bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure-based approach to rationally design a chimeric protein for an effective vaccine against Group B
Streptococcus
infections
Authors: Nuccitelli Annalisa , Cozzi Roberta , Gourlay Louise J. , Donnarumma Danilo , Necchi Francesca , Norais Nathalie , Telford John L. , Rappuoli Rino , Bolognesi Martino , Maione Domenico , Grandi Guido , Rinaudo C. Daniela
Published: May 2011

Structural vaccinology is an emerging strategy for the rational design of vaccine candidates. We successfully applied structural vaccinology to design a fully synthetic protein with multivalent protection activity. In Group B
Streptococcus
, cell-surface pili have aroused great interest because of their direct roles in virulence and importance as protective antigens. The backbone subunit of type 2a pilus (BP-2a) is present in six immunogenically different but structurally similar variants. We determined the 3D structure of one of the variants, and experimentally demonstrated that protective antibodies specifically recognize one of the four domains that comprise the protein. We therefore constructed a synthetic protein constituted by the protective domain of each one of the six variants and showed that the chimeric protein protects mice against the challenge with all of the type 2a pilus-carrying strains. This work demonstrates the power of structural vaccinology and will facilitate the development of an optimized, broadly protective pilus-based vaccine against Group B
Streptococcus
by combining the uniquely generated chimeric protein with protective pilin subunits from two other previously identified pilus types. In addition, this work describes a template procedure that can be followed to develop vaccines against other bacterial pathogens.
Variation of the magnetic properties of Ni2MnGa Heusler alloy upon tetragonalization: a first-principles study
Authors: Galanakis I , Şaşıoğlu E
Published: May 2011

We study the influence of the tetragonalization occurring during the martensitic phase transition on the exchange interactions in Ni2MnGa Heusler alloy using first-principles calculations in conjunction with the frozen-magnon approximation. We show that the tetragonalization alters only the exchange constants characterizing the Mn–Mn interactions. Calculated Curie temperatures within the random-phase approximation are found to agree with experimental data. Moreover, we study the temperature dependence of the magnetization and the small deviation from the experimental data exactly at the temperature of the phase transition is discussed. Obtained results agree with previous theoretical results using Liechtenstein's formula to calculate the exchange constants and the Monte Carlo simulation technique to estimate the Curie temperature.
Crossover in domain wall potential polarity as a function of anti-notch geometry
Authors: Sekhar M Chandra , Goolaup S , Purnama I , Lew W S
Published: May 2011

We have carried out a systematic study on domain wall (DW) pinning at an anti-notch in a Ni80Fe20 nanowire. Micromagnetic studies reveal that the potential polarity experienced by the DW at the anti-notch is a function of both DW chirality and anti-notch geometry. A transition in the potential disruption experienced by the DW is observed when the anti-notch height-to-width ratio (H
AN/W
AN) is 2. This transition is due to the relative orientation of the spins in the anti-notch with respect to the transverse component of the DW. When the anti-notch acts as a potential barrier, the DW undergoes damped oscillations prior to coming to an equilibrium position. The equilibrium position is a strong function of the anti-notch dimensions when the H
AN/W
AN ratio <2 and is constant for H
AN/W
AN ⩾ 2. The effect of the relative orientation between the spins in the anti-notch and the transverse component of the DW on the shape of the potential is discussed.
Effect of Al gate on the electrical behaviour of Al-doped Ta2O5 stacks
Authors: Skeparovski A , Novkovski N , Atanassova E , Paskaleva A , Lazarov V K
Published: May 2011

The electrical behaviour of Al-doped Ta2O5 films on nitrided silicon and implemented in Al-gated MIS capacitors has been studied. The dopant was introduced into the Ta2O5 through its surface by deposing a thin Al layer on the top of Ta2O5 followed by an annealing process. The HRTEM images reveal that the initial double-layer structure of the stacks composed of doped Ta2O5 and interfacial SiON layer undergoes changes during the formation of the Al gate and transforms into a three-layer structure with an additional layer between the Al electrode and the doped Ta2O5. This layer, being a result of reaction between the Al gate and the Al-doped Ta2O5, affects the overall electrical properties of the stacks. Strong charge trapping/detrapping processes have been established in the vicinity of the doped Ta2O5/SiON interface resulting in a large C–V hysteresis effect. The charge trapping also influences the current conduction in the layers keeping the current density level rather low even at high electric fields (J < 10−6 A cm−2 at 7 MV cm−1). By employing a three-layer model of the stack, the permittivity of both, the Al-doped Ta2O5 and the additional layer, has been estimated and the corresponding conduction mechanisms identified.
Low-temperature synthesis of microcrystalline 3C-SiC film by high-pressure hydrogen-plasma-enhanced chemical transport
Authors: Ohmi Hiromasa , Hori Takahiro , Mori Tetsuya , Kakiuchi Hiroaki , Yasutake Kiyoshi
Published: May 2011

