bluuebunny/crossref_metadata_2025 huggingface dataset:
Microwave-assisted magnetic recording at lower transverse oscillating field
Authors: Goh Chi-Keong , Yuan Zhi-min , Zhou Tiejun , Wang Li , Liu Bo
Published: March 2009

Microwave-assisted magnetization reversal is a promising approach to overcome thermal instabilities and to achieve high magnetic recording densities. In this work, micromagnetic simulations are conducted to investigate the influence of square resonance fields on magnetic recording. We observe that lower switching field can be achieved with square microwave fields as compared to sinusoidal transverse fields because it has a larger spectral energy and a wider Fourier spectra. The wide Fourier spectra also induce a second switching field minimal at a lower frequency, implying that assisted switching can potentially be achieved at around 1/3 of the frequency of pure sinusoidal resonance field. It is found that the presence of the third harmonic component is sufficient to produce similar magnetic behavior. This observation forms the design basis of our modified spin torque oscillator, which generates a transverse field containing a strong power spectrum density at the first and the third harmonics, for microwave-assisted recording. With the inherent tradeoff between field strength and frequency, the new oscillator has a distinct advantage because field strength is contributed mainly by the low frequency component.
Structural transformation of grains and grain boundaries with introducing boron atoms into CoPtCr magnetic layer investigated by ultrasoft pseudopotential calculation and transmission electron microscopy analysis
Authors: Shoda Kaoru , Takeda Seiji
Published: March 2009

We have investigated the effect of introducing boron (B) into grains and grain boundaries of CoPtCr magnetic layer on the structural property by using ultrasoft pseudopotential calculation and advanced transmission electron microscopy (TEM) analysis. We have estimated the preferential substitutional and interstitial B atomic sites in a hexagonal close packed (hcp) structure, and the effect of additional B atoms on lattice parameters through an optimization process. The comparison of the calculated lattice parameters with experimental lattice parameters has led to the concept that B atoms may occupy both substitutional and interstitial sites at small Pt content and may transfer from substitutional sites to interstitial sites with an increase in Pt content. We also discuss how the addition of B atoms affects the atomic arrangement of the hcp structure and causes the transformation into amorphous structure. TEM analysis clearly shows that B segregates to the center of a boundary region that corresponds to the amorphous area observed in the TEM imaging, while Cr is more evenly distributed over a larger area at the boundary, indicating that B is responsible for the amorphous grain boundary structure.
Dispersion relations of electron density fluctuations in a Hall thruster plasma, observed by collective light scattering
Authors: Tsikata S. , Lemoine N. , Pisarev V. , Grésillon D. M.
Published: March 2009

Kinetic models and numerical simulations of E⃗×B⃗ plasma discharges predict microfluctuations at the scales of the electron cyclotron drift radius and the ion plasma frequency. With the help of a specially designed collective scattering device, the first experimental observations of small-scale electron density fluctuations inside the plasma volume are obtained, and observed in the expected ranges of spatial and time scales. The anisotropy, dispersion relations, form factor, amplitude, and spatial distribution of these electron density fluctuations are described and compared to theoretical expectations.
Kinetic dissipation and anisotropic heating in a turbulent collisionless plasma
Authors: Parashar T. N. , Shay M. A. , Cassak P. A. , Matthaeus W. H.
Published: March 2009

The kinetic evolution of the Orszag–Tang vortex is studied using collisionless hybrid simulations. In magnetohydrodynamics (MHD) this configuration leads rapidly to broadband turbulence. At large length scales, the evolution of the hybrid simulations is very similar to MHD, with magnetic power spectra displaying scaling similar to a Kolmogorov scaling of −5/3. At small scales, differences from MHD arise, as energy dissipates into heat almost exclusively through the magnetic field. The magnetic energy spectrum of the hybrid simulation shows a break where linear theory predicts that the Hall term in Ohm’s law becomes significant, leading to dispersive kinetic Alfvén waves. A key result is that protons are heated preferentially in the plane perpendicular to the mean magnetic field, creating a proton temperature anisotropy of the type observed in the corona and solar wind.
Does water need a λ-type transition?
Authors: Johari G. P. , Tombari Elpidio , Salvetti Giuseppe , Mallamace Francesco
Published: March 2009

After ascertaining that the Cp of water confined to 1.1 nm diameter pores had been used to reach the conjecture for a λ-transition in supercooled bulk water, we argue that only three H2O molecules can fit across the 1.1 nm diameter pore. Two of these form a (one-molecule thick) nanoshell hydrogen bonded to the SiO2 pore wall. Hydrogen bonding or cooperative motions of the remaining one H2O molecule would not produce a “λ-type transition.”
Rate constants calculation with a simple mixed quantum/classical implementation of the flux-flux correlation function method
Authors: Palma Juliana
Published: March 2009

