Contributors: Arash Kamari, Farhad Gharagheizi, Amir H. Mohammadi, Deresh Ramjugernath

Date: 2016-04-01

... In this communication, a corresponding states-based model for the calculation/estimation of the gas compressibility factor (z-factor) of natural gasses is proposed. The method applies the gene expression programming (GEP) algorithm. The parameters of the new model comprise the pseudo-reduced pressure and pseudo-reduced temperature. For assessing the performance and accuracy of the developed model, several statistical and graphical error analyses have been applied simultaneously. Additionally, comparisons have been made between this method and the most widely-used correlations and equations of state (EoS) available in the literature. Various statistical parameters are also used to evaluate the validity and the predictive capability of the newly developed method. Furthermore, the Leverage approach (Williams plot) is used to determine the realm of prediction capability of the new z-factor model and to detect any probable erroneous data points. The results obtained demonstrate that the newly proposed model is more reliable and more effective than the empirical models and EoS methods for prediction of z-factors of natural gasses.

Contributors: Esmaeil Fatemi-Behbahani, Ebrahim Farshidi, Karim Ansari-Asl

Date: 2016-04-01

... In this paper a new digital background correction and calibration technique for redundant multi-bit pipeline stages is presented. In this method output voltage of each stage in converter is defined as sum of the ideal product and error signal, which error voltage include of linear non-ideal section or first order error and nonlinearity undesired signal or third order error. Linear error is formed by capacitor mismatch, op-amp offset, comparator offset and finite op-amp gain effects. Nonlinear error is deformed the output voltage depend on the nonlinear results of open loop residue amplifier. Correction begins with separately calculation and cancelation of the nonlinear and linear errors respectively. For calibration of each stage at first step, the nonlinear effects in digital output of backend ADC is eliminated and then by digital modeling of first order analog error the influence of this unfavorable signal is diminished from digital equivalent of input voltage. Therefore for cancelation of non-ideal impairment in each stage a digital filter consist of linear and nonlinear channel in digital domain is designed. The first order and third order coefficients of designed digital function are unknown and should by a pertinent method be estimated simultaneously. Adaptive filter are best choose for this method. Simulation results show that INL/DNL parameters of 14-bit radix-4 pipelined converter are improved from 17LSB/3LSB to 0.45LSB/0.41LSB after calibration. The SNDR/SFDR parameters are increased from 30dB/36dB to 83dB/90dB.

Contributors: Eric Gabin Kilama

Date: 2016-04-01

... From the perspective of recipients, the increasing influence of China and emerging donors in the aid landscape represents an opportunity to attract additional resources to finance development and improve their control over their development agenda. This paper investigates how African countries and other LMICs deal with this complex and changing aid landscape and explores how government fiscal behaviors and private agent anticipations regarding aid flows are affected.

Contributors: Niels Anthonisen

Date: 2016-03-01

... The distribution of firm-sizes in the U.S. – or at least its upper tail – appears to be well-described by a Pareto distribution with infinite variance. This fact forms the basis of the granular hypothesis proposed by Gabaix in his paper “The Granular Origins of Aggregate Fluctuations” (Econometrica, (2011)). The granular hypothesis provides a mechanism whereby independent firm-level shocks are capable of generating macroeconomic fluctuations. This paper considers the granular hypothesis in a new framework. It develops a DSGE model by superimposing a stochastic overlapping generations framework on a network. Idiosyncratic output shocks to individual firms are transmitted across the economy through income–expenditure channels. Specifically, firms represent vertices of the network, and a firm x is linked to another firm y if x employs one or more workers who purchase commodities produced by y. The paper’s findings agree closely with results first discovered by Gabaix: if firm-sizes in an economy are described by a Pareto distribution, then independent firm-level shocks can generate macroeconomic fluctuations in accordance with the granular hypothesis. Furthermore, the model is capable of generating aggregate volatility of the same order of magnitude as occurs in reality. Thus the paper describes a new general equilibrium framework where macroeconomic fluctuations can arise as the consequence of independent firm-level shocks.

Contributors: J. Janová, D. Hampel

Date: 2016-03-01

... When using alpha-design for plant variety testing under space restrictions, ex post design modifications must be implemented to prevent variety self-proximity on plots and, consequently, to prevent damage-induced loss of experimental information. This is done ad hoc for each experiment; the unsystematic modification is, however, commonly not only unable to resolve all existing proximities, but may introduce secondary undesired proximities. In this paper, a procedure is developed for the universal construction of modified alpha-design that covers all existing proximity constraints while keeping the efficiency level of the original design. Using extensive real data simulation, we validate the procedure and confirm high damage robustness of the modified designs. The procedure has been implemented as a Matlab function and is available as on-line supplement to the paper. The function enables to design the damage-robust experiments automatically using only standard computer equipment.

