bluuebunny/crossref_metadata_2025 huggingface dataset:
The KCNQ5 potassium channel mediates a component of the afterhyperpolarization current in mouse hippocampus
Authors: Tzingounis Anastassios V. , Heidenreich Matthias , Kharkovets Tatjana , Spitzmaul Guillermo , Jensen Henrik S. , Nicoll Roger A. , Jentsch Thomas J.
Published: May 2010

Mutations in KCNQ2 and KCNQ3 voltage-gated potassium channels lead to neonatal epilepsy as a consequence of their key role in regulating neuronal excitability. Previous studies in the brain have focused primarily on these KCNQ family members, which contribute to M-currents and afterhyperpolarization conductances in multiple brain areas. In contrast, the function of KCNQ5 (Kv7.5), which also displays widespread expression in the brain, is entirely unknown. Here, we developed mice that carry a dominant negative mutation in the KCNQ5 pore to probe whether it has a similar function as other KCNQ channels. This mutation renders KCNQ5dn-containing homomeric and heteromeric channels nonfunctional. We find thatKcnq5dn/dnmice are viable and have normal brain morphology. Furthermore, expression and neuronal localization of KCNQ2 and KCNQ3 subunits are unchanged. However, in the CA3 area of hippocampus, a region that highly expresses KCNQ5 channels, the medium and slow afterhyperpolarization currents are significantly reduced. In contrast, neither current is affected in the CA1 area of the hippocampus, a region with low KCNQ5 expression. Our results demonstrate that KCNQ5 channels contribute to the afterhyperpolarization currents in hippocampus in a cell type-specific manner.
Cluster of Pseudoinfections withBurkholderia cepaciaAssociated with a Contaminated Washer-Disinfector in a Bronchoscopy Unit
Authors: Rosengarten Dror , Block Colin , Hidalgo-Grass Carlos , Temper Violeta , Gross Ilana , Budin-Mizrahi Anna , Berkman Neville , Benenson Shmuel
Published: May 2010

In December 2008, bronchoalveolar lavage fluid samples obtained from 3 patients were positive forBurkholderia cepaciacomplex on culture. Samples obtained from bronchoscopes and rinse-water samples obtained from the washer-disinfector were found to be positive forB. cepaciacomplex. The cause of this pseudo-outbreak was that the washer-disinfector was installed without the required antibacterial filter.
Physics of magnetic resonance imaging: from spin to pixel
Authors: Gossuin Yves , Hocq Aline , Gillis Pierre , Quoc Lam Vuong
Published: May 2010

Magnetic resonance imaging has become a major diagnostic tool in modern medicine. MRI makes it possible to obtain highly contrasted body images without ionizing radiation. Using the magnetic properties of hydrogen protons, MRI is at the crossroads between physics, electronics, signal processing and informatics. In this introductory text, the basic physical principles of MRI image formation are explained. Some important clinical applications are also presented.
SPICE modelling of magnetic tunnel junctions written by spin-transfer torque
Authors: Guo W , Prenat G , Javerliac V , Baraji M El , de Mestier N , Baraduc C , Diény B
Published: May 2010

Spintronics aims at extending the possibility of conventional electronics by using not only the charge of the electron but also its spin. The resulting spintronic devices, combining the front-end complementary metal oxide semiconductor technology of electronics with a magnetic back-end technology, employ magnetic tunnel junctions (MTJs) as core elements. With the intent of simulating a circuit without fabricating it first, a reliable MTJ electrical model which is applicable to the standard SPICE (Simulation Program with Integrated Circuit Emphasis) simulator is required. Since such a model was lacking so far, we present a MTJ SPICE model whose magnetic state is written by using the spin-transfer torque effect. This model has been developed in the C language and validated on the Cadence Virtuoso Platform with a Spectre simulator. Its operation is similar to that of the standard BSIM (Berkeley Short-channel IGFET Model) SPICE model of the MOS transistor and fully compatible with the SPICE electrical simulator. The simulation results obtained using this model have been found in good accord with those theoretical macrospin calculations and results.
Incidence of in situ annealing on the nanoscale topographical/electrical properties of the tunnel barrier in sputtered epitaxial Fe/MgO/Fe multilayers
Authors: Kim D J , Arabski J , Costa V Da , Schmerber G , Bowen M , Boukari S , Beaurepaire E
Published: May 2010

Technological improvements in the magnetotransport performance of Fe/MgO/Fe stacks require nanoscale control over the topographical and electrical properties of the ultrathin MgO barrier. We have statistically investigated the incidence of in situ annealing of the lower Fe layer on the nanoscale topographical/electrical properties of Fe/MgO bilayers and the structural and magnetic properties of Fe/MgO/Fe/Co multilayers prepared by sputtering. This annealing step improves the crystal quality of both the lower Fe and the upper Fe/Co layers, leading to an enhanced saturated magnetic moment. Finally, this annealing step substantially mitigates the presence of nanohills on the lower Fe layer and improves the uniformity of the height and/or the thickness of the MgO tunnel barrier. Our results pave the way for studies of nanoscale transport on micrometre-sized devices through a better understanding of, and control over, nanoscale hotspots in the tunnel barrier.
Influence of Co layer thickness on the structural and magnetic properties of
multilayers
Authors: Zarefy A , Lechevallier L , Lardé R , Chiron H , Le Breton J-M , Baltz V , Rodmacq B , Dieny B
Published: May 2010

