hazardous byproducts, molecular oxygen (O2) is an ideal oxidant. However, relatively limited methodologies are available that use O2 efficiently in selective organic transformations.Recently, the use of metal catalysts coupled with the reduction of O2 has become an attractive approach for aerobic oxidation. In particular, Pd complexes have shown great potential for the development of versatile aerobic reactions because of their ability to directly couple O2 reduction. As a result, these complexes have attracted tremendous research attention and afford new opportunities for selective oxidation chemistry.In this Acc...
TL;DR: The novel microsphere-like BiOI hierarchical material synthesized by a one-step solution method at room temperature exhibits an excellent photocatalytic degradation and mineralization capability to TC under visible light irradiation, which comes from its electronic band structure, high surface area and high surface-to-volume ratio.
TL;DR: Although enzyme applications are being developed in full swing, breakthroughs are needed to overcome their weaknesses in maintaining activities during the catalytic processes and strategies of metagomic analysis, cell surface display technology and cell-free system might give valuable solutions in novel enzyme exploiting and enzyme engineering.
Abstract: Enzymes are protein molecules functioning as specialized catalysts for chemical reactions. They have contributed greatly to the traditional and modern chemical industry by improving existing processes. In this article, we first give a survey of representative industrial applications of enzymes, focusing on the technical applications, feed industry, food processing and cosmetic products. The recent important developments and applications of enzymes in industry are reviewed. Then large efforts are dedicated to the worldwide enzyme market from the demand and production perspectives. Special attention is laid on the Chinese enzyme market. Although enzyme applications are being developed in full swing, breakthroughs are needed to overcome their weaknesses in maintaining activities during the catalytic processes. Strategies of metagomic analysis, cell surface display technology and cell-free system might give valuable solutions in novel enzyme exploiting and enzyme engineering.
TL;DR: In this paper, the paraffin/expanded graphite (EG) composite phase change material (PCM) was prepared by absorbing liquid Paraffin into the expanded graphite, in which paraffIN was chosen as the PCM.
TL;DR: HTC processes were studied using two different biomass feedstocks and the resulting lignite-like solid products contained mainly lignin with a high degree of aromatization and a large amount of oxygen-containing groups, which may be desirable feedstocks for biodiesel and chemical production.
TL;DR: A series of room temperature ionic liquids, in which cholinium acts as the cation and amino acids as the anions, were prepared via a simple and green chemical route and characterized, and dissolved lignin efficiently and selectively.
TL;DR: Current isolation and purification strategies are summarized, and the bioconversion of hemicelluloses including pretreatment, enzymatic hydrolysis, and fermentation are discussed.
TL;DR: These first ant methylomes and their intra- and interspecies comparison reveal an exonic methylation pattern that points to a connection between DNA methylation and splicing, suggesting roles in genome regulation in these social insects.
TL;DR: It is reported that in the superconducting iron chalcogenides, a secondsuperconducting phase suddenly re-emerges above 11.5 GPa, after the Tc drops from the first maximum of 32 K at 1 GPa.
Abstract: Pressure has an essential role in the production(1) and control(2,3) of superconductivity in iron-based superconductors. Substitution of a large cation by a smaller rare-earth ion to simulate the pressure effect has raised the superconducting transition temperature T-c to a record high of 55 K in these materials(4,5). In the same way as T-c exhibits a bell-shaped curve of dependence on chemical doping, pressure-tuned T-c typically drops monotonically after passing the optimal pressure(1-3). Here we report that in the superconducting iron chalcogenides, a second superconducting phase suddenly re-emerges above 11.5 GPa, after the T-c drops from the first maximum of 32 K at 1 GPa. The T-c of the re-emerging superconducting phase is considerably higher than the first maximum, reaching 48.0-48.7 K for Tl0.6Rb0.4Fe1.67Se2, K0.8Fe1.7Se2 and K0.8Fe1.78Se2.
TL;DR: In this paper, the photocatalytic activity, the amounts adsorbed of CO 2 and the visible light absorption capability of Bi 2 S 3 -modified TNTs photocatalyst are all better than those of CdS-modified TNTs.
TL;DR: In this article, the authors investigated the effect of cultural values on travel motivation and behavioral intention in Chinese tourists and found that both internal and external values exert a significantly positive effect on the travel motivation.
Abstract: Culture has been widely proposed by marketing theorists as one of the underlying determinants of consumer behavior. Empirical inquiries in the field of tourism remain scarce, particularly in the understanding of its behavioral influences. The study reported in this article aims to fill the gap by investigating the effect of cultural values on travel motivation and behavioral intention. The analysis of survey data from outbound Chinese tourists reveals that both internal and external values exert a significantly positive effect on travel motivation. Behavioral intention is affected only by internal values. The novelty dimension of travel motivation directly affects behavioral intention. The findings are examined in the context of the rising significance and uniqueness of Chinese outbound tourism. Pragmatic and theoretical implications are discussed.