The synthesis of microcrystalline 3C-SiC films on glass substrates at relatively low temperatures (⩽600 °C) by the plasma-enhanced chemical transport method was carried out using a high-pressure pure hydrogen glow discharge. This method used the chemical erosion products of graphite and silicon in the hydrogen plasma as the deposition source. The temperature dependence of the etching rate of graphite and the generated volatile C-species were investigated by exposing sintered graphite to a pure hydrogen plasma at 100 Torr. Infrared absorption gas analysis indicated that the C-related film precursor generated from the graphite was mainly CH4. The etch rate of graphite reached a maximum at a sample temperature of 200 °C. The deposition rate of the SiC film prepared at a hydrogen pressure of 200 Torr increased monotonically from 14 to 29 nm min−1 with an increase in substrate temperature (T
sub) from 100 to 600 °C. The Si/C composition ratio in the films was independent of T
sub and all the film compositions were nearly stoichiometric. The prepared SiC films were microcrystalline 3C-SiC. Raman spectroscopy indicated that the film quality significantly depends on T
sub. The electrical conductivity of the films at room temperature was found to increase exponentially from 3 × 10−4 to 1.7 S cm−1 with T
sub.
Stably inverse shadowable transitive sets and dominated splitting
Authors: Lee Keonhee , Lee Manseob
Published: May 2011

Let

f
f

be a diffeomorphism of a closed

n
n

-dimensional smooth manifold. In this paper, we show that if

f
f

has the

C
1

C^1

-stably inverse shadowing property on a transitive set, then it admits a dominated splitting.
A uniqueness theorem for meromorphic mappings with two families of hyperplanes
Authors: Dethloff Gerd , Duc Quang Sy , Tan Tran
Published: May 2011

In this paper, we extend the uniqueness theorem for meromorphic mappings to the case where the family of hyperplanes depends on the meromorphic mapping and where the meromorphic mappings may be degenerate.
Mms1 and Mms22 stabilize the replisome during replication stress
Authors: Vaisica Jessica A. , Baryshnikova Anastasija , Costanzo Michael , Boone Charles , Brown Grant W.
Published: May 2011

Mms1 and Mms22 form a Cul4Ddb1-like E3 ubiquitin ligase with the cullin Rtt101. In this complex, Rtt101 is bound to the substrate-specific adaptor Mms22 through a linker protein, Mms1. Although the Rtt101Mms1/Mms22ubiquitin ligase is important in promoting replication through damaged templates, how it does so has yet to be determined. Here we show that mms1Δ and mms22Δ cells fail to properly regulate DNA replication fork progression when replication stress is present and are defective in recovery from replication fork stress. Consistent with a role in promoting DNA replication, we find that Mms1 is enriched at sites where replication forks have stalled and that this localization requires the known binding partners of Mms1—Rtt101 and Mms22. Mms1 and Mms22 stabilize the replisome during replication stress, as binding of the fork-pausing complex components Mrc1 and Csm3, and DNA polymerase ε, at stalled replication forks is decreased in mms1Δ and mms22Δ. Taken together, these data indicate that Mms1 and Mms22 are important for maintaining the integrity of the replisome when DNA replication forks are slowed by hydroxyurea and thereby promote efficient recovery from replication stress.
CDK promotes interactions of Sld3 and Drc1 with Cut5 for initiation of DNA replication in fission yeast
Authors: Fukuura Masayoshi , Nagao Koji , Obuse Chikashi , Takahashi Tatsuro S. , Nakagawa Takuro , Masukata Hisao
Published: May 2011

Cyclin-dependent kinase (CDK) plays essential roles in the initiation of DNA replication in eukaryotes. Although interactions of CDK-phosphorylated Sld2/Drc1 and Sld3 with Dpb11 have been shown to be essential in budding yeast, it is not known whether the mechanism is conserved. In this study, we investigated how CDK promotes the assembly of replication proteins onto replication origins in fission yeast. Phosphorylation of Sld3 was found to be dependent on CDK in S phase. Alanine substitutions at CDK sites decreased the interaction with Cut5/Dpb11 at the N-terminal BRCT motifs and decreased the loading of Cut5 onto replication origins. This defect was suppressed by overexpression of drc1+. Phosphorylation of a conserved CDK site, Thr-111, in Drc1 was critical for interaction with Cut5 at the C-terminal BRCT motifs and was required for loading of Cut5. In a yeast three-hybrid assay, Sld3, Cut5, and Drc1 were found to form a ternary complex dependent on the CDK sites of Sld3 and Drc1, and Drc1–Cut5 binding enhanced the Sld3–Cut5 interaction. These results show that the mechanism of CDK-dependent loading of Cut5 is conserved in fission yeast in a manner similar to that elucidated in budding yeast.
The eisosome core is composed of BAR domain proteins
Authors: Olivera-Couto Agustina , Graña Martin , Harispe Laura , Aguilar Pablo S.
Published: May 2011

Eisosomes define sites of plasma membrane organization. In Saccharomyces cerevisiae, eisosomes delimit furrow-like plasma membrane invaginations that concentrate sterols, transporters, and signaling molecules. Eisosomes are static macromolecular assemblies composed of cytoplasmic proteins, most of which have no known function. In this study, we used a bioinformatics approach to analyze a set of 20 eisosome proteins. We found that the core components of eisosomes, paralogue proteins Pil1 and Lsp1, are distant homologues of membrane-sculpting Bin/amphiphysin/Rvs (BAR) proteins. Consistent with this finding, purified recombinant Pil1 and Lsp1 tubulated liposomes and formed tubules when the proteins were overexpressed in mammalian cells. Structural homology modeling and site-directed mutagenesis indicate that Pil1 positively charged surface patches are needed for membrane binding and liposome tubulation. Pil1 BAR domain mutants were defective in both eisosome assembly and plasma membrane domain organization. In addition, we found that eisosome-associated proteins Slm1 and Slm2 have F-BAR domains and that these domains are needed for targeting to furrow-like plasma membrane invaginations. Our results support a model in which BAR domain protein–mediated membrane bending leads to clustering of lipids and proteins within the plasma membrane.
Targeted inactivation of integrin-linked kinase in hair follicle stem cells reveals an important modulatory role in skin repair after injury
Authors: Nakrieko Kerry-Ann , Rudkouskaya Alena , Irvine Timothy S. , D'souza Sudhir J. A. , Dagnino Lina
Published: May 2011

