A hybrid framework of iterative MapReduce and MPI for molecular dynamics applications

Developing platforms for large scale data processing has been a great interest to scientists. Hadoop is a widely used computational platform which is a fault-tolerant distributed system for data storage due to HDFS (Hadoop Distributed File System) and performs fault-tolerant distributed data processing in parallel due to MapReduce framework. It is quite often that actual computations require multiple MapReduce cycles, which needs chained MapReduce jobs. However, Design by Hadoop is poor in addressing problems with iterative structures. In many iterative problems, some invariant data is required by every MapReduce cycle. The same data is uploaded to Hadoop file system in every MapReduce cycle, causing repeated data delivering and unnecessary time cost in transferring this data. In addition, although Hadoop can process data in parallel, it does not support MPI in computing. In any Map/Reduce task, the computation must be serial. This results in inefficient scientific computations wrapped in Map/Reduce tasks because the computation can not be distributed over a Hadoop cluster, especially a Hadoop cluster on a traditional high performance computing cluster. Computational technologies have been extensively investigated to be applied into many application domains. Since the presence of Hadoop, scientists have applied the MapReduce framework to biological sciences, chemistry, medical sciences, and other areas to efficiently process huge data sets. In our research, we proposed a hybrid framework of iterative MapReduce and MPI for molecular dynamics applications. We carried out molecular dynamics simulations with the implemented hybrid framework. We improved the capability and performance of Hadoop by adding a MPI module to Hadoop. The MPI module enables Hadoop to monitor and manage the resources of Hadoop cluster so that computations incurred in Map/Reduce tasks can be performed in a parallel manner. We also applied the local caching mechanism to avoid data delivery redundancy to make the computing more efficient. Our hybrid framework inherits features of Hadoop and improves computing efficiency of Hadoop. The targeting application domain of our research is molecular dynamics simulation. However, the potential use of our iterative MapReduce framework with MPI is broad. It can be used by any applications which contain single or multiple MapReduce iterations, invoke serial or parallel (MPI) computations in Map phase or Reduce phase of Hadoop

Didymin improves UV irradiation resistance in C. elegans

Didymin, a type of flavono-o-glycoside compound naturally present in citrus fruits, has been reported to be an effective anticancer agent. However, its effects on stress resistance are unclear. In this study, we treated Caenorhabditis elegans with didymin at several concentrations. We found that didymin reduced the effects of UV stressor on nematodes by decreasing reactive oxygen species levels and increasing superoxide dismutase (SOD) activity. Furthermore, we found that specific didymin-treated mutant nematodes daf-16(mu86) & daf-2(e1370), daf-16(mu86), akt-1(ok525), akt-2(ok393), and age-1(hx546) were susceptible to UV irradiation, whereas daf-2(e1371) was resistant to UV irradiation. In addition, we found that didymin not only promoted DAF-16 to transfer from cytoplasm to nucleus, but also increased both protein and mRNA expression levels of SOD-3 and HSP-16.2 after UV irradiation. Our results show that didymin affects UV irradiation resistance and it may act on daf-2 to regulate downstream genes through the insulin/IGF-1-like signaling pathway

Physiological effects of tree growth regulators on several tree species

Physiological effects of two tree growth regulators (TGRs), flurprimidol and paclobutrazol, on eleven species located in Indiana and Louisiana were studied. Five experiments were designed with mature trees, saplings, seedlings, or isolated mitochondria to investigate effects of TGRs on wound healing, cambial growth, vegetative growth of progeny seedlings, and electron transport by leaf mitochondria. Species investigated were: Quercus rubra L., Q. alba L., Q. falcata var. pagodaefolia Elliott, Juglans nigra L., Alnus glutinosa L., Liquidambar styraciflua L., Fraxinus americana L., Pinus strobus L., P. taeda L., Liriodendron tulipifera L., and Platanus occidentalis L. Closure of bark wounds was reduced in paclobutrazol-treated white oak, red oak, sweetgum, black walnut and white ash in Indiana, and sweetgum and cherrybark oak in Louisiana. There was no difference in bark wound closure between treated and untreated European black alder, yellow poplar, white pine, or American sycamore. Closure of pruning wounds was reduced in white oak, red oak, sweetgum, European black alder, and black walnut in Indiana, and sweetgum and cherrybark oak in Louisiana. The inhibitory effect on closure of both bark and pruning wounds in some species persists at least three or four years. TGRs were transported to developing seeds of silver maple and reduced growth of the progeny when the seeds were collected one month after treatment. The growth of progeny seedlings was enhanced when seeds were collected one year after treatment and was not affected when seeds were collected two years after treatment with TGRs. The effect of paclobutrazol on cambial growth, annual shoot growth, and total tree height growth varied with species and treatment duration. Paclobutrazol reduced cambial growth in white oak, red oak, cherrybark oak, sweetgum, European black alder, and white pine with the effect varying among species, vertical location of the cross-section, and years after treatment. TGRs accumulated in seeds of treated European black alder and silver maple reduced or stimulated electron transport in leaf mitochondria of the progeny seedlings. The inhibition and stimulation effects depending on the number of growing seasons after treatment of the parent trees related to growth responses, indicating another mode of action of TGRs

Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate

Abstract Background Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active potent signalling compounds. Developing inhibitors for LOX is of high interest to researchers. Modelling the interactions between LOX and its substrate arachidonic acid is critical for developing LOX specific inhibitors. Currently, there are no LOX-substrate structures. Recently, the structure of a coral LOX, 8R-LOX, which is 41% sequence identical to the human 5-LOX was solved to 1.85Å resolution. This structure provides a foundation for modelling enzyme-substrate interactions. Methods In this research, we applied a computational method, Internal Coordinate Mechanics (ICM), to model the interactions between 8R-LOX and its substrate arachidonic acid. Docking arachidonic acid to 8R-LOX was performed. The most favoured docked ligand conformations were retained. We compared the results of our simulation with a proposed model and concluded that the binding pocket identified in this study agrees with the proposed model partially. Results The results showed that the conformation of arachidonic acid docked into the ICM-identified docking site has less energy than that docked into the manually defined docking site for pseudo wild type 8R-LOX. The mutation at I805 resulted in no docking pocket found near Fe atom. The energy of the arachidonic acid conformation docked into the manually defined docking site is higher in mutant 8R-LOX than in wild type 8R-LOX. The arachidonic acid conformations are not productive conformations. Conclusions We concluded that, for the wild type 8R-LOX, the conformation of arachidonic acid docked into the ICM-identified docking site is more stable than that docked into the manually defined docking site. Mutation affects the structure of the putative active site pocket of 8R-LOX, and leads no docking pockets around the catalytic Fe atom. The docking simulation in a mutant 8R-LOX demonstrated that the structural change due to the mutation impacts the enzyme activity. Further research and analysis is required to obtain the 8R-LOX-substrate model.</p

Revised Aggregation-tree Used in Metadata Extraction from SVG Images

Many of the multimedia researchers have focused on the issue of the retrieval of images using indexed image collections. A number of spatial data structures based on Minimum Bounding Rectangles (MBRs) have been developed. Previously, we presented aggregation-tree structure to extract metadata from Scalable Vector Graphics (SVG) documents [8]. In this paper, we revised the aggregation-tree to better model the data in SVG and reduce the size of the aggregation-tree. Aggregation-tree is constructed based on aggregation rules for different topological relations between objects

Online monitoring method of mine-used high voltage cable insulatio

In order to monitor insulation condition of mine-used high voltage cable in real time, an online monitoring method of mine-used high voltage cable insulation based on wide area measurement system(WAMS) was proposed. In the method, real-time voltage and current of cable ends are obtained synchronously by use of WAMS, and insulation resistance and equivalent capacitance of cable are derived through establishment of equivalent circuit model of cable to ground, so as to realize dynamic monitoring of cable insulation condition. The simulation results show that measurement error of the method decreases with increase of cable insulation deterioration, which meets precision requirement of online monitoring of mine-used high voltage cable insulation

Ingredients in Zijuan Pu’er Tea Extract Alleviate β-Amyloid Peptide Toxicity in a <i>Caenorhabditis elegans</i> Model of Alzheimer’s Disease Likely through DAF-16

Amyloid-&#946;, one of the hallmarks of Alzheimer&#8217;s disease (AD), is toxic to neurons and can also cause brain cell death. Oxidative stress is known to play an important role in AD, and there is strong evidence that oxidative stress is associated with amyloid-&#946;. In the present study we report the protective effect of Zijuan Pu&#8217;er tea water extract (ZTWE) and the mixture of main ingredients (+)-catechins, caffeine and procyanidin (MCCP) in ZTWE on &#946;-amyloid-induced toxicity in transgenic Caenorhabditis elegans (C. elegans) CL4176 expressing the human A&#946;1&#8315;42 gene. ZTWE, (+)-catechins, caffeine, procyanidin and MCCP delayed the &#946;-amyloid-induced paralysis to different degrees. The MCCP treatment did not affect the transcript abundance of amyloid-&#946; transgene (amy-1); however, Thioflavin T staining showed a significant decrease in A&#946; accumulation compared to untreated worms. Further research using transgenic worms found that MCCP promoted the translocation of DAF-16 from cytoplasm to nucleus and increased the expression of superoxide dismutase 3 (SOD-3). In addition, MCCP decreased the reactive oxygen species (ROS) content and increased the SOD activity in CL4176 worms. In conclusion, the results suggested that MCCP had a significant protective effect on &#946;-amyloid-induced toxicity in C. elegans by reducing &#946;-amyloid aggregation and inducing DAF-16 nuclear translocation that could activate the downstream signal pathway and enhance resistance to oxidative stress

Ellagic Acid Increases Stress Resistance via Insulin/IGF-1 Signaling Pathway in Caenorhabditis elegans

Ellagic acid is a natural polyphenol found in various fruits and vegetables. Numerous studies have shown that ellagic acid has beneficial effects on human health. In this study, we investigated the stress resistant action of ellagic acid in Caenorhabditis elegans (C. elegans). Notably, 50 &mu;M ellagic acid prolonged the lifespan of C. elegans by 36.25%, 36.22%, 155.1%, and 79.07% under ultraviolet radiation stress, heat stress, oxidative stress, and Pseudomonas aeruginosa infection stress, respectively. Furthermore, the mechanism by which ellagic acid reduces the damage caused by ultraviolet radiation in C. elegans was explored. Ellagic acid could significantly induce the nucleus translocation of DAF-16 and, thereby, activate a series of target genes to resist ultraviolet radiation stress. Moreover, ellagic acid also significantly increased the expression of SOD-3 by 3.61 times and the activity of superoxide dismutase by 3.70 times to clean out harmful reactive oxygen species in C. elegans exposed to ultraviolet radiation stress. In both daf-16 mutant and daf-2; daf-16 double-mutant worms exposed to ultraviolet radiation, ellagic acid could no longer prolong their lifespan. These results indicate that ellagic acid plays an important role in resisting ultraviolet radiation stress in C. elegans, probably in an insulin/IGF-1 signaling pathway-dependent way