The correlated effects of the insertion of a Pt spacer between ferromagnetic and antiferromagnetic layers and of the variation of the Co layers' thickness on the structural and magnetic properties of
multilayers have been studied. Samples with n = 1 and 7, t
Co = 0.4 and 0.6 nm, t
Pt = 0 and 0.4 nm have been investigated by tomographic atom probe and superconducting quantum interference device magnetometry. For spacer-free samples (t
Pt = 0), the structural investigation shows that when t
Co = 0.4 nm, Mn and Ir atoms diffuse deeply into the (Pt/Co)3 multilayers. In contrast for t
Co = 0.6 nm, the Mn and Ir diffusion is much reduced. Because Pt acts as a barrier against the Mn and Ir diffusion, this difference is less pronounced in samples with Pt insertion. The hysteresis loops shapes, the exchange bias fields and the saturation magnetization values were correlated with the structural properties of these samples and discussed, taking into account the susceptibility, exchange stiffness and perpendicular magnetic anisotropy.
Influence of edge roughness on graphene nanoribbon resonant tunnelling diodes
Authors: Liang Gengchiau , Khalid Sharjeel Bin , Lam Kai-Tak
Published: May 2010

The edge roughness effects of graphene nanoribbons on their application in resonant tunnelling diodes with different geometrical shapes (S, H and W) were investigated. Sixty samples for each 5%, 10% and 15% edge roughness conditions of these differently shaped graphene nanoribbon resonant tunnelling diodes were randomly generated and studied. Firstly, it was observed that edge roughness in the barrier regions decreases the effective barrier height and thickness, which increases the broadening of the quantized states in the quantum well due to the enhanced penetration of the wave-function tail from the electrodes. Secondly, edge roughness increases the effective width of the quantum well and causes the lowering of the quantized states. Furthermore, the shape effects on carrier transport are modified by edge roughness due to different interfacial scattering. Finally, with the effects mentioned above, edge roughness has a considerable impact on the device performance in terms of varying the peak-current positions and degrading the peak-to-valley current ratio.
Influence of temperature and illumination on the electrical properties of p-ZnTe/n-CdTe heterojunction grown by molecular beam epitaxy
Authors: Farag A A M , Yahia I S , Wojtowicz T , Karczewski G
Published: May 2010

A set of p-ZnTe/n-CdTe heterojunctions were grown on conducting GaAs substrates by molecular beam epitaxy. The current density–voltage (J–V) and capacitance–voltage (C–V) characteristics measured in the temperature range 300–400 K were analysed in order to reveal the dominant carrier transport mechanisms through the junctions. The C–V measurements show that the device is linearly graded. The temperature dependence of the built-in potential and the impurity gradient of the device were determined. The deep defect states govern the current flow through the junctions. The measurements under the lower voltage region (V < 0.35 V) reveal at the p-ZnTe/n-CdTe interface, the presence of deep defect states with the activation energy of 0.52 eV. Under the higher forward bias voltage (V > 0.35 V), the space-charge-limited current governed the J–V characteristics with a single traps level, ΔE
t = 0.55 eV. The p-ZnTe/n-CdTe device under different illumination intensities exhibit a significant photosensitivity proving that this kind of heterostructure can be regarded as a good candidate for photodiode applications.
On basic processes sustaining constricted glow discharge in longitudinal N2 flow at atmospheric pressure
Authors: Akishev Yu , Grushin M , Karalnik V , Petryakov A , Trushkin N
Published: May 2010

The results of numerical calculations on a steady-state constricted discharge in N2 flow at atmospheric pressure are presented. Basic elementary processes responsible for sustaining the constricted discharge at low and high currents are found. It is shown that the charged particle generation in both regimes is controlled predominantly by an associative ionization
. However, metastable states are created in these regimes by different processes. In low-current discharge N2(A) and N2(a′) metastables are created due to mutual collisions of the vibrationally excited molecules, and their collision frequency is determined by the vibration energy distribution function. In high-current discharge these metastables are excited by energetic electrons, and inelastic collision frequency is determined by the electron energy distribution function. The charged particle dynamic balance in the high-current constricted discharge in atmospheric pressure N2 is non-local and sustained by ionization and ambipolar diffusion like that in a low-current diffusive discharge in a tube at low pressure. It was demonstrated that blowing of the discharge by longitudinal gas flow leads to a more pronounced constriction.
A study of ternary Cu2SnS3 and Cu3SnS4 thin films prepared by sulfurizing stacked metal precursors
Authors: Fernandes P A , Salomé P M P , Cunha A F da
Published: May 2010

Thin films of Cu2SnS3 and Cu3SnS4 were grown by sulfurization of dc magnetron sputtered Sn–Cu metallic precursors in a S2 atmosphere. Different maximum sulfurization temperatures were tested which allowed the study of the Cu2SnS3 phase changes. For a temperature of 350 °C the films were composed of tetragonal (I-42m) Cu2SnS3. The films sulfurized at a maximum temperature of 400 °C presented a cubic (F-43m) Cu2SnS3 phase. On increasing the temperature up to 520 °C, the Sn content of the layer decreased and orthorhombic (Pmn21) Cu3SnS4 was formed. The phase identification and structural analysis were performed using x-ray diffraction (XRD) and electron backscattered diffraction (EBSD) analysis. Raman scattering analysis was also performed and a comparison with XRD and EBSD data allowed the assignment of peaks at 336 and 351 cm−1 for tetragonal Cu2SnS3, 303 and 355 cm−1 for cubic Cu2SnS3, and 318, 348 and 295 cm−1 for the Cu3SnS4 phase. Compositional analysis was done using energy dispersive spectroscopy and induced coupled plasma analysis. Scanning electron microscopy was used to study the morphology of the layers. Transmittance and reflectance measurements permitted the estimation of absorbance and band gap. These ternary compounds present a high absorbance value close to 104 cm−1. The estimated band gap energy was 1.35 eV for tetragonal (I-42m) Cu2SnS3, 0.96 eV for cubic (F-43m) Cu2SnS3 and 1.60 eV for orthorhombic (Pmn21) Cu3SnS4. A hot point probe was used for the determination of semiconductor conductivity type. The results show that all the samples are p-type semiconductors. A four-point probe was used to obtain the resistivity of these samples. The resistivities for tetragonal Cu2SnS3, cubic Cu2SnS3 and orthorhombic (Pmn21) Cu3SnS4 are 4.59 × 10−2 Ω cm, 1.26 × 10−2 Ω cm, 7.40 × 10−4 Ω cm, respectively.
Comparison of Sasang Constitutional Medicine, Traditional Chinese Medicine and Ayurveda
Authors: Kim Jong Yeol , Pham Duong Duc , Koh Byung Hee
Published: May 2010