Integrin-linked kinase (ILK) is key for normal epidermal morphogenesis, but little is known about its role in hair follicle stem cells and epidermal regeneration. Hair follicle stem cells are important contributors to newly formed epidermis following injury. We inactivated the Ilk gene in the keratin 15–expressing stem cell population of the mouse hair follicle bulge. Loss of ILK expression in these cells resulted in impaired cutaneous wound healing, with substantially decreased wound closure rates. ILK-deficient stem cells produced very few descendants that moved toward the epidermal surface and into the advancing epithelium that covers the wound. Furthermore, those few mutant cells that homed in the regenerated epidermis exhibited a reduced residence time. Paradoxically, ILK-deficient bulge stem cells responded to anagen growth signals and contributed to newly regenerated hair follicles during this phase of hair follicle growth. Thus ILK plays an important modulatory role in the normal contribution of hair follicle stem cell progeny to the regenerating epidermis following injury.
CDK-dependent phosphorylation of Mob2 is essential for hyphal development inCandida albicans
Authors: Gutiérrez-Escribano Pilar , González-Novo Alberto , Suárez M. Belén , Li Chang-Run , Wang Yue , de Aldana Carlos R. Vázquez , Correa-Bordes Jaime
Published: May 2011

Nuclear Dbf2-related (NDR) protein kinases are essential components of regulatory pathways involved in cell morphogenesis, cell cycle control, and viability in eukaryotic cells. For their activity and function, these kinases require interaction with Mob proteins. However, little is known about how the Mob proteins are regulated. In Candida albicans, the cyclin-dependent kinase (CDK) Cdc28 and the NDR kinase Cbk1 are required for hyphal growth. Here we demonstrate that Mob2, the Cbk1 activator, undergoes a Cdc28-dependent differential phosphorylation on hyphal induction. Mutations in the four CDK consensus sites in Mob2 to Ala significantly impaired hyphal development. The mutant cells produced short hyphae with enlarged tips that displayed an illicit activation of cell separation. We also show that Cdc28 phosphorylation of Mob2 is essential for the maintenance of polarisome components at hyphal tips but not at bud tips during yeast growth. Thus we have found a novel signaling pathway by which Cdc28 controls Cbk1 through the regulatory phosphorylation of Mob2, which is crucial for normal hyphal development.
Fast accessibility-based prediction of RNA–RNA interactions
Authors: Tafer Hakim , Amman Fabian , Eggenhofer Florian , Stadler Peter F. , Hofacker Ivo L.
Published: May 2011

Motivation: Currently, the best RNA–RNA interaction prediction tools are based on approaches that consider both the inter- and intramolecular interactions of hybridizing RNAs. While accurate, these methods are too slow and memory-hungry to be employed in genome-wide RNA target scans. Alternative methods neglecting intramolecular structures are fast enough for genome-wide applications, but are too inaccurate to be of much practical use.

Results: A new approach for RNA–RNA interaction was developed, with a prediction accuracy that is similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup. This is achieved by using a combination of precomputed accessibility profiles with an approximate energy model. This approach is implemented in the new version of RNAplex. The software also provides a variant using multiple sequences alignments as input, resulting in a further increase in specificity.

Availability:  RNAplex is available at www.bioinf.uni-leipzig.de/Software/RNAplex.

Contact:  htafer@bioinf.uni-leipzig.de; ivo@tbi.univie.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Evaluation of drug–human serum albumin binding interactions with support vector machine aided online automated docking
Authors: Zsila Ferenc , Bikadi Zsolt , Malik David , Hari Peter , Pechan Imre , Berces Attila , Hazai Eszter
Published: May 2011

Motivation: Human serum albumin (HSA), the most abundant plasma protein is well known for its extraordinary binding capacity for both endogenous and exogenous substances, including a wide range of drugs. Interaction with the two principal binding sites of HSA in subdomain IIA (site 1) and in subdomain IIIA (site 2) controls the free, active concentration of a drug, provides a reservoir for a long duration of action and ultimately affects the ADME (absorption, distribution, metabolism, and excretion) profile. Due to the continuous demand to investigate HSA binding properties of novel drugs, drug candidates and drug-like compounds, a support vector machine (SVM) model was developed that efficiently predicts albumin binding. Our SVM model was integrated to a free, web-based prediction platform (http://albumin.althotas.com). Automated molecular docking calculations for prediction of complex geometry are also integrated into the web service. The platform enables the users (i) to predict if albumin binds the query ligand, (ii) to determine the probable ligand binding site (site 1 or site 2), (iii) to select the albumin X-ray structure which is complexed with the most similar ligand and (iv) to calculate complex geometry using molecular docking calculations. Our SVM model and the potential offered by the combined use of in silico calculation methods and experimental binding data is illustrated.

