Performance, reliability, and performability of a hybrid RAID array and a comparison with traditional RAID1 arrays

We describe a hybrid mirrored disk organization patented by LSI Logic Corp. and compare its performance, reliability, and performability with traditional mirrored RAID1 disk organizations and RAID(4+?), ?≥1. LSI RAID has the same level of redundancy as mirrored disks, but also utilizes parity coding. Unlike RAID1, which cannot tolerate all two disk failures, LSI RAID similarly to RAID6 is 2?Disk Failure Tolerant (2DFT), but in addition it can tolerate almost all three disk failures, while RAID1 organizations are generally 1DFT. We list analytic expressions for the reliability of various RAID1 organizations and use enumeration when the reliability expression cannot be obtained analytically. An asymptotic expansion method based on disk unreliabilities is used for an easy comparison of RAID reliabilities. LSI RAID performance is evaluated with the Read-Modify-Write (RMW) and ReConstruct Write (RCW) methods to update parities. The combination of the two methods is used to balance data and parity disk loads, which results in maximizing the I/O throughput. The analysis shows that LSI RAID has an inferior performance with respect to basic mirroring in processing an OLTP workload, but it outperforms RAID6. LSI RAID in spite of its higher Mean Time to Data Loss (MTTDL) is outperformed by other RAID1 organizations as far as its performability is concerned, i.e., the number of I/Os carried out by the disk array operating at maximum I/Os Per Second (IOPS) until data loss occurs. A survey of RAID1 organizations and distributed replicated systems is also included.     

Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis

The acetylation level of histones on lysine residues regulated by histone acetyltransferases and histone deacetylases plays an important but under‐studied role in the control of gene expression in plants. With the aim of characterizing the Arabidopsis RPD3/HDA1 family histone deacetylase HDA5, we present evidence showing that HDA5 displays deacetylase activity. Mutants defective in the expression of HDA5 displayed a late‐flowering phenotype. Expression of the flowering repressor genes FLC and MAF1 was up‐regulated in hda5 mutants. Furthermore, the gene activation markers, histone H3 acetylation and H3K4 trimethylation on FLC and MAF1 chromatin were increased in hda5‐1 mutants. Chromatin immunoprecipitation analysis showed that HDA5 binds to the chromatin of FLC and MAF1. Bimolecular fluorescence complementation assays and co‐immunoprecipitation assays showed that HDA5 interacts with FVE, FLD and HDA6, indicating that these proteins are present in a protein complex involved in the regulation of flowering time. Comparing gene expression profiles of hda5 and hda6 mutants by RNA‐seq revealed that HDA5 and HDA6 co‐regulate gene expression in multiple development processes and pathways.     

Mirrored disk rouing and scheduling

Disk mirroring or RAID level 1 stores the same data twice, on two independent disks, to ensure that all single disk failures can be tolerated. This high storage overhead is acceptable in view of the drop in storage cost per gigabyte and rapidly increasing disk capacities. Disk access time, on the other hand, is improving at a very slow pace, so that another important advantage of disk mirroring is the doubling of the disk access bandwidth in processing read requests. Efficient routing of read requests to disks and local disk scheduling can be used to improve performance even further. We are primarily concerned with two RAID1 configurations: (i) source-initiated routing with the independent queues—IQ method; (ii) destination-initiated routing with the shared queue—SQ method. Static, dynamic, and affinity-based (AB) routing methods are used to distribute requests with the IQ method. We compare the performance of various IQ and SQ based routing policies using a random number-driven simulation. While there is some improvement in performance with the more sophisticated routing policies, performance is dominated by the local disk scheduling policy. The SQ method allows resource sharing, so that it tends to outperform the IQ based routing, but it requires the scheduler to keep track of the state of the disk drives. As a further means to improve performance, we consider the effect of prioritizing reads with respect to writes, transposed data allocation, and replicating data more than twice. We acknowledge the support of NSF through Grant 0105485 in Computer Systems Architecture. Alexander Thomasian (ACM) is a Professor of Computer Science at New Jersey Institute of Technology. He was a faculty member at Case Western University and University of Southern California and an adjunct professor at Columbia University, while a Research Staff Member at the IBM T. J. Watson Research Center (1985–1998). He received his PhD in Computer Science from UCLA. Dr. Thomasian’s research has more recently been focused on indexing high-dimensional datasets and especially the performance of storage systems. He is the author of Database Concurrency Control: Methods, Performance, and Analysis, Kluwer 1996. Dr. Thomasian is a Fellow of IEEE.     