Sasang constitutional medicine (SCM), traditional Chinese medicine (TCM) and Ayurveda are three different forms of Asian traditional medicine. Although these traditions share a lot in common as holistic medicines, the different philosophical foundations found in each confer distinguishing attributes and unique qualities. SCM is based on a constitution‐based approach, and is in this way relatively more similar to the Ayurvedic tradition than to the TCM, although many of the basic SCM theories were originally derived from TCM, a syndrome‐based medicine. SCM and TCM use the same botanical materials that are distributed mainly in the East Asian region, but the basic principles of usage and the underlying rationale are completely different from each other. Meanwhile, the principles of the Ayurvedic use of botanical resources are very similar to those seen in SCM, but the medicinal herbs used in Ayurveda generally originate from the West Asian region which displays a different spectrum of flora.
Rebuilding depleted fish stocks: biology, ecology, social science, and management strategies
Authors: Hammer Cornelius , Kjesbu Olav Sigurd , Kruse Gordon H. , Shelton Peter A.
Published: May 2010

Hammer, C., Kjesbu, O. S., Kruse, G. H., and Shelton, P. A. 2010. Rebuilding depleted fish stocks: biology, ecology, social science, and management strategies. – ICES Journal of Marine Science, 67: 1825–1829. This is an introduction to an ICES/PICES symposium entitled as in the title of this manuscript. During the symposium, five theme sessions embraced the subject material under the headings “Impact of fisheries and environmental impacts on stock structure, reproductive potential, and recruitment dynamics”, “Trophic controls on stock recovery”, “Methods for analysing and modelling stock recovery”, “Social and economic aspects of fisheries management and governance”, and “Management and recovery strategies”. A panel discussion provided a valuable overview of current understanding and research focus.
Morphological and genetic evidence that Octopus vulgaris Cuvier, 1797 inhabits Amsterdam and Saint Paul Islands (southern Indian Ocean)
Authors: Guerra Ángel , Roura Álvaro , González Ángel F. , Pascual Santiago , Cherel Yves , Pérez-Losada Marcos
Published: May 2010

Guerra, Á., Roura, Á., González, Á. F., Pascual, S., Cherel, Y., and Pérez-Losada, M. 2010. Morphological and genetic evidence that Octopus vulgaris Cuvier, 1797 inhabits Amsterdam and Saint Paul Islands (southern Indian Ocean). – ICES Journal of Marine Science, 67: 1401–1407. The coastal octopus at Saint Paul and Amsterdam Islands is Octopus vulgaris Cuvier 1797. Meristic and morphological characters, along with phylogenetic analysis of COI and COIII DNA sequences, were used to identify 11 animals collected in 2000 or 2001. The range of the species is therefore expanded to include the oceanic islands of the central southern Indian Ocean. The trees also depicted the genus Octopus as polyphyletic and O. vulgaris sense Cuvier or sensu stricto as monophyletic.
Parental Perceptions of Research After Completion of Placebo‐controlled Trials in Pediatric Gastroenterology
Authors: Perez Maria E , Langseder Annette , Lazar Eric , Youssef Nader N
Published: May 2010

Background and Objectives:

Investigators may have concerns that parents will not allow their children to participate in placebo‐controlled trials (PCTs). The aim of the present study was to identify potential differences between parental perceptions in families who successfully completed (CO) a clinical trial compared with those who were noncompleters (NC).

Patients and Methods:

Parents of both CO and NC children enrolled in pediatric gastrointestinal studies performed in the previous year were eligible. NC were defined as those who were screen failures or treatment nonresponders or had adverse events. One hundred seven parents were identified and mailed a 26‐item questionnaire eliciting perceptions regarding participation in research. Questionnaires were sent 6 months after participation in research ended.

Results:

Seventy‐eight (69%) parents returned the survey. Characteristics included maternal responders (98%), English as primary language (97%), and education beyond high school (85%). Five parents (4.7%) had children involved in previous research trials. There were no significant differences in responses found between CO (n = 49; 63%) and NC (n = 29; 37%) in regard to importance of research, perceptions of risk to child, benefits to child, and more attention in the study. Statistical significance was approached in regard to the comfort with the research team, with a greater portion of CO stating that the researcher put the parent at ease and the NC feeling less positive about the interaction (P = 0.05).

Conclusions:

A positive perception about participation in research is not stratified by successful completion of a PCT. These results should encourage investigators and institutional review boards that if properly designed and conducted, pediatric PCTs can result in a positive experience for parents.
A Comparison of Presentation and Management Trends in Acute Pancreatitis Between Infants/Toddlers and Older Children
Authors: Park Alexander J , Latif Sahibzada U , Ahmad Mahwish U , Bultron Gilberto , Orabi Abrahim I , Bhandari Vineet , Husain Sohail Z
Published: May 2010

Objectives:

Acute pancreatitis is a necroinflammatory disease that leads to 210,000 hospitalizations in the United States annually. Recent reports suggest that there may be important differences in clinical features between infants/toddlers and older children. Thus, in this study we make a direct comparison between the pediatric age groups in presentation and management trends of acute pancreatitis.

Patients and Methods:

We examined all children (ages 0 to 20 years) admitted to Yale‐New Haven Children's Hospital with pancreatitis between 1994 and 2007.

Results:

Two hundred seventy‐one cases met inclusion criteria for acute pancreatitis. Infants and toddlers manifested fewer signs and symptoms of abdominal pain, epigastric tenderness, and nausea compared with older children (43% vs 93%; 57% vs 90%; and 29% vs 76%, respectively; P < 0.05 for all comparisons). They were more likely to be diagnosed by serum lipase than by amylase and to undergo radiographic evaluation (P < 0.05). They had a longer hospital stay (19.5 vs 4 days; P < 0.05) and were less likely to be directly transitioned to oral nutrition (14% vs 71%; P < 0.05).

Conclusions:

Infants and toddlers with acute pancreatitis present with fewer classical symptoms and are managed differently from older children. We believe these data will be helpful in evaluating and understanding treatment practices in this age group.
Development and Assessment of a Modified Pediatric Crohn Disease Activity Index
Authors: Leach Steven T , Nahidi Lily , Tilakaratne Samantha , Day Andrew S , Lemberg Daniel A
Published: May 2010

The Pediatric Crohn Disease Activity Index (PCDAI) is an established and validated measure of disease activity in children with Crohn disease. However, its use in the research setting can be limited because of ambiguity of the subjective and anthropometric components of the index. Here we propose and evaluate a modified PCDAI (Mod PCDAI) consisting of the laboratory measures of the PCDAI plus C‐reactive protein. This Mod PCDAI can provide an indication of disease activity because it correlates with the PCDAI, physicians' global assessment, and fecal calprotectin, and therefore may provide a suitable alternative to the PCDAI when required.
Gastric Electrical Activity Becomes Abnormal in the Upright Position in Patients With Postural Tachycardia Syndrome
Authors: Safder Shaista , Chelimsky Thomas C , O'Riordan Mary Ann , Chelimsky Gisela
Published: May 2010

Objectives:

Some patients with functional abdominal pain report worsening of symptoms in the upright position. Many of these have a postural tachycardia syndrome (POTS). We investigated whether the electrical activity of the stomach changes during the upright portion of a tilt table test in patients with and without POTS.

Patients and Methods:

All of the children undergoing autonomic testing were offered enrollment in this institutional review board–approved prospective study between October 2007 and January 2009. Electrogastrography was recorded 10 minutes in the supine position and during the entire upright portion of tilt. Children were divided into 2 groups: POTS and No‐POTS. Findings were correlated with this grouping using Fisher exact test and either Student t test or Wilcoxon rank sum test as appropriate.

Results:

Forty‐nine patients participated (35 girls), with a mean age of 14.7 + 3.5 years, 25 with POTS and 24 without. The POTS and No‐POTS groups did not differ in baseline normal gastric activity. The change from supine to standing showed a significant difference in the electrogastrographic tracing between the POTS and No‐POTS groups (P < 0.04–0.09), best seen in channels 1 and 4. In particular, gastric activity became more abnormal in the upright position in the POTS group, whereas the opposite occurred in the No‐POTS group.

Conclusions:

The electrical activity of the stomach changes during the upright position in children with POTS, but not in children without this diagnosis. These changes could relate to their report of worsening pain in the upright position.
β‐Carotene Deficiency in Cholestatic Liver Disease of Childhood Is Caused by β‐Carotene Malabsorption
Authors: Socha Piotr , Skorupa Ewa , Pawlowska Joanna , Wierzbicka Aldona , Dhawan Anil , Jankowska Irena , Karczmarewicz Ela , Kubalska Jolanta , Łukaszkiewicz Jacek , Lorenc Roman
Published: May 2010

Background:

Depletion of β‐carotene (b‐c) has not been extensively studied in children with chronic cholestatic liver disease.

Patients and Methods:

We assessed b‐c serum concentration in 53 children with cholestatic liver disease: 19 patients operated on for biliary atresia, 12 with Alagille syndrome, and 22 with progressive familial intrahepatic cholestasis. To test b‐c absorption, 6 children with chronic cholestasis received a load of 10 mg b‐c/kg body weight.

Results:

We found decreased b‐c concentrations in 45 patients. The absorption of b‐c was not detectable in 5 of 6 children studied.

Conclusions:

b‐c depletion is a common problem of chronic cholestatic liver disease in childhood that can be attributed to disturbed intestinal absorption.
Intestinal Microbiota of 6‐week‐old Infants Across Europe: Geographic Influence Beyond Delivery Mode, Breast‐feeding, and Antibiotics
Authors: Fallani Matteo , Young David , Scott Jane , Norin Elisabeth , Amarri Sergio , Adam Rüdiger , Aguilera Marga , Khanna Sheila , Gil Angel , Edwards Christine A , Doré Joël ,   Other Members of the INFABIO Team
Published: May 2010

Objectives:

There are many differences in diet and lifestyle across Europe that may influence the development of the infant gut microbiota. This work aimed to assess the impact of geographic area, mode of delivery, feeding method, and antibiotic treatment on the fecal microbiota of infants from 5 European countries with different lifestyle characteristics: Sweden, Scotland, Germany, Italy, and Spain.

Patients and Methods:

Fecal samples from 606 infants (age 6 weeks) recruited within the European project INFABIO were analyzed by fluorescent in situ hybridization combined with flow cytometry using a panel of 10 rRNA targeted group‐ and species‐specific oligonucleotide probes. Information on factors potentially affecting gut microbiota composition was collected with questionnaires and associations were evaluated with multivariate analyses.

Results:

The Bifidobacterium genus was predominant (40% average proportion of total detectable bacteria), followed by Bacteroides (11.4%) and enterobacteria (7.5%). Northern European countries were associated with higher proportions of bifidobacteria in infant feces, whereas a more diverse microbiota with more bacteroides characterized southern countries. Bifidobacteria dominated the microbiota of breast‐fed infants, whereas formula‐fed babies had significantly higher proportions of Bacteroides and members of the Clostridium coccoides and Lactobacillus groups. Newborns delivered by cesarean section or from mothers treated with antibiotics perinatally had lower proportions of Bacteroides and members of the Atopobium cluster.

Conclusions:

Delivery mode and feeding method influenced the fecal microbiota of European infants at 6 weeks, as expected, but the effect of country of birth was more pronounced, with dominant bifidobacteria in northern countries and greater early diversification in southern European countries.
Medical Management of Alagille Syndrome
Authors: Kamath Binita M , Loomes Kathleen M , Piccoli David A
Published: May 2010

Alagille syndrome is a highly variable, autosomal dominant disorder that affects the liver, heart, eyes, face, skeleton, kidneys, and vascular system. Much has been learned about the genetics of this disorder, which is caused primarily by mutations in the Notch signaling pathway ligandJAGGED1; however, the medical management of this condition is complex and continues to generate controversy. The significant variability of organ involvement requires the managing physician to have an understanding of the breadth and interplay of the variable manifestations. Furthermore, the liver disease in particular requires an appreciation of the natural history and evolution of the profound cholestasis.
Purified chicken intestinal mucin attenuates Campylobacter jejuni pathogenicity in vitro
Authors: Alemka Abofu , Whelan Sarah , Gough Ronan , Clyne Marguerite , Gallagher Mary E. , Carrington Stephen D. , Bourke Billy
Published: May 2010

Campylobacter jejuni is a major causative agent of diarrhoeal disease worldwide in the human population. In contrast, heavy colonization of poultry typically does not lead to disease and colonized chickens are a major source of Campylobacter infections in humans. Previously, we have shown that chicken (but not human) intestinal mucus inhibits C. jejuni internalization. In this study, we test the hypothesis that chicken mucin, the main component of mucus, is responsible for this inhibition of C. jejuni virulence. Purified chicken intestinal mucin attenuated C. jejuni binding and internalization into HCT-8 cells depending on the site of origin of the mucin (large intestine>small intestine>caecum). C. jejuni invasion of HCT-8 cells was preferentially inhibited compared to bacterial binding to cells. Exposure of the mucin to sodium metaperiodate recovered bacterial invasion levels, suggesting a glycan-mediated effect. However, fucosidase or sialidase pre-treatment of mucin failed to abrogate the inhibition of C. jejuni pathogenicity. In conclusion, differences in the composition of chicken and human intestinal mucin may contribute to the differential outcome of Campylobacter infection of these hosts.
Prevalence of varicella-zoster virus genotypes in Australia characterized by high-resolution melt analysis and ORF22 gene analyses
Authors: Toi Cheryl S. , Dwyer Dominic E.
Published: May 2010

DNA sequence variation analysis has divided varicella-zoster virus (VZV; Human herpesvirus 3) into distinct geographical clades: European, Asian, African and Japanese. These genotypes are becoming increasingly prevalent within regions atypical to their original source and there has been the suggestion of recombination between genotypes. Seventy-eight clinical isolates from hospitalized patients with varicella were collected in New South Wales, the Northern Territory, Western Australia and Victoria from 2006 to 2009. The wild-type strains and the vaccine strain (vOka) were differentiated by single nucleotide polymorphism detection using high-resolution melt analysis of five target genes (ORF1, -21, -37, -60 and -62), and by DNA sequence analysis of a 484 bp region of ORF22. Phylogenetic analysis showed that 46 % (36/78) of the clinical isolates were European clade 1 (C/E1) strains, 21 % (16/78) were European clade 3 (B/E2) strains, 12 % (9/78) were Asian/African clade 5 (A/M1) strains, 10 % (8/78) were clade 4 (J2/M2), 6 % (5/78) were clade 2 (J/J) and 5 % (4/78) belonged to the novel clade VI. No significant association was shown between VZV genotype and region, age or gender. Although European strains were most common, the results suggest an increase in African/Asian, Japanese and clade VI genotypes circulating in Australia.
Binding and degradation of fibrinogen by Bacteroides fragilis and characterization of a 54 kDa fibrinogen-binding protein
Authors: Houston Simon , Blakely Garry W. , McDowell Andrew , Martin Lorraine , Patrick Sheila
Published: May 2010

