bluuebunny/crossref_metadata_2025 huggingface dataset:
Egyptian faience and rose gold at Mochlos, Crete
Authors: Giumlia-Mair A R G , Soles J
Published: January 2013

The Mycenaean necklace found in a tomb in the Limenaria cemetery at Mochlos, Crete, consists of a row of faience beads and a central gold bead, and it is dated to the LM IIIA period (about 1400–1300 BC). Studies on faience have shown that different production technologies were used in this period: efflorescence, cementation and direct application methods. The efflorescence method was used in Egypt. The manufacture of the faience from Mochlos indicates an Egyptian origin, but the shape and the style are Aegean. The gold bead shows a deliberately applied rose patination on one side and a normal golden colour on the other. The analyses showed that the composition of the pink film is very similar to that on Tutankhamun's sequins. The technique of colouring gold is known from objects found in royal tombs in Egypt. This piece of jewelry shows, like the faience, a strong Egyptian technological influence.
In situ synthesis ZrB2/Fe cladding layer by PTA process
Authors: Guo L J , Wang X B , Zang P P , Wang H B
Published: January 2013

ZrB2/Fe cladding layer was in situ synthesised by plasma transferred arc powder cladding on mild steel substrate using Zr and B4C as the precursor powders. The phase composition and microstructure were investigated by X-ray diffraction analysis, optical microscope, scanning electron microscopy and energy dispersive spectrum. Microhardness of the layer was examined at room temperature. The results show that the phases of the cladding layer are ZrB2 and iron. ZrB2 particles have three morphologies: acicular, short rod and block. Reaction process could be divided into four stages according to the state of reactants. ZrB2 particles gradient distribute in substrate from surface to bottom of the layer. Skeleton-like structure and cluster structure of ZrB2 are formed in the surface part, and particulate reinforced structure is formed in the middle and bottom part of the layer. The microhardness was greatly improved due to the presence of ZrB2 particles in comparison with the substrate.
High Tech in 5100 BC: multianalytical approach for characterisation of decorated pottery from Tappeh-Zaghe
Authors: Emami M-A , Trettin R
Published: January 2013

Tappeh-Zaghe is an important archaeological site, located in the northern part of the Persian plateau, and dated to prehistoric times (∼5100 BC). The pottery from Tappeh-Zaghe shows an astonishingly fine manufacture. Multianalytical methods have been applied to determine the general chemical composition and the manufacturing process of the ceramic of this period. The results of this investigation show that the pottery from Tappeh-Zaghe was locally produced. The samples are characterised by three distinguishable layers, consisting of clay materials in the core and fine processed quartz aggregates mixed with lime paste on the surface. The external layer is decorated with a painted reddish decoration. The well processed quartz aggregates indicate that the potters applied the external layer on the surface to obtain a structure providing better conditions for decorating and painting, and also more resistant against thermal shock.
Structural and mechanical properties of nanostructured tungsten oxide thin films
Authors: Hasan M M , Haseeb A S M A , Masjuki H H
Published: January 2013

This study presents structural and mechanical properties of WO3 thin films deposited on glass substrates at different temperatures by radio frequency reactive magnetron sputtering. WO3 films deposited at temperatures up to 200°C are found as amorphous, but crystalline at 300 and 400°C. Chemical analysis reveals the overstoichiometry of the films. The diffusion of sodium ions from glass substrates occurs at higher temperatures. The adhesion critical loads of WO3 films deposited at room temperature and at 200, 300 and 400°C are found to be 670, 990, 1080 and 830 mN respectively using microscratch tests with a 25 μm probe. Scratch hardness increases with the rise of temperature. The depth of penetration and wear track width decrease with temperature, indicating an improved penetration and wear resistance at temperatures up to 300°C. Scanning electron microscopy images reveal that the coatings fail due to wedge and recovery spallation during scratch and wear tests respectively.
Gilding of cultural heritage artefacts: an elaborated technology
Authors: Darque-Ceretti E , Felder E , Aucouturier M
Published: January 2013

