bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes
Authors: Chen Gwo-Liang , Chang Yun-Juan , Hsueh Chun-Hway 
Published: August 2013

Abstract
Motivation: Prokaryotic genome annotation has been focused mainly on identifying all genes and their protein functions. However, &lt;30% of the prokaryotic genomes submitted to GenBank contain partial repeat features of specific types and none of the genomes contain complete repeat annotations. Deciphering all repeats in DNA sequences is an important and open task in genome annotation and bioinformatics. Hence, there is an immediate need of a tool capable of identifying full spectrum repeats in the whole genome.
Results: We report the PRAP (Prokaryotic Repeats Annotation Program software package to automate the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared with the major existing repeat finding tools, PRAP exhibits competitive or better results. The results are consistent with manually curated and experimental data. Repeats can be identified and grouped into families to define their relevant types. The final output is parsed into the European Molecular Biology Laboratory (EMBL)/GenBank feature table format for reading and displaying in Artemis, where it can be combined or compared with other genome data. It is currently the most complete repeat finder for prokaryotes and is a valuable tool for genome annotation.
Availability: https://sites.google.com/site/prapsoftware/
Contact: hsuehc@ntu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data
Authors: Imholte Greg C. , Scott-Boyer Marie-Pier , Labbe Aurélie , Deschepper Christian F. , Gottardo Raphael 
Published: August 2013

Abstract
Motivation: Recently, mapping studies of expression quantitative loci (eQTL) (where gene expression levels are viewed as quantitative traits) have provided insight into the biology of gene regulation. Bayesian methods provide natural modeling frameworks for analyzing eQTL studies, where information shared across markers and/or genes can increase the power to detect eQTLs. Bayesian approaches tend to be computationally demanding and require specialized software. As a result, most eQTL studies use univariate methods treating each gene independently, leading to suboptimal results.
Results: We present a powerful, computationally optimized and free open-source R package, iBMQ. Our package implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. Model parameters are estimated using a Markov chain Monte Carlo algorithm. The free and widely used openMP parallel library speeds up computation. Using a mouse cardiac dataset, we show that iBMQ improves the detection of large trans-eQTL hotspots compared with other state-of-the-art packages for eQTL analysis.
Availability: The R-package iBMQ is available from the Bioconductor Web site at http://bioconductor.org and runs on Linux, Windows and MAC OS X. It is distributed under the Artistic Licence-2.0 terms.
Contact: christian.deschepper@ircm.qc.ca or rgottard@fhcrc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Efficient inference of local ancestry
Authors: Yang James J. , Li Jia , Buu Anne , Williams L. K. 
Published: August 2013

Abstract
Motivation: The inference of local ancestry of admixed individuals at every locus provides the basis for admixture mapping. Local ancestry information has been used to identify genetic susceptibility loci.
Results: In this study, we developed a statistical method, efficient inference of local ancestry (EILA), which uses fused quantile regression and k-means classifier to infer the local ancestry for admixed individuals. We also conducted a simulation study using HapMap data to evaluate the performance of EILA in comparison with two competing methods, HAPMIX and LAMP. In general, the performance declined as the ancestral distance decreased and the time since admixture increased. EILA performed as well as the other two methods in terms of computational efficiency. In the case of closely related ancestral populations, all the three methods performed poorly. Most importantly, when the ancestral distance was large or moderate, EILA had higher accuracy and lower variation in comparison with the other two methods.
Availability and implementation: EILA is implemented as an R package, which is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/).
Contact: jyangstat@gmail.com
Sampling selectivity in acoustic-trawl surveys of Pacific sardine (Sardinops sagax) biomass and length distribution†
Authors: Demer David A. , Zwolinski Juan P. , Cutter George R. , Byers Kyle A. , Macewicz Beverly J. , Hill Kevin T. 
Published: August 2013