TL;DR: Three-dimensional BiOI/BiOCl composite microspheres with enhanced visible-light photodegradation activity of bisphenol-A (BPA) synthesized by a simple, one-pot, template-free, solvothermal method exhibited a high mineralization ratio, high stability and easy separation for recycling use, suggesting that it is a promising photocatalyst for the removal of BPA pollutants.
TL;DR: It is found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice.
Abstract: DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.
TL;DR: A series of bismuth oxyhalides with controllable composition and band structure have been successfully synthesized by a facile and general one-pot hydrothermal route using Bi2O3 as the starting material.
Abstract: A series of bismuth oxyhalides with controllable composition and band structure have been successfully synthesized by a facile and general one-pot hydrothermal route using Bi2O3 as the starting material; their band structures and visible-light-induced photocatalytic performances are investigated
06 Jun 2012
TL;DR: A hybrid BCI that uses the motor imagery-based mu rhythm and the P300 potential to control a brain-actuated simulated or real wheelchair is introduced to provide a greater number of commands with increased accuracy to the BCI user.
Abstract: Brain-computer interfaces (BCIs) are used to translate brain activity signals into control signals for external devices. Currently, it is difficult for BCI systems to provide the multiple independent control signals necessary for the multi-degree continuous control of a wheelchair. In this paper, we address this challenge by introducing a hybrid BCI that uses the motor imagery-based mu rhythm and the P300 potential to control a brain-actuated simulated or real wheelchair. The objective of the hybrid BCI is to provide a greater number of commands with increased accuracy to the BCI user. Our paradigm allows the user to control the direction (left or right turn) of the simulated or real wheelchair using left- or right-hand imagery. Furthermore, a hybrid manner can be used to control speed. To decelerate, the user imagines foot movement while ignoring the flashing buttons on the graphical user interface (GUI). If the user wishes to accelerate, then he/she pays attention to a specific flashing button without performing any motor imagery. Two experiments were conducted to assess the BCI control; both a simulated wheelchair in a virtual environment and a real wheelchair were tested. Subjects steered both the simulated and real wheelchairs effectively by controlling the direction and speed with our hybrid BCI system. Data analysis validated the use of our hybrid BCI system to control the direction and speed of a wheelchair.
TL;DR: Experimental results revealed that the CS/PAA- MCM had greater adsorption capacity than CS-MCM, and PAA played an important role for the adsorbent of Cu(II) ions, which indicated the significant separability of the MCM in the aqueous suspensions.
TL;DR: In this paper, the authors proposed a first-principles theory to study the linear dispersions in phononic and photonic crystals, which is capable of predicting accurately the linear slopes of Dirac and Dirac-like cones at various symmetry points in a Brillouin zone, independent of frequency and lattice structure.
Abstract: By using the $\stackrel{\ensuremath{\rightharpoonup}}{k}\ifmmode\cdot\else\textperiodcentered\fi{}\stackrel{\ensuremath{\rightharpoonup}}{p}$ method, we propose a first-principles theory to study the linear dispersions in phononic and photonic crystals. The theory reveals that only those linear dispersions created by doubly degenerate states can be described by a reduced Hamiltonian that can be mapped into the Dirac Hamiltonian and possess a Berry phase of $\ensuremath{-}\ensuremath{\pi}$. Linear dispersions created by triply degenerate states cannot be mapped into the Dirac Hamiltonian and carry no Berry phase, and, therefore should be called Dirac-like cones. Our theory is capable of predicting accurately the linear slopes of Dirac and Dirac-like cones at various symmetry points in a Brillouin zone, independent of frequency and lattice structure.
TL;DR: In this paper, the production of cellulose nanofibrils (CNF) from a bleached eucalyptus pulp using a commercial stone grinder was reported.
Abstract: This study reports the production of cellulose nanofibrils (CNF) from a bleached eucalyptus pulp using a commercial stone grinder Scanning electronic microscopy and transmission electronic microscopy imaging were used to reveal morphological development of CNF at micro and nano scales, respectively Two major structures were identified: (1) highly kinked, naturally helical, and untwisted fibrils that serve as backbones of CNF networks, and (2) entangled, less distinctively kinked (or curled) and twisted “soft looking” nanofibrils These two major structures appeared in different features of CNF network such as “trees”, “net”, “flower”, single fibril, etc Prolonged fibrillation can break the nanofibrils into nanowhiskers from the untwisted fibrils with high crystallinity Energy input for mechanical fibrillation is on the order of 5–30 kWh/kg The gradual reduction in network size of CNF with time may be used to fractionate CNF
TL;DR: The degradation of p -chloroaniline (PCA) by persulfate (S 2 O 8 2 - ) activated with zero-valent iron (ZVI) was investigated through batch experiments as discussed by the authors.