bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypothalamo-pituitary and immune-dependent adrenal regulation during systemic inflammation
Authors: Kanczkowski Waldemar , Alexaki Vasileia-Ismini , Tran Nguyen , Großklaus Sylvia , Zacharowski Kai , Martinez Antoine , Popovics Petra , Block Norman L. , Chavakis Triantafyllos , Schally Andrew V. , Bornstein Stefan R.
Published: August 2013

Significance

In several critically ill patients the homeostatic regulation of adrenocortical hormone secretion is impaired. Toll-like receptors (TLR) play a substantial role in HPA axis activation in the course of systemic inflammation. Here, using mice with conditional deletion of a crucial TLR adapter protein, MyD88, we investigated the role of systemic and local adrenal TLR signaling in the activation of adrenal glucocorticoid responses to stress and regulation of immune-adrenal crosstalk during systemic inflammatory response syndrome. Our results suggest that immune cells, rather than adrenal cells, are major regulators of the systemic and intra-adrenal inflammatory response to LPS. However, the full HPA axis activation in SIRS is not entirely dependent on systemic TLR signaling.
Relative Vulnerability of PIT‐Tagged Subyearling Fall Chinook Salmon to Predation by Caspian Terns and Double‐Crested Cormorants in the Columbia River Estuary
Authors: Sebring Scott H. , Carper Melissa C. , Ledgerwood Richard D. , Sandford Benjamin P. , Matthews Gene M. , Evans Allen F.
Published: August 2013

We quantified the percentage of PIT‐tagged subyearling fall Chinook Salmon Oncorhynchus tshawytscha that were consumed by Caspian terns Hydroprogne caspia and double‐crested cormorants Phalacrocorax auritus nesting on East Sand Island in the Columbia River estuary by electronically recovering PIT tags that were deposited on the bird colonies. We released 23 groups of PIT‐tagged subyearling fall Chinook Salmon from hatcheries in the lower Columbia River downstream of Bonneville Dam from 2002 to 2010. Vulnerability to avian predation was compared between PIT‐tagged subyearlings of two Columbia River basin stocks: tule and upriver bright (URB). Recoveries of PIT tags revealed that overall predation rates were significantly different between the tule stock (22%) and URB stock (3%); for fish that were detected as entering the lower Columbia River during the same week, predation rates also differed between stocks (tule: 21%; URB: 2%). Minimum predation rates on tule subyearlings originating from hatcheries downstream of Bonneville Dam were among the highest documented for any salmonid species in the Columbia River basin to date, occasionally exceeding 35% of the available fish. The ratio of URB fish consumed by the two avian predators indicated that the percentages were nearly equal (cormorant [%]: tern [%] = 51:49), whereas the ratio for tule‐stock fish consumed by the two avian species was not uniform (cormorant: tern = 81:19). Differences in predation rates between the tule stock and the URB stock may be attributable to migration behaviors exhibited in the estuary. We estimate that more than 8 million tule fall Chinook Salmon subyearlings released from hatcheries annually are consumed by double‐crested cormorants and Caspian terns nesting on East Sand Island; ongoing management actions by multiple federal, state, and tribal governments, if successful, will decrease predation on fall Chinook Salmon stocks.
Sharp Hamilton’s Laplacian estimate for the heat kernel on complete manifolds
Authors: Wu Jia-Yong
Published: August 2013

In this paper we give Hamilton’s Laplacian estimates for the heat equation on complete noncompact manifolds with nonnegative Ricci curvature. As an application, combining Li-Yau’s lower and upper bounds of the heat kernel, we give an estimate on Laplacian form of the heat kernel on complete manifolds with nonnegative Ricci curvature that is sharp in the order of time parameter for the heat kernel on the Euclidean space.
Values of the Euler 𝜙-function not divisible by a given odd prime, and the distribution of Euler-Kronecker constants for cyclotomic fields
Authors: Ford Kevin , Luca Florian , Moree Pieter
Published: August 2013

Let

ϕ
\phi

denote Euler’s phi function. For a fixed odd prime

q
q

we investigate the first and second order terms of the asymptotic series expansion for the number of

n
⩽
x

n\leqslant x

such that

q
∤
ϕ
(
n
)

q\nmid \phi (n)

. Part of the analysis involves a careful study of the Euler-Kronecker constants for cyclotomic fields. In particular, we show that the Hardy-Littlewood conjecture about counts of prime

k
k

-tuples and a conjecture of Ihara about the distribution of these Euler-Kronecker constants cannot be both true.
A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
Authors: Abrishami V. , Zaldívar-Peraza A. , de la Rosa-Trevín J. M. , Vargas J. , Otón J. , Marabini R. , Shkolnisky Y. , Carazo J. M. , Sorzano C. O. S.
Published: August 2013

Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives.

Results: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time.

Availability: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es.

Contact:  vabrishami@cnb.csic.es or coss@cnb.csic.es

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis
Authors: Reese Sarah E. , Archer Kellie J. , Therneau Terry M. , Atkinson Elizabeth J. , Vachon Celine M. , de Andrade Mariza , Kocher Jean-Pierre A. , Eckel-Passow Jeanette E.
Published: August 2013

Motivation: Batch effects are due to probe-specific systematic variation between groups of samples (batches) resulting from experimental features that are not of biological interest. Principal component analysis (PCA) is commonly used as a visual tool to determine whether batch effects exist after applying a global normalization method. However, PCA yields linear combinations of the variables that contribute maximum variance and thus will not necessarily detect batch effects if they are not the largest source of variability in the data.

Results: We present an extension of PCA to quantify the existence of batch effects, called guided PCA (gPCA). We describe a test statistic that uses gPCA to test whether a batch effect exists. We apply our proposed test statistic derived using gPCA to simulated data and to two copy number variation case studies: the first study consisted of 614 samples from a breast cancer family study using Illumina Human 660 bead-chip arrays, whereas the second case study consisted of 703 samples from a family blood pressure study that used Affymetrix SNP Array 6.0. We demonstrate that our statistic has good statistical properties and is able to identify significant batch effects in two copy number variation case studies.

Conclusion: We developed a new statistic that uses gPCA to identify whether batch effects exist in high-throughput genomic data. Although our examples pertain to copy number data, gPCA is general and can be used on other data types as well.

Availability and implementation: The gPCA R package (Available via CRAN) provides functionality and data to perform the methods in this article.

Contact:  reesese@vcu.edu or eckel@mayo.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
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

Motivation: Prokaryotic genome annotation has been focused mainly on identifying all genes and their protein functions. However, <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

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

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

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.
Phytophthora Database 2.0: Update and Future Direction
Authors: Park Bongsoo , Martin Frank , Geiser David M. , Kim Hye-Seon , Mansfield Michele A. , Nikolaeva Ekaterina , Park Sook-Young , Coffey Michael D. , Russo Joseph , Kim Seong H. , Balci Yilmaz , Abad Gloria , Burgess Treena , Grünwald Niklaus J. , Cheong Kyeongchae , Choi Jaeyoung , Lee Yong-Hwan , Kang Seogchan
Published: August 2013

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.
Slow–fast dynamics of a time-delayed electro-optic oscillator
Authors: Weicker Lionel , Erneux Thomas , D'Huys Otti , Danckaert Jan , Jacquot Maxime , Chembo Yanne , Larger Laurent
Published: August 2013

Square-wave oscillations exhibiting different plateau lengths have been observed experimentally by investigating an electro-optic oscillator. In a previous study, we analysed the model delay differential equations and determined an asymptotic approximation of the two plateaus. In this paper, we concentrate on the fast transition layers between plateaus and show how they contribute to the total period. We also investigate the bifurcation diagram of all possible stable solutions. We show that the square waves emerge from the first Hopf bifurcation of the basic steady state and that they may coexist with stable low-frequency periodic oscillations for the same value of the control parameter.
Amplitude death in networks of delay-coupled delay oscillators
Authors: Höfener Johannes M. , Sethia Gautam C. , Gross Thilo
Published: August 2013

Amplitude death is a dynamical phenomenon in which a network of oscillators settles to a stable state as a result of coupling. Here, we study amplitude death in a generalized model of delay-coupled delay oscillators. We derive analytical results for degree homogeneous networks which show that amplitude death is governed by certain eigenvalues of the network's adjacency matrix. In particular, these results demonstrate that in delay-coupled delay oscillators amplitude death can occur for arbitrarily large coupling strength
k
. In this limit, we find a region of amplitude death which already occurs at small coupling delays that scale with 1/
k
. We show numerically that these results remain valid in random networks with heterogeneous degree distribution.
Complexity in electro-optic delay dynamics: modelling, design and applications
Authors: Larger Laurent
Published: August 2013

Nonlinear delay dynamics have found during the last 30 years a particularly prolific exploration area in the field of photonic systems. Besides the popular external cavity laser diode set-ups, we focus in this article on another experimental realization involving electro-optic (EO) feedback loops, with delay. This approach has strongly evolved with the important technological progress made on broadband photonic and optoelectronic devices dedicated to high-speed optical telecommunications. The complex dynamical systems performed by nonlinear delayed EO feedback loop architectures were designed and explored within a huge range of operating parameters. Thanks to the availability of high-performance photonic devices, these EO delay dynamics led also to many successful, efficient and diverse applications, beyond the many fundamental questions raised from the observation of experimental behaviours. Their chaotic motion allowed for a physical layer encryption method to secure optical data, with a demonstrated capability to operate at the typical speed of modern optical telecommunications. Microwave limit cycles generated in similar EO delay oscillators showed significantly improved spectral purity thanks to the use of a very long fibre delay line. Last but not least, a novel brain inspired computational principle has been recently implemented physically in photonics for the first time, again on the basis of an EO delay dynamical system. In this latter emerging application, the computed result is obtained by a proper ‘read-out’ of the complex nonlinear transients emerging from a fixed point, the transient being issued by the injection of the information signal to be processed.
Amplitude and phase dynamics in oscillators with distributed-delay coupling
Authors: Kyrychko Y. N. , Blyuss K. B. , Schöll E.
Published: August 2013

This paper studies the effects of distributed-delay coupling on the dynamics in a system of non-identical coupled Stuart–Landau oscillators. For uniform and gamma delay distribution kernels, the conditions for amplitude death are obtained in terms of average frequency, frequency detuning and the parameters of the coupling, including coupling strength and phase, as well as the mean time delay and the width of the delay distribution. To gain further insights into the dynamics inside amplitude death regions, the eigenvalues of the corresponding characteristic equations are computed numerically. Oscillatory dynamics of the system is also investigated, using amplitude and phase representation. Various branches of phase-locked solutions are identified, and their stability is analysed for different types of delay distributions.
Bifurcation analysis of delay-induced patterns in a ring of Hodgkin–Huxley neurons
Authors: Kantner Markus , Yanchuk Serhiy
Published: August 2013

Rings of delay-coupled neurons possess a striking capability to produce various stable spiking patterns. In order to reveal the mechanisms of their appearance, we present a bifurcation analysis of the Hodgkin–Huxley (HH) system with delayed feedback as well as a closed loop of HH neurons. We consider mainly the effects of external currents and communication delays. It is shown that typically periodic patterns of different spatial form (wavenumber) appear via Hopf bifurcations as the external current or time delay changes. The Hopf bifurcations are shown to occur in relatively narrow regions of the external current values, which are independent of the delays. Additional patterns, which have the same wavenumbers as the existing ones, appear via saddle–node bifurcations of limit cycles. The obtained bifurcation diagrams are evidence for the important role of communication delays for the emergence of multiple coexistent spiking patterns. The effects of a short-cut, which destroys the rotational symmetry of the ring, are also briefly discussed.
Two-parameter study of square-wave switching dynamics in orthogonally delay-coupled semiconductor lasers
Authors: Masoller C. , Sciamanna M. , Gavrielides A.
Published: August 2013