Adaptive Sector Grouping to Reduce False Sharing in Distributed RAID

Distributed redundant array of inexpensive disks (RAID) is often embedded in a cluster architecture. In a centralized RAID subsystem, the false sharing problem does not exist, because the disk array allows only mutually exclusive access by one user at a time. However, the problem does exist in a distributed RAID architecture, because multiple accesses may occur simultaneously in a distributed environment. This problem will seriously limit the effectiveness of collective I/O operations in network-based, cluster computing. Traditional accesses to disks in a RAID are done at block level. The block granularity is large, say 32 KB, often resulting in false sharing among fragments in the block. The false sharing problem becomes worse when the block size or the stripe unit becomes too large. To solve this problem, we propose an adaptive sector grouping approach to accessing a distributed RAID. Each sector has a fine grain of 512 B. Multiple sectors are grouped together to match with the data block size. The grouped sector has a variable size that can be adaptively adjusted by software. Benchmark experiments reveal the positive effects of this adaptive access scheme on the performance of a RAID. Our scheme can reduce the collective I/O access time without increasing the buffer size. Both theoretical analysis and experimental results demonstrate the performance gain in using grouped sectors for fast access of distributed RAID.     

HISTONE DEACETYLASE 6 represses pathogen defence responses in Arabidopsis thaliana

Plant defence mechanisms are suppressed in the absence of pathogen attack to prevent wasted energy and growth inhibition. However, how defence responses are repressed is not well understood. Histone deacetylase 6 (HDA6) is a negative regulator of gene expression, and its role in pathogen defence response in plants is not known. In this study, a novel allele of hda6 (designated as shi5) with spontaneous defence response was isolated from a forward genetics screening in Arabidopsis. The shi5 mutant exhibited increased resistance to hemibiotrophic bacterial pathogen Pst DC3000, constitutively activated expression of pathogen‐responsive genes including PR1, PR2, etc. and increased histone acetylation levels at the promoters of most tested genes that were upregulated in shi5. In both wild type and shi5 plants, the expression and histone acetylation of these genes were upregulated by pathogen infection. HDA6 was found to bind to the promoters of these genes under both normal growth conditions and pathogen infection. Our research suggests that HDA6 is a general repressor of pathogen defence response and plays important roles in inhibiting and modulating the expression of pathogen‐responsive genes in Arabidopsis.     

Chemical composition and antimicrobial activity of volatiles from Degenia velebitica, a European stenoendemic plant of the Brassicaceae family

Free and glucosidic bound leaf volatiles of Degenia velebitica were isolated and fractionated simultaneously into H₂O‐soluble, H₂O‐insoluble, and highly volatile compounds by hydrodistillation–adsorption (HDA) and analyzed by GC/MS. Among the 24 constituents identified, the main compounds obtained by the HDA method were S‐ and/or N‐atom containing compounds, i.e., 6‐(methylsulfanyl)hexanenitrile ( 10 ; 26.78%), dimethyl trisulfide ( 6 ; 26.35%), 3,4,5‐trimethylpyrazole ( 17 ; 13.33%), hex‐5‐enenitrile ( 2 ; 10.11%), dimethyl tetrasulfide ( 8 ; 4.93%), and pent‐4‐enyl isothiocyanate ( 7 ; 4.45%). In addition, O‐glycosidically bound volatiles and free volatiles were isolated by solvent extraction. Sixteen volatile O‐aglycones and twelve free volatile components were identified. The main O‐aglycones were eugenol ( 19 ; 24.15%), 2‐methoxy‐4‐vinylphenol ( 11 ; 11.50%), and benzyl alcohol ( 20 ; 9.49%), and the main free volatiles were (9Z,12Z)‐octa‐9,12‐dienic acid (38.35%), hexadecanoic acid (22.64%), and phytol (5.80%). The H₂O‐soluble volatile fraction obtained by HDA, containing mostly glucosinolate degradation products and 3,4,5‐trimethylpyrazole ( 17 ), was evaluated for antimicrobial activity by determining inhibition zones with the diffusion method as well as minimal inhibitory concentrations (MIC) and minimal microbicidal concentrations (MMC) with the micro‐dilution method. The fraction expressed activity against the tested Gram‐positive and Gram‐negative bacteria as well as against yeast, with MIC values equal to or lower than 16.7 μg/ml.     

Regulating the molar fraction of 4-hydroxybutyrate in Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) by biological fermentation and enzymatic degradation

