bluuebunny/crossref_metadata_2025 huggingface dataset:
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences
Authors: He David , Parkinson John
Published: February 2008

Summary: Low-complexity, repetitive protein sequences with a limited amino acid palette are abundant in nature, and many of them play an important role in the structure and function of certain types of proteins. However, such repetitive sequences often do not have rigidly defined motifs. Consequently, the identification of these low-complexity repetitive elements has proven challenging for existing pattern-matching algorithms. Here we introduce a new web-tool SubSeqer (http://compsysbio.org/subseqer/) which uses graphical visualization methods borrowed from protein interaction studies to identify and characterize repetitive elements in low-complexity sequences. Given their abundance, we suggest that SubSeqer represents a valuable resource for the study of typically neglected low-complexity sequences.

Contact:  jparkin@sickkids.ca
Crystal structure of enoyl–acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor
Authors: Saito Jun , Yamada Mototsugu , Watanabe Takashi , Iida Maiko , Kitagawa Hideo , Takahata Sho , Ozawa Tomohiro , Takeuchi Yasuo , Ohsawa Fukuichi
Published: February 2008

Enoyl–acyl carrier protein (ACP) reductases are critical for bacterial type II fatty acid biosynthesis and thus are attractive targets for developing novel antibiotics. We determined the crystal structure of enoyl–ACP reductase (FabK) from Streptococcus pneumoniae at 1.7 Å resolution. There was one dimer per asymmetric unit. Each subunit formed a triose phosphate isomerase (TIM) barrel structure, and flavin mononucleotide (FMN) was bound as a cofactor in the active site. The overall structure was similar to the enoyl–ACP reductase (ER) of fungal fatty acid synthase and to 2‐nitropropane dioxygenase (2‐ND) from Pseudomonas aeruginosa, although there were some differences among these structures. We determined the crystal structure of FabK in complex with a phenylimidazole derivative inhibitor to envision the binding site interactions. The crystal structure reveals that the inhibitor binds to a hydrophobic pocket in the active site of FabK, and this is accompanied by induced‐fit movements of two loop regions. The thiazole ring and part of the ureido moiety of the inhibitor are involved in a face‐to‐face π–π stacking interaction with the isoalloxazine ring of FMN. The side‐chain conformation of the proposed catalytic residue, His144, changes upon complex formation. Lineweaver–Burk plots indicate that the inhibitor binds competitively with respect to NADH, and uncompetitively with respect to crotonoyl coenzyme A. We propose that the primary basis of the inhibitory activity is competition with NADH for binding to FabK, which is the first step of the two‐step ping‐pong catalytic mechanism.
NMR solution structure of KP‐TerB, a tellurite‐resistance protein from Klebsiella pneumoniae
Authors: Chiang Sheng‐Kuo , Lou Yuan‐Chao , Chen Chinpan
Published: February 2008

Klebsiella pneumoniae (KP), a Gram‐negative bacterium, is a common cause of hospital‐acquired bacterial infections worldwide. Tellurium (Te) compounds, although relatively rare in the environment, have a long history as antimicrobial and therapeutic agents. In bacteria, tellurite (TeO3 −2) resistance is conferred by the ter (Ter) operon (terZABCDEF). Here, on the basis of 2593 restraints derived from NMR analysis, we report the NMR structure of TerB protein (151 amino acids) of KP (KP‐TerB), which is mainly composed of seven α‐helices and a 310 helix, with helices II to V apparently forming a four‐helix bundle. The ensemble of 20 NMR structures was well‐defined, with a RMSD of 0.32 ± 0.06 Å for backbone atoms and 1.11 ± 0.07 Å for heavy atoms, respectively. A unique property of the KP‐TerB structure is that the positively and negatively charged clusters are formed by the N‐terminal positively and C‐terminal negatively charged residues, respectively. To the best of our knowledge, the protein sequence and structures of KP‐TerB are unique.
Improvement in Mechanical Properties of Powder‐Processed MoSi2 by the Addition of Sc2O3 and Y2O3
Authors: Suzuki Yoshikazu , Morgan Peter E. D. , Niihara Koichi
Published: February 2008

Additions of 1‐20 mol% Sc2O3 or Y2O3 to MoSi2 eliminate glassy SiO2, which improves mechanical properties at both ambient and high temperatures. In particular, only 1 mol% ScO3 additions dramatically enhance three‐point bending strength from 521 to 1081 MPa. Vickers hardness, Young's modulus, fracture toughness, and high‐temperature strength are also improved by this low level of additive. The improvement of mechanical properties is attributed to the formation of crystalline silicates: Sc2Si2O7, Y2Si2O7, Y2SiO5, and Y4Si3O12, which are analyzed by XRD, SEM‐EDS, and TEM‐EDS methods.
Dependence of Oxidation Modes on Zirconia Content in Silicon Carbide/Zirconia/Mullite Composites
Authors: Tsai Cheng‐Yuan , Lin Chien‐Cheng
Published: February 2008