Abstract
Demer, D. A., Zwolinski, J. P., Cutter, G. R. Jr, Byers, K. A., Macewicz, B. J., and Hill, K. T. Sampling selectivity in acoustic-trawl surveys of Pacific sardine (Sardinops sagax) biomass and length distribution. – ICES Journal of Marine Science, 70: . To annually assess the northern stock of Pacific sardine (Sardinops sagax) in the California Current and set harvest quotas for the US fishery, managers have used an age-structured stock synthesis model fitted with results from acoustic-trawl (ATM), daily-egg-production, and aerial-photogrammetric survey methods, fishery landing and individual-length data, and many assumed or empirically derived parameters. In these assessments, sardine landed at ports spanning from Ensenada, México to Vancouver Island, Canada were assumed to be solely from the northern stock. It was also assumed that the ATM estimates of sardine biomass were negligibly biased for the sizes of fish sampled by the survey trawls (i.e., catchability q = 1 for sardine standard length (SL) values greater than ∼17 cm). Due to these catchability and length-selectivity assumptions, the ATM- and assessment-estimated abundances are mostly similar for larger sardine. However, the assessment estimates include large abundances of small sardine (SL values less than ∼15 cm) that are not represented in either the ATM-survey results or the fishery landings, and generally did not recruit to the migrating northern stock sampled by the ATM surveys. We considered four explanations for this disparity: (i) the ATM length-selectivity assumption is correct; (ii) the non-recruiting small fish may comprise a smaller portion of the stock than indicated by the assessments; (iii) during years of low recruitment success, those size classes may be virtually completely fished by the Ensenada and San Pedro fisheries; or (iv) they may belong to the southern sardine stock. This investigation emphasizes the previously identified importance of differentiating samples from the northern and southern stocks and surveying their entire domains.
Exploring the discharge of e-countability by charities
Authors: Connolly Ciaran , Dhanani Alpa 
Published: August 2013

Purpose
– This research explores the use of the internet, a mechanism that provides the opportunity to reach vast audiences efficiently and cost effectively, by United Kingdom (UK) charities to discharge accountability.

Design/methodology/approach
– This research combines a content analysis of the web sites of large UK charities and semi-structured interviews with key charity personnel responsible for the formulation and dissemination of information to stakeholders.

Findings
– The results indicate that, in most cases, charity web sites, as accountability mechanisms, appear to play a wide role, being directed at both upward and downward stakeholders. However, while the web sites are usually professionally created with appropriate web site presentation and page design, the discharge of fiduciary accountability via the internet is not universal.

Research limitations/implications
– This research focuses on large UK charities. This, together with the nature of the items captured by the content analysis checklist and the semi-structured interviews, inevitably affects its generalisability.

Practical implications
– Accepting that charities have a duty to account to their stakeholders, and that the input of accounting practitioners is vital in this process, this research extends our understanding of how the internet is employed by charities to fulfil this duty.

Originality/value
– The charity sector has grown extensively in size and prominence in recent years and policymakers have come to embrace the role that charities play in societal development. This paper provides a crucial insight into the discharge of accountability by charities through the internet.
Determinants and value relevance of corporate disclosure
Authors: A. Bokpin Godfred 
Published: August 2013

Purpose
– The purpose of this paper is to document the determinants and value relevance of corporate disclosure and transparency on the Ghana Stock Exchange (GSE).

Design/methodology/approach
– The paper employs the Fama and French model by relating firm value to firm level characteristics, with a sample of 27 firms on the GSE over a six-year period (2003-2008)

Findings
– The author found positive though statistically insignificant relationship between corporate disclosure and firm value represented by market to book value ratio and negative for stock price. Consistent with the political cost, signalling, agency and economic theories of corporate disclosure, the author found firm size, financial leverage, audit quality, age and profitability to be significant firm level characteristics determining corporate disclosure in Ghana. Though the adoption of IFRS is significant, it has marginally improved disclosure, though perhaps it is observed more in breach than in compliance and practical steps must be taken to improve disclosure practice on the GSE.

Originality/value
– The main value of the paper lies in providing further evidence of the value relevance and determinants of corporate disclosure using emerging data.
Reaping the benefits of two worlds
Authors: Cohen Sandra , Kaimenakis Nikolaos , Venieris George 
Published: August 2013

Purpose
– The purpose of this paper is to explore the coexistence of cash accounting and accrual accounting systems through an investigation of the roles they fulfill in Greek municipalities.

Design/methodology/approach
– The survey results are based on the answers of the financial department principals of 106 municipalities to a structured questionnaire. The roles of accounting investigated are informed by Ansari and Euske's model.

Findings
– It appears that cash accounting information prevails in the major function of decision making, with accrual accounting information playing a secondary role. Larger municipalities seem to use accounting data more extensively than smaller ones for negotiations, both in accrual and cash terms.

Originality/value
– The study sheds light on the actual use of accrual accounting information in a public sector setting, where customarily decisions were based on cash accounting considerations.
Corrosion of inhibitor treated mild steel immersed in distilled water and a simulated salt solution
Authors: Malaibari Zuhair , Kahraman Ramazan , Rauf Abdur 
Published: August 2013