We perform a detailed numerical analysis of square-wave (SW) polarization switching in two semiconductor lasers with time-delayed, orthogonal mutual coupling. An in-depth mapping of the dynamics in the two-parameter plane coupling strength versus frequency detuning shows that stable SWs occur in narrow parameter regions that are localized close to the boundary of stability of the pure-mode solution. In this steady state, the two coupled lasers emit orthogonal polarizations. We also show that there are various types of SW forms and that stable switching does not need the inclusion of noise or nonlinear gain in the model. As these narrow regions of deterministic and stable SWs occur for quite different combinations of parameters, they could potentially explain the waveforms that have been observed experimentally. However, on the other hand, these regions are narrow enough to be in fact considered as experimentally unreachable. Therefore, our results indicate that further experimental statistical studies are needed in order to distinguish deterministic and stationary square waveforms from long transients because of noise.
Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil
Authors: Vandamme Peter , De Brandt Evie , Houf Kurt , Salles Joana Falcão , Dirk van Elsas Jan , Spilker Theodore , LiPuma John J.
Published: August 2013

Analysis of partial gyrB gene sequences revealed six taxa in a group of 17

Burkholderia glathei

-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA–DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented

Burkholderia zhejiangensis

, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934T = CCUG 63059T), Burkholderia choica sp. nov. (type strain, LMG 22940T = CCUG 63063T), Burkholderia telluris sp. nov. (type strain, LMG 22936T = CCUG 63060T), Burkholderia udeis sp. nov. (type strain, LMG 27134T = CCUG 63061T) and Burkholderia terrestris sp. nov. (type strain, LMG 22937T = CCUG 63062T).
MHC class I immune proteins are critical for hippocampus-dependent memory and gate NMDAR-dependent hippocampal long-term depression
Authors: Nelson P. Austin , Sage Jennifer R. , Wood Suzanne C. , Davenport Christopher M. , Anagnostaras Stephan G. , Boulanger Lisa M.
Published: August 2013

Memory impairment is a common feature of conditions that involve changes in inflammatory signaling in the brain, including traumatic brain injury, infection, neurodegenerative disorders, and normal aging. However, the causal importance of inflammatory mediators in cognitive impairments in these conditions remains unclear. Here we show that specific immune proteins, members of the major histocompatibility complex class I (MHC class I), are essential for normal hippocampus-dependent memory, and are specifically required for NMDAR-dependent forms of long-term depression (LTD) in the healthy adult hippocampus. Inβ2m−/−TAP−/−mice, which lack stable cell-surface expression of most MHC class I proteins, NMDAR-dependent LTD in area CA1 of adult hippocampus is abolished, while NMDAR-independent forms of potentiation, facilitation, and depression are unaffected. Altered NMDAR-dependent synaptic plasticity in the hippocampus ofβ2m−/−TAP−/−mice is accompanied by pervasive deficits in hippocampus-dependent memory, including contextual fear memory, object recognition memory, and social recognition memory. Thus normal MHC class I expression is essential for NMDAR-dependent hippocampal synaptic depression and hippocampus-dependent memory. These results suggest that changes in MHC class I expression could be an unexpected cause of disrupted synaptic plasticity and cognitive deficits in the aging, damaged, and diseased brain.
Reinvestigation of tricyclic acyclovir: characterization of a `proton-wire' model
Authors: Meepripruk Montha , Haller Kenneth J.
Published: August 2013

The crystal structure of a dihydrate of the title compound, 3-[(2-hydroxyethoxy)methyl]-6-methyl-3H-imidazolo[1,2-a]-purin-9(5H)-one, C11H13N5O3·2H2O, has been reinvestigated. The asymmetric unit contains two molecules of tricyclic acyclovir and four molecules of water. The structure consists of a three-dimensional network of strong hydrogen bonds that integrates all of the components. While the crystal structure and the formation of an (H2O)8solvent water molecule cluster through a disordered strong hydrogen bond [O...O = 2.807 (3) Å] between two water molecules across an inversion centre has been described previously [Suwińska, Golankiewicz & Zielenkiewicz (2001).Acta Cryst.C57, 767–769], the disorder was incompletely modelled. In this work, the disorder model is extended and includes disorder of one tricyclic acyclovir hydroxy group across another inversion centre [O...O = 2.644 (4) Å]. The resulting infinite O—H...O hydrogen-bonded water–hydroxy chains, analogous to the `proton wires' found in the membrane protein gramicidin A, are discussed and an unusual disorder model involving infinite concerted chains of O—H...O hydrogen bonds is provided.
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

Purpose

The 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/approach

Corrosion 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.