Two basic oxidation modes of silicon carbide/zirconia/mullite (SiC/ZrO2/mullite) composites were defined based on the plotted curve of the gradient of the silica (SiO2) layer thickness (formed on individual SiC particles) versus depth. Mode I, where oxygen diffusivity was much slower in the matrix than in the SiO2 layer, exhibited a relatively large gradient and limited oxidation depth. Mode II, where oxygen diffusivity was much faster in the matrix than in the SiO2 layer, displayed a relatively small gradient and an extensive oxidation depth. When the volume fraction of ZrO2 was below a threshold limit, the composites exhibited Mode I behavior; otherwise, Mode II behavior was observed. For composites with a ZrO2 content above the threshold limit, the formation of zircon (ZrSiO4), as a result of the reaction between ZrO2 and the oxidation product (i.e., SiO2), might change the oxidation behavior from Mode II to Mode I.
Ab‐Initio Total Energy Calculation of α‐ and β‐Silicon Nitride and the Derivation of Effective Pair Potentials with Application to Lattice Dynamics
Authors: Ching Wai‐Yim , Xu Yong‐Nian , Gale Julian D. , Rühle Manfred
Published: February 2008

The ground state total energies of α‐ and β‐Si3N4 crystals are calculated by an ab‐initio method based on local density functional theory. The calculated bulk modulus and pressure coefficients for both crystals are in good agreement with recent experimental measurements. Interatomic pair potentials of the Buckingham form with an additional repulsive term are derived using ab‐initio effective charges and total energy data. The effective pair potentials give excellent results on equilibrium lattice parameters, elastic constants, phonon spectra, and lattice specific heat for both crystals. The zone‐center optical phonon modes are in good agreement with measured infrared and Raman spectra. The pair potentials for α‐ and β‐Al2O3 are similar but not the same, despite their similarities in the local short‐range order. Applications of the pair potentials to the simulation and modeling of surfaces and interfaces in Si3N4 ceramics are discussed.
Synthesis of TiC, TiC‐Cu Composites, and TiC‐Cu Functionally Graded Materials by Electrothermal Combustion
Authors: Shon In‐Jin , Munir Zuhair A.
Published: February 2008

Titanium carbide and composites and functionally graded materials (FGMs) of TiC–xCu were synthesized by an electrothermal combustion (ETC) method. TiC synthesized by ETC showed small amounts of porosity relative to those synthesized by ignition using radiative heating. Composites and FGMs with higher copper content can be synthesized by ETC. In the FGM products a nearly linear change in composition in the graded region was observed in samples with 0 ≤x (wt%) ≤ 75.
Ferroelectric Thin Films of Bismuth‐Containing Layered Perovskites: Part II, PbBi2Nb2O9
Authors: Du Xiaofeng , Chen I‐Wei
Published: February 2008

Ferroelectric thin films of bismuth‐containing layered perovskite PbBi2Nb2O9 have been prepared by a metalorganic decomposition (MOD) method. Random and highly c‐oriented films of the same starting composition have been obtained under different intermediate‐ and high‐temperature heat treatments. A comparison of their crystallization and properties with those of Bi4Ti3O12 films reveals similar trends that are common to bismuth‐containing Aurivillius compounds. Heterogeneous nucleation of the perovskite phase either on the pyrochlore (444) plane because of lattice matching or on the substrate surface because of lower interfacial energy is proposed as the cause of orientation selection during crystallization. The different thickness of the pseudoperovskite subunits in these layered compounds may be responsible for the systematic difference in the anisotropic ferroelectric properties. Smaller polarization and higher coercive field are expected for PbBi2Nb2O9, which has thinner pseudoperovskite units than Bi4Ti3O12.
Contamination Effects on Interfacial Porosity during Cyclic Oxidation of Mullite‐Coated Silicon Carbide
Authors: Lee Kang N.
Published: February 2008

Plasma‐sprayed mullite (3Al2O32SiO2) and mullite/yttria‐stabilized zirconia (mullite/YSZ) dual‐layer coatings have been developed to protect silicon‐based ceramics from environmental attack. The mullite/SiC system develops interfacial pores during cyclic oxidation. The development of pores at the mullite/sintered SiC interface in air has been investigated as a function of the purity of mullite at 1230°–1350°C in an atmospheric‐pressure furnace. The silica scale is readily contaminated by impurities of alkali or alkaline‐earth metal oxides from the mullite coating. The contamination enhances oxidation and reduces the scale viscosity by forming alkali or alkaline‐earth metal silicates. The porosity increases as the temperature and contamination increase and decreases as the purity of the mullite increases.
Interleukin‐8 increases vascular endothelial growth factor and neuropilin expression and stimulates ERK activation in human pancreatic cancer
Authors: Li Min , Zhang Yuqing , Feurino Louis W. , Wang Hao , Fisher William E. , Brunicardi F. Charles , Chen Changyi , Yao Qizhi
Published: February 2008

Interleukin‐8 (IL‐8) is associated with tumorigenesis by promoting angiogenesis and metastasis. Although up‐regulation of IL‐8 is indicated in many cancers, its function in pancreatic cancer has not been well characterized. In this study we examined the expression of IL‐8 on pancreatic cancer cells and clinical tissue specimens, and investigated the effect of exogenous IL‐8 on gene expression, and signaling in human pancreatic cancer cells. We found that pancreatic cancer cells expressed higher amount of IL‐8 mRNA than normal human pancreatic ductal epithelium cells. IL‐8 mRNA was also substantially overexpressed in 11 of 14 (79%) clinical pancreatic‐adenocarcinoma samples compared with that in their surrounding normal tissues. Exogenous IL‐8 up‐regulated the expression of vascular endothelial growth factor165, and neuropilin (NRP)‐2 in BxPC‐3 cells, one of human pancreatic cancer cell lines. IL‐8 expression was inducible by hypoxia mimicking reagent cobalt chloride. In addition, IL‐8 activated extracellular signal‐regulated kinase (ERK)1/2 signaling pathway in BxPC‐3 cells. Our studies suggest that IL‐8 might be a malignant factor in human pancreatic cancer by induction of vascular endothelial growth factor and NRP‐2 expression and ERK activation. Targeting IL‐8 along with other antiangiogenesis therapy could be an effective treatment for this malignancy. (Cancer Sci 2008, 99: 733–737)
Positive association of up‐regulated Cripto‐1 and down‐regulated E‐cadherin with tumour progression and poor prognosis in gastric cancer
Authors: Zhong X‐Y , Zhang L‐H , Jia S‐Q , Shi T , Niu Z‐J , Du H , Zhang G‐G , Hu Y , Lu A‐P , Li J‐Y , Ji J‐F
Published: February 2008

Aims:  Cripto‐1 may be capable of up‐regulating signalling molecules associated with epithelial‐to‐mesenchymal transition (EMT), an important event characterized by loss of E‐cadherin during malignant tumour progression and metastasis. The aim was to investigate the expression of Cripto‐1 and E‐cadherin in relation to clinicopathological features and patient prognosis of gastric cancer.

Methods and results:  The expression of Cripto‐1 and E‐cadherin was studied by immunohistochemistry in 118 gastric cancer cases. Up‐regulated Cripto‐1 (CR+) was found in 54% (64/118) of cases, whereas down‐regulated E‐cadherin (E‐cad−) was found in 70% (83/118) of cases. Either CR+ or E‐cad− was associated with lymph node metastasis, liver metastasis and late TNM stage (P < 0.05). Patients with either CR− or E‐cad+ showed higher 5‐year survival rates than those with CR+ or E‐cad− (P = 0.0012 and P = 0.0017, respectively). When combined, evaluation of these two proteins, simultaneous CR+ and E‐cad− (CR+/E‐cad−) in cancer was strongly associated with the above three aggressive clinicopathological features (P < 0.001) and indicated the worst patient survival (P = 0.0001). Multivariate analysis revealed that CR+/E‐cad− was an independent prognostic factor in gastric cancer.

Conclusions:  Combined analysis of Cripto‐1 and E‐cadherin has significant value in evaluating the metastatic potential of gastric cancer and predicting patient prognosis.
Dentine demineralization when subjected to EDTA with or without various wetting agents: a co‐site digital optical microscopy study
Authors: De‐Deus G. , Reis C. , Fidel S. , Fidel R. , Paciornik S.
Published: February 2008

Aim  To analyse quantitatively the chelating ability of ethylenediaminetetraacetic acid (EDTA) and three common EDTA‐based associations with wetting agents.

Methodology  Twelve maxillary human molars were selected, from which 3 mm thick discs were obtained from the cervical third of the root. Following the creation of standardized smear layer co‐site microscopy image sequences of the dentine surface submitted to EDTA, EDTA plus 0.1% cetavlon® (Sigma Chemical Co., St Louis, MO, USA), EDTA plus 1.25% sodium lauryl ether sulphate and SmearClear™ (Sybron Endo, Orange, CA, USA) were obtained after several cumulative demineralization times. Sixteen images were obtained of each dentine sample for each experimental time, at 1000× magnification. An image processing and analysis sequence was used to measure the area of open tubules for each experimental time. Thus, it was possible to follow the demineralization process and quantitatively analyse the effect of the various substances. The Student’s t‐test was used to assess differences between experimental groups.

Results  EDTA solution had the strongest effect at all experimental times whilst the association of EDTA with wetting agents showed a weaker chelating effect and this difference was statistically significant (P < 0.05).

Conclusions  (i) The EDTA solution had the strongest effect at all experimental times (P < 0.05); (ii) the association of EDTA with wetting agents did not improve the chelating power of the solution; (iii) co‐site optical microscopy represents a powerful approach to compare directly, longitudinally and quantitatively the ability of the chelating solutions.
Bond strengths of three types of fibre‐reinforced post systems in various regions of root canals
Authors: D’Arcangelo C. , Zazzeroni S. , D’Amario M. , Vadini M. , De Angelis F. , Trubiani O. , Caputi S.
Published: February 2008

Aim  To evaluate the bond strengths of three adhesive/resin cement/fibre post systems to coronal, middle and apical thirds of post space dentine.

Methodology  Three types of glass‐fibre post systems were selected for the study. Saremco Post Non‐stop Fibre (Saremco), FRC Postec Plus (Ivoclar Vivadent) and Anatomical Post (Dentalica) were luted in prepared root canals using adhesive system and resin cement provided by the respective manufacturer. The luting agent was placed into the root canal using a specific syringe with needle. A push‐out test was performed on sections from the apical, middle and coronal parts of each specimen to measure bond strength. All fractured specimens were observed using a stereomicroscope to identify the modes of failure.

Results  Bond strength values were significantly affected both by the post–adhesive–cement system used and by root region (P < 0.05). Additionally, there was no significant interaction between the post system and region of canal factors (P > 0.05). The highest bond strength values were found in the coronal third for all experimental groups. The middle and apical thirds exhibited similar bond strengths with no statistically significant differences amongst them. Saremco and Precision post systems had the highest retentive strengths, whilst the Ivoclar post system had the lowest values. Microscopic analysis of the specimens revealed a prevalence of post–cement and mixed failures.

Conclusions  Type of post–adhesive–cement system and root position had a significant effect on fibre post retention. The coronal region of the canals was characterized by significantly higher bond strengths.
Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples
Authors: Teletchea Fabrice , Bernillon Jacques , Duffraisse Marilyne , Laudet Vincent , Hänni Catherine
Published: February 2008

Molecular identification of animal or plant species in fresh and degraded products (e.g. food, faeces, hair and other organic remains) has become a very important issue in both conservation biology and food science.

In this proof‐of‐concept study, we developed a microarray‐based method using cytochrome b‐derived probes to identify the main commercial and/or endangered vertebrate species in both food and forensic samples.

This method allowed the unambiguous identification of 71 out of 77 species tested. In the remaining six cases, identification was hampered due to false sequences deposited in GenBank and high intraspecific variability. Our evaluation of this DNA chip for routine control demonstrated its effectiveness for the simultaneous identification of at least five species, and that its sensitivity varied according to the type of sample analysed.

Synthesis and applications. Taken together, our results suggest that cytb‐based microarray is a reliable and powerful identification tool for vertebrates, and more generally highlights the significant role of both molecular and traditional taxonomy in the development of molecular identification methods.
Polyphosphate at the Streptomyces lividans cytoplasmic membrane is enhanced in the presence of the potassium channel KcsA
Authors: HEGERMANN J. , LÜNSDORF H. , OVERBECK J. , SCHREMPF H.
Published: February 2008

The distribution of polyphosphate (polyP) within the cytoplasmic membrane of Streptomyces lividans hyphae or protoplasts has been determined at high spatial resolution by elemental mapping using energy‐filtered electron microscopy (EFTEM). The results revealed that polyP was best traceable after its interaction with lead ions followed by their precipitation as lead sulphide. Concomitant studies of the S.lividans wildtype (WT) strain and its co‐embedded mutant ΔK (lacking a functional kcsA gene) were conducted by labelling as the surface matrix of either one was labelled by cationic colloidal thorium dioxide. Within the WT strain, additional polyP was found to accumulate distinctly at the inner face of the cytoplasmic membrane. After removal of the cell wall (within protoplasts), the polyP‐derived lead‐sulphide (PbS) precipitate formed clusters of fibrillar material extending up to 50 nm into the cytoplasm. This feature was absent in the ΔK mutant strain. Together the results revealed that the presence of the KcsA channel and the structured polyP coincide.
Observation of the ion‐mirror effect during microscopy of insulating materials
Authors: CROCCOLO F. , RICCARDI C.
Published: February 2008

Utilizing the ion beam of a focused ion beam (FIB)/scanning electron microscope (SEM) microscope to investigate non‐conductive samples, we observe a mirror image very much similar to the one that is commonly obtained with the electron beam and the same samples. To our knowledge this is the first observation of what can be called ‘Ion‐Mirror Effect’. This effect is produced by a positive charging of the sample obtained by rastering with high‐energy ions (30 kV) and a subsequent imaging with low energy ones (5 kV). The proposed explanation is that first a positive charge is trapped within the sample and eventually the lower energy ions are deflected back by the latter, and hit the surface of the microscope chamber very similar to what happens in the ‘Electron‐Mirror Effect’. The mirror image is produced after detection of the electrons produced by the interaction between ions and the chamber materials.
Orientation fields of nonlinear biological fibrils by second harmonic generation microscopy
Authors: ODIN C. , LE GRAND Y. , RENAULT A. , GAILHOUSTE L. , BAFFET G.
Published: February 2008

The orientation of fibrils within biological tissues is of primary importance. In this study, we propose a simple method based on second harmonic generation (SHG) microscopy to map, pixel by pixel, the orientation of the symmetry axis of the second‐order nonlinear susceptibility tensor of fibrils that produce SHG. The method uses only four images acquired at specific polarizations of the input laser beam, and can be easily and cheaply implemented on a confocal microscope. In addition to orientation informations, the method also provides polarization independent images and estimations of the ratio of the nonlinear susceptibility components. We demonstrate the relevance of our concept by studying the orientation fields of the collagen meshwork in a healthy rat liver that provides well separated fibrils. By correlating the mean orientation of the nonlinear susceptibility to the fibril orientation itself for many fibril segments, and using circular statistics, it is shown that both orientations are truly parallel at the fibril scale. Our polarimetric method allows to map fibril orientation fields, independently of individual fibril contrast in the SHG image.
Parental conceptions of self‐mutilation among Finnish adolescents
Authors: RISSANEN M.‐L. , KYLMÄ J. P. O. , LAUKKANEN E. R.
Published: February 2008

The purpose of this paper is to describe self‐mutilation from the viewpoint of parents of self‐mutilating Finnish adolescents. Four parents of self‐mutilating adolescents were interviewed in depth. Qualitative content analysis was applied. Four main categories emerged: the phenomenon of self‐mutilation, factors contributing to self‐mutilation, the purposes of self‐mutilation and sequels of self‐mutilation. Factors contributing to self‐mutilation could be divided into those relating to the adolescent and those relating to the family, especially the mother. The purposes of self‐mutilation were purposes relating to the adolescent and those relating to others, while sequels of self‐mutilation could be divided into sequels for the adolescent and those for the parents. Sequels of self‐mutilation for the adolescent could be further divided into sequels for the adolescent herself and for the relationship with significant others, including parents, siblings and peers, and sequels in relation to healthcare staff. While knowledge of self‐mutilation is inadequate among parents, it evokes strong negative emotions when it occurs in their own family. Self‐mutilation should be raised by healthcare professionals and discussed in health promotion or in parents' meetings at schools.
‘It is still so deep‐seated, the fear’: psychological stress reactions as consequences of intimate partner violence
Authors: SCHEFFER LINDGREN M. , RENCK B.
Published: February 2008