Bacteroides fragilisis a bacterium that resides in the normal human gastro-intestinal tract; however, it is also the most commonly isolated Gram-negative obligate anaerobe from human clinical infections, such as intra-abdominal abscesses, and the most common cause of anaerobic bacteraemia. Abscess formation is important in bacterial containment, limiting dissemination of infection and bacteraemia. In this study, we investigatedB. fragilisbinding and degradation of human fibrinogen, the major structural component involved in fibrin abscess formation. We have shown thatB. fragilisNCTC9343 binds human fibrinogen. A putativeBacteroidesfragilisfibrinogen-binding protein, designated BF-FBP, identified in the genome sequence of NCTC9343, was cloned and expressed inEscherichia coli. The purified recombinant BF-FBP bound primarily to the human fibrinogen Bβ-chain. In addition, we have identified fibrinogenolytic activity inB. fragilisexponential phase culture supernatants, associated with fibrinogenolytic metalloproteases in NCTC9343 and 638R, and cysteine protease activity in YCH46. All nine clinical isolates ofB. fragilisexamined degraded human fibrinogen; with eight isolates, initial Aα-chain degradation was observed, with varying Bβ-chain andγ-chain degradation. With one blood culture isolate, Bβ-chain andγ-chain degradation occurred first, followed by subsequent Aα-chain degradation. Our data raise the possibility that the fibrinogen-binding protein ofB. fragilis, along with a variety of fibrinogenolytic proteases, may be an important virulence factor that facilitates dissemination of infection via reduction or inhibition of abscess formation.
Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors
Authors: Ogasawara Hiroshi , Yamada Kayoko , Kori Ayako , Yamamoto Kaneyoshi , Ishihama Akira
Published: May 2010

Under stressful conditions in nature, Escherichia coli forms biofilms for long-term survival. Curli fimbriae are an essential architecture for cell–cell contacts within biofilms. Structural components and assembly factors of curli are encoded by two operons, csgBA and csgDEFG. The csgD gene product controls transcription of both operons. Reflecting the response of csgD expression to external stresses, a number of transcription factors participate in the regulation of the csgD promoter. Analysis of the csgD mRNA obtained from E. coli mutants in different transcription factors indicated that CpxR and H-NS act as repressors while OmpR, RstA and IHF act as activators. An acid-stress response regulator, RstA, activates csgD only under acidic conditions. These five factors bind within a narrow region of about 200 bp upstream of the csgD promoter. After pair-wise promoter-binding assays, the increase in csgD transcription in the stationary phase was suggested to be due, at least in part, to the increase in IHF level cancelling the silencing effect of H-NS. In addition, we propose a novel regulation model of this complex csgD promoter through cooperation between the two positive factors (OmpR–IHF and RstA–IHF) and also between the two negative factors (CpxR–H-NS).
Siderophore-mediated iron acquisition in Bacillus anthracis and related strains
Authors: Hotta Kinya , Kim Chu-Young , Fox David T. , Koppisch Andrew T.
Published: May 2010

Recent observations have shed light on some of the endogenous iron-acquisition mechanisms of members of the Bacillus cereus
sensu
lato group. In particular, pathogens in the B. cereus group use siderophores with both unique chemical structures and biological roles. This review will focus on recent discoveries in siderophore biosynthesis and biology in this group, which contains numerous human pathogens, most notably the causative agent of anthrax, Bacillus anthracis.
Outer membrane pore protein prediction in mycobacteria using genomic comparison
Authors: Mah Nancy , Perez-Iratxeta Carolina , Andrade-Navarro Miguel A.
Published: May 2010

Proteins responsible for outer membrane transport across the unique membrane structure of Mycobacterium spp. are attractive drug targets in the treatment of human diseases caused by the mycobacterial pathogens, Mycobacterium tuberculosis, M. bovis, M. leprae and M. ulcerans. In contrast with Escherichia coli, relatively few outer-membrane proteins (OMPs) have been identified in Mycobacterium spp., largely due to the difficulties in isolating mycobacterial membrane proteins and our incomplete understanding of secretion mechanisms and cell wall structure in these organisms. To further expand our knowledge of these elusive proteins in mycobacteria, we have improved upon our previous method of OMP prediction in mycobacteria by taking advantage of genomic data from seven mycobacteria species. Our improved algorithm suggests 4333 sequences as putative OMPs in seven species with varying degrees of confidence. The most virulent pathogenic mycobacterial species are slightly enriched in these selected sequences. We present examples of predicted OMPs involved in horizontal transfer and paralogy expansion. Analysis of local secondary structure content allowed identification of small domains predicted to perform as OMPs; some examples show their involvement in events of tandem duplication and domain rearrangements. We discuss the taxonomic distribution of these discovered families and architectures, often specific to mycobacteria or the wider taxonomic class of Actinobacteria. Our results suggest that OMP functionality in mycobacteria is richer than expected and provide a resource to guide future research of these understudied proteins.
Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis
Authors: Fong Jiunn C. N. , Syed Khalid A. , Klose Karl E. , Yildiz Fitnat H.
Published: May 2010

Biofilm formation enhances the survival and persistence of the facultative human pathogenVibrio choleraein natural ecosystems and its transmission during seasonal cholera outbreaks. A major component of theV. choleraebiofilm matrix is theVibriopolysaccharide (VPS), which is essential for development of three-dimensional biofilm structures. Thevpsgenes are clustered in two regions, thevps-I cluster (vpsU,vpsA–K, VC0916–27) and thevps-II cluster (vpsL–Q, VC0934–39), separated by an intergenic region containing therbmgene cluster that encodes biofilm matrix proteins. In-frame deletions of thevpsclusters and genes encoding matrix proteins drastically altered biofilm formation phenotypes. To determine which genes within thevpsgene clusters are required for biofilm formation and VPS synthesis, we generated in-frame deletion mutants for all thevpsgenes. Many of these mutants exhibited reduced capacity to produce VPS and biofilms. Infant mouse colonization assays revealed that mutants lacking eithervpsclusters orrbmA(encoding secreted matrix protein RbmA) exhibited a defect in intestinal colonization compared to the wild-type. Understanding the roles of the variousvpsgene products will aid in the biochemical characterization of the VPS biosynthetic pathway and elucidate howvpsgene products contribute to VPS biosynthesis, biofilm formation and virulence inV. cholerae.
Overexpression of AtDOF4.7, an Arabidopsis DOF Family Transcription Factor, Induces Floral Organ Abscission Deficiency in Arabidopsis
Authors: Wei Peng-Cheng , Tan Feng , Gao Xin-Qi , Zhang Xiu-Qing , Wang Gao-Qi , Xu Heng , Li Li-Juan , Chen Jia , Wang Xue-Chen
Published: May 2010