Findings

During 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/value

The 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

Purpose

The aim of this study was to investigate the effectiveness of restoration of gold foils on Dazu Grottoes using different parylene coatings.

Design/methodology/approach

The 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.

Findings

The 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/value

The 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

Purpose

The 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/approach

The 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).

Findings

Inhibition 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/implications

More inhibitor concentrations can be studied in order to draw more comprehensive conclusions on the efficiency of the tested inhibitor.

Practical implications

The 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/value

The 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

Purpose

The 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/approach

A 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.

Findings

The results of coated samples were satisfactory as compared to those of uncoated carbon steel, as the former were better protected against corrosion.

Originality/value

This 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

Purpose

The 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/approach

An 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.

Findings

Simulation 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/value

The 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

Purpose

The 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/approach

The paper explores the importance of studying business model in the Chinese market and summarises the eight papers in this issue.

Findings

The 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/implications

Further investigation is needed into the interaction among Chinese firms' activities on business model design and operation and the institutional, technological, and market environment.

Originality/value

Overall, 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

Purpose

This 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/approach

At 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.

Findings

The 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 implications

The method exposed in the paper can be used on soil organic matter content hyper‐spectral inversion and even for other similar forecast problems.

Originality/value

The 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.
Image denoising method based on grey relational threshold
Authors: Hong‐jun Li , Wei Hu , Zheng‐guang Xie , Wei Wang
Published: August 2013

Purpose

The paper aims to do some further research on grey relational analysis applied in wavelet transform, and proposed a grey relational threshold algorithm for image denoising. This study tries to suppress the noise while retaining the edges and important structures as much as possible.

Design/methodology/approach

The paper analyzed the characters of noises and edges distribution in different subbands; then used the grey relational value to calculate the relationship of scale, direction and noise deviation. This paper used the grey relational value of scale, direction and noise deviation as influenced factors, and proposed a grey relational threshold algorithm.

Findings

Grey relational analysis used in threshold setting has the superiority in image denoising. The simulation results have already certified both in visual effect and peak signal to noise ratio (PSNR).

Originality/value

This paper applied grey relation theory into image denoising, and proposed a grey relational threshold algorithm. It provides a novel method for image denoising.
Measuring child and adolescent health literacy: a systematic review of literature
Authors: Ormshaw Michael J. , Paakkari Leena T. , Kannas Lasse K.
Published: August 2013

Purpose

A systematic review of literature was conducted to compile, analyse and describe the methodology and measurement of childhood/adolescent health literacy.

Design/methodology/approach

Six online databases (ERIC, PubMed, CINAHL, Biomed Central, Web of Science and Sports Discuss) were systematically searched to identify English language, peer‐reviewed articles, published between 1980 and April 2011, which reported on the measurement of health literacy in a population under the age of 18. The search identified 16 articles to be included in the final review, from which, data were systematically extracted in order to answer four review questions concerning several aspects of the method and effectiveness of the completed studies.

Findings

The majority (n=13) of the studies described the use of newly developed measurement tools and enquiry methods. The majority (n=14) assessed health literacy via task performance as opposed to examining self‐reported health literacy. Thirteen health topics and nine distinct components of health literacy were identified as being scrutinised by the 16 articles. Examination of the intended measurement aims of each study, in comparison with the actual measurement methods revealed that six studies fully succeeded in examining what they intended to measure. It is concluded that even though research in this field is escalating, clear definitions and measurement methods of childhood health literacy must be developed in order to effectively expand the field further and comprehensively assess childhood health literacy.

Originality/value

This review is to our knowledge the first to collate and examine studies concentrating solely on the measurement of health literacy in a child and/or adolescent population.