The negative mental health consequences of intimate partner violence have been well documented in recent years. One aim of the present study was to examine psychological distress and mental problems in assaulted women who have left their relationships. Another aim was to explore these women's sense of coherence (SOC). A combination of qualitative in‐depth interviews and quantitative measurement instruments was used. Data were collected from 14 assaulted women with a mean age of 38, living in different places in Sweden. Impact of event scale‐revised and symptom checklist‐90‐R show that the violence creates long‐term psychological stress reactions and confirm previous research on the subject. Twelve of the 14 women have symptoms of post‐traumatic stress disorder (PTSD). The result of the interviews confirmed complex PTSD and disorders of extreme stress not otherwise specified. On the other hand we found a surprisingly high SOC level among several of the respondents, a fact which could explain why these women finally managed to leave mainly by their own efforts. We call for more both qualitative and quantitative studies on this serious public health issue.
Substitution rate of the hepatitis B virus surface gene
Authors: Zaaijer H. L. , Bouter S. , Boot H. J.
Published: February 2008

Summary.  Molecular epidemiology of hepatitis B virus (HBV) often relies on the comparison of HBV surface (S) gene sequences, although little is known about the substitution rate of the HBV S‐gene. In this study, we compared HBV S‐gene sequences in longitudinal sample pairs of 40 untreated, chronically HBV‐infected patients, spanning 210 years of cumulative follow‐up. The 40 patients included HBV e‐antigen positive and negative persons; with HBV DNA levels ranging from 103 to 109 cps/mL and belonging to HBV genotypes A, B, C, D and E. In the 40 sample pairs, 70 nucleotide changes occurred in the HBV S‐gene (0–8 per patient), resulting in an average substitution rate of 5.1 × 10−4 nucleotide changes/site/year (range: 0–1.3 × 10−2). Surprisingly, the number of substitutions was strongly associated with the inverse level of viremia; and only weakly with the duration of follow‐up: in 11 highly viremic patients (HBV DNA ≥108 cps/mL), only four substitutions occurred despite a cumulative observation period of 56 years (substitution rate: 1.1 × 10−4), while in the 10 patients with viremia below 104 cps/mL, 29 substitutions occurred during 30 years of follow‐up (substitution rate: 14.6 × 10−4). We conclude that in chronic hepatitis B virus infection the rate of nucleotide substitution in the HBV S‐gene is inversely related to the level of viremia and thus varies widely from person to person; hampering the phylogenetic analysis of possible chains of HBV infection.
Risk of hepatitis C virus transmission through drug preparation equipment: a systematic and methodological review
Authors: De P. , Roy É. , Boivin J.‐F. , Cox J. , Morissette C.
Published: February 2008

Summary.  The use of blood‐contaminated drug preparation equipment is believed to be associated with the transmission of hepatitis C virus (HCV) among injection drug users (IDUs), but the extent of HCV infection risk is unclear. The objective of this review was to appraise the evidence regarding HCV incidence associated with the use of drug preparation equipment such as drug mixing containers, filters and water. In June 2007, cohort and case–control studies examining the association of HCV incidence with the sharing of drug preparation equipment were identified by searching electronic reference databases as well as the reference lists of published papers. Ten studies (seven cohort and three nested case–control) met the inclusion criteria for the review. The relative risk of HCV infection associated with drug preparation equipment were mainly between 2.0 and 5.9; however, the precision of the estimates from individual studies were marked by wide confidence intervals. Few studies exist to allow an adequate assessment of the individual contributions of containers, filters and water to HCV incidence. The major methodological limitations of reviewed studies were short follow‐up times, inadequate control of confounders and lack of exclusion of periods when IDUs were not at risk for HCV infection through drug injection. Current evidence implicating the association of drug preparation equipment with HCV incidence is limited by several methodological concerns.
Monoclonal antibody recognizing N‐terminal epitope of hepatitis C virus nonstructural 5B inhibits viral RNA replication
Authors: Kang S. M. , Choi S. H. , Park C. Y. , Kim M. H. , Kim T. K. , Park J. M. , Koh M. S. , Kang H. J. , Hwang S. B.
Published: February 2008

Summary. The nonstructural 5B (NS5B) protein of hepatitis C virus (HCV) is an RNA‐dependent RNA polymerase (RdRp) with a key role in HCV replication. To characterize the functional roles of NS5B in HCV replication, we produced a panel of 10 monoclonal antibodies (mAbs) directed against NS5B protein from mice immunized with functionally active RdRp. The epitopes of eight mAbs are localized in the middle region (amino acid 240–263) of NS5B protein. On the other hand, the epitopes of two mAbs are mapped to amino acids 67–88 at the N‐terminus of NS5B protein. To examine the effects of mAbs on HCV‐RNA replication, we performedin vitroRdRp assay using either the 3′‐untranslated region (UTR) or the full‐length of HCV‐RNA as a template in the presence of each mAb. mAbs specific for the middle region of NS5B had no effect on RdRp activity. Surprisingly, mAb recognizing the N‐terminal region of NS5B inhibited RdRp activity in a dose‐dependent manner. We have confirmed the same result using the other subclass of mAb, whose epitope is also localized to the same N‐terminal region of NS5B. These data show that NS5B contains a B‐cell epitope located between amino acid residues 67 and 88. Binding of this epitope with an antibody interferes with the enzymatic function of NS5B.
Jr‐ZFP2, encoding a Cys2/His2‐type transcription factor, is involved in the early stages of the mechano‐perception pathway and specifically expressed in mechanically stimulated tissues in woody plants
Authors: LEBLANC‐FOURNIER NATHALIE , COUTAND CATHERINE , CROUZET JEROME , BRUNEL NICOLE , LENNE CATHERINE , MOULIA BRUNO , JULIEN JEAN‐LOUIS
Published: February 2008