Contact:  eszter.hazai@virtuadrug.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA
Authors: Troshin Peter V. , Procter James B. , Barton Geoffrey J.
Published: May 2011

Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts.

Availability and Implementation: JABAWS is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws.

Contact:  g.j.barton@dundee.ac.uk
An ensemble biclustering approach for querying gene expression compendia with experimental lists
Authors: De Smet Riet , Marchal Kathleen
Published: May 2011

Motivation: Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query. This approach, however, leaves the user with a tedious post-processing of partially redundant biclustering results. The fact that for each query-gene multiple parameter settings need to be tested in order to detect the ‘most optimal bicluster size’ adds to the redundancy problem.

Results: To aid with this post-processing, we developed an ensemble approach to be used in combination with query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible parameter settings are merged in a statistically robust way. Clustering of this matrix results in distinct, non-redundant consensus biclusters that maximally reflect the information contained within the original query-based biclustering results. The usefulness of the developed approach is illustrated on a biological case study in Escherichia coli.

Availability and implementation: Compiled Matlab code is available from http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_DeSmet_2011/.

Contact:  kathleen.marchal@biw.kuleuven.be

Supplementary information:Supplementary data are available at Bioinformatics online.
The helper component-proteinase of the Zucchini yellow mosaic virus inhibits the Hua Enhancer 1 methyltransferase activity in vitro
Authors: Jamous Rana M. , Boonrod Kajohn , Fuellgrabe Marc W. , Ali-Shtayeh Mohammed S. , Krczal Gabi , Wassenegger Michael
Published: May 2011

The helper component-proteinase (HC-Pro) is a multifunctional protein found among potyviruses. With respect to its silencing suppressor function, small RNA binding appears to be the major activity of HC-Pro. HC-Pro could also exhibit other suppressor activities. HC-Pro may inhibit the Hua Enhancer 1 (HEN1) activity. There is indirect evidence showing that either transient or stable expression of HC-Pro in plants results in an increase of non-methylated small RNAs. Here, we demonstrated that recombinant Zucchini yellow mosaic virus (ZYMV) HC-Pro inhibited the methyltransferase activity of HEN1 in vitro. Moreover, we found that the HC-ProFINK mutant, which has lost small RNA-binding activity, inhibited HEN1 activity, while the truncated proteins and total soluble bacterial proteins did not. Using the ELISA-binding assay, we provided evidence that the HC-ProFRNK wild-type and HC-ProFINK both bound to HEN1, with HC-ProFRNK binding stronger than HC-ProFINK. Motif mapping analysis revealed that the amino acids located between positions 139 and 320 of ZYMV HC-Pro were associated with HEN1 interaction.
The NS1 protein of influenza A virus suppresses interferon-regulated activation of antigen-presentation and immune-proteasome pathways
Authors: Tisoncik Jennifer R. , Billharz Rosalind , Burmakina Svetlana , Belisle Sarah E. , Proll Sean C. , Korth Marcus J. , García-Sastre Adolfo , Katze Michael G.
Published: May 2011

The NS1 protein of influenza virus counters host antiviral defences primarily by antagonizing the type I interferon (IFN) response. Both the N-terminal dsRNA-binding domain and the C-terminal effector domain are required for optimal suppression of host responses during infection. To better understand the regulatory role of the NS1 effector domain, we used an NS1-truncated mutant virus derived from human H1N1 influenza isolate A/Texas/36/91 (Tx/91) and assessed global transcriptional profiles from two independent human lung cell-culture models. Relative to the wild-type Tx/91-induced gene expression, the NS1 mutant virus induced enhanced expression of innate immune genes, specifically NF-κB signalling-pathway genes and IFN-α and -β target genes. We queried an experimentally derived IFN gene set to gauge the proportion of IFN-responsive genes that are suppressed specifically by NS1. We show that the C-terminally truncated NS1 mutant virus is less efficient at suppressing IFN-regulated gene expression associated with activation of antigen-presentation and immune-proteasome pathways. This is the first report integrating genomic analysis from two independent human culture systems, including primary lung cells, using genetically similar H1N1 influenza viruses that differ only in the length of the NS1 protein.
Relation of genetic phylogeny and geographical distance of tick-borne encephalitis virus in central Europe
Authors: Weidmann M. , Růžek D. , Křivanec K. , Zöller G. , Essbauer S. , Pfeffer M. , Zanotto P. M. de A. , Hufert F. T. , Dobler G.
Published: May 2011

Tick-borne encephalitis virus (TBEV) is the most important arboviral agent causing disease of the central nervous system in central Europe. In this study, 61 TBEV E gene sequences derived from 48 isolates from the Czech Republic, and four isolates and nine TBEV strains detected in ticks from Germany, covering more than half a century from 1954 to 2009, were sequenced and subjected to phylogenetic and Bayesian phylodynamic analysis to determine the phylogeography of TBEV in central Europe. The general Eurasian continental east-to-west pattern of the spread of TBEV was confirmed at the regional level but is interlaced with spreading that arises because of local geography and anthropogenic influence. This spread is reflected by the disease pattern in the Czech Republic that has been observed since 1991. The overall evolutionary rate was estimated to be approximately 8×10−4substitutions per nucleotide per year. The analysis of the TBEV E genes of 11 strains isolated at one natural focus in Žďár Kaplice proved for the first time that TBEV is indeed subject to local evolution.
Modulation of hepatitis C virus replication by iron and hepcidin in Huh7 hepatocytes
Authors: Bartolomei Giody , Cevik Recep Emrah , Marcello Alessandro
Published: May 2011