Gilding has been used to decorate, one may say sublimate, the surface appearance of artworks since the beginning of gold use in art. Gold foils and leaves were used first, thanks to the high ductility of that metal, and the progress of gilding art through centuries has been linked to: (1) the evolution of the thickness of the gold film used for the process; (2) the continuous research for efficient adhesive materials adapted to the various substrates; and (3) the development of techniques of direct adhesion of the gold coating, especially on metals. This paper, based on recent laboratory results obtained through laboratory studies of various museum artworks, discusses these three aspects. First, it shall develop a mechanical modelling of gold leaf beating. Second, it shall detail the properties of the main classes of adhesive materials used for leaf gilding on various materials. Finally, the importance of the diffusion phenomena at the interface between a metal substrate and a gold coating shall be discussed, especially in the case of gilding involving a high temperature treatment.
Si doped ZnO thin films for transparent conducting oxides
Authors: Qin H , Liu H F , Yuan Y Z
Published: January 2013

Transparent conductive silicon doped zinc oxide (SZO, 3%Si) thin films are grown by direct current magnetron sputtering on glass substrates at room temperature. Experimental results show that the sputtering time has a significance impact on the growth rate, crystal quality and electrical properties of the films, and have little impact on the optical properties of the films. The growth rate decreases with the sputtering time. The resistivity of ZnO/Si films decreases as the sputtering time increases from 8 to 20 min. However, as the sputtering time increases further, the electrical resistivity increases instead. When other sputtering conditions are kept unchanged, it is found that the optimum sputtering time is 20 min and the achieved lowest resistivity is 4·92×10−4 Ω cm (sheet resistance = 11·5 Ω/sq for thickness 427·5 nm). The UV-vis transmission spectrum shows that all film samples present a transmission of above 90·0% in the visible range.
Corrosion behaviour of electrodeposited Ni–Sn–P alloys
Authors: Wang H Z , Song Y , Zhang Z X , Yao S W , Zhang W G
Published: January 2013

Ni–Sn–P alloys with a stannous content of 2·91–4·05 wt-% and a phosphorous content of 13·54–14·56 wt-% produced as a coating on copper by constant current electrodeposition were studied, with regard to their corrosion behaviour upon immersion in 10 wt-% H2SO4 solutions. The corrosion resistance of Ni–Sn–P alloy improved with increasing stannous content. X-ray photoelectron spectroscopy and energy dispersive X-ray spectroscopy confirmed the formation of Sn and P enriched layers at the alloy surface. After corrosion, a layer of passive film composed of SnO2, Ni(OH)2 and Ni3(PO4)2 was formed on the surface, which could prevent the contact between metal surface and corrosive liquid.
Gold nanoparticles deposited on polyaniline nanofibres as for electro-oxidation of hydrazine
Authors: Hosseini M G , Momeni M M , Zeynali S
Published: January 2013

Gold nanoparticles (Au-NPs) dispersed in polyaniline (PAni) matrixes coated on titanium substrate, as a novel electrode (PAni/Ti). Scanning electron microscopy results show that Au-NPs are distributed at the surface of the PAni film. The electrochemical behaviour and electrocatalytic activity of Au-NPs/PAni/Ti electrodes were examined for electrocatalytic activity toward oxidation of hydrazine, and the results show that these modified electrodes are highly active for electrocatalytic oxidation of hydrazine.
High temperature tribology of nanocrystalline Ni–P–Ag coating
Authors: Alirezaei S , Monirvaghefi S M , Saatchi A , Ürgen M , Motallebzadeh A
Published: January 2013

In this study, silver particles were embedded in Ni–P matrix by electroless deposition on medium carbon steel substrates to produce Ni–P–Ag composite coating. The structure of as plated and heat treated coatings were evaluated by X-ray diffraction analysis. Tribological properties of the coatings were investigated by pin on disc test method using 52100 steel pin as counter body at room and high temperatures. Three-dimensional optical profiler was employed to determine wear rate of the deposits. Surface morphology, cross-section of coatings and wear scars were studied by using scanning electron microscopy equipped with EDS analysis. The results showed that nanocrystalline Ni–P–Ag composite coating had a self-lubricating property at room and high temperatures. It was concluded that diffusion and nucleation of silver on the surface of Ni–P–Ag coating and also formation of a silver thin layer on the sliding surface led to decrease the friction coefficient of Ni–P–Ag coating.
Corrosion behaviour of electroless Ni–P–TiO2 nanocomposite coatings using Taguchi
Authors: Hosseini J , Bodaghi A
Published: January 2013

This paper reports an experimental study of corrosion characteristics of electroless Ni–P–TiO2 nanocomposite coatings. Coating process parameters are optimised for maximum corrosion resistance based on L9 Taguchi orthogonal design with four process parameters, namely, concentration of nickel source solution, concentration of reducing agent, concentration of TiO2 powder and bath temperature. Corrosion behaviour of the electroless Ni–P–TiO2 nanocomposite coatings was evaluated in 3·5 wt-%NaCl aqueous solution using polarisation technique. Scanning electron microscopy and energy dispersive X-ray spectroscopy analysis were used for studying surface morphology and chemical composition of the electroless Ni–P–TiO2 nanocomposite coatings. The results showed that incorporation of TiO2 in coating causes an increase in corrosion resistance and improves surface morphology. Finally, optimum conditions were achieved as follows: concentration of nickel source solution, 50 g L−1; concentration of reducing agent, 10 g L−1; concentration of TiO2 powder, 10 g L−1; and bath temperature, 85°C.
Hyperdiploidy with 58-66 chromosomes in childhood B-acute lymphoblastic leukemia is highly curable: 58951 CLG-EORTC results
Authors: Dastugue Nicole , Suciu Stefan , Plat Geneviève , Speleman Frank , Cavé Hélène , Girard Sandrine , Bakkus Marleen , Pagès Marie Pierre , Yakouben Karima , Nelken Brigitte , Uyttebroeck Anne , Gervais Carine , Lutz Patrick , Teixeira Manuel R. , Heimann Pierre , Ferster Alice , Rohrlich Pierre , Collonge Marie Agnès , Munzer Martine , Luquet Isabelle , Boutard Patrick , Sirvent Nicolas , Karrasch Matthias , Bertrand Yves , Benoit Yves
Published: January 2013

Key Points

Patients with 58-66 chromosomes have 99% event-free survival and 100% overall survival in the 58951 EORTC-CLG study. The higher the ploidy, the better the prognosis in the 58951 EORTC-CLG study.
Hyers-Ulam stability of functional equations in matrix normed spaces
Authors: Lee Jung Rye , Shin Dong Yun , Park Choonkil
Published: January 2013

In this paper, we prove the Hyers-Ulam stability of the Cauchy additive functional equation and the quadratic functional equation in matrix normed spaces.

MSC:47L25, 39B82, 46L07, 39B52.
Mojo Hand, a TALEN design tool for genome editing applications
Authors: Neff Kevin L , Argue David P , Ma Alvin C , Lee Han B , Clark Karl J , Ekker Stephen C
Published: January 2013

Background

Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications.

Results

We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method.

Conclusions

Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.
CySBGN: A Cytoscape plug-in to integrate SBGN maps
Authors: Gonçalves Emanuel , Iersel Martijn van , Saez-Rodriguez Julio
Published: January 2013

Background

A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.

Results

We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network.

Conclusions

CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Authors: Seitzer Phillip , Huynh Tu Anh , Facciotti Marc T
Published: January 2013

Background

Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.

Results

Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.

Conclusions

JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.
Random generalized linear model: a highly accurate and interpretable ensemble predictor
Authors: Song Lin , Langfelder Peter , Horvath Steve
Published: January 2013

Background

Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature selection tends to overfit the data and leads to low predictive accuracy. Therefore, it remains an important research goal to combine the advantages of ensemble predictors (high accuracy) with the advantages of forward regression modeling (interpretability). To address this goal several articles have explored GLM based ensemble predictors. Since limited evaluations suggested that these ensemble predictors were less accurate than alternative predictors, they have found little attention in the literature.

Results

Comprehensive evaluations involving hundreds of genomic data sets, the UCI machine learning benchmark data, and simulations are used to give GLM based ensemble predictors a new and careful look. A novel bootstrap aggregated (bagged) GLM predictor that incorporates several elements of randomness and instability (random subspace method, optional interaction terms, forward variable selection) often outperforms a host of alternative prediction methods including random forests and penalized regression models (ridge regression, elastic net, lasso). This random generalized linear model (RGLM) predictor provides variable importance measures that can be used to define a “thinned” ensemble predictor (involving few features) that retains excellent predictive accuracy.

Conclusion

RGLM is a state of the art predictor that shares the advantages of a random forest (excellent predictive accuracy, feature importance measures, out-of-bag estimates of accuracy) with those of a forward selected generalized linear model (interpretability). These methods are implemented in the freely available R software packagerandomGLM.
Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus
Authors: Cabanillas Laura , Arribas María , Lázaro Ester
Published: January 2013

Background

When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine.

Results

The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics.

Conclusions

Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salarL.)
Authors: Ozerov Mikhail , Vasemägi Anti , Wennevik Vidar , Niemelä Eero , Prusov Sergey , Kent Matthew , Vähä Juha-Pekka
Published: January 2013

Background

New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salarL.) populations using an Illumina SNP-chip.

Results

In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r> 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample.

Conclusions

Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits.
Genetic variation and expression diversity between grain and sweet sorghum lines
Authors: Jiang Shu-Ye , Ma Zhigang , Vanitha Jeevanandam , Ramachandran Srinivasan
Published: January 2013

Background

Biological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period.

Results

We implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence.

Conclusion

Substantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.
Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses
Authors: Humbert Sabrina , Subedi Sanjeena , Cohn Jonathan , Zeng Bin , Bi Yong-Mei , Chen Xi , Zhu Tong , McNicholas Paul D , Rothstein Steven J
Published: January 2013

Background

Water and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunately, tremendous progress has been made in the past decades in terms of modeling to assist growers in the decision making process and many tools are now available to achieve more sustainable practices both environmentally and economically. Nevertheless large gaps remain between our empirical knowledge of the physiological changes observed in the field in response to nitrogen and water stresses, and our limited understanding of the molecular processes leading to those changes.

Results

This work examines in particular the impact of simultaneous stresses on the transcriptome. In a greenhouse setting, corn plants were grown under tightly controlled nitrogen and water conditions, allowing sampling of various tissues and stress combinations. A microarray profiling experiment was performed using this material and showed that the concomitant presence of nitrogen and water limitation affects gene expression to an extent much larger than anticipated. A clustering analysis also revealed how the interaction between the two stresses shapes the patterns of gene expression over various levels of water stresses and recovery.

Conclusions

Overall, this study suggests that the molecular signature of a specific combination of stresses on the transcriptome might be as unique as the impact of individual stresses, and hence underlines the difficulty to extrapolate conclusions obtained from the study of individual stress responses to more complex settings.
Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies
Authors: Goh Wilson Wen Bin , Fan Mengyuan , Low Hong Sang , Sergot Marek , Wong Limsoon
Published: January 2013

Background

Proteomics Signature Profiling (PSP) is a novel hit-rate based method that proved useful in resolving consistency and coverage issues in proteomics. As a follow-up study, several points need to be addressed: 1/ PSP’s generalisability to pathways, 2/ understanding the biological interplay between significant complexes and pathway subnets co-located on the same pathways on our liver cancer dataset, 3/ understanding PSP’s false positive rate and 4/ demonstrating that PSP works on other suitable proteomics datasets as well as expanding PSP’s analytical resolution via the use of specialised ontologies.

Results

1/ PSP performs well with Pathway-Derived Subnets (PDSs). Comparing the performance of PDSs derived from various pathway databases, we find that an integrative approach is best for optimising analytical resolution. Feature selection also confirms that significant PDSs are closely connected to the cancer phenotype.

2/ In liver cancer, correlation studies of significant PSP complexes and PDSs co-localised on the same pathways revealed an interesting relationship between the purine metabolism pathway and two other complexes involved in DNA repair. Our work suggests progression to poor stage requires additional mutations that disrupt DNA repair enzymes.

3/ False positive analysis reveals that PSP, applied on both complexes and PDSs, is powerful and precise.

4/ Via an expert-curated lipid ontology, we uncovered several interesting lipid-associated complexes that could be associated with cancer progression. Of particular interest is the HMGB1-HMGB2-HSC70-ERP60-GAPDH complex which is also involved in DNA repair. We also demonstrated generalisability of PSP using a non-small-cell lung carcinoma data set.

Conclusions

PSP is a powerful and precise technique, capable of identifying biologically coherent features. It works with biological complexes, network-predicted clusters as well as PDSs. Here, an instance of the interplay between significant PDSs and complexes, possibly significantly involved in liver cancer progression but not well understood as yet, is demonstrated. Also demonstrated is the enhancement of PSP’s analytical resolution using specialised ontologies.
Role of N-terminal protein formylation in central metabolic processes in Staphylococcus aureus
Authors: Mader Diana , Liebeke Manuel , Winstel Volker , Methling Karen , Leibig Martina , Götz Friedrich , Lalk Michael , Peschel Andreas
Published: January 2013

Background

Bacterial protein biosynthesis usually depends on a formylated methionyl start tRNA but Staphylococcus aureus is viable in the absence of Fmt, the tRNAMet formyl transferase. fmt mutants exhibit reduced growth rates indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation.

Results

In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the exometabolome of an S. aureus fmt mutant was compared with that of the parental strain and the transcription of corresponding enzymes was analyzed to identify possible regulatory changes. The mutant consumed glucose and other carbon sources slower than the wild type. While the turnover of several metabolites remained unaltered fmt inactivation led to increases pyruvate release and, concomitantly, reduced pyruvate dehydrogenase activity. In parallel, the release of the pyruvate-derived metabolites lactate, acetoin, and alanine was reduced. The anaerobic degradation of arginine was also reduced in the fmt mutant compared to the wild-type strain. Moreover, the lack of formylated proteins caused increased susceptibility to the antibiotics trimethoprim and sulamethoxazole suggesting that folic acid-dependant pathways were perturbed in the mutant.

Conclusions

These data indicate that formylated proteins are crucial for specific bacterial metabolic processes and they may help to understand why it has remained important during bacterial evolution to initiate protein biosynthesis with a formylated tRNAMet.
Evaluation of intravenous voriconazole in patients with compromised renal function
Authors: Lilly Craig M , Welch Verna L , Mayer Thomas , Ranauro Paul , Meisner Joanne , Luke David R
Published: January 2013

Background

Incorporation of the solubilizing excipient, sulfobutylether-β-cyclodextrin (SBECD), in the intravenous (IV) formulation of voriconazole has resulted in the recommendation that this formulation be used with caution in patients with creatinine clearances (Clcr) < 50 mL/min. This study evaluated the safety of IV voriconazole compared with two other IV antifungals not containing SBECD in patients with compromised renal function.

Methods

A total of 128 patients aged 11–93 years who had a baseline Clcr < 50 mL/min between January 1, 2007 and December 31, 2010 were identified from a database of a university-affiliated inpatient healthcare system; of these, 55 patients received caspofungin, 54 patients received fluconazole, and 19 patients received voriconazole. Changes in serum creatinine (Scr) and Clcr levels while on therapy were compared with baseline values and between groups.

Results

The groups had similar characteristics apart from the larger proportion of females that received fluconazole. Baseline Scr was higher in those receiving caspofungin, but maximal increases of Scr and decreases in Clcr were greatest for the fluconazole group. Acute kidney injury (AKI), assessed by RIFLE criteria, was more frequent in the fluconazole vs. the caspofungin group (p < 0.01); incidence of AKI in the voriconazole group was not significantly different than found in the other two groups. The infecting organism was a predictor of AKI and formulation with SBECD was not.

Conclusions

Treatment of fungal infections in patients with compromised renal function with an SBECD-containing antifungal agent was not associated with AKI in clinical practice. Since the infecting organism was associated with AKI, decision on which antifungal to use should be determined by susceptibilities to the organism and not the incorporation of SBECD in the IV formulation.
Debate around infection-dependent hemophagocytic syndrome in paediatrics
Authors: Ansuini Valentina , Rigante Donato , Esposito Susanna
Published: January 2013

Background

Hemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. The most consistent association is with viral infections but, as it is still debated whether any micro-organisms are involved in its pathogenesis, we critically appraised the literature concerning HPS and its relationship with infections.

Discussion

Infection-dependent HPS has been widely observed, but there are no data concerning its incidence in children. A better understanding of the pathophysiology of HPS may clarify the interactions between the immune system and the variously implicated potential infectious agents. Epstein-Barr virus (EBV) infection has been prominently associated with HPS, with clonal proliferation and the hyperactivation of EBV-infected T cells. However, a number of other viral, bacterial, fungal, and parasitic infections have been reported in association with HPS. In the case of low-risk HPS, corticosteroids and/or intravenous immunoglobulin or cyclosporine A may be sufficient to control the biological process, but etoposide is recommended as a means of reversing infection-dependent lymphohistiocytic dysregulation in high-risk cases.

HPS is a potential complication of various infections. A polymerase chain reaction search for infectious agents including EBV, cytomegalovirus andLeishmaniais recommended in clinical settings characterised by non-remitting fever, organomegaly, cytopenia and hyperferritinemia.
Rifampin-associated tubulointersititial nephritis and Fanconi syndrome presenting as hypokalemic paralysis
Authors: Min Hong Ki , Kim Eun Oh , Lee Sang Ju , Chang Yoon Kyung , Suh Kwang Sun , Yang Chul Woo , Kim Suk Young , Hwang Hyeon Seok
Published: January 2013

Background

Rifampin is one of the most important drugs in first-line therapies for tuberculosis. The renal toxicity of rifampin has been reported sporadically and acute tubulointerstitial nephritis (ATIN) is a frequent histological finding. We describe for the first time a case of ATIN and Fanconi syndrome presenting as hypokalemic paralysis, associated with the use of rifampin.

Case presentation

A 42-year-old man was admitted with sudden-onset lower extremity paralysis and mild renal insufficiency. He had been treated for pulmonary tuberculosis with isoniazid, rifampin, and ethambutol for 2 months. Laboratory tests revealed proteinuria, profound hypokalemia, hyperchloremic metabolic acidosis with a normal anion gap, positive urine anion gap, hypophosphatemia with hyperphosphaturia, hypouricemia with hyperuricosuria, glycosuria with normal serum glucose level, generalized aminoaciduria, and β2-microglobulinuria. A kidney biopsy revealed findings typical of ATIN and focal granular deposits of immunoglubulin A and complement 3 in the glomeruli and tubules. Electron microscopy showed epithelial foot process effacement and electron-dense deposits in the subendothelial and mesangial spaces. Cessation of rifampin resolved the patient’s clinical presentation of Fanconi syndrome, and improved his renal function and proteinuria.

Conclusion

This case demonstrates that rifampin therapy can be associated with Fanconi syndrome presenting as hypokalemic paralysis, which is a manifestation of ATIN. Kidney function and the markers of proximal tubular injury should be carefully monitored in patients receiving rifampin.
Mineral metabolism and outcomes in chronic kidney disease stage 2–4 patients
Authors: Chartsrisak Kamonwan , Vipattawat Kotcharat , Assanatham Montira , Nongnuch Arkom , Ingsathit Atiporn , Domrongkitchaiporn Somnuek , Sumethkul Vasant , Distha-Banchong Sinee
Published: January 2013

Background

Marked hyperphosphatemia, hyperparathyroidism and 25-hydroxyvitamin D deficiency are associated with mortality in dialysis patients. Such data in chronic kidney disease stage 2–4 population are limited. It has been suggested that high-normal serum phosphate predicts worse renal and patient outcomes. The data regarding parathyroid hormone and outcomes in this population is limited. The present study examined mineral metabolism and its association with the development of end-stage renal disease and mortality in stage 2–4 chronic kidney disease patients.