After flower pollination, a programmed process called abscission occurs in which unwanted floral organs are actively shed from the main plant body. We found that a member of the DOF (for DNA binding with one finger) transcription factor family, Arabidopsis (Arabidopsis thaliana) DOF4.7, was expressed robustly in the abscission zone. The Arabidopsis 35S::AtDOF4.7 lines with constitutive expression of AtDOF4.7 exhibited an ethylene-independent floral organ abscission deficiency. In these lines, anatomical analyses showed that the formation of the abscission zone was normal. However, dissolution of the middle lamella failed to separate between the cell walls. AtDOF4.7 was identified as a nucleus-localized transcription factor. This protein had both in vitro and in vivo binding activity to typical DOF cis-elements in the promoter of an abscission-related polygalacturonase (PG) gene, PGAZAT. Overexpression of AtDOF4.7 resulted in down-regulation of PGAZAT. AtDOF4.7 interacted with another abscission-related transcription factor, Arabidopsis ZINC FINGER PROTEIN2. Taken together, our results suggest that AtDOF4.7 participates in the control of abscission as part of the transcription complex that directly regulates the expression of cell wall hydrolysis enzymes.
Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants
Authors: Nakagami Hirofumi , Sugiyama Naoyuki , Mochida Keiichi , Daudi Arsalan , Yoshida Yuko , Toyoda Tetsuro , Tomita Masaru , Ishihama Yasushi , Shirasu Ken
Published: May 2010

Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa  japonica ‘Nipponbare’), an economically important crop. Using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins. To investigate the conservation of phosphoproteomes between plant species, we developed a novel phosphorylation-site evaluation method and performed a comparative analysis of rice and Arabidopsis (Arabidopsis thaliana). The ratio of tyrosine phosphorylation in the phosphoresidues of rice was equivalent to those in Arabidopsis and human. Furthermore, despite the phylogenetic distance and the use of different cell types, more than 50% of the phosphoproteins identified in rice and Arabidopsis, which possessed ortholog(s), had an orthologous phosphoprotein in the other species. Moreover, nearly half of the phosphorylated orthologous pairs were phosphorylated at equivalent sites. Further comparative analyses against the Medicago phosphoproteome also showed similar results. These data provide direct evidence for conserved regulatory mechanisms based on phosphorylation in plants. We also assessed the phosphorylation sites on nucleotide-binding leucine-rich repeat proteins and identified novel conserved phosphorylation sites that may regulate this class of proteins.
Reversible phase transition of pyridinium-3-carboxylic acid perchlorate
Authors: Ye Heng-Yun , Chen Li-Zhuang , Xiong Ren-Gen
Published: May 2010

Pyridinium-3-carboxylic acid perchlorate was synthesized and separated as crystals. Differential scanning calorimetry (DSC) measurements show that this compound undergoes a reversible phase transition at ∼ 135 K with a wide hysteresis of 15 K. Dielectric measurements confirm the transition at ∼ 127 K. Measurement of the unit-cell parameters versus temperature shows that the values of the c axis and β angle change abruptly and remarkably at 129 (2) K, indicating that the system undergoes a first-order transition at T
c = 129 K. The crystal structures determined at 103 and 298 K are all monoclinic in P21/c, showing that the phase transition is isosymmetric. The crystal contains one-dimensional hydrogen-bonded chains of the pyridinium-3-carboxylic acid cations, which are further linked to perchlorate anions by hydrogen bonds to form well separated infinite planar layers. The most distinct differences between the structures of the higher-temperature phase and the lower-temperature phase are the change of the distance between the adjacent pyridinium ring planes within the hydrogen-bonded chains and the relative displacement between the hydrogen-bonded layers. Structural analysis shows that the driving force of the transition is the reorientation of the pyridinium-3-carboxylic acid cations. The degree of order of the perchlorate anions may be a secondary order parameter.
Charge-density analysis of the ground state of a photochromic 1,10-phenanthroline zinc(II) bis(thiolate) complex
Authors: Scheins Stephan , Zheng Shao-Liang , Benedict Jason B. , Coppens Philip
Published: May 2010

The charge density of the title compound was determined at 90 K, using a spherical crystal of 150 µm diameter. The proper treatment of the Zn atom in the pseudo-tetrahedral environment is considered in detail. A satisfactory refinement is only obtained when anharmonic Gram–Charlier parameters are included as variables in the refinement. A successful combined anharmonic/multipole refinement indicates a small polarization of the 4sshell in the anisotropic environment. One of the two toluenethiols is approximately π-stacked with the phenanthroline ligand. A bond path is found connecting the two ligands. In addition the Zn—S bond to this ligand is slightly extended compared with the same bond to the second toluenethiol. A separate photocrystallographic and theoretical study indicates the long wavelength emission of the title compound to be due to a ligand-to-ligand charge transfer (LLCT) from a toluenethiol to the phenanthroline ligand. The charge-density results do not provide a basis for deciding which of the thiole ligands is the source of the transferred electron density. This result is in agreement with the theoretical calculations, which show comparable oscillator strengths for charge transfer from either of the ligands.
Persistence of the stereochemical activity of the Bi3+lone electron pair in Bi2Ga4O9up to 50 GPa and crystal structure of the high-pressure phase
Authors: Friedrich Alexandra , Juarez-Arellano Erick A. , Haussühl Eiken , Boehler Reinhard , Winkler Björn , Wiehl Leonore , Morgenroth Wolfgang , Burianek Manfred , Mühlberg Manfred
Published: May 2010