Plants respond to environmental mechanical stimulation, such as wind, by modifying their growth and development. To study the molecular effects of stem bending on 3‐week‐old walnut trees, a cDNA‐AFLP approach was developed. This study allowed the identification of a cDNA, known as Jr‐ZFP2, encoding a Cys2/His2‐type two‐zinc‐fingered transcription factor. Reverse transcriptase‐polymerase chain reaction analysis confirmed that Jr‐ZFP2 mRNA accumulation is rapidly and transiently induced after mechanical stimulation. After bending, Jr‐ZFP2 transcript increase was restricted to the stem, the organ where the mechanical solicitation was applied. Furthermore, other abiotic factors, such as cold or salt, did not modify Jr‐ZFP2 mRNA accumulation in walnut stems under our experimental conditions, whereas growth studies demonstrated that salt stress was actually perceived by the plants. These results suggest that the regulation of Jr‐ZFP2 expression is more sensitive to mechanical stimulus. This gene will be a good marker for studying the early stages of mechanical perception in woody plants.
A survey of patients with self‐reported severe food allergies in Japan
Authors: Imamura T. , Kanagawa Y. , Ebisawa M.
Published: February 2008

Food allergies have increased in recent years in Japan. Details of causative foods, places where anaphylaxis developed, and other allergic factors remain unknown, and we investigated them. A‘questionnaire survey for the prevention of food allergies’ was conducted using a nationwide group of patients with food allergies. A total of 1383 patients from 878 families (including 319 patients who experienced anaphylaxis) provided valid answers to the questionnaire. The average age of the first anaphylactic attack was 3.20 ± 6.327 yr. The most common allergens causing anaphylaxis were in order milk, eggs, wheat, peanuts, and soybeans, followed by sesame and buckwheat. The most common place where anaphylaxis developed was the patient’s own home, followed by fast food restaurants, places visited, restaurants, and schools. In patients’ own homes, fast food restaurants (buffet), places visited and schools, the most common allergens were milk, eggs, and wheat. In restaurants and accommodation facilities, eggs were the most common allergen followed by milk. As possible food allergies can cause anaphylaxis, it is necessary to provide precise information for consumers regarding packaged and processed foods.
Effects of using thermally treated lupins instead of soybean meal and rapeseed meal in total mixed rations on in vitro microbial yield and performance of dairy cows
Authors: Boguhn J. , Kluth H. , Bulang M. , Engelhard T. , Spilke J. , Rodehutscord M.
Published: February 2008

The objective was to study whether thermally treated lupins (TTL) can replace solvent‐extracted soybean meal (SBM) and rapeseed meal (RSM) in dairy cow rations. Three total mixed rations (TMR) were used. They differed in the inclusion of the main protein feeds (TTL alone, TTL + RSM and RSM + SBM) but were equal in organic matter digestibility and metabolizable energy content. In vitro organic matter fermentation was not significantly different between the TMR. Efficiency of microbial crude protein (MCP) synthesis was significantly higher for TMR RSM + SBM than for TTL. In vitro gas production potential was similar for the three TMR. The maximal rate of gas production was achieved later in TMR TTL than in RSM + SBM. Feed intake of dairy cows was significantly lower when TMR TTL was fed than when TMR TTL + RSM or RSM + SBM were fed. Milk yield was significantly lower with the high inclusion rate of TTL in comparison with the other TMR. The contents of milk protein and milk fat were significantly lower when the two TTL containing TMR were fed in comparison with the RSM + SBM ration. Effects of TTL inclusion on MCP synthesis may affect the amino acid supply to the duodenum of cows to a greater extent than differences in the degradability of feed proteins.
Musculoskeletal disorders and comorbid depression: Implications for practice
Authors: Lloyd Chris , Waghorn Geoff , McHugh Cate
Published: February 2008

Background:  The physical demands of work have a substantial impact on the incidence of work‐related musculoskeletal disorders. Depression is often associated with work‐related injuries and may influence a person's success or otherwise return to work. There is pressure for occupational rehabilitation providers to produce good return‐to‐work outcomes in a timely and financially responsible manner. The aim was to examine current evidence for any added impact of depression on return‐to‐work prospects among people with work‐related musculoskeletal disorders.

Methods:  A review of the literature was conducted to determine the extent to which depression comorbid with musculoskeletal disorders affected labour force participation and the outcomes obtained in occupational rehabilitation.

Results:  Australian population level data show that people of working age with depression comorbid with musculoskeletal disorders have extensive labour force disadvantage and reduced return‐to‐work outcomes when participating in occupational rehabilitation.