A simple mixed quantum/classical (mixed-Q/C) implementation of the flux-flux correlation function method has been applied to evaluate rate constants for a two-dimensional model system. The model consists of an Eckart barrier resembling the collinear H+H2 reaction, linearly coupled to a harmonic oscillator. Results are presented for a broad range of parameters for temperatures between 140 and 300 K. It is found that the mixed-Q/C method gives fairly accurate results as long as the reaction does not involve too many recrossings. This suggests that the methodology could be extended to treat direct polyatomic reactions in gas phase.
Dynamics of liquid jets and threads under the action of radial electric fields: Microthread formation and touchdown singularities
Authors: Wang Qiming , Mählmann S. , Papageorgiou D. T.
Published: March 2009

We study theoretically the axisymmetric nonlinear dynamics of viscous conducting liquid jets or threads under the action of a radial electric field. The field is generated by a potential difference between the jet surface and a concentrically placed electrode of given radius. We develop a long wave nonlinear model that is used to predict the dynamics of the system and, in particular, to address the effect of the radial electric field on jet breakup. Two canonical regimes are identified that depend on the size of the gap between the outer electrode and the unperturbed jet surface. For relatively large gap sizes, long waves are stabilized for sufficiently strong electric fields but remain unstable as in the nonelectrified case for electric field strengths below a critical value. For relatively small gaps, an electric field of any strength enhances the instability of long waves as compared to the nonelectrified case. We carry out numerical simulations based on our nonlinear models to describe the nonlinear evolution and terminal states in these two regimes. We find that jet pinching does not occur irrespective of the parameters. We identify regimes where capillary instability leads to the formation of stable quasistatic microthreads (connected to large main drops) whose radius decreases with the strength of the electric field. The generic ultimate singular event described by our models is the attraction of the jet surface toward the enclosing electrode and its contact with the electrode in finite time. A self-similar closed form solution is found that describes this event with the interface near touchdown having locally a cusp geometry. The theory is compared to the time-dependent simulations with excellent agreement.
Size-induced elastic stiffening of ZnO nanostructures: Skin-depth energy pinning
Authors: Liu X. J. , Li J. W. , Zhou Z. F. , Yang L. W. , Ma Z. S. , Xie G. F. , Pan Y. , Sun Chang Q.
Published: March 2009

It has long been puzzling regarding the trends and physical origins of the size-effect on the elasticity of ZnO nanostructures. An extension of the atomic “coordination-radius” correlation premise of Pauling and Goldschmidt to energy domain has enabled us to clarify that the elastic modulus is intrinsically proportional to the sum of bond energy per unit volume and that the size-induced elastic stiffening arises from (i) the broken-bond-induced local strain and skin-depth energy pinning and (ii) the tunable fraction of bonds between the undercoordinated atoms, and therefore, the elastic modulus of ZnO nanostructures should increase with the inverse of feature size.
Zero thermal expansion in a pure-form antiperovskite manganese nitride
Authors: Takenaka K. , Takagi H.
Published: March 2009

A zero thermal expansion material in a pure form is fabricated using an antiperovskite manganese nitride. The isotropic zero thermal expansion is achieved by optimizing the heat treatment and the chemical composition. The present study suggests that the heat treatment affects the thermal expansion mainly via the nitrogen content of the material. The obtained materials exhibit a low expansion of |α|<0.5×10−6 K−1 (α is the coefficient of linear thermal expansion) over a broad temperature range, which includes room temperature. They are desirable for many fields of industry as reliable, mechanically hard, and low-cost zero thermal expansion materials.
Highly stable and symmetric boron caged B@Co12@B80 core-shell cluster
Authors: Wang Jian-Tao , Chen Changfeng , Wang E. G. , Wang Ding-Sheng , Mizuseki H. , Kawazoe Y.
Published: March 2009

The geometry, stability, and electronic properties of B@Co12@Bn and Co13@Bn clusters with a wide range n=55 up to 92 are studied by ab initio calculations. We find that B@Co12@B80 and Co13@B80 with closed B80 shell are two stable magic clusters with nearly perfect icosahedral symmetry, and B@Co12@B80 is more stable than Co13@B80 energetically. The strong core-shell bonding yields a very large energy gain of ∼30 eV. This high stability is attributed to the favorable closed-shell atomic and electronic structures. The B@Co12@B80 exhibits a large highest occupied and lowest unoccupied energy gap (0.96 eV) that is close to the value for isolated B80 fullerene.
The universe, yours to discover
Authors: Feder Toni
Published: March 2009

