Search

An expanded GGGGCC hexanucleotide of more than 30 repeats (termed (G4C2)30+) within C9orf72 is the most prominent mutation in familial frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis (ALS) (termed C9+). Through an unbiased large-scale screen of (G4C2)49-expressing Drosophila we identify the CDC73/PAF1 complex (PAF1C), a transcriptional regulator of RNA polymerase II, as a suppressor of G4C2-associated toxicity when knocked-down. Depletion of PAF1C reduces RNA and GR dipeptide production from (G4C2)30+ transgenes. Notably, in Drosophila, the PAF1C components Paf1 and Leo1 appear to be selective for the transcription of long, toxic repeat expansions, but not shorter, nontoxic expansions. In yeast, PAF1C components regulate the expression of both sense and antisense repeats. PAF1C is upregulated following (G4C2)30+ expression in flies and mice. In humans, PAF1 is also upregulated in C9+-derived cells, and its heterodimer partner, LEO1, binds C9+ repeat chromatin. In C9+ FTD, PAF1 and LEO1 are upregulated and their expression positively correlates with the expression of repeat-containing C9orf72 transcripts. These data indicate that PAF1C activity is an important factor for transcription of the long, toxic repeat in C9+ FTD. The (G4C2)30+ repeat expansion is the most prominent mutation in familial FTD and ALS. Here the PAF1 complex is identified as a transcriptional regulator of this unique mutation. Data from FTD tissue positive for the C9orf72 mutation support the relevance of this complex in disease.

Sulfamerazine (SMR) as a persistent organic pollutant in waste streams is of growing environmental concern. This study explores the extraction SMR from water into an acetic acid (AA) solution using granular activated carbon (GAC), and removal of SMR by ozonation in AA solution. Systematic experiments have shown that GAC can be used as an adsorbent to transfer sulfamerazine from water to AA solution. SMR removal efficiency is 99.5% in 10% AA aqueous solution, which is better than in water. The removal rate of SMR in the AA solution decreased as the initial molar ratio of SMR and O3 increased. The removal rate of SMR decreased with Fe3+ present in the reactive system. The removal of SMR is dominated by indirect ozonation in water, while the SMR removal is an effect of both direct and indirect ozonation in AA solution. It is a very efficient process for the degradation of SMR in micro polluted water when using combined GAC adsorption–desorption in AA solution and ozonation of the resulting solution.

In this work, we reported a kind of deflecting air cavity generation strategy by controlling the superhydrophobic (SHB) area occupancy and the impact angle of water entry. The influence of SHB area occupancy and the impact angle on the water entry dynamics and drag reduction characteristics of spheres are also explored through both experimental and theoretical analysis. For a hemispherically coated sphere, it is found that the formed air cavity would reach a maximum deflecting angle when the impact angle of water entry is 90°. With the increasing impact angle, the deflection displacement of the hemispherically coated sphere in the horizontal direction first increases and then decreases. When the impact angle is 90°, the deflection displacement reaches the maximum. The deflection displacement of the SHB region-modulated sphere in the horizontal direction has the same variation trend. Moreover, the SHB region-modulated sphere exhibits different air cavity morphologies (no cavity, transition state seal, deep seal, and surface seal) at different impact velocities for impact angles of 0° and 180°. The air cavity pinch-off depth and pinch-off time first increase and then stabilize as the SHB area occupancy increases, regardless of whether the impact angle is 0° or 180°, and the value of ( Zpinch − Zp)/ Zpinch is not affected by the SHB area occupancy (α ∼ 0°). Finally, we demonstrate that SHB region-modulated spheres all move faster than the original spheres, and the sphere with a SHB area occupancy of 0.25 ( α ∼ 180°) is able to reduce the drag reduction coefficient to 0.055.

Pre-salting is an important pre-treatment during production of Suancai as it provides flavor precursor and microbial community for subsequent fermentation. To investigate the effect of pre-salting duration on fermentation of Suancai, the physicochemical properties, microbial composition, non-volatile and volatile organic compounds profiles of Suancai pre-salted for 1 month (1 M) and 7 months (7 M) were analyzed during fermentation for 30 days. Results showed that 7 M led to higher salt content, faster depletion of reducing sugars, and more titratable acidity. Additionally, more lactic acid and acetic acid, and less umami amino acid (Glu) and GABA were observed in 7 M. Longer pre-salting duration (7 M) promoted formation of mild-flavor volatile compounds, and significantly reduced isothiocyanates with pungent off-flavor. Moreover, 7 M promoted abundance of genera Chromohalobacter, Vibrio and Pichia, while reducing abundance of Lactobacillus, Debaryomyces and Kazachstania throughout fermentation. These results implicated that longer pre-salting duration facilitated more acidic, milder flavor and less pungent off-odor in Suancai. This study provided a perspective for pre-salting as a control point for improving quality of fermented vegetable.