Several clinical observations point to an intricate crosstalk between iron (Fe) metabolism and chronic hepatitis C virus (HCV) infection. In this study, we wanted to investigate the molecular control that Fe levels exert on HCV replication at the hepatocyte level. In keeping with previous observations we confirmed that supra-physiological intracellular Fe induced by haemin treatment down-modulated HCV replication from subgenomic replicons. We also found that RNAi-mediated knockdown of the key Fe modulator hepcidin increased intracellular ferritin and inhibited HCV replication. Conversely, HCV replication did not modulate ferritin content in hepatocytes. Finally, we demonstrated that hepcidin is modulated at the mRNA level by alpha interferon through STAT3. We propose that in Huh7 cells hepcidin modulation leads to an unfavourable intracellular environment for HCV replication. These data may therefore contribute to a better understanding of the complex interplay between HCV and cellular physiology during infection.
Identification of promiscuous HLA‐DR‐restricted CD4+ T‐cell epitopes on the cancer‐testis antigen HCA587
Authors: Wen Weigang , Zhang Lijie , Peng Jirun , Chen Juanjuan , Hao Jiaqing , Li Xiaofeng , Qian Xiaoping , Zeng Pumei , Zhang Yu , Yin Yanhui
Published: May 2011

The cancer testis antigen HCA587 is an attractive candidate for T cell‐based immunotherapy because it is overexpressed in a wide spectrum of malignant tumors but not normal tissues, except testis. Several CTL epitopes derived from HCA587 have been described. Our aim was to identify helper T lymphocyte epitopes of HCA587 for the optimization of T cell‐based immunotherapies against HCA587‐expressing tumors. Candidate helper T lymphocyte epitopes for HCA587 were predicted using the SYFPEITHI algorithm and were tested for their ability to induce helper T lymphocyte responses by in vitro peptide vaccination of CD4+ T lymphocytes from healthy individuals and hepatocellular carcinoma patients. Four CD4+ T‐cell epitopes for HCA587 (p43–57, p145–159, p186–200 and p249–263) were identified. Among them, the p43–57 epitope was shown to be naturally processed and presented by HCA587‐expressing tumor cells as well as autologous dendritic cells pulsed with whole‐protein HCA587. Notably, this epitope behaved as a promiscuous T‐cell epitope as it stimulated T cells in the context of more than one HLA class II allele. Thus, p43–57 is the first HCA587‐derived major histocompatibility complex class II‐restricted epitope to fulfil all prerequisites for use as a peptide vaccine in patients with HCA587‐expressing tumors. (Cancer Sci 2011; 102: 1455–1461)
Carbon storage, structure and composition of miombo woodlands in Tanzania’s Eastern Arc Mountains
Authors: Shirima Deo D. , Munishi Pantaleo K. T. , Lewis Simon L. , Burgess Neil D. , Marshall Andrew R. , Balmford Andrew , Swetnam Ruth D. , Zahabu Eliakimu Mnkondo
Published: May 2011

We determine the aboveground biomass and carbon storage (ABGC) of trees and the herbaceous layer in miombo woodland in the Eastern Arc Mountains (EAM) of Tanzania. In four 1‐ha sample plots in Nyanganje and Kitonga Forests, we measured all trees ≥10 cm diameter alongside height and wood mass density. The plots contained an average of 20 tree species ha−1 (range 11–29) and 344 stems ha−1 (range 281–382) with Shannon diversity values of 1.05 and 1.25, respectively. We weighted nine previously published woody savannah allometric models based on whether: (i) the model was derived from the same geographical region; (ii) the model included tree height/wood mass density in addition to stem diameter; and (iii) sample size was used to fit the model. The weighted mean ABGC storage from the nine models range from 13.5 ± 2 to 29.8 ± 5 Mg ha−1. Measured ABGC storage in the herbaceous layer, using the wet combustion method, adds 0.55 ± 0.02 Mg C ha−1. Estimates suggest that EAM miombo woodlands store a range of 13–30 Mg ha−1 of carbon. Although the estimates suggest that miombo woodlands store significant quantities of carbon, caution is required as this is the first estimate based on in situ data.
Paracetamol prescribing in primary care: too little and too much?
Authors: Kazouini Ammar , Mohammed Baba S. , Simpson Colin R. , Helms Peter J. , McLay James S.
Published: May 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Paracetamol is the most frequently prescribed analgesic and antipyretic in children.

• The adherence to paracetamol dosage recommendation in children is poor, with paracetamol prescriptions alone accounting for 30% of off label prescribing as a result of dose violation.

WHAT THIS STUDY ADDS

• Our study has identified that approximately a fifth of paracetamol prescriptions issued to children by their GP are off label, with the most common reason being either too small or too high a dose.

• Both overdosing in young children and underdosing in older children together with their associated risks of toxicity or under treatment occur relatively frequently.

AIMS To assess the level of paracetamol off label prescribing in the community and the potential for paracetamol under or overdosing.

METHODS The Scottish Practice Team Information (PTI) database containing prescribing data for approximately 35 839 children aged (0–12 years) was analysed for paracetamol prescriptions for the year 2006. Off label prescribing was defined as prescribing outside the BNFc age and dose recommendations.