PurposeThe purpose of this study was to investigate the performances of three inhibitors in controlling corrosion of local mild steel products in distilled water and a simulated salt solution.Design/methodology/approachCorrosion inhibition of mild steel was investigated using electrochemical techniques. Untreated and inhibitor treated specimens were fully immersed in two test solutions, distilled water and the simulated solution of 2.0 wt.% NaCl and 1.0 wt.% Na2SO4.FindingsDuring full immersion in the simulated salt solution, sodium dihydrogen orthophosphate was not effective at all, resulting in even higher corrosion rates than that of the untreated specimens. Sodium benzoate was effective for three days only. Dicyclohexylamine nitrite was the most effective of them all, keeping its effectiveness for as much as 20 days. When the specimens were immersed in distilled water, all three inhibitors were effective during the 60 days of immersion while dicyclohexylamine nitrite and sodium benzoate treated specimens performed better than those treated with sodium dihydrogen orthophosphate.Originality/valueThe objective of this research was to investigate the performances of three inhibitors – sodium dihydrogen orthophosphate (inorganic) at 10 mM concentration, dicyclohexylamine nitrite (organic) and sodium benzoate (organic) at 100 mM concentration – in controlling the corrosion of local mild steel products fully immersed in two test solutions, distilled water and the simulated salt solution. All three inhibitors are film forming and anodic type inhibitors. According to the authors' literature review, this study is original and will add value to the studies of inhibition of steel corrosion under similar environments.
The effect of parylene coating for restoration of gold foil on Dazu Grottoes
Authors: Tian Xingling , Li Naisheng , Zhang Zhiguo , Chen Xu , Wang Yang , Weinhold Wolfgang Peter 
Published: August 2013

PurposeThe aim of this study was to investigate the effectiveness of restoration of gold foils on Dazu Grottoes using different parylene coatings.Design/methodology/approachThe gold foil samples were applied with two types of parylene coating with six different thicknesses, C‐10, C‐15, C‐20, N‐10, N‐20, N‐25, respectively. Electrochemical impedance, surface morphology, and hydrophobicity properties were used to examine the behavior of the coatings.FindingsThe results showed that an increase in electrochemical corrosion resistance was observed as the degree of coating thickness was increased for both C‐parylene and N‐parylene coatings. In addition, the surface morphology study, using 3D topography measurement, indicated that the surface roughness was decreased for all parylene coatings. Furthermore, the parylene‐C coating was comparatively more effective than was the parylene‐N coating.Originality/valueThe results obtained from the three methods were in close agreement. This is an indication that the parylene‐C coating can be used to restore the gold foils on Dazu Grottoes and to support future restoration and consolidation to be applied on site on the Grottoes.
Effect of an alkyl amine‐based corrosion inhibitor for 1018 carbon steel pipeline in sea water
Authors: Shawabkeh Reyad , Rihan Rihan , AL‐Baker Nawaf 
Published: August 2013

PurposeThe paper aims to report an experimental investigation of the effectiveness of an alkyl amine‐based inhibitor on the corrosion behavior of 1018 carbon steel in sea water. The adsorption equilibrium for this corrosion inhibitor on carbon steel was also investigated. The corrosion inhibitor was evaluated based on parameters such as inhibitor concentration, temperature, stirring speed and pH.Design/methodology/approachThe experimental setup employed an autoclave with a flow circulation system. Weight loss determinations and electrochemical techniques such as polarization resistance and potentiodynamic polarization were used to detect and monitor the performance of the corrosion inhibitor. Surface examination of the steel substrate before and after applying different doses of inhibitor was undertaken using Fourier transform infrared spectroscopy (FT‐IR), scanning electron microscopy (SEM), and energy dispersive spectrometry (EDS).FindingsInhibition efficiency was enhanced by adsorption of amine‐containing functional groups on the steel surface. This adsorption capacity was measured and fitted Langmuir and Shawabkeh‐Tutunji isotherms and was found to require a maximum requirement of 1.08 mg of corrosion inhibitor to provide a monolayer of cover on the carbon steel surface. The inhibition efficiency increased with increasing the inhibitor concentration and solution pH. Moreover, increasing the solution temperature and stirring speed had an adverse effect on inhibition efficiency. Polarization data fitted by the Butler‐Volmer Equation showed the values of anodic and cathodic Tafel coefficients were an average of 0.8 and 0.2, respectively. The measured corrosion rates decreased rapidly within the first hour after commencing the experiments, which is related to the formation of a protective oxide film.Research limitations/implicationsMore inhibitor concentrations can be studied in order to draw more comprehensive conclusions on the efficiency of the tested inhibitor.Practical implicationsThe effect of alkyl amine‐based inhibitor on the corrosion inhibition characteristic of 1018 carbon steel (CS) in sea water was determined at different inhibitor concentrations, temperatures, stirring speeds and pH.Originality/valueThe new information reported in this paper is the effect of alkyl amine‐based inhibitor on the corrosion characteristics of 1018 carbon steel in seawater using an autoclave with a flow circulation system. The paper is valuable to researchers in the area of corrosion inhibitors and oil and gas industry.
Analysis of the formation of a vinyltrimethoxysilane film on 1010 carbon steel using electrochemical techniques
Authors: Souza Fernandes Bruno , Gustavo da Silva Souza Kleber , Vieira Aoki Idalina , Dani Rico Amado Franco 
Published: August 2013