In this work, we proposed a facile underwater air cavity generation strategy based on rough microstructured spheres and explored its water entry dynamics and drag reduction characteristics. Under the assistance of microstructures, the three-phase contact line is pinned near the sphere equator and inhibits the wetting of the liquid film along the sphere surface, so that leading the formation of air cavity. The water entry process is mainly divided into four stages: flow formation, cavity opening and stretching, cavity closure and entrapment, and cavity collapse. With the Froude number Fr, the pinch-off depth of air cavity obviously increases, and the pinch-off time is also delayed, which contributes to the formation of a longer bottom air cavity. In addition, the spheres with a larger impact velocity would fall faster in water during the initial falling period, while the terminal velocities are nearly the same for all the spheres when they are in a stable falling period. It is worth noting that for a same sphere, the larger impact velocity could not only contribute to the formation of a longer air cavity but also makes the generated air cavity keep in a stable and streamlined shape at different underwater depth, which is vitally important for achieving continuous drag reduction. Finally, we demonstrated numerically that the stable streamlined sphere-in-cavity structure could reduce the hydrodynamic resistance levels up to 91.3% at Re ∼ 3.12 × 104, which is related to the boundary slip caused by an air layer trapped in the microstructures.

Spinocerebellar ataxia type 2 is a polyglutamine (polyQ) disease associated with an expanded polyQ domain within the protein product of the ATXN2 gene. Interestingly, polyQ repeat expansions in ATXN2 are also associated with amyotrophic lateral sclerosis (ALS) and parkinsonism depending upon the length of the polyQ repeat expansion. The sequence encoding the polyQ repeat also varies with disease presentation: a pure CAG repeat is associated with SCA2, whereas the CAG repeat in ALS and parkinsonism is typically interrupted with the glutamine encoding CAA codon. Here, we asked if the purity of the CAG sequence encoding the polyQ repeat in ATXN2 could impact the toxicity of the ataxin-2 protein in vivo in Drosophila. We found that ataxin-2 encoded by a pure CAG repeat conferred toxicity in the retina and nervous system, whereas ataxin-2 encoded by a CAA-interrupted repeat or CAA-only repeat failed to confer toxicity, despite expression of the protein at similar levels. Furthermore, the CAG-encoded ataxin-2 protein aggregated in the fly eye, while ataxin-2 encoded by either a CAA/G or CAA repeat remained diffuse. The toxicity of the CAG-encoded ataxin-2 protein was also sensitive to the translation factor eIF4H, a known modifier of the toxic GGGGCC repeat in flies. These data indicate that ataxin-2 encoded by a pure CAG versus interrupted CAA/G polyQ repeat domain is associated with differential toxicity, indicating that mechanisms associated with the purity of the sequence of the polyQ domain contribute to disease., Graphical Abstract Graphical Abstract

A systematic monitoring campaign of pharmaceuticals and personal-care products (PPCPs) was performed in the Taige Canal basin, which is located in a rural area of the Yangtze River Delta. A total of 55 out of 61 monitored PPCPs were detected, with concentrations up to 647 ng/L. The maximum concentrations of 75% of monitored antibiotics and 80% of non-antibiotics were above the median values of previously reported maximum concentrations in China, indicating that the basin is heavily contaminated. It is estimated that the PPCP mass flow of the Taige Canal (0.06–0.58 kg/day) entering into Lake Taihu is similar to that of the influent of a wastewater treatment plant. Analysis of the seasonal variation shows that, during the wet season, the average total concentration of sulfonamides was 8 and 11 times that of the normal season and dry season, respectively. The concentration of sulfachlorpyridazine accounted for 40.37% of total antibiotics, suggesting heavy pollution from the animal-breeding industry in this area. The PPCP mass flow rates observed in 2019 were lower than those of 2018 in the same season, and this interannual variation is mainly attributable to water pollution controls in the watershed. Combined analysis of ordination and clustering indicates that the distribution of PPCPs in the Taige Canal is affected by the confluence with Yong'an River and human activities such as water pollution control. Water–sediment distribution analysis demonstrates that the sediment–water distribution coefficients of quinolone and macrolide were higher than those of sulfonamide, lincosamide and chloramphenicol.

Background: Genotype imputation as a service is developed to enable researchers to estimate genotypes on haplotyped data without performing whole genome sequencing. However, genotype imputation is computation intensive and thus it remains a challenge to satisfy the high performance requirement of genome wide association study (GWAS). Objective: In this paper, we propose a high performance computing solution for genotype imputation on supercomputers to enhance its execution performance. Method: We design and implement a multi-level parallelization that includes job level, process level and thread level parallelization, enabled by job scheduling management, message passing interface (MPI) and OpenMP, respectively. It involves job distribution, chunk partition and execution, parallelized iteration for imputation and data concatenation. Due to the design of multi-level parallelization, we can exploit the multi-machine/multi-core architecture to improve the performance of genotype imputation. Results: Experiment results show that our proposed method can outperform the Hadoop-based implementation of genotype imputation. Moreover, we conduct the experiments on supercomputers to evaluate the performance of the proposed method. The evaluation shows that it can significantly shorten the execution time, thus improving the performance for genotype imputation. Conclusion: The proposed multi-level parallelization, when deployed as an imputation as a service, will facilitate bioinformatics researchers in Singapore to conduct genotype imputation and enhance the association study.

Existing Hadoop MapReduce fault tolerance strategy causes the computing jobs suffering from high performance penalty during failure recovery. In this paper, we propose Fast Recovery MapReduce (FAR-MR) to improve MapReduce performance in failure recovery. FAR-MR includes a novel fault tolerance strategy that combines distributed checkpointing and proactive push mechanism to support fast recovery from task failure and node failure. With distributed checkpointing, computing progress of each task is recorded as checkpoints periodically and kept in distributed data storage. The recovered task can obtain the last progress of the failed task from the distributed storage during failure recovery. In addition, the proactive push mechanism enables the computing results of map tasks to be proactively transmitted to the nodes hosting reduce tasks of the same computing job. When a failure happens, the partial output results being pushed to the reducer nodes can be used by the reduce tasks without the necessity of re-compute. FAR-MR allows a failed task to be recovered efficiently at any node in the cluster. The performance evaluation has shown that the proposed FAR-MR can improve computing job performance by up to 62% and 45% compared to Hadoop MapReduce in the case of task failure recovery and node failure recovery, respectively.

The ribosomal DNA (rDNA) repeats of more and more species have been found to be polymorphic in the genome, and the understanding of this polymorphism is conducive not only to eliminating potential chaos in the metagenomic analysis (MGA), but also to providing rich information on rDNA evolution. In this study, the MGA previously used for the study of environmental microbial diversity was improved and extended to detect the intragenomic polymorphism (IGP) of rDNA in three species of Camellia L. The 3′‐end region of 26S rDNA of three individuals was amplified using degenerate primer pairs. Three annealing temperatures were applied to obtain as many ribotypes as possible, and equimolar amplicons from the three species were then pooled and sequenced using the Illumina MiSeq platform. An incredibly high level of IGP of rDNA was found in all three species. Nearly all of the ribotypes detected from this study were rDNA pseudogenes, and most of them have existed for a long time in the genome, with some generated from several rapid expansions. Our procedure provided an effective technique for detection of IGP of rDNA, and the particular evolutionary information of rDNAs in Camellia was also exploited.

To study the phenolics in grains of hulless barley varieties harvested in the Qinghai-Tibet plateau region, free, esterified, and insoluble-bound phenolic fractions were extracted from grain of fourteen varieties. The phenolic components and antioxidant activity of the fractions were studied. Identification of phenolics profile in QB35 variety was studied using ultra-high-performance liquid chromatography-diode array with quadrupole time-of-flight and tandem mass spectrometry (UPLC-QTOF-MS/MS), which revealed fourteen phenolics in the free form, four in the esterified form, and seventeen in the insoluble-bound form. Total phenolic contents (TPC) of the fractions were tested finding significantly (p

In view of the problems of exposure bias and insufficient annotation data in the existing Chinese short text summary algorithms, a new pre-training short text summary algorithm named ERNIE-GEN-CTS based on ERNIE-GEN is proposed. This paper uses pre-training language model to realize the double attention of word level and word level for short text, and fills the sub block with semantic information to optimize the exposure bias problem. After the pre-training model of large-scale Chinese corpus, the results are improved in LCSTS data set after the task tuning of the downstream summary, and the validity and stability of the model are verified.

Federated cloud enables data sharing across different organizations. This paper proposes a distributed search index (DS-index) solution to provide distributed search capability in federated cloud, with the target to support multi-attribute range queries with secondary indexes. DS-index deploys a three-layer architecture with a multi-attribute index overlay, a tree-based P2P network layer, and a federated cloud layer. We present a distributed search algorithm with the three-layer architecture. In order to facilitate distributed search, we propose a dynamic mapping algorithm for DS-index to map between different layers. In addition, a Markov Chain-based cost model is defined to facilitate node selection and mapping. With the dynamic mapping algorithm and cost model, the proposed DS-index solution is more cost-effective than the traditional P2P networks as it can reduce the network cost in terms of index maintenance cost and node selection cost. The experiments demonstrate that, our DS-index solution along with its cost model can save the computation resource and reduce network bandwidth consumption by around 30% comparing to the one without cost model. It can also reduce the number of node splits/merges by around 20% comparing to the state-of-the-art solution.

Aqueous solutions of ethanol and ascorbic acid alone and in combination were compared to a commonly used sanitizer, sodium hypochlorite, and a leading commercial antibrowning agent containing calcium ascorbate (CA) for their efficacy to inhibit microbial growth and browning on fresh-cut lotus root. Fresh-cut lotus root slices were immersed in one of 7 treatment solutions including water (control), 30% ethanol (v/v), 30% ethanol (v/v) plus 30 g L −1 ascorbic acid (AA), 30% ethanol (v/v) plus 30 g L −1 CA, 30 g L −1 AA, 30 g L −1 CA and 100 mg L −1 sodium hypochlorite for 2 min, and then packaged in polyethylene bags and stored for 28 d at 4 °C. Packages were monitored for headspace gas composition, color, texture, aerobic mesophilic bacteria, and yeast and mold populations, electrolyte leakage and sensory attributes. The results indicate that all ethanol treatments, with and without added AA or CA, not only inhibited microbial growth, but also delayed browning more effectively than either AA or CA alone. The combined treatments of Ethanol 30% (v/v) along with 30 g L −1 AA or 30 g L −1 CA were even more effective than ethanol alone in maintaining quality of fresh-cut lotus slices during cold storage. Increasing ethanol concentration within the range of 5–30% (v/v) when accompanied by 30 g L −1 AA, decreased microbial populations and had little effect on quality maintenance of fresh-cut lotus root during cold storage. Ethanol concentrations of 20–30% (v/v) in conjunction with 30 g L −1 AA have the potential to inhibit browning and maintain quality of fresh-cut lotus root slices for more than 14 d when stored at 4 °C. This is the first use of ethanol as a dual control for both browning and microbial growth in fresh-cut lotus root.