Astronomy enthusiasts the world over are hosting activities from puppet shows to telescope viewings to get the public to say ‘wow!’
DOE, NSF get billions in R&D funding from stimulus act
Authors: Kramer David
Published: March 2009

Agencies are planning to quickly spend their shares of recovery monies; further budget increases are provided in omnibus spending bill.
Introducing the black hole
Authors: Ruffini Remo , Wheeler John A.
Published: March 2009

According to present cosmology, certain stars end their careers in a total gravitational collapse that transcends the ordinary laws of physics.
John Wheeler’s mentorship: An enduring legacy
Authors: Christensen Terry M.
Published: March 2009

“We all know that the real reason universities have students is in order to educate the professors.” —John Archibald Wheeler, 1976
The true identities of the slipper lobsters Nisto laevis and Nisto asper (Crustacea: Decapoda: Scyllaridae) verified by DNA analysis
Authors: Palero Ferran , Guerao Guillermo , Clark Paul F. , Abelló Pere
Published: March 2009

In 1885, Sarato created Nisto as a new genus of slipper lobster and assigned two species to his taxon, namely Nisto laevis and N. asper. Bouvier later regarded these two species as post-larval stages of Scyllarus arctus (Linnaeus, 1758). This viewpoint of two post-larval stages has been accepted and retained, including being cited in the most recent scyllarid literature. The discovery of N. laevis and N. asper specimens in the reference collection of the Natural History Museum, London and the capture of three nisto-stage individuals, one in the north-western Mediterranean Sea and two in the Gulf of Cádiz (eastern Atlantic Ocean) have facilitated a historical review into the post-larval stages of S. arctus, as well as new detailed morphological descriptions. From the present study, it has been possible to describe and illustrate the nisto stages of S. arctus and S. pygmaeus (Bate, 1888) and to resolve the true identities of N. laevis and N. asper by DNA analysis. Accordingly, N. laevis has been identified as the nisto stage of S. pygmaeus and N. asper as that of S. arctus.
Effect of season and landscape position on the aluminium geochemistry of tropical acid sulfate soil leachate
Authors: Hicks W. S. , Bowman G. M. , Fitzpatrick R. W.
Published: March 2009

Acid sulfate soils (ASS) occupy an estimated 5.8 × 106 ha of coastal Australia. In tropical Australia, the processes operating in these soils, and their environmental hazards, are poorly understood. Drainage of a tropical estuarine wetland containing extensive ASS deposits left the area in a highly degraded condition. Surface and soil water pH values from the site were consistently <5 and commonly <3.5. Aluminium activity was several orders of magnitude greater than the level set for the protection of aquatic ecosystems, with a seasonal variation of 3 orders of magnitude. Aluminium behaved conservatively at the discharge point to receiving waters. In drainage lines and soil solution, aluminium activity was limited by elevated sulfate activity. Aluminium was commonly supersaturated with respect to alunite and behaved as though an aluminium species with the stoichiometry Al:OH:SO4 regulated its activity, which was 2–5 orders of magnitude lower than if gibbsite or amorphous aluminium hydroxide solubility was the control. While jurbanite (AlOHSO4.5H2O) is no longer considered a potential mineral in ASS, these data again raise the question of a satisfactory explanation of aluminium activity. Sulfate activity was influenced by seasonal factors. Wet season conditions were reducing and favoured the dissolution of acid iron oxidation products. The dry season oxidising and drying conditions favoured their precipitation, resulting in seasonal cycling. Based on our findings we developed a landscape geochemical process model for the site.
Synthesis and characterization of a new structure of gas hydrate
Authors: Yang L. , Tulk C. A. , Klug D. D. , Moudrakovski I. L. , Ratcliffe C. I. , Ripmeester J. A. , Chakoumakos B. C. , Ehm L. , Martin C. D. , Parise J. B.
Published: March 2009

Atoms and molecules <0.9 nm in diameter can be incorporated in the cages formed by hydrogen-bonded water molecules making up the crystalline solid clathrate hydrates. For these materials crystallographic structures generally fall into 3 categories, which are 2 cubic forms and a hexagonal form. A unique clathrate hydrate structure, previously known only hypothetically, has been synthesized at high pressure and recovered at 77 K and ambient pressure in these experiments. These samples contain Xe as a guest atom and the details of this previously unobserved structure are described here, most notably the host-guest ratio is similar to the cubic Xe clathrate starting material. After pressure quench recovery to 1 atmosphere the structure shows considerable metastability with increasing temperature (T <160 K) before reverting back to the cubic form. This evidence of structural complexity in compositionally similar clathrate compounds indicates that the reaction path may be an important determinant of the structure, and impacts upon the structures that might be encountered in nature.
Examining the conspicuousness and prominence of two required warnings on OTC pain relievers
Authors: Bix Laura , Bello Nora M. , Auras Rafael , Ranger Jon , Lapinski Maria K.
Published: March 2009