Conclusions:  Although more research is needed, there is already sufficient evidence to support the introduction of systems and practices to detect and integrate treatment for comorbid depression in order to prevent occupational rehabilitation failure.
South Australian school teachers’ perceptions of occupational therapy reports
Authors: Vincent Robyn , Stewart Hugh , Harrison Jo
Published: February 2008

Background/aim:  The qualitative research reported here investigated the perceptions of primary school teachers regarding the usefulness of occupational therapy reports from the Flinders Medical Centre. The reports included either recommendations alone or in conjunction with written programs for the students.

Methods:  This qualitative descriptive study employed in‐depth semistructured interviews to gather the perspectives of four school teachers from primary schools in the southern suburbs of Adelaide. The interviews were audiotaped, transcribed, and analysed using a thematic inductive approach.

Results:  Four themes emerged from the data in relation to teachers’ perceptions of the reports: (i) Understandable but not always useful; (ii) It's important ... we can't do it all; (iii) We never actually speak; and (iv) It's probably impossible but ... in an ideal world.

Conclusions:  The research findings provide an insight into the professional relationship between education and health professionals in the presence of minimal collaboration. The participants in this study described the occupational therapy reports as useful but they all wanted a higher level of interaction with therapists. The participants also gave suggestions for improving the current procedure to increase collaboration between health and education professionals. Such improvements could enhance educational outcomes for South Australian children with a disability.
Social competence and learning difficulties: Teacher perceptions
Authors: Wight Megan , Chapparo Christine
Published: February 2008

Background/aim:  Social competence has been linked to children's classroom performance with three out of four children with learning difficulties reported to have problems with social skills. Social participation remains a predominant childhood occupation and a key indicator of school performance. Occupational therapists work with teachers to accurately assess the social performance of children in context and to provide targeted intervention. There is limited research about what teachers perceive are the specific nature of social difficulties experienced by children with learning difficulties in the classroom. This study investigated teacher perceptions of the social competence of a small sample of Australian boys with learning difficulties within the classroom context.

Methods:  The Teacher Skillstreaming Checklist was used to investigate teacher perceptions of the social abilities of 21 primary school aged boys with learning difficulties compared to a control group. A correlational analysis was used to examine the relationship.

Results and conclusions:  The study identified that the boys with learning difficulties were perceived by their teachers as having poorer social performance across multiple domains when compared to their typically developing peers. Implications of these findings are that children's social performance may negatively impact learning and classroom participation and that for some children, social competence should be a focus of occupational therapy assessment and treatment.
FLUORESCENCE ACTIVATED CELL SORTING OF TRANSIENTLY TRANSFECTED As4.1 CELLS SHOWS RENIN ENHANCER DIRECTS ON/OFF SWITCHING OF RENIN PROMOTER IN VITRO
Authors: Morris Brian J
Published: February 2008

The proximal promoter of the renin gene is weak and its activity is influenced by a strong, far‐upstream enhancer. This and the ability of renin expression in renal afferent arteriolar cells to be ‘recruited’ under chronic stimulation is consistent with the on/off switching (variegation) model of gene expression. If true, this would provide an example in which variegation controls a physiologically regulable gene.

The present study tested the hypothesis that renin promoter activity may accord with the variegation model, at least in individual juxtaglomerular (mouse As4.1) cells in vitro.

As4.1 cells were transiently transfected with constructs containing the mouse renin (Ren‐1c) enhancer adjacent to the Ren‐1c promoter and a linked reporter gene encoding enhanced green fluorescent protein (EGFP). The EGFP signal from individual cells was monitored by fluorescence activated cell sorting.

In the presence of the renin enhancer there was 10‐fold higher EGFP expression in transfected cells compared with cells transfected with EGFP constructs containing the promoter alone. There was, moreover, an 8‐fold increase in the number of EGFP expressing cells. However, EGFP expression in individual transfected cells was similar in the presence or absence of the enhancer.

Results from the in vitro system used suggest that the Ren‐1c enhancer does not regulate the rate of promoter activity, but rather increases the probability of achieving an active transcriptional state. Limitations of these findings are discussed.
SEARCHING FOR FUNCTIONAL GENETIC VARIANTS IN NON‐CODING DNA
Authors: Cobb Joanna , Büsst Cara , Petrou Steven , Harrap Stephen , Ellis Justine
Published: February 2008

The search for DNA sequence variants for complex human polygenic conditions has been a strong focus of recent genetic research. While gene loci have been identified, few variants in the coding sequences of these genes have been found, suggesting that non‐coding sequence variation may underlie many complex conditions.

Non‐coding DNA harbours regulatory elements capable of making changes to gene expression. However, regulatory DNA sequences are currently difficult to recognize and their function is poorly understood, complicating the task of assigning potential functional significance to non‐coding variation.

Comparative genomics, the study of evolutionary DNA conservation, has enabled the emergent field of non‐coding DNA identification in human disease analysis.

This brief review will focus on the potential of a relatively high throughput technique based on comparative genomics, that may aid in the identification of functionally important non‐coding sequence variation in complex diseases.
EXAMINATION OF CHROMOSOME 7p22 CANDIDATE GENES RBaK, PMS2 AND GNA12 IN FAMILIAL HYPERALDOSTERONISM TYPE II
Authors: Jeske YWA , So A , Kelemen L , Sukor N , Willys C , Bulmer B , Gordon RD , Duffy D , Stowasser M
Published: February 2008

There are two types of familial hyperaldosteronism (FH): FH‐I and FH‐II. FH‐I is caused by a hybrid CYP11B1/CYP11B2 gene mutation. The genetic cause of FH‐II, which is more common, is unknown. Adrenal hyperplasia and adenomas are features. We previously reported linkage of FH‐II to a ~5 Mb region on chromosome 7p22. We subsequently reported finding no causative mutations in the retinoblastoma‐associated Kruppel‐associated box gene (RBaK), a candidate at 7p22 involved in tumorigenesis and cell cycle control.