Macamides and Macaenes are the bioactive marker compounds in maca (Lepidium meyenii Walp., Brassicaceae) tuber. To simultaneously quantify these two types of compound, HPLC method was studied. To distinguish and group the growing regions of different maca samples, Hierarchical cluster analysis, a chemometric method, was applied to analyze the HPLC data. The calibration curves obtained using the HPLC method showed satisfactory linearity with determination coefficients >0.9998. The precision and repeatability relative standard deviation values were

Microbial communities in fermented food are shaped by a myriad of abiotic factors. The respective roles of abiotic factors in shaping the dynamic bacterial community of paocai during aging remain unclear. In the present study, 100 paocai samples (pH: 2.95–5.23; NaCl content: 0.13–15.41%; total acid: 6.61–18.33 mg/mL; total sugars: 7.96–487.90 μg/mL; total viable count: 3.55–8.99 LogCFU/mL; aging time: 5 day–15 year) were analyzed through high-throughput sequencing and the results revealed five dominant bacterial genera across different samples, including Lactobacillus, Pediococcus, Leuconostoc, Lactococcus and unclassified genera. Both NaCl and total acid (TA) were the major factors regulating bacterial community divergence in paocai. Based on these results, the microbial communities were reconstructed by manipulating the TA and NaCl contents in vitro to validate the effectiveness of these factors in shaping microbial communities during paocai fermentation. Results showed that roles of abiotic factors differentiated during fermentation. At the early stage, salt was the first abiotic filter, mainly working through promoting the abundance of Lactococcus and Leuconostoc. As the TA content increased, the selective role of salt weakened while acid became the dominant at the later stage, as evidenced by the increased abundance of Lactobacillus and Pediococcus following the increase of TA content.

The objective of the present study was to investigate the effect of reused brine and fresh salt brine on nitrites and biogenic amines production in low-salt Paocai during fermentation, with insights into the impact of initial microbial loading and acidification. By monitoring the changes in microbial counts, physicochemical properties as well as the production of nitrites, biogenic amines and precursor amino acid nitrogen (AAN) in Paocai fermented with reused brine (RB), microorganism-reduced reused brine (MRRB), fresh salt brine (SB) and acidified fresh salt brine (ASB), the results showed that RB promoted the growth of lactic acid bacteria (LAB) and yeasts, causing a rapid consumption of reducing sugar. MRRB and RB inhibited the undesirable enterobacteria, while SB and ASB failed. Among the treatments, RB achieved highest AAN contents and lowest contents of nitrites (1.10 mg/kg), histamine (0.29 mg/kg), tyramine (0.79 mg/kg) and cadaverine (not detected) after fermentation. Comparing SB with ASB, it was found that initial acidification of salt brine eliminated cadaverine and reduced histamine contents by 33.93%. These results suggested that the initial microbial loading and acidification of brine could reduce nitrites and biogenic amines production in Paocai during fermentation, which might provide guidance for production of fermented vegetable with higher safety.

Reduction of biogenic amine and nitrites is of practical importance for promoting the safety of fermented vegetable. The aim of this study was to analyze the efficacy of package types in reducing biogenic amine and nitrite levels of Paocai during storage. And the related parameters including microbial growth, pH and generation of amino acid nitrogen (AAN) were also evaluated. The results showed that when compared with aerobic package (AP) and NaCl solution package (NP), vacuum package (VP) reduced the counts of lactic acid bacteria and yeasts to 6.98 and 1.21 LogCFU/g, respectively. The pH of Paocai was not significantly different among treatments. VP was more effective than AP and NP in suppressing the accumulation of histamine, tyramine and putrescine in Paocai, as evidenced by the contents that were 0.19, 0.15 and 0.43 mg/kg after storage, respectively. Additionally, VP and AP prevented cadaverine production throughout the storage while NP accelerated its production. For Paocai in VP and NP, the AAN content rose by 66.67% and 33.33%, respectively, while AAN in AP increased by 133.33% after storage. Meanwhile, nitrite accumulation in Paocai was mitigated by VP, as shown by nitrite content that were 56.04% and 36.31% lower than those in AP and NP groups, respectively, at the end of storage. Therefore, compared with conventional NP, VP was the most effective in suppressing the production of biogenic amines, nitrite and AAN, while AP accelerated the accumulation of these nitrogenous compounds, possibly implicated the application of VP to produce fermented vegetable with higher safety property.

Due to consistent improvements in memory and processor technology, object storage devices (OSDs) have greater memory space and more powerful processing power, which allow the OSDs to execute user-defined programs. Shifting part of an application's processing to the disk drives drops the amount of data transferred across the network and explores the parallelism of large-scale distributed storage systems, reducing the execution time for many basic data analytics tasks. In this paper, we propose a large-scale object-based active storage platform, named Gem, for data analytics in the internet of things (IoT). All data from the IoT that resides in disk drives form objects with attributes, methods and policies. For some applications such as data analytics, application-specific operations are executed by the drive processors. In this way, only the results are returned to clients, rather than data files being read by the clients. Therefore, the platform Gem is able to greatly reduce the overhead of data analytics applications in the Internet of Things. By conducting performance evaluation, experimental results demonstrate the effectiveness and scalability of Gem.