Methods

This is a prospective cohort study that included 466 non-dialysis chronic kidney disease stage 2–4 patients. Mineral parameters were obtained at the time of enrollment and the patients were followed prospectively for 25 (1–44) months or until they reached the endpoints of end-stage renal disease or mortality.

Results

Hyperparathyroidism and 25-hydroxyvitamin D deficiency began to occur in the early stages of chronic kidney disease, whereas significant hyperphosphatemia only developed in the later stages. High-normal and mildly elevated serum phosphate (>4.2 mg/dL) predicted the composite outcome of end-stage renal disease or mortality after adjustments for cardiovascular risk factors, chronic kidney disease stage and other mineral parameters. Parathyroid hormone levels above the upper limit of normal (>65 pg/mL) predicted the future development of end-stage renal disease and the composite outcome of end-stage renal disease or mortality after adjustments. 25-hydroxyvitamin D deficiency (<15 ng/mL) was also associated with worse outcomes.

Conclusions

In chronic kidney disease, hyperparathyroidism developed prior to significant hyperphosphatemia confirming the presence phosphate retention early in the course of chronic kidney disease. High-normal serum phosphate and mildly elevated parathyroid hormone levels predicted worse renal and patient outcomes. This data emphasizes the need for early intervention in the care of chronic kidney disease stage 2–4 patients.
The risk of upper gastrointestinal bleeding in patients treated with hemodialysis: a population-based cohort study
Authors: Kuo Chien-Chun , Kuo Hsin-Wei , Lee I-Ming , Lee Chien-Te , Yang Chun-Yuh
Published: January 2013

Background

There are no prior studies that have estimated the risk of upper gastrointestinal bleeding (UGIB) among the dialysis population relative to the general population. The aim of this study was to examine the risk of UGIB among end-stage renal disease (ESRD) patients during a 6-year period following their initiation of hemodialysis (HD) therapy in Taiwan- a country with the highest incidence of ESRD in the world, using general population as an external comparison group.

Methods

Data were obtained from the Taiwan National health Insurance Research Database. In total, 796 patients who were beginning HD between 1999 and 2003 were recruited as the study cohort and 3,184 patients matched for age and sex were included as comparison cohort. Multivariate Cox proportional hazard regression models were used to adjust for confounding and to compare the 6-year UGIB-free survival rate between these two cohorts.

Results

The incidence rate of UGIB (42.01 per 1000 person-year) was significantly higher in the HD cohort than in the control cohort (27.39 per 1000 person-years). After adjusting for potential confounders, the adjusted hazard ratios for UGIB during the 6-year follow-up periods for HD patients was 1.27 (95% CI=1.03-1.57) compared to patients in the comparison cohort.

Conclusions

We conclude that HD patients were at an increased risk for UGIB compared with the general population.
Prevention and management of excessive gestational weight gain: a survey of overweight and obese pregnant women
Authors: Leslie W S , Gibson A , Hankey C R
Published: January 2013

Background

Excessive gestational weight gain is associated with adverse infant, childhood and maternal outcomes and research to develop interventions to address this issue is ongoing. The views of women on gestational weight gain and the resources they would consider helpful in addressing this are however largely unknown. This survey aimed to determine the views of newly pregnant women, living in areas of social disadvantage, on 1) their current body weight and potential gestational weight gain and 2) the resources or interventions they would consider helpful in preventing excessive gestational weight gain.

Methods

A convenience sample of overweight and obese pregnant women living in Fife, UK, were invited to complete a short anonymised questionnaire at their 12 week booking visit.