In the current study we investigated RBaK regulatory regions and two other candidate genes: postmeiotic segregation increased 2 (PMS2, involved in DNA mismatch repair and tumour predisposition) and guanine nucleotide‐binding protein alpha‐12 (GNA12, a transforming oncogene).

The GNA12 and PMS2 genes were examined in two affected (A1, A2) and two unaffected (U1, U2) subjects from a large 7p22‐linked FH‐II family (family 1). No mutations were found.

The RBaK and PMS2 distal promoters were sequenced to –2150 bp from the transcription start site for RBaK and–2800 bp for PMS2. Five unreported single nucleotide polymorphisms (SNPs) were found in subjects A1, A2 but not in U1 or U2; A(–2031 bp)T, T(–2030 bp)G, G(–834 bp)C, C(–821 bp)G in RBaK and A(–876 bp)G in PMS2. Additional affected and unaffected subjects from family 1 and from two other 7p22‐linked FH‐II families and 58 unrelated normotensive control subjects were genotyped for these SNPs.

The five novel SNPs were found to be present in a significant proportion of normotensive controls. The four RBaK promoter SNPs were found to be in linkage disequilibrium in the normal population. The RBaK promoter (–)2031T/2030G/834C/821T allele was found to be in linkage disequilibrium with the causative mutation in FH‐II family 1, but not in families 2 and 3. The PMS2 promoter (–)876G allele was also found to be linked to affected phenotypes in family 1.

The RBaK and PMS2 promoter SNPs alter the binding sites for several transcription factors. Although present in the normal population, it is possible that the RBaK (–)2031T/2030G/834C/821T and PMS2 (–)876G alleles may have functional roles contributing to the FH‐II phenotype in family 1.
TIME‐COURSE REDUCTION OF RENAL FUNCTION IN RATS ON HIGH SODIUM INTAKE: ACUTE REVERSAL BY POTASSIUM CANRENOATE
Authors: Rugale Caroline , Cordaillat Magali , Mimran Albert , Jover Bernard
Published: February 2008

Time course of renal alterations associated with long‐term (since weaning) administration of a high sodium (HS, 8% NaCl) diet was assessed in Sprague‐Dawley rats. Reversal by acute administration of the mineralocorticoid receptor antagonist, potassium canrenoate (40 mg/kg, i.p.) or the type 1 angiotensin II receptor antagonist, losartan (10 mg/kg, i.v.), was evaluated at the age of 5 months (i.e. after 21 weeks of HS feeding).

High sodium intake had no detectable effect on blood pressure; however, albuminuria was always higher in the HS than control group. Glomerular filtration rate, renal plasma flow and filtration fraction decreased significantly after 12 weeks of HS diet by approximately 50, 30 and 20%, respectively. Canrenoate was effective and markedly reversed the renal hypofiltration associated with HS feeding without change in systemic blood pressure. In contrast, losartan reduced blood pressure and it was devoid of a beneficial effect on renal function.

The present observations indicate that hypofiltration and hypoperfusion of the kidney occurred progressively and require a long period of exposure to a high sodium intake. Albuminuria, which increased before detectable changes in renal function, may represent an early marker of renal dysfunction. The beneficial effect of acute administration of potassium canrenoate favours the participation of aldosterone, at least partially, in the sustained deterioration of renal function after 21 weeks of high sodium feeding.
RENIN INHIBITION WITH ALISKIREN
Authors: Wuerzner Grégoire , Azizi Michel
Published: February 2008

Initial attempts to inhibit renin in humans have faced numerous difficulties. Molecular modelling and X‐ray crystallography of the active site of renin have led to the development of new orally active renin inhibitors, such as aliskiren.

Aliskiren has a low bioavailality (between 2.6 and 5.0%) compensated by its high potency to inhibit renin (IC50: 0.6 nmol/L) and a long plasma half‐life (23–36 h), which makes it suitable for once‐daily dosing.

The once‐daily administration of aliskiren to hypertensive patients lowers BP as strongly as standard doses of established angiotensin II type 1 (AT1) receptor blockers (losartan, valsartan, irbesartan), hydrochlorothiazide, angiotensin converting enzyme inhibitors (ramipril and lisinopril) or long acting calcium channel blockers (amlodipine). In combination therapy, aliskiren further decreases blood pressure when combined with either hydrochlorothiazide, amlodipine, irbesartan or ramipril.

The biochemical consequences of renin inhibition differ from those of angiotensin I‐converting enzyme (ACE) inhibition and Ang II antagonism, particularly in terms of angiotensin profiles and interactions with the bradykinin‐nitric oxide‐cyclic guanosine monophosphate pathway and possibly the (pro)renin receptor.

Blockade of the renin angiotensin system (RAS) with ACE inhibitors, AT1 receptor blockers or a combination of these drugs has become one of the most successful therapeutic approaches in medicine. However, it remains unclear how to optimize RAS blockade to maximize cardiovascular and renal benefits. In this context, renin inhibition to render the RAS fully quiescent is a new possibility requiring further study.