RESULTS Two thousand seven hundred and sixty‐one children aged 0–12 years were issued with 4423 prescriptions for paracetamol. (1446 males). Children 1–5 years (1329, 42.2%) accounted for 48.9% (2164) of all paracetamol prescriptions. Eighteen per cent (793) of individual prescriptions were off label and after accounting for repeat prescriptions 625 (22.75%) individuals were exposed to off label prescriptions. A further 15% (668) of prescriptions contained insufficient dosage data to determine their status, 13.3% (368) being underdosed and 4.4% (121) overdosed at least once during the study year. In total 11.3% (502) of all prescriptions were classified as underdose, 2.9% (127) as overdose and 15% (667) had no dosage instructions. Age was significantly related to non recommended dosage (χ2 test, P < 0.001). Children 1–3 months old were at highest risk of being overdosed; 27% of prescriptions recommended actual or potential overdosage and 25% (354) of children aged 6–12 years were prescribed an actual or potential underdose. Overall 57.2% of all prescriptions failed to comply with current BNFc recommendations.

CONCLUSION Paracetamol off label prescribing is common in primary care, with relatively high levels of potential overdosing in the youngest children and potential underdosing in the oldest children.
Validation of the cantharidin‐induced skin blister as an in vivo model of inflammation
Authors: Dinh Phong Huy Duc , Corraza Francis , Mestdagh Kristel , Kassengera Zaina , Doyen Virginie , Michel Olivier
Published: May 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Techniques to create aseptic inflammatory reactions provide information regarding acute inflammatory pathways and may be used to assess the anti‐inflammatory properties of novel drugs.

WHAT THIS STUDY ADDS

• In this study, we have shown that the cantharidin‐induced blister is a local inflammatory reaction, safe and well tolerated, with a good intra‐subject inter‐day reproducibility. This induced blister is inhibited by specific (anti‐tumour necrosis factor (TNF)) and non specific (corticosteroids) systemic anti‐inflammatory agents. This model could be of interest to evaluate anti‐inflammatory agents in their early phase development.

AIM Pharmacological profiling techniques, such as the cantharidin‐induced skin blister, may be used to assess the anti‐inflammatory properties of novel drugs. However, no data are available on the reproducibility of this technique or on the blocking effect of anti‐inflammatory drugs, such as anti‐TNF and corticosteroids.

METHODS A group of 30 healthy subjects were randomized into three parallel groups treated with placebo, oral methylprednisolone 20 mg day−1 for 7 days or anti‐tumour necrosis factor (TNF) (adalimumab, Humira®, Abbott) 40 mg s.c. single dose. A first blister was induced at baseline and collected, immediately before the start of treatment and a second blister was obtained 7 days after the start of treatment. The total number of cells, the cell viability and the differential cell count were evaluated by two independent observers, who were blind to treatment. anova was used to compare change from baseline among the three groups before pairwise comparisons.

RESULTS Among the placebo group, there was no significant difference in the total cell count, neutrophils, eosinophils and monocytes between day 1 and day 7. Methylprednisolone inhibited the eosinophil influx in mean % (95% CI) (−1.0 (−1.7, −0.3); P < 0.02) and absolute (P < 0.02) values, while anti‐TNF inhibited the neutrophil influx in mean % (95% CI) (−19.3 (−29.5, −9.1); P < 0.01) and absolute (P < 0.05) values.

CONCLUSIONS The cantharidin‐induced skin blister is a safe, well tolerated and reproducible procedure. Pre‐treatment with anti‐TNF or methylprednisolone inhibited the neutrophilic or eosinophilic trafficking, respectively. It could be useful in profiling anti‐inflammatory drugs regarding their effects on the cellular inflammatory response.
Long‐term safety and efficacy of deferasirox (Exjade®) for up to 5 years in transfusional iron‐overloaded patients with sickle cell disease
Authors: Vichinsky Elliott , Bernaudin Françoise , Forni Gian Luca , Gardner Renee , Hassell Kathryn , Heeney Matthew M. , Inusa Baba , Kutlar Abdullah , Lane Peter , Mathias Liesl , Porter John , Tebbi Cameron , Wilson Felicia , Griffel Louis , Deng Wei , Giannone Vanessa , Coates Thomas
Published: May 2011

To date, there is a lack of long‐term safety and efficacy data for iron chelation therapy in transfusion‐dependent patients with sickle cell disease (SCD). To evaluate the long‐term safety and efficacy of deferasirox (a once‐daily oral iron chelator), patients with SCD completing a 1‐year, Phase II, randomized, deferoxamine (DFO)‐controlled study entered a 4‐year extension, continuing to receive deferasirox, or switching from DFO to deferasirox. Average actual deferasirox dose was 19·4 ± 6·3 mg/kg per d. Of 185 patients who received at least one deferasirox dose, 33·5% completed the 5‐year study. The most common reasons for discontinuation were withdrawal of consent (23·8%), lost to follow‐up (9·2%) and adverse events (AEs) (7·6%). Investigator‐assessed drug‐related AEs were predominantly gastrointestinal [including nausea (14·6%), diarrhoea (10·8%)], mild‐to‐moderate and transient in nature. Creatinine clearance remained within the normal range throughout the study. Despite conservative initial dosing, serum ferritin levels in patients with ≥4 years deferasirox exposure significantly decreased by −591 μg/l (95% confidence intervals, −1411, −280 μg/l; P = 0·027; n = 67). Long‐term deferasirox treatment for up to 5 years had a clinically acceptable safety profile, including maintenance of normal renal function, in patients with SCD. Iron burden was substantially reduced with appropriate dosing in patients treated for at least 4 years.
Three stories about mother: narratives by women who have lived in care
Authors: Eronen Tuija
Published: May 2011