Radish paocai is a representative of fermented vegetables in China. The objective of the present study was to evaluate the potential of cold plasma (CP) treatment as decontamination technology for packaged paocai. By comparing with heat pasteurization, the effect of CP on microbial, physicochemical and organoleptic properties of paocai during storage was investigated. Results showed that CP efficiently eliminated yeasts, especially gas-producing yeast, while allowing retention of lactic acid bacteria. Compared with pasteurization at 70 °C for 30 min which eliminated 5.00 logCFU/g of microorganisms, more reducing sugar was consumed by CP-treated paocai, leading to the increase of total acid content by 72.34% and a lower pH at 3.98 after storage of 7 days. Additionally, nitrite content in CP group was 48.54% lower than that of control and was 22.22% higher than that of pasteurization group, with no significant effect on salt content and amino acid nitrogen. As for organoleptic property, firmness and b* value of CP treated samples was 12.53% higher and 26.26% lower than those of pasteurization group after storage, respectively, indicating that CP could alleviate the softening and browning of paocai. Therefore, compared with control, CP could improve the storage stability of packaged paocai, meanwhile achieving similar safety quality as pasteurization, highlighting its potential in preserving packaged fermented vegetables.

As modern data centers continue to grow in size and complexity to host different kinds of applications, it is required to have an efficient proactive failure management for Data Center reliability. Although Software-Defined Networking (SDN) and its implementation OpenFlow facilitate dynamic management and the configuration of Data center networks, network failure recovery in a timely manner remains great challenging. The centralized SDN controller is responsible for monitoring the entire network health status and maintain the end-to-end connectivity between the hosts. In the event of a link failure, the controller either computes a new backup path reactively on demand and creates flow table entries for the new backup path, or pro-actively computes the backup path a-priori and set up flow table rules for the pre-defined backup path. Switching to the predefined backup path locally results in faster recovery time compared to switching to the backup path that establish on demand. In this paper, we propose a proactive mechanism to provide fast recovery upon a link failure. With the proposed proactive approach, we compute the recovery (or backup) paths for the flows prior to failures and install appropriate rules in the forwarding tables at the switches in advance. Such recovery paths are adaptively updated based on the current load state of the network to improve resource efficiency and reduce congestion. By providing the backup forwarding rules in advance, upon a failure, the failed traffic is rerouted without interacting with the controller, thus ensuring fast recovery. We demonstrate the effectiveness of the proposed mechanisms using an experimental testbed with Openstack platform and simulated environment with Mininet.

The macroscopic and microscopic morphologies and indigo and indirubin concentration of the traditional Chinese medicine herbs Isatis indigotica Fort., Polygonum tinctorium Ait., and Baphicacanthus cusia (Nees) Bremek, all commonly known as “daqingye”, were determined and compared. The morphological analyses indicated that I. indigotica has leaves with winged petioles and no glandular hairs or crystals, P. tinctorium has leaves with membranous ocrea and clusters of calcium oxalate, and B. cusia has palisade cells in the mesophyll running over the main vein and single cells containing calcium carbonate crystals. Indigo and indirubin are chemical constituents that have been previously isolated from daqingye and were selected in this study as identification markers for high-performance liquid chromatography analysis due to their pharmacological activities. The chromatographic results showed that indigo and indirubin concentration varied significantly among the three species: high concentration of both indigo and indirubin were observed in I. indigotica, the highest concentration among the three daqingye plants was found in P. tinctorium but with low levels of indirubin, and the concentration of indigo and indirubin was quite low in B. cusia. In summary, three different species commonly known as daqingye were accurately distinguished by morphological observation, internal leaf anatomy analysis, and chromatographic analysis.

Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.

Without a central authority, blockchains can easily enable the management of transactions. Smart contracts stored on blockchains are self-executing contractual states that are not controlled by anybody, so they can be trusted. In addition, due to increasing improvements in processor and memory technology, IoT (Internet of Things) devices have more powerful processing power and greater memory space, which allow them to execute user-defined programs, e.g., smart contracts. Shifting part of applications’ tasks to IoT devices reduces the transferred data amount over the IoT network. The parallelism of large-scale storage systems is employed to decrease many basic data analytics tasks’ execution time. Blockchain can be used as smart contracts that facilitate and enforce the negotiation of a contract in the IoT. This chapter proposes a blockchain-based storage system, named Sapphire, for data analytics applications in the Internet of Things. All the IoT data from the devices forms objects with IDs, attributes, policies, and methods. We present an OSD-based smart contract (OSC) approach employed in Sapphire as a transaction protocol, where IoT devices interact with such blockchains. For data analytics applications, the IoT device processors execute application-specific operations. By doing so, only the results are returned to clients instead of data files read by them. Therefore, the Sapphire system can greatly decrease the overhead of data analytics in the Internet of Things.