The regulation of 4-hydroxybutyrate (4HB) molar fraction in the poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] of a local isolate Cupriavidus sp. USMAA1020 was attempted by employing a feeding strategy through fed-batch fermentation in 100-L fermenter. The growth of Cupriavidus sp. USMAA1020 was enhanced by frequently feeding carbon and nitrogen at a ratio of 5 (C/N 5) using a DO-stat with cascade mode at 20% (v/v) dissolved oxygen (DO). The feeding of C/N 5 and the use of the DO-stat mode were able to regulate the 4HB composition from 0–67 mol% by sequential feeding of γ-butyrolactone and supplementing oleic acid. A high 4HB molar fraction of 67 mol% with a PHA concentration of 5.2 g/L was successfully obtained by employing this feeding strategy. Notably, enzymatic degradation carried out enhanced the 4HB composition of the copolymer synthesized. PHB depolymerase enzyme from Acidovorax sp. was used to degrade this P(3HB-co-70-mol%4HB) copolymer and the 4HB composition could be increased up to 83 mol%. The degradation process was observed by monitoring the time-dependent change in the weight loss of copolymer films. The percentage of weight loss of solvent-cast film increased proportionally up to 19% within 3 h, whereas salt-leached films showed 90% of weight loss within 3 h of incubation and were completely degraded by 4 h. The molecular weight (M _n ) of the films treated with enzyme demonstrated a slight decrease. SEM observation exhibited a rough surface morphology of the copolymer degraded with depolymerase enzyme.     

Biological monitoring of hexamethylene diisocyanate by determination of 1,6-hexamethylene diamine as the trifluoroethyl chloroformate derivative using capillary gas chromatography with thermoionic and selective-ion monitoring

A GC method using a novel derivatization reagent, 2′,2′,2-trifluoroethyl chloroformate (TFECF), for the derivatization of primary and secondary aliphatic amines with the formation of carbamate esters is presented. The method is based on a derivatization procedure in a two-phase system, where the carbamate ester is formed. The method is applied to the determination of 1,6-hexamethylene diamine (HDA) in aqueous solutions and human urine, using capillary GC. Detection was performed using thermionic specific detection (TSD) and mass spectrometry (MS)—selective-ion monitoring (SIM) using electron-impact (EI) and chemical ionization (CI) with ammonia monitoring both positive (CI)⁺ and negative ions (CI)⁻. Quantitative measurements were made in the chemical ionization mode monitoring both positive and negative ions. Tetra-deuterium-labelled HDA (TDHDA; H₂NC²H₂(CH₂)₄C²H₂NH₂) was used as the internal standard for the GC—MS analysis. In CI⁺ the m/z 386 and the m/z 390 ions corresponding to the [M + 18]⁺ ions (M = molecular ion) of HDA—TFECF and TDHDA—TFECF were measured; in CI⁻ the m/z 267 and the m/z 271 ions corresponding to the [M — 101]⁻ ions. The overall recovery was found to be 97 ± 5% for a HDA concentration of 1000 μg/l in urine. The minimal detectable concentration in urine was found to be less than 20 μg/l using GC—TSD and 0.5 μg/l using GC—SIM. The overall precision for the work-up procedure and GC analysis was ca. 3% (n = 5) for 1000 μg/l HDA-spiked urine, and ca. 4% (n = 5) for 100 μg/l. The precision using GC—SIM for urine samples spiked to a concentration of 5 μg/l was found to be 6.3% (n = 10).     

INJECTION OF 6-HYDROXYDOPAMINE AND HYDROGEN PEROXIDE INTO THE SUBSTANTIA NIGRA AND LATERAL VENTRICLE OF THE CAT: SPECIFIC AND NONSPECIFIC EFFECTS ON STRIATAL BIOGENIC AMINES1

Attempting to clarify the mechanism by which intracerabral injection of 6-hydroxydopamine (60HDA) reduces catecholamines in the caudate nucleus (CN), we have tested two hypotheses: (1) 60HDA specifically attacks catecholaminergic neurons; (2) 60HDA liberates hydrogen peroxide (H₂O₂) which destroys neurons indiscriminately. To this end, we have injected high or low doses of 60HDA or equimolar amounts of H₂O₂ stereotaxically into the substantia nigra (SN) or the lateral ventricle of cats and have placed electrocoagulative lesions in the SN. We determined the CN levels of dopamine (DA), norepinephrine (NE) and serotonin (5HT) 7-10 days later. Nigral injections of high doses (8 μ mol) of either agent or low doses (80 nmol) of 60HDA decreased both DA and NE and induced similar histologic damage in the SN with neuronal drop-out at the periphery of the lesions. Injection of 80 nmol of H₂O₂ into the SN did not decrease CN amine levels and did not produce histologic damage in the SN. Electrocoagulation of the SN decreased CN DA and NE, but the histologic lesions failed to show any peripheral neuronal drop-out. Ventricular injections of high doses (16 μmol) of 60HDA or H₂O₂ reduced not only DA and NE but also 5HT levels in the ipsilateral CN. Low intraventricular doses (0-16 μmol) of 60HDA decreased only DA and NE without affecting 5HT levels in the CN whereas 0.16 μmol of H₂O₂ had no effect on any of the CN amines. The catecholamine-depleting effects of low doses (80 nmol) of 60HDA were significantly potentiated by inhibiting brain monoamine oxidase by 90 percent or more at the time and site of injection of 60HDA. These results suggest that the extracellular liberation of H₂O₂ from 60HDA could explain some possibly nonspecific effects of high doses of 60HDA; at lower doses, however, 60HDA may act via selective uptake into catecholaminergic neurons with subsequent intracellular release of H₂O₂.     

