Optimizing egalitarian performance in the side-effects model of colocation for data center resource management

In data centers, up to dozens of tasks are colocated on a single physical machine. Machines are used more efficiently, but tasks' performance deteriorates, as colocated tasks compete for shared resources. As tasks are heterogeneous, the resulting performance dependencies are complex. In our previous work [18] we proposed a new combinatorial optimization model that uses two parameters of a task - its size and its type - to characterize how a task influences the performance of other tasks allocated to the same machine. In this paper, we study the egalitarian optimization goal: maximizing the worst-off performance. This problem generalizes the classic makespan minimization on multiple processors (P||Cmax). We prove that polynomially-solvable variants of multiprocessor scheduling are NP-hard and hard to approximate when the number of types is not constant. For a constant number of types, we propose a PTAS, a fast approximation algorithm, and a series of heuristics. We simulate the algorithms on instances derived from a trace of one of Google clusters. Algorithms aware of jobs' types lead to better performance compared with algorithms solving P||Cmax. The notion of type enables us to model degeneration of performance caused by using standard combinatorial optimization methods. Types add a layer of additional complexity. However, our results - approximation algorithms and good average-case performance - show that types can be handled efficiently.Comment: Author's version of a paper published in Euro-Par 2017 Proceedings, extends the published paper with addtional results and proof

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N-2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N-2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N2O, but N-2 production was reduced by 84% compared to the control. In parallel with greater N2O production, we observed an increase in the fungi: bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N2O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N2O production due to the inhibitory effects on nosZ-II-carrying communities

Seasonal and Spatial Variation in the Location and Reactivity of a Nitrate‐Contaminated Groundwater Discharge Zone in a Lakebed

Groundwater discharge delivering anthropogenic N from surrounding watersheds can impact lake nutrient budgets. However, upgradient groundwater processes and changing dynamics in N biogeochemistry at the groundwater‐lake interface are complex. In this study, seasonal water‐level variations in a groundwater flow‐through lake altered discharge patterns of a wastewater‐derived groundwater contaminant plume, thereby affecting biogeochemical processes controlling N transport. Pore water collected 15 cm under the lakebed along transects perpendicular to shore varied from oxic to anoxic with increasing nitrate concentrations (10–75 μM) and corresponding gradients in nitrite and nitrous oxide. Pore water depth profiles of nitrate concentrations and stable isotopic compositions largely reflected upgradient groundwater N sources and N cycle processes, with minor additional nitrate reduction in the near‐surface lakebed sediments. Potential denitrification rates determined in laboratory microcosms were 10–100 times higher in near‐surface sediments (0–5 cm) than in deeper sediments (5–30 cm) and were correlated with sediment carbon content and abundance of denitrification genes (nirS, nosZI, and nosZII). Potential anammox‐driven N2 production was detectable in deeper anoxic sediments. Injection of bromide and nitrite in the lake sediments showed that the highest net nitrite consumption rates were within the top 10 cm. However, short transit times owing to rapid upward pore water velocities (4–5 cm hr−1) limited removal of the contaminant nitrate transiting through the sediments. Results demonstrate that local hydrologic and biogeochemical processes at the point of discharge affect the distribution and discharge rate of N through lakebed sediments, but processes in the upgradient groundwater can be more important for affecting N speciation and concentration

Dual pulse shaping transmission with complementary nyquist pulses

© 2019 IEEE. The concept of complementary Nyquist pulse is introduced in this paper. Making use of a half rate Nyquist pulse and its complementary one, a dual pulse shaping transmission scheme is proposed, which achieves full Nyquist rate transmission with only a half of the sampling rate required by conventional Nyquist pulse shaping. This is essential for realizing high-speed digital communication systems with available and affordable data conversion devices. The condition for cross-symbol interference free transmission with the proposed dual pulse shaping is proved in theory, and two classes of ideal complementary Nyquist pulses are formulated assuming raised-cosine pulse shaping. Simulation results are also presented to demonstrate the improved spectral efficiency with dual pulse shaping and compare other system performance against conventional Nyquist pulse shaping

Statistically validated networks in bipartite complex systems

Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1-5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6-9], email accounts and emails [10], plants and animals that pollinate them [11, 12]. Bipartite networks are often very heterogeneous in the number of relationships that the elements of one set establish with the elements of the other set. When one constructs a projected network with nodes from only one set, the system heterogeneity makes it very difficult to identify preferential links between the elements. Here we introduce an unsupervised method to statistically validate each link of the projected network against a null hypothesis taking into account the heterogeneity of the system. We apply our method to three different systems, namely the set of clusters of orthologous genes (COG) in completely sequenced genomes [13, 14], a set of daily returns of 500 US financial stocks, and the set of world movies of the IMDb database [15]. In all these systems, both different in size and level of heterogeneity, we find that our method is able to detect network structures which are informative about the system and are not simply expression of its heterogeneity. Specifically, our method (i) identifies the preferential relationships between the elements, (ii) naturally highlights the clustered structure of investigated systems, and (iii) allows to classify links according to the type of statistically validated relationships between the connected nodes.Comment: Main text: 13 pages, 3 figures, and 1 Table. Supplementary information: 15 pages, 3 figures, and 2 Table

The Quantized Hall Insulator: A New Insulator in Two-Dimensions

Quite generally, an insulator is theoretically defined by a vanishing conductivity tensor at the absolute zero of temperature. In classical insulators, such as band insulators, vanishing conductivities lead to diverging resistivities. In other insulators, in particular when a high magnetic field (B) is added, it is possible that while the magneto-resistance diverges, the Hall resistance remains finite, which is known as a Hall insulator. In this letter we demonstrate experimentally the existence of another, more exotic, insulator. This insulator, which terminates the quantum Hall effect series in a two-dimensional electron system, is characterized by a Hall resistance which is approximately quantized in the quantum unit of resistance h/e^2. This insulator is termed a quantized Hall insulator. In addition we show that for the same sample, the insulating state preceding the QHE series, at low-B, is of the HI kind.Comment: 4 page

Evolution of Th2 responses : Characterization of IL-4/13 in sea bass (Dicentrarchus labrax L.) and studies of expression and biological activity

Acknowledgements This research was funded by the European Commission under the 7th Framework Programme for Research and Technological Development (FP7) of the European Union (Grant Agreement 311993 TARGETFISH). T.W. received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (grant reference number HR09011) and contributing institutions.Peer reviewedPublisher PD

Allelic based gene-gene interactions in rheumatoid arthritis

The detection of gene-gene interaction is an important approach to understand the etiology of rheumatoid arthritis (RA). The goal of this study is to identify gene-gene interaction of SNPs at the allelic level contributing to RA using real data sets (Problem 1) of North American Rheumatoid Arthritis Consortium (NARAC) provided by Genetic Analysis Workshop 16 (GAW16). We applied our novel method that can detect the interaction by a definition of nonrandom association of alleles that occurs when the contribution to RA of a particular allele inherited in one gene depends on a particular allele inherited at other unlinked genes. Starting with 639 single-nucleotide polymorphisms (SNPs) from 26 candidate genes, we identified ten two-way interacting genes and one case of three-way interacting genes. SNP rs2476601 on PTPN22 interacts with rs2306772 on SLC22A4, which interacts with rs881372 on TRAF1 and rs2900180 on C5, respectively. SNP rs2900180 on C5 interacts with rs2242720 on RUNX1, which interacts with rs881375 on TRAF1. Furthermore, rs2476601 on PTPN22 also interacts with three SNPs (rs2905325, rs1476482, and rs2106549) in linkage disequilibrium (LD) on IL6. The other three SNPs (rs2961280, rs2961283, and rs2905308) in LD on IL6 interact with two SNPs (rs477515 and rs2516049) on HLA-DRB1. SNPs rs660895 and rs532098 on HLA-DRB1 interact with rs2834779 and four SNPs in LD on RUNX1. Three-way interacting genes of rs10229203 on IL6, rs4816502 on RUNX1, and rs10818500 on C5 were also detected

High resolution mapping of a novel late blight resistance gene Rpi-avll, from the wild Bolivian species Solanum avilesii

Both Mexico and South America are rich in Solanum species that might be valuable sources of resistance (R) genes to late blight (Phytophthora infestans). Here, we focus on an R gene present in the diploid Bolivian species S. avilesii. The genotype carrying the R gene was resistant to eight out of 10 Phytophthora isolates of various provenances. The identification of a resistant phenotype and the generation of a segregating population allowed the mapping of a single dominant R gene, Rpi-avl1, which is located in an R gene cluster on chromosome 11. This R gene cluster is considered as an R gene “hot spot”, containing R genes to at least five different pathogens. High resolution mapping of the Rpi-avl1 gene revealed a marker co-segregating in 3890 F1 individuals, which may be used for marker assisted selection in breeding programs and for further cloning of Rpi-avl