Expanded non-coding RNA repeats of CUG and CCUG are the underlying genetic causes for myotonic dystrophy type 1 (DM1) and type 2 (DM2), respectively. A gain-of-function of these pathogenic repeat expansions is mediated at least in part by their abnormal interactions with RNA-binding proteins such as MBNL1 and resultant loss of activity of these proteins. To study pathogenic mechanisms of CCUG-repeat expansions in an animal model, we created a fly model of DM2 that expresses pure, uninterrupted CCUG-repeat expansions ranging from 16 to 720 repeats in length. We show that this fly model for DM2 recapitulates key features of human DM2 including RNA repeat-induced toxicity, ribonuclear foci formation and changes in alternative splicing. Interestingly, expression of two isoforms of MBNL1, MBNL135 and MBNL140, leads to cleavage and concurrent upregulation of the levels of the RNA-repeat transcripts, with MBNL140 having more significant effects than MBNL135. This property is shared with a fly CUG-repeat expansion model. Our results suggest a novel mechanism for interaction between the pathogenic RNA repeat expansions of myotonic dystrophy and MBNL1.

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh = 0.0002-0.0013, mc = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST = 0.343). High within-population genetic variation (HE = 0.377-0.515), relatively large effective population sizes (Ne = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon.

Prompt response to data access requests is the key performance concern of parallel storage systems. Sort partition (SP) is one of the most promising file allocation solutions for the static scenario due to its sorted partition and placing mechanism. The online variant of SP, hybrid partition (HP), however, does not perform well in the dynamic scenario. The recently proposed balanced allocation with sort (BAS) and its online version balanced allocation with sort for batch (BASB) try to compete with SP and HP by providing better load balancing together with sorting. BAS's performance is close to SP, and BASB greatly outperforms HP. In this paper, we proposed new file placement solutions for the parallel storage systems: Optimized Sort Partition (OSP) for the static scenario and Optimized Sort Partition Online (OSPOnline) for the dynamic scenario. By eliminating the drawbacks of SP/HP and BAS/BASB in the file assignment, OSP and OSPOnline can achieve optimized system response time. Conducted simulations show that OSP and OSPOnline steadily outperform their competitors under various conditions.

In this paper, we propose a new reference-based data compression method for efficient compressing of genome sequencing data in FASTQ format. With the advance of the next sequencing technology, the genome data can be generated faster and cheaper, which brings the challenges for efficient storage of these data when used in cloud computing. In order to efficiently store these types of genome data in cloud, content-aware compressing methods have to be developed to make use of the specific file structures. Compared with existing genome-specific compression methods, our proposed content-aware method focused on high compression ratio by taking advantages of repetitive nature of DNA sequence, and using reference genomes in compressing the sequences inside the FASTQ files. The benchmark results of 8 datasets show that our method can achieve highest compression ratio compared with existing FASTQ file compressors.

Federated cloud facilitates data sharing across multiple organizations. Existing distributed storage systems cannot support efficient data search with complicated query requirements. This paper proposes a DS-index solution to provide distributed search in federated cloud, targeting to support multi-attribute range search with secondary index. DS-index includes a three-layer architecture with a multi-attribute index overlay, a tree-based P2P network layer, and a federated cloud layer. In addition, a dynamic mapping algorithm has been presented for DS-index to map between different layers. We have also defined a Markov Chain-based cost model to facilitate node selection and mapping. The proposed DS-index solution is capable to support multi-attribute range queries in the federated cloud. The experiments have shown that, the DS-index solution with cost model can save the computation resource and reduce network bandwidth consumption by around 30% comparing to the one without cost model. It can also reduce the splitting/ merging times by around 20% comparing to the state-of-the-art solution.

The objective of this research was to characterize the high level of resistance to stripe that has been observed in the released wheat cultivar, Chuanmai45. A combination of classic genetic analysis, molecular and cytogenetic methods were used to characterize resistance in an F2 population derived from Chuanmai45 and the susceptible Chuanmai42. Inheritance of resistance was shown to be conferred by two genes in Chuanmai45. Fluorescence in situ hybridization (FISH) was used along with segregation studies to show that one gene was located on a 1RS.1BL translocation. Molecular markers were employed to show that the other locus was located on chromosome 4B. The defeated gene, Yr24/26, on chromosome 1BL was present in the susceptible parent and lines that recombined this gene with the 1RS.1BL translocation were identified. The germplasm, loci, and associated markers identified in this study will be useful for application in breeding programs utilizing marker-assisted selection.

Entodon is taxonomically revised for East Asia. All taxa previously considered to occur in this region were studied. Among the morphological observations, special attention is paid to peristome structure by means of the scanning electron microscope. Thirty-three species are recognized for East Asia. Nineteen new synonyms are proposed at the specific level. A key to the identification of the species is provided, and for each species synonymy, illustrations, descriptions, habitat, distribution and representative specimens examined are given.

Dynamic bandwidth allocation (DBA) is an open and hot topic in the Ethernet passive optical network (EPON), which is regarded as one of the best choices for next-generation access networks. This paper proposes an estimation-based scheme, interleaved polling with adaptive cycle time with grant estimation (IPACT-GE), for effective upstream channel sharing among multiple optical network units (ONUs) in EPONs. By estimating the amount of new packets arriving between two consecutive pollings and granting ONUs with extra estimated amount, the proposed IPACT-GE scheme can achieve shorter waiting delay and less buffer occupancy at the light load than IPACT, a significant DBA scheme in EPONs. Moreover, when combined with the strict priority queue (SPQ) mechanism to provide differentiated services, IPACT-GE can greatly mitigate the light load penalty that is obvious in the IPACT solution combined with SPQ.