Families and social work interventions in their lives are at the core of child welfare. Child welfare practices can shape children's and parents' family memories and narratives of different family relations. However, there is little social work research so far based on the personal narratives of people who have lived in care. The study data consist of the written life stories and biographical interviews of three women who have lived part of their childhood in children's homes. In their narratives, the most central family relation was their relationship to the mother. They used different narrative strategies in their stories while trying to manage both living their childhood in care and presenting their mother morally in the same story. The central moral and emotional stance in the narratives of the mother–daughter relationship was love. Through the analysis, three moral characters of the mother were constructed. The first told about an absent mother, the second a loved and loving mother and in the third, the mother's moral character was continuously negotiated and contested. Constructing a personal story and moral character of oneself and of one's mother can be truly risky in the context of a childhood in care.
A comparison of systems and outcomes for safeguarding children in Australia and Norway
Authors: Kojan Bente Heggem , Lonne Bob
Published: May 2011

Using aggregated national data, this paper compares outcomes of Australian ‘child protection’ (CP) and Norwegian ‘child welfare services’ (CWS). We highlight each nation's context and key elements of their CP/CWS organizations, with emphasis on policy and programme orientation. System outcomes are examined along with the implications of their different approaches. The main policy focus in Australia is protection and risk, while Norway's systemic approach stresses prevention, early intervention and support. These differences influence practitioner's intervention strategies and how the needs of children and parents are met. In Norway, approximately 80% of the children in the CWS receive some sort of supportive services. In contrast, Australian services for supporting families are narrowly targeted. Both countries share the ‘best interest of the child’ principle and an increased focus on children's rights, and have experienced increased service demands and rates of children in out‐of‐home care. The paper explores the relative merits of these systems.
A prospective study of lymphocyte subpopulations and regulatory T cells in patients with chronic hepatitis C virus infection developing interferon‐induced thyroiditis
Authors: Soldevila Berta , Alonso Núria , Martínez‐Arconada Maria J. , Granada Maria L. , Baía Diogo , Vallejos Virginia , Fraile Manuel , Morillas Rosa M. , Planas Ramon , Pujol‐Borrell Ricardo , Martínez‐Cáceres Eva M. , Sanmartí Anna M.
Published: May 2011

Objective  One of the side effects of interferon‐alpha (IFN‐α) therapy is interferon‐induced thyroiditis (IIT). The role of lymphocyte subpopulations in IIT remains to be defined. The aim of this study was to assess different peripheral blood lymphocyte subpopulations, mainly CD4+CD25+CD127low/‐FoxP3+ regulatory T cells (Tregs), in patients with chronic hepatitis C virus (HCV) infection who developed IIT.

Design, patients and methods  From 120 patients with chronic HCV who started antiviral treatment, those who developed IIT (IIT patients) were selected and compared with patients who did not develop IIT (Co‐HCV). Peripheral blood mononuclear cells were obtained before treatment (BT), mid‐treatment (MT), end of treatment (ET), 24 weeks post‐treatment (PT) and at appearance of IIT (TT).

Results  Eleven patients developed IIT: three Hashimoto’s thyroiditis, one Graves’disease, one positive antithyroidal antibodies, one nonautoimmune hypothyroidism and five destructive thyroiditis. During antiviral treatment, an increase in CD8+ and in Tregs was observed in both groups. A decrease in CD3+, CD19+ and NKT lymphocyte subpopulations was also observed (all P < 0·05). However, no changes were observed in the percentage of CD4+, CD3+γδ+ and iNKT lymphocytes, Th1/Th2 balance and Bcl2 expression on B cells when BT was compared with ET. At the appearance of IIT (TT), IIT patients had a higher Th1 response (CCR5+CCR7−) (P < 0·01) and a higher Tregs percentage (P < 0·05) than Co‐HCV.

Conclusions  Our results point to the immunomodulatory effects of IFN‐α on different lymphocyte subpopulations and a possible role of Th1 response and Tregs in patients with HCV who developed IIT.
Added value of CAC in risk stratification for cardiovascular events: a systematic review
Authors: Peters Sanne A. E. , Bakker Marina , den Ruijter Hester M. , Bots Michiel L.
Published: May 2011

Eur J Clin Invest 2012; 42 (1): 110–116

Background  Identification of individuals at high risk for cardiovascular disease (CVD) is important to initiate adequate treatment and to prevent future events. Moreover, identification of low‐risk individuals is important to refrain from unneeded therapy. Current risk prediction models do not accurately predict the risk of CVD in individuals, and new markers have been sought to improve the risk assessment in individuals. Coronary artery calcification (CAC) is a marker of atherosclerosis that might improve current risk assessment when added to traditional risk factors.

Materials and methods  We performed a systematic review on PubMed search (1 February 2011) on studies reporting on the added value of CAC in risk prediction in asymptomatic individuals.

Results  Of 39 publications on CAC and CVD, nine studies were carried out in asymptomatic individuals. All studies showed an increase in area under the curve ranging from 0·05 to 0·20 when CAC was added to the risk model. Four studies reported on improvements of individuals in low‐, intermediate‐, and high‐risk categories. Addition of CAC to the risk model resulted in a net reclassification improvement ranging from 14% to 30%, meaning that CAC measurement reclassified a substantial proportion of individuals into correct risk categories. This improvement was most pronounced in those at intermediate Framingham risk.