The crystal structure of the high-pressure phase of bismuth gallium oxide, Bi2Ga4O9, was determined up to 30.5 (5) GPa fromin situsingle-crystal in-house and synchrotron X-ray diffraction. Structures were refined at ambient conditions and at pressures of 3.3 (2), 6.2 (3), 8.9 (1) and 14.9 (3) GPa for the low-pressure phase, and at 21.4 (5) and 30.5 (5) GPa for the high-pressure phase. The mode-Grüneisen parameters for the Raman modes of the low-pressure structure and the changes of the modes induced by the phase transition were obtained from Raman spectroscopic measurements. Complementary quantum-mechanical calculations based on density-functional theory were performed between 0 and 50 GPa. The phase transition is driven by a large spontaneous displacement of one O atom from a fully constrained position. The density-functional theory (DFT) model confirmed the persistence of the stereochemical activity of the lone electron pair up to at least 50 GPa in accordance with the crystal structure of the high-pressure phase. While the stereochemcial activity of the lone electron pair of Bi^{3+} is reduced at increasing pressure, a symmetrization of the bismuth coordination was not observed in this pressure range. This shows an unexpected stability of the localization of the lone electron pair and of its stereochemical activity at high pressure.
Structure of pyrrhotite 5C(Fe9S10)
Authors: Elliot Alexander Dean
Published: May 2010

The distribution of vacancies throughout the underlying NiAs structure of pyrrhotite 5Cwas analysed through the application of vacancy avoidance and the closeness condition in conjunction with order–disorder layering. Two crystallographically equivalent structure solutions (chiral enantiomers) were produced consisting of layers containing one vacancy in every eight iron sites broken by a fully occupied layer every fifth iron layer, and best described by monoclinic statistical models. The statistical 5Cstructures were verified using synchrotron powder diffraction data as well as published electron-diffraction patterns. An order–disorder structure description is proposed for the intermediate pyrrhotites of which pyrrhotite 5Cis an end-member.
Octahedral tilting in Pb-based relaxor ferroelectrics at high pressure
Authors: Maier Bernd J. , Angel Ross J. , Marshall William G. , Mihailova Boriana , Paulmann Carsten , Engel Jens M. , Gospodinov Marin , Welsch Anna-Maria , Petrova Dimitrina , Bismayer Ulrich
Published: May 2010

We have employed a combination of powder neutron diffraction and single-crystal synchrotron X-ray diffraction to characterize the pressure-induced phase transitions that occur in the perovskite-type relaxor ferroelectric PbSc0.5Ta0.5O3 (PST) and Pb0.78Ba0.22Sc0.5Ta0.5O3 (PST-Ba). At ambient pressure the symmetry of the average structure for both compounds is Fm\bar{3}m as a result of partial ordering of the Sc and Ta cations on the octahedral sites. At pressures above the phase transition both the neutron and X-ray diffraction patterns exhibit an increase in the intensities of h,k,l = all odd reflections and no appearance of additional Bragg reflections. Synchrotron single-crystal X-ray diffraction data show that the intensity of hhh peaks, h = 2n + 1, does not change with pressure. This indicates that the structural distortion arising from the phase transition has a glide-plane pseudo-symmetry along the 〈111〉 cubic directions. Rietveld refinement to the neutron powder data shows that the high-pressure phase has either R\bar{3}c or R\bar{3} symmetry, depending on whether the presence of 1:1 octahedral cation ordering is neglected or taken into account, and comprises octahedral tilts of the type a
−
a
−
a
− that continuously evolve with pressure. The cubic-to-rhombohedral transition is also marked by a large increase in the anisotropy of the displacement ellipsoids of the Pb cations, indicating larger displacements of Pb cations along the rhombohedral threefold axis rather than within the perpendicular plane. For PST the anisotropy of the Pb displacement parameters decreases at approximately 3 GPa above the phase-transition pressure. For both PST and PST-Ba the average magnitudes of Pb-cation displacements expressed in terms of isotropic displacement ellipsoids gradually decrease over the entire pressure range from ambient to 7.35 GPa.
Structures of relevant ammonium salts in fertilizers
Authors: Montejo-Bernardo J. M. , García-Granda S. , Fernández-González A.
Published: May 2010

The crystal structures of two double salts of ammonium nitrate (AN) and ammonium sulfate (AS) are reported. The double salts 2NH4NO3·(NH4)2SO4 (2AN·AS) and 3NH4NO3·(NH4)2SO4 (3AN·AS) show a very similar crystal structure packing with alternating layers of anions and cations. The solid-state ionic distribution is controlled by an extensive hydrogen-bonding network with ammonium groups as the donors and O atoms acting as the acceptors. Crystallographic studies were conducted at both room temperature (293 K) and 100 K. Increasing the temperature involves shortening the
b
axis in the case of the 3AN·AS salt. Quantification of fertilizer mixtures using the Rietveld method was also carried out by means of the structural models reported in this paper for both salts.