Ag-based catalysts supported on various metal oxides, Al2O3, TiO2, and TiO2–Al2O3, were prepared by the sol–gel method. The effect of SO2 on catalytic activity was investigated for NO reduction with propene under lean burn condition. The results showed the catalytic activities were greatly enhanced on Ag/TiO2–Al2O3 in comparison to Ag/Al2O3 and Ag/TiO2, especially in the low temperature region. Application of different characterization techniques revealed that the activity enhancement was correlated with the properties of the support material. Silver was highly dispersed over the amorphous system of TiO2–Al2O3. NO3− rather than NO2− or NOx reacted with the carboxylate species to form CN or NCO. NO2 was the predominant desorption species in the temperature programmed desorption (TPD) of NO on Ag/TiO2–Al2O3. More amount of formate (HCOO−) and CN were generated on the Ag/TiO2–Al2O3 catalyst than the Ag/Al2O3 catalyst, due to an increased number of Lewis acid sites. Sulfate species, resulted from SO2 oxidation, played dual roles on catalytic activity. On aged samples, the slow decomposition of accumulated sulfate species on catalyst surface led to poor NO conversion due to the blockage of these species on active sites. On the other hand, catalytic activity was greatly enhanced in the low temperature region because of the enhanced intensity of Lewis acid site caused by the adsorbed sulfate species. The rate of sulfate accumulation on the Ag/TiO2–Al2O3 system was relatively slow. As a consequence, the system showed superior capability for selective adsorption of NO and SO2 toleration to the Ag/Al2O3 catalyst.

The failure characteristics of the contact material Ag-SnO2 were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), and X-ray energy dispersive spectroscopy (EDS). Phase analysis showed that there were Ag, SnO2, and Sn on the contact surfaces at the time of failure under the load condition of 30 A and 220 V (AC), which means that SnO2 decomposed in service. When the contacts were tested under airproof ambient condition, half-spherical bulges came into being on the contact surfaces, which resulted in early failure and dispersive characteristics. But half-spherical bulges were not found when the contacts were tested under open ambient condition. The temperature change of the contacts during the life testing under airproof ambient condition was different from that under open ambient condition.

SO2 strongly decreased the catalytic activities of low loading Ag/Al2O3 below 500 °C in selective catalytic reduction (SCR) of NOx by propene with or without the assistance of non-thermal plasma (NTP), which was mainly attributed to the competition between SO2 and NO. By controlling the loadings of Ag and Ag+ over alumina, the resistance of SO2 was remarkably enhanced between 400 °C and 500 °C in thermal SCR. In the NTP-assisted SCR, most of the NOx conversions were also apparently recovered from 250 °C to 500 °C.

An In2O3/Al2O3 catalyst shows high activity for the selective catalytic reduction of NO with propene in the presence of oxygen. The presence of SO2 in feed gas suppressed the catalytic activity dramatically at high temperatures; however it was enhanced in the low temperature range of 473–573 K. In TPD and FT-IR studies, the formation of sulfate species on the surface of the catalyst caused an inhibition of NOX adsorption sites, and the absorbance ability of NO was suppressed by the presence of SO2, and the amount of ad-NO3− species decreased obviously. This leads to a decrease of catalytic activity at higher temperatures. However, addition of SO2 enhanced the formation of carboxylate and formate species, which can explain the promotional effect of SO2 at low temperature, because active C3H6 (partially oxidized C3H6) is crucial at low temperature.

The hybrid betweenBrassica napusandB. rapadisplays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis forB. napus(AnAnCCgenome),B. rapa(ArArgenome), and its hybrid F1 (AnArCgenome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified usingB. rapa(AA genome) andB. oleracea(CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aidBrassicaimprovement.

While backbone networks have experienced substantial changes in the last decade, access networks have not changed much. Recently, passive optical networks (PONs) seem to be ready for commercial deployment as access networks, due to the maturity of a number of enabling technologies. Among the PON technologies, Ethernet PON (EPON) standardized by the IEEE 802.3ah Ethernet in the First Mile (EFM) Task Force is the most attractive one because of its high speed, low cost, familiarity, interoperability, and low overhead. In this paper, we consider the issue of upstream channel sharing in the EPONs. We propose a novel multiple-access control scheme to provide bandwidth-guaranteed service for high-demand customers, while providing best effort service to low-demand customers according to the service level agreement (SLA). The analytical and simulation results prove that the proposed scheme performs best in what it is designed to do compared to another well-known scheme that has not considered providing differentiated services. With business customers preferring premium services with guaranteed bandwidth and residential users preferring low-cost best effort services, our scheme could benefit both groups of subscribers, as well as the operators.

The ever increasing amounts of digital data being stored in public and private clouds are challenging users to access and manage the data. With the corresponding storage system reaches Petabyte-scale, or even Exabyte-scale, metadata access will become a severe performance bottleneck. Hence, this paper proposes an efficient multi-dimensional metadata index and search solution for cloud data. By proposing some new mechanism for K-D-B tree based index/search and implementing index partitioning technique, our system can achieve optimized performance in terms of memory utilization and search speed. Experiments show that our system performs much better as compared with existing solutions. In addition, our system can safely scale out in a distributed manner with guaranteed performance.