Conclusions  The available studies consistently showed that CAC scoring improves risk stratification in CVD risk categories when added to traditional risk factors only, especially among individuals at intermediate risk for CVD. Cost‐effectiveness analyses together with a randomized controlled trial are needed before widespread introduction of CAC in clinical care.
Phospholipase Cγ2 is required for basal but not oestrogen deficiency–induced bone resorption
Authors: Kertész Zsuzsanna , Győri Dávid , Körmendi Szandra , Fekete Tünde , Kis‐Tóth Katalin , Jakus Zoltán , Schett Georg , Rajnavölgyi Éva , Dobó‐Nagy Csaba , Mócsai Attila
Published: May 2011

Eur J Clin Invest 2012; 42 (1): 49–60

Background  Osteoclasts play a critical role in bone resorption under basal conditions, but they also contribute to pathological bone loss during diseases including postmenopausal osteoporosis. Phospholipase Cγ2 (PLCγ2) is an important signalling molecule in diverse haematopoietic lineages. Here, we tested the role of PLCγ2 in basal and ovariectomy‐induced bone resorption, as well as in in vitro osteoclast cultures using PLCγ2‐deficient (PLCγ2−/−) mice.

Materials and methods  The trabecular architecture of long bone metaphyses was tested by micro‐CT and histomorphometric analyses. Postmenopausal osteoporosis was modelled by surgical ovariectomy. Osteoclast development and function, gene expression and PLCγ2 phosphorylation were tested on in vitro osteoclast and macrophage cultures.

Results  PLCγ2−/− mice had significantly higher trabecular bone mass under basal conditions than wild‐type mice. PLCγ2 was required for in vitro development and resorptive function of osteoclasts, but not for upregulation of osteoclast‐specific gene expression. PLCγ2 was phosphorylated in a Src‐family‐dependent manner upon macrophage adhesion but not upon stimulation by M‐CSF or RANKL. Surprisingly, ovariectomy‐induced bone resorption in PLCγ2−/− mice was similar to, or even more robust than, that in wild‐type animals.

Conclusions  Our results indicate that PLCγ2 participates in bone resorption under basal conditions, likely because of its role in adhesion receptor signalling during osteoclast development. In contrast, PLCγ2 does not appear to play a major role in ovariectomy‐induced bone loss. These results suggest that basal and oestrogen deficiency–induced bone resorption utilizes different signalling pathways and that PLCγ2 may not be a suitable therapeutic target in postmenopausal osteoporosis.
Improving the effectiveness of wood‐ash fertilization in mixed mountain pastures
Authors: Ferreiro A. , Merino A. , Díaz N. , Piñeiro J.
Published: May 2011

Mountain pastures can be improved by the application of wood ash, but its effectiveness as a source of N, P and other elements requires improved management practices. Two application rates of wood ash (6 and 12 t ha−1) were tested in a 4‐year trial on a low‐input fertilized pasture. Ash was complemented with mineral P, and N fixation was encouraged by sowing white clover. Wood‐ash application led to increased pasture yield (by 100%) and to increased proportions of white clover and ryegrass (60%), thus improving pasture feed value. N fixation by white clover, and possibly increased mineralization because of higher pH, may have compensated for lack of N in the wood ash. Addition of mineral fertilizer improved the supply of P, although incorporation of the wood ash into the soil may also have enhanced release of P from non‐extractable components. High amounts of compounds containing Ca and Mg contributed to the long‐term maintenance of soil reserves of these elements. Despite high inputs of K (175–350 mg kg−1) from wood ash, annual additions of K are required to counteract depletion via plant uptake and leaching. Increased Mn availability after the treatment (up to 400 mg kg−1) may limit repeated applications of wood ash, at least on poorly aerated soils.
C1272F: a novel type 2A von Willebrand’s disease mutation in A1 domain; its clinical significance
Authors: WOODS A. I. , SANCHEZ‐LUCEROS A. , KEMPFER A. C. , POWAZNIAK Y. , CALDERAZZO PEREYRA J. C. , BLANCO A. N. , MESCHENGIESER S. S. , LAZZARI M. A.
Published: May 2011

Summary.  Most mutations identified in 2A VWD patients are localized in the A2 domain, although missense substitutions have also been recognized in the A1 domain. We describe a novel heterozygous missense mutation in the A1 domain of VWF gene responsible for type 2A phenotype. Analysis of the complete exon 28 was carried out in a patient and his mother with life‐long histories of moderate to severe bleeding and laboratory data of type 2A VWD. The analysis of exon 28 of VWF gene showed a 3815 G→T transversion resulting in C1272F mutation. It is probably associated with a group I mechanism according to patients’ clinical symptoms, and, in the case of the propositus, the lack of clinical response to treatment with desmopressin. The mutation was not found in 100 normal alleles. This substitution affected the normal S–S bound between C1272 and C1458, which is involved in A1 loop structure, altering the normal multimerization and function of VWF. The VWFpp/VWF:Ag ratio in the propositus and his mother was >3, suggesting a shortened survival of VWF. We believe it is important to report the complete clinical phenotype corresponding to the new mutation to increase the knowledge in the clinical field.