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

Histone deacetylases have central functions in regulating stress defenses and development in plants. However, the knowledge about the deacetylase functions is largely limited to histones, although these enzymes were found in diverse subcellular compartments. In this study, we determined the proteome‐wide signatures of the RPD3/HDA1 class of histone deacetylases in Arabidopsis. Relative quantification of the changes in the lysine acetylation levels was determined on a proteome‐wide scale after treatment of Arabidopsis leaves with deacetylase inhibitors apicidin and trichostatin A. We identified 91 new acetylated candidate proteins other than histones, which are potential substrates of the RPD3/HDA1‐like histone deacetylases in Arabidopsis, of which at least 30 of these proteins function in nucleic acid binding. Furthermore, our analysis revealed that histone deacetylase 14 (HDA14) is the first organellar‐localized RPD3/HDA1 class protein found to reside in the chloroplasts and that the majority of its protein targets have functions in photosynthesis. Finally, the analysis of HDA14 loss‐of‐function mutants revealed that the activation state of RuBisCO is controlled by lysine acetylation of RuBisCO activase under low‐light conditions.     

A Gracefully Degradable Declustered RAID Architecture

A new layout method Prime-groups is proposed to evenly distribute parity groups for declustered RAID. Prime-groups satisfies most of the layout goals for a good declustered RAID layout. For the goals that are not satisfied, it is near optimal. A new layout goal maximal write and reconstruction parallelism is also proposed. If a layout satisfies the new goal, all the surviving disks can be read in parallel and can be rewritten in parallel during reconstruction and reconfiguration. Prime-groups satisfies the new goal when the write request begins in the first disk of the array. It is also near optimal in term of declustering ratio when p is a prime. Prime-groups can compliment the layouts proposed by Alvarez et al. [2] for the criteria to obtain a good layout is quite different between Prime-groups and those proposed by Alvarez et al. [2].     

Removal of nonionic surfactants from wastewater using a constructed wetland

Removal of nonionic surfactants from municipal wastewater using a constructed wetland with a horizontal subsurface flow was studied in 2009 and 2010. Extraction spectrophotometry with 3′,3″,5′,5″‐tetrabromophenolphthalein ethyl ester and KCl served to determine the analyte concentrations. Triton^® X‐100 was used as a standard to express the nonionic‐surfactant concentrations. Anionic and cationic surfactants were shown not to interfere during the determination. Nonionic surfactants were degraded (to products undeterminable by the method) with a high average efficiency that reached 98.1% in 2009 and 99.1% in 2010, respectively. The average concentration of nonionic surfactants at the inflow was 0.978 mg/l, while it was close to the limit of quantification at the outflow (0.014 mg/l). A significant fraction of nonionic surfactants (38.7%) was already degraded during the pretreatment, and only 14.0% of the nonionic surfactants remained in the interstitial H₂O taken in the vegetation bed at a distance of 1 m from the inflow zone at a 50‐cm depth. Nonionic surfactants were degraded both under aerobic and anaerobic conditions.     

Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen

The Butyrivibrio group comprises Butyrivibrio fibrisolvens and related Gram-positive bacteria isolated mainly from the rumen of cattle and sheep. The aim of this study was to investigate phenotypic characteristics that discriminate between different phylotypes. The phylogenetic position, derived from 16S rDNA sequence data, of 45 isolates from different species and different countries was compared with their fermentation products, mechanism of butyrate formation, lipid metabolism and sensitivity to growth inhibition by linoleic acid (LA). Three clear sub-groups were evident, both phylogenetically and metabolically. Group VA1 typified most Butyrivibrio and Pseudobutyrivibrio isolates, while Groups VA2 and SA comprised Butyrivibrio hungatei and Clostridium proteoclasticum, respectively. All produced butyrate but strains of group VA1 had a butyrate kinase activity <40 U (mg protein)⁻¹, while strains in groups VA2 and SA all exhibited activities >600 U (mg protein)⁻¹. The butyrate kinase gene was present in all VA2 and SA bacteria tested but not in strains of group VA1, all of which were positive for the butyryl-CoA CoA-transferase gene. None of the bacteria tested possessed both genes. Lipase activity, measured by tributyrin hydrolysis, was high in group VA2 and SA strains and low in Group VA1 strains. Only the SA group formed stearic acid from LA. Linoleate isomerase activity, on the other hand, did not correspond with phylogenetic position. Group VA1 bacteria all grew in the presence of 200 μg LA ml⁻¹, while members of Groups VA2 and SA were inhibited by lower concentrations, some as low as 5 μg ml⁻¹. This information provides strong links between phenotypic and phylogenetic properties of this group of clostridial cluster XIVa Gram-positive bacteria.