MicroRNAs (miRNAs) are 20- to ∼24-nucleotide (nt) small RNAs that impact a variety of biological processes, from development to age-associated events. To study the role of miRNAs in aging, studies have profiled the levels of miRNAs with time. However, evidence suggests that miRNAs show heterogeneity in length and sequence in different biological contexts. Here, by examining the expression pattern of miRNAs by Northern blot analysis, we found that Drosophila miRNAs show distinct isoform pattern changes with age. Surprisingly, an increase of some miRNAs reflects increased 2′-O-methylation of select isoforms. Small RNA deep sequencing revealed a global increase of miRNAs loaded into Ago2, but not into Ago1, with age. Our data suggest increased loading of miRNAs into Ago2, but not Ago1, with age, indicating a mechanism for differential loading of miRNAs with age between Ago1 and Ago2. Mutations in Hen1 and Ago2, which lack 2′-O-methylation of miRNAs, result in accelerated neurodegeneration and shorter life span, suggesting a potential impact of the age-associated increase of 2′-O-methylation of small RNAs on age-associated processes. Our study highlights that miRNA 2′-O-methylation at the 3′ end is modulated by differential partitioning of miRNAs between Ago1 and Ago2 with age and that this process, along with other functions of Ago2, might impact age-associated events in Drosophila.

The computational science community is approaching petascale level simulations that will produce massive amount of datasets. While the computational power of supercomputers keep increasing, the I/O systems have not kept pace, resulting in a significant performance bottle neck. We propose a solution, VisDSI, to address the problem by 1) using traditional high performance clusters with disks directly attached within each node, 2) deploying a data-intensive distributed file system on the cluster, and 3) developing a POSIX-compatible I/O layer to enable the traditional visualization applications to smoothly port to this new platform as well as to provide a new I/Osemantic of retrieving the data location with respect to the POSIX standards. In particular, VisDSI guarantees the colocated compute and data storage by introducing a scheduling of work assignments to nodes with local copies of needed data. Compared with the original visualization application, our solution runs at least 10 times faster.

Premise of the study: Microsatellite loci are described for Rhodiola, a medicinal herb genus widely used in traditional Chinese medicine. Methods and Results: A total of 17 polymorphic microsatellite primer pairs were developed using the combined biotin-capture method. The number of alleles per locus ranged from one to 12 across 192 individuals from R. bupleuroides, R. crenulata, R. fastigiata, and R. sacra, and the mean observed and expected heterozygosities ranged from 0.177 to 0.412 and from 0.363 to 0.578, respectively. Conclusions: The results demonstrate the potential use of this new set of microsatellite markers for genotyping individuals and estimating genetic diversity in Rhodiola.

Data Center Ethernet is likely to be deployed as the communication infrastructure for future data centers, which carries multiple types of traffic with very different characteristics and handling requirements. Conventional Spanning Tree Protocol STP cannot meet the requirement of a Data Center Ethernet framework because of its poor bandwidth utilization and lack of multipathing capability. In this paper, we propose a layer2 multipathing solution, namely optimized dynamic load-balancing multipathing ODLBMP, to be deployed in Data Center Ethernet. Our proposed method utilizes all available links and ports for frame delivery and can split traffic of a communication pair along multiple paths. In ODLBMP, the traffic loads of all paths are continuously monitored so that traffic assigned to each path can be dynamically adjusted to avoid path/link over-utilization. Per-flow forwarding is observed in ODLBMP to guarantee the in-order delivery, which is important for most storage traffic. In addition, ODLBMP finely differentiates flows from application perspective so it has more flexibility in traffic splitting and route selection, and achieves better multipath load balancing. Computer simulations show that our proposed algorithm performs better than other compared algorithms, including STP, Transparent Interconnection of Lots of Links, and DLBMP, in all simulation scenarios in terms of frame delivery ratio and network throughput. Copyright © 2013 John Wiley & Sons, Ltd.

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed-shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative "nonshattering" sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative "nonshattering" allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative "nonshattering" allele (frequency ∼26%) with shattering phenotype. All weedy rice accessions are the "nonshattering" genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation ("G"/"T") of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.

Human neurodegenerative diseases have the temporal hallmark of afflicting the elderly population. Ageing is one of the most prominent factors to influence disease onset and progression, yet little is known about the molecular pathways that connect these processes. To understand this connection it is necessary to identify the pathways that functionally integrate ageing, chronic maintenance of the brain and modulation of neurodegenerative disease. MicroRNAs (miRNA) are emerging as critical factors in gene regulation during development; however, their role in adult-onset, age-associated processes is only beginning to be revealed. Here we report that the conserved miRNA miR-34 regulates age-associated events and long-term brain integrity in Drosophila, providing a molecular link between ageing and neurodegeneration. Fly mir-34 expression exhibits adult-onset, brain-enriched and age-modulated characteristics. Whereas mir-34 loss triggers a gene profile of accelerated brain ageing, late-onset brain degeneration and a catastrophic decline in survival, mir-34 upregulation extends median lifespan and mitigates neurodegeneration induced by human pathogenic polyglutamine disease protein. Some of the age-associated effects of miR-34 require adult-onset translational repression of Eip74EF, an essential ETS domain transcription factor involved in steroid hormone pathways. Our studies indicate that miRNA-dependent pathways may have an impact on adult-onset, age-associated events by silencing developmental genes that later have a deleterious influence on adult life cycle and disease, and highlight fly miR-34 as a key miRNA with a role in this process.