Results

428 women, BMI>25 kg/m2, completed the questionnaire. Fifty-four per cent of respondents were obese (231) and 62% were living in areas of mild to moderate deprivation. Over three-quarters of participants felt dissatisfied with their current weight (81%). The majority of women (60%) expressed some concern about potential weight gain. Thirty-nine percent were unconcerned about weight gain during their pregnancy, including 34 women (19%) who reported having retained weight gained in earlier pregnancies. Amongst those concerned about weight gain advice on physical activity (41%) and access to sports/leisure facilities were favoured resources (36%). Fewer women (12%) felt that group sessions on healthy eating or attending a clinic for individualised advice (14%) would be helpful. “Getting time off work” was the most frequently cited barrier (48%) to uptake of resources other than leaflets.

Conclusions

These data suggest a lack of awareness amongst overweight and obese women regarding excessive gestational weight gain. Monitoring of gestational weight gain, and approaches for its management, should be formally integrated into routine antenatal care. Barriers to the uptake of resources to address weight gain are numerous and must be considered in the design of future interventions and services.
Reproductive patterns among twins - a Swedish register study of men and women born 1973-1983
Authors: Bladh Marie , Josefsson Ann , Carstensen John , Finnström Orvar , Sydsjö Gunilla
Published: January 2013

Background

During the last decades there has been a steady increase of twin births. A combination of improved medical treatment of preterm and small-for-gestational age children has contributed to a higher number of surviving twins. Prematurity is known to affect reproduction in a negative way. Few studies have focused on the potential effect twinning may have on future reproduction. Thus, the aim of this study was to investigate the effect of being born a twin compared to being born a singleton have on future reproduction.

Methods

In a national population-based register study, all individuals born between 1973–1983 who were alive and living in Sweden at 13 years of age (n = 1 016 908) constituted the sample. Data on each study subject’s own birth as well as the birth of their first offspring, and parental socio-demographic factors were collected from Swedish population based registers. Hazard ratios and corresponding 95% CI was calculated using Cox proportional hazards model.

Results

Twins, both men and women, had a reduced likelihood of reproducing compared to singletons (women: HR = 0.89, 95% CI = 0.86-0.93; men: HR = 0.92, 95% CI = 0.87-0.97). This difference in birth rates can only partly be explained by diverging birth characteristics. Amongst men and women born very preterm, twins had an increased likelihood of reproducing compared to singletons (women: HR = 1.25, 95% CI = 1.02-1.62; men: HR = 1.34, 95% CI = 1.01-1.78).

Conclusions

Twins have lower reproduction rates compared to singletons, which only to a certain degree can be explained by diverging birth characteristics.
Need for insulin to control gestational diabetes is reflected in the ambulatory arterial stiffness index
Authors: Kärkkäinen Henna , Laitinen Tomi , Heiskanen Nonna , Saarelainen Heli , Valtonen Pirjo , Lyyra-Laitinen Tiina , Vanninen Esko , Heinonen Seppo
Published: January 2013

Background

The aim was to evaluate the metabolic profile in conjunction with vascular function using the ambulatory arterial stiffness index (AASI) in women with uncomplicated pregnancies and in women with gestational diabetes mellitus (GDM).

Methods

Plasma glucose, lipids, HOMA –IR (homeostasis model assessment of insulin resistance) and AASI, as obtained from 24-hour ambulatory blood pressure monitoring in third trimester pregnancy and at three months postpartum, were measured in three groups of women: controls (N = 32), women with GDM on diet (N = 42) and women with GDM requiring insulin treatment (N = 10).

Results

Women with GDM had poorer glycemic control and higher HOMA-IR during and after pregnancy and their total and LDL (low density lipoprotein) cholesterol levels were significantly higher after pregnancy than in the controls. After delivery, there was an improvement in AASI from 0.26 ± 0.10 to 0.17 ± 0.09 (P = 0.002) in women with GDM on diet, but not in women with GDM receiving insulin whose AASI tended to worsen after delivery from 0.30 ± 0.23 to 0.33 ± 0.09 (NS), then being significantly higher than in the other groups (P = 0.001-0.047).

Conclusions

Women with GDM had more unfavorable lipid profile and higher blood glucose values at three months after delivery, the metabolic profile being worst in women requiring insulin. Interestingly, the metabolic disturbances at three months postpartum were accompanied by a tendency towards arterial stiffness to increase in women requiring insulin.