Contributors: Ning Wang, En-Hua Xia, Li-Zhi Gao

Date: 2016-03-01

... WRKY transcription factors play critical roles in plant growth and development, as well as the response to biotic and abiotic stresses. Despite the fact that WRKY gene family has been characterized in a number of plant species, very little is known in the common bean, Phaseolus vulgaris. The recently released genome sequences provide us a good opportunity for genome-wide analysis of WRKY genes in this legume crop. In this study, a total of 90 WRKY genes (PvWRKYs) were identified and classified into three groups, of which the second group was further separated into five subgroups based on the structure of the conserved domains. All the WRKY genes were located on chromosomes 1 to 11 with a non-uniformed distribution. The phylogenetic analysis revealed that the majority of the PvWRKY genes were clustered with those from soybean, indicating that most of the WRKY genes may be originated from the same ancestor with Glycine max; both tandem and segmental duplications have played an important role in the evolution and diversification of the WRKY gene family in P. vulgaris. The variety and complexity of protein structure indicate that WRKY genes may be of significance in plant growth regulation and stress responses. The analysis of expression profiles revealed that the majority of WRKY genes showed tissue-specific expression, which is indicative of diverged expression during the development of common bean.

Contributors: Adelchi Azzalini, Ryan P. Browne, Marc G. Genton, Paul D. McNicholas

Date: 2016-03-01

... We examine some skew distributions used extensively within the model-based clustering literature in recent years, paying special attention to claims that have been made about their relative efficacy. Theoretical arguments are provided as well as real data examples.

Contributors: Youhong Fang, Jingjing Quan, Xiaoting Hua, Ye Feng, Xi Li, Jianfeng Wang, Zhi Ruan, Shiqiang Shang, Yunsong Yu

Date: 2016-03-01

... Acinetobacter baumannii is an important bacterium that emerged as a significant nosocomial pathogen worldwide. The rise of A. baumannii was due to its multi-drug resistance (MDR), while it was difficult to treat multi-drug resistant A. baumannii with antibiotics, especially in pediatric patients for the therapeutic options with antibiotics were quite limited in pediatric patients. A. baumannii ST208 was identified as predominant sequence type of carbapenem resistant A. baumannii in the United States and China. As we knew, there was no complete genome sequence reproted for A. baumannii ST208, although several whole genome shotgun sequences had been reported. Here, we sequenced the 4087-kilobase (kb) chromosome and 112-kb plasmid of A. baumannii XH386 (ST208), which was isolated from a pediatric hospital in China. The genome of A. baumannii XH386 contained 3968 protein-coding genes and 94 RNA-only encoding genes. Genomic analysis and Minimum inhibitory concentration assay showed that A. baumannii XH386 was multi-drug resistant strain, which showed resistance to most of antibiotics, except for tigecycline. The data may be accessed via the GenBank accession number CP010779 and CP010780.

Contributors: Larissa Mara de Andrade, Paula Macedo Nobile, Rafael Vasconcelos Ribeiro, João Felipe Nebó Carlos de Oliveira, Antonio Vargas de Oliveira Figueira, Luis Tadeu Marques Frigel, Daniel Nunes, Dilermando Perecin, Michael dos Santos Brito, Regina Célia de Matos Pires

Date: 2016-03-01

... Aquaporins (AQPs) are proteins that facilitate the transport of water, small neutral solutes and gases across membranes and have an important role in plant physiology and drought stress responses. The sugarcane (Saccharum spp.) transcriptome was searched for AQPs, also known as major intrinsic proteins. Phylogenetic analysis based on nucleotide sequences identified 33 isoforms that fit into four AQP subfamilies previously described for monocotyledonous: 13 plasma membrane intrinsic protein (PIPs), 11 tonoplast intrinsic proteins (TIPs), six nodulin 26-like intrinsic proteins (NIPs) and three small basic intrinsic proteins (SIPs). Among the PIPs, five proteins were classified as PIP1 type and eight were classified as PIP2 type. The expression profiles of three PIP2 isoforms (ShPIP2;1, ShPIP2;5 and ShPIP2;6), which are counterparts of previously described isoforms involved in drought stress in leaves of higher plants, were aligned with monocots and dicot PIP2 protein sequence showing high identity with maize proteins. Furthermore, the transcript abundance of these three genes was evaluated through quantitative PCR (qPCR) in two sugarcane genotypes (‘IACSP94-2094’ and ‘IACSP97-7065’) subjected to water deficit under field and greenhouse conditions. ShPIP2;1, ShPIP2;5 and ShPIP2;6 isoforms were responsive to water deficit and their expression patterns were dependent on genotype, experimental condition and duration of drought stress. Taken together, our results show that the three APQs have their expression in leaves changed under drought, suggesting that these proteins constitute an important target for functional characterization in sugarcane, particularly focusing the performance of plants under varying water availability.

Contributors: Anna V. Williams, Joseph T. Miller, Ian Small, Paul G. Nevill, Laura M. Boykin

Date: 2016-03-01

... Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences.