A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Background: Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Results: Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in "fed" mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. Conclusions: The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome

Classification of building design information

The more widely used classification/coding systems for building elements and components, such as CI /SfB and UDC, were developed to classify documents. A classification/coding system for use with computer aided design has to be able to convey detailed information about the features and properties of components. Previous studies of the use of information in the construction industry, in particular the CACCI Reports, have examined the logical structure of design operations and how this influences the structure of a corresponding information system. This Thesis examines also the traditional roles of the participants in the design team and demonstrates that these roles modify the ideal structure. A number of existing classification systems are analysed to provide, with an analysis of the theory of classification, the desirable features of a practical classification system. The CACCI Report proposed the development of a national commodity file. In the Section on an outline of a possible classification system it is argued that the function of a national commodity file could be replaced by a three-level classification/code with responsibility for information being divided between manufacturer, trade sector organisation and the design team, responsibility for information rests with the participant-most-concerned. Examples are provided of an individual participant's use of the proposed system and how the system would be used by several participants. In the absence of a national system, it is suggested that the proposed system would allow teams of designers to proceed with the development of a data base for computer aided design

[O III] Equivalent Width and Orientation Effects in Quasars

The flux of the [OIII] line is considered to be a good indicator of the bolometric emission of quasars. The observed continuum emission from the accretion disc should instead be strongly dependent on the inclination angle theta between the disc axis and the line of sight. Based on this, the equivalent width (EW) of [OIII] should provide a direct measure of theta. Here we analyze the distribution of EW([OIII]) in a sample of ~6,000 SDSS quasars, and find that it can be accurately reproduced assuming a relatively small intrinsic scatter and a random distribution of inclination angles. This result has several implications: 1) it is a direct proof of the disc-like emission of the optical continuum of quasars; 2) the value of EW([OIII]) can be used as a proxy of the inclination, to correct the measured continuum emission and then estimate the bolometric luminosity of quasars; 3) the presence of almost edge-on discs among broad line quasars implies that the accretion disc is not aligned with the circumnuclear absorber, and/or that the covering fraction of the latter is rather small. Finally, we show that a similar analysis of EW distributions of broad lines (Hbeta, Mg II, C IV) provides no evidence of inclination effects, suggesting a disc-like geometry of the broad emission line region.Comment: 8 pages, 5 figures. Accepted for publication in MNRA

Overview of Caching Mechanisms to Improve Hadoop Performance

Nowadays distributed computing environments, large amounts of data are generated from different resources with a high velocity, rendering the data difficult to capture, manage, and process within existing relational databases. Hadoop is a tool to store and process large datasets in a parallel manner across a cluster of machines in a distributed environment. Hadoop brings many benefits like flexibility, scalability, and high fault tolerance; however, it faces some challenges in terms of data access time, I/O operation, and duplicate computations resulting in extra overhead, resource wastage, and poor performance. Many researchers have utilized caching mechanisms to tackle these challenges. For example, they have presented approaches to improve data access time, enhance data locality rate, remove repetitive calculations, reduce the number of I/O operations, decrease the job execution time, and increase resource efficiency. In the current study, we provide a comprehensive overview of caching strategies to improve Hadoop performance. Additionally, a novel classification is introduced based on cache utilization. Using this classification, we analyze the impact on Hadoop performance and discuss the advantages and disadvantages of each group. Finally, a novel hybrid approach called Hybrid Intelligent Cache (HIC) that combines the benefits of two methods from different groups, H-SVM-LRU and CLQLMRS, is presented. Experimental results show that our hybrid method achieves an average improvement of 31.2% in job execution time

稲垣足穂『少年愛の美学』の読書論的研究 --念者としての語り--

千葉大学大学院人文社会科学研究科研究プロジェクト報告書第144集 『パフォーマンスの民族誌的研究』橋本裕之

SEH: Size Estimate Hedging for Single-Server Queues

For a single server system, Shortest Remaining Processing Time (SRPT) is an optimal size-based policy. In this paper, we discuss scheduling a single-server system when exact information about the jobs' processing times is not available. When the SRPT policy uses estimated processing times, the underestimation of large jobs can significantly degrade performance. We propose a simple heuristic, Size Estimate Hedging (SEH), that only uses jobs' estimated processing times for scheduling decisions. A job's priority is increased dynamically according to an SRPT rule until it is determined that it is underestimated, at which time the priority is frozen. Numerical results suggest that SEH has desirable performance when estimation errors are not unreasonably large

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus

BACKGROUND: Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the epigenome is involved in diabetic nephropathy. We assessed whether epigenetic modification of DNA methylation is associated with diabetic nephropathy in a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease. METHODS: We performed DNA methylation profiling in bisulphite converted DNA from cases and controls using the recently developed Illumina Infinium(R) HumanMethylation27 BeadChip, that enables the direct investigation of 27,578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14,495 genes. RESULTS: Singular Value Decomposition (SVD) analysis indicated that significant components of DNA methylation variation correlated with patient age, time to onset of diabetic nephropathy, and sex. Adjusting for confounding factors using multivariate Cox-regression analyses, and with a false discovery rate (FDR) of 0.05, we observed 19 CpG sites that demonstrated correlations with time to development of diabetic nephropathy. Of note, this included one CpG site located 18 bp upstream of the transcription start site of UNC13B, a gene in which the first intronic SNP rs13293564 has recently been reported to be associated with diabetic nephropathy. CONCLUSION: This high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy

Linearized Data Center Workload and Cooling Management

With the current high levels of energy consumption of data centers, reducing power consumption by even a small percentage is beneficial. We propose a framework for thermal-aware workload distribution in a data center to reduce cooling power consumption. The framework includes linearization of the general optimization problem and proposing a heuristic to approximate the solution for the resulting Integer Linear Programming (ILP) problems. We first define a general nonlinear power optimization problem including several cooling parameters, heat recirculation effects, and constraints on server temperatures. We propose to study a linearized version of the problem, which is easier to analyze. As an energy saving scenario and as a proof of concept for our approach, we also consider the possibility that the red-line temperature for idle servers is higher than that for busy servers. For the resulting ILP problem, we propose a heuristic for intelligent rounding of the fractional solution. Through numerical simulations, we compare our heuristics with two baseline algorithms. We also evaluate the performance of the solution of the linearized system on the original system. The results show that the proposed approach can reduce the cooling power consumption by more than 30 percent compared to the case of continuous utilizations and a single red-line temperature