PurposeThe application of coatings on metal substrates can provide an increase in corrosion resistance in the environment where the material is employed. The use of silane causes low environmental impact and may represent an alternative to replace chromates and phosphates applied as a pretreatment prior to surface painting. The objective of this study was to evaluate experimental parameters for the investigation of the formation of a vinyltrimethoxysilane (VTMOS) monolayer on 1010 carbon steel applying electrochemical techniques.Design/methodology/approachA total of 24 types of coated samples were obtained, following three 23 factorial design of experiments (DOE), and one uncoated. The VTMOS monolayer was formed by hand dip process, followed by curing in a stove, using substrates of sanded, pickled and degreased 1010 carbon steel and hydrolyzed silane.FindingsThe results of coated samples were satisfactory as compared to those of uncoated carbon steel, as the former were better protected against corrosion.Originality/valueThis paper shows an evaluation of experimental parameters that influence the formation of a film of silane VTMOS on 1010 carbon steel by means of electrochemical techniques. The results indicated that the silane monolayer VTMOS promotes enhanced properties that prevent corrosion of 1010 carbon steel and the method of film formation directly influences the properties of such protection.
Attitude scheme for satellite with defective inertia characteristic
Authors: Jin Jin , Baoyin Hexi , Li Junfeng 
Published: August 2013

PurposeThe purpose of this paper is to propose an attitude determination and control scheme for a low‐cost Micro‐satellite with defective inertia. Restricted by the payload design, the z‐axis inertia of this satellite is larger than the x and y axes, which is unstable for natural attitude dynamics.Design/methodology/approachAn original operation mode is designed to avoid z axis from long‐time pointing to the sun during damping, which avoids some unexpected damage. In attitude determination design, EKF and UKF algorithms are compared on estimation accuracy, convergence time and computation complexity in attitude estimation design, which is referred to determine the final estimation scheme. A DSP‐based hardware solution is achieved and a semi‐physical testing and simulation system is built.FindingsSimulation results show the 3‐axis stable mode can be built with the proposed scheme, and the unprotected facet of the satellite can be kept away from long‐time pointing to the sun.Originality/valueThe proposed ADCS scheme can be a reference for the future Micro‐satellite programs which share the similar configuration.
Mastering Chinese business model by conducting indigenous management research
Authors: Xi Youmin , Zhang Xiaojun 
Published: August 2013

PurposeThe purpose of this paper is to explore the topic of the Chinese business model and provide a brief introduction to the papers in this special issue.Design/methodology/approachThe paper explores the importance of studying business model in the Chinese market and summarises the eight papers in this issue.FindingsThe papers in this special issue address what the business model is in China, how it influences organizational outcomes, and how to build the business model in the Chinese market. These papers may be germane to both researchers and practitioners concerned with managing business model in China. For scholars, these papers broaden the understanding of business model and extend the theoretical boundaries of the business model from the Western to the Eastern context. For practitioners doing business in China, these papers give implications on how to build business models in China as well as what institutional and technological factors should be considered when designing their business models.Research limitations/implicationsFurther investigation is needed into the interaction among Chinese firms' activities on business model design and operation and the institutional, technological, and market environment.Originality/valueOverall, these papers make remarkable contributions to our understanding of Chinese business model. The topics of these studies are various and the methods are also multiplex. Several interesting Chinese business models are addressed such as Bandit business model and “a company + farmers”.
Soil organic matter content GM(0,N) estimation model based on hyper‐spectral technique
Authors: Xi‐can Li , Zheng Yuan , Guangbo Zhang 
Published: August 2013

PurposeThis paper attempts to establish the grey GM(0,N) estimation model of the soil organic matter content spectral inversion under the uncertainties between soil organic matter contents and spectral characteristics and the theory of grey system.Design/methodology/approachAt first, based on the uncertainty of the relationship between the soil organic matter content and spectral characteristics, using the ordered grey accumulation generation and grey GM(0, N) model to establish hyper‐spectral grey estimation model of soil organic matter content. Second, the presented model is used to estimate soil organic matter of Hengshan County in Shanxi province in the last part of the paper.FindingsThe results are convincing: not only that soil organic matter content spectral inversion grey GM(0, N) model based on the ordered grey accumulation generation theory is valid, but also the model's prediction accuracy is higher, with the sample's average prediction accuracy being 93.662 per cent.Practical implicationsThe method exposed in the paper can be used on soil organic matter content hyper‐spectral inversion and even for other similar forecast problems.Originality/valueThe paper succeeds in realising both prediction pattern and application of soil organic matter content hyper‐spectral inversion by using the newest developed theories: grey GM(0, N) model based on the ordered grey accumulation generation.