The labeling of over-the-counter (OTC) drugs is critical to their safe and effective use, and certain warnings are meant to be read at the point of purchase (POP). Examples include (
i
) warnings that alert consumers to the fact that the package is not child-resistant and (
ii
) warnings that alert consumers to potential product tampering. U.S. law mandates these warnings be “conspicuous” and “prominent” so that it is likely that consumers will read them before leaving the store. Our objective was to quantify the relative prominence and conspicuousness of these warnings. Sixty-one participants reviewed the packages of 5 commercially available analgesics to evaluate the prominence and conspicuousness of these warnings. Evaluated data included (
i
) the time spent examining the warnings compared with other areas of the label (using a bright pupil eye tracker), (
ii
) the ability to recall information from the OTCs viewed, and (
iii
) the legibility of the warnings relative to other elements of the labels (as measured by ASTM D7298-06). Eye-tracking data indicated that warnings were viewed by fewer participants and for less time than other elements of the packages. Recall and legibility data also indicated that the warning statements compared unfavorably with other elements of the labels tested. Evidence presented in this study suggests that 2 required warnings on 5 different OTCs are not prominent or conspicuous when compared with other elements of tested labels.
Craniosynostosis in the Middle Pleistocene human Cranium 14 from the Sima de los Huesos, Atapuerca, Spain
Authors: Gracia Ana , Arsuaga Juan Luis , Martínez Ignacio , Lorenzo Carlos , Carretero José Miguel , Bermúdez de Castro José María , Carbonell Eudald
Published: March 2009

We report here a previously undescribed human Middle Pleistocene immature specimen, Cranium 14, recovered at the Sima de los Huesos (SH) site (Atapuerca, Spain), that constitutes the oldest evidence in human evolution of a very rare pathology in our own species, lambdoid single suture craniosynostosis (SSC). Both the ecto- and endo-cranial deformities observed in this specimen are severe. All of the evidence points out that this severity implies that the SSC occurred before birth, and that facial asymmetries, as well as motor/cognitive disorders, were likely to be associated with this condition. The analysis of the present etiological data of this specimen lead us to consider that Cranium 14 is a case of isolated SSC, probably of traumatic origin. The existence of this pathological individual among the SH sample represents also a fact to take into account when referring to sociobiological behavior in Middle Pleistocene humans.
Abstracts
Authors: Dix David J.
Published: March 2009

The U.S. Environmental Protection Agency (EPA), National Toxicology Program (NTP), and National Institutes of Health (NIH) Chemical Genomics Center (NCGC) have complementary research programs designed to improve chemical toxicity evaluations by developing high throughput screening (HTS) methods that evaluate the impact of environmental chemicals on key toxicity pathways. These federal partners are coordinating an extension of the EPA’s ToxCast program, the NTP’s HTS initiative, and the NCGC’s Molecular Libraries Initiative into a collaborative research program focused on identifying toxicity pathways and developing in vitro assays to characterize the ability of chemicals to perturb those pathways. The goal is to develop new paradigm for high throughput toxicity testing that collects mechanistic and quantitative data from in vitro assays measuring chemical modulation of biological processes involved in the progression to toxicity. As toxicity pathways are identified, the in vitro assays can be optimized for comparison to in vivo animal studies, and for predicting effects in humans. Subsequent computational modeling of toxicity pathway responses and appropriate chemical dosimetry will need to be developed to make these predictions relevant for human health risk assessment. This work was reviewed by EPA and approved for publication but does not necessarily reflect official Agency policy.

Index Terms:

Toxicogenomics, High Throughput Screening/Testing, EPA ToxCast, Chemical Risk Assessment
Chronic Inhalation Exposure of Rats for up to 104 Weeks to a Non–Carbon-Based Magnetite Photocopying Toner
Authors: Slesinski Ronald S. , Turnbull Duncan
Published: March 2009

Male and female Han Wistar rats were exposed for 6 h/day, 5 days/week for 13 or 104 weeks (whole body) to a magnetite photocopying toner. The toner contained 45% to 50% magnetite, with 45% to 50% styrene acrylic resin and less than 5% external additives, including hydrophobic amorphous silica and proprietary surface functional modifiers. Exposure levels were 1, 5, and 25 mg/m3 for the 13-week study and 1, 4, and 16 mg/m3 for the 104-week study. Lung toner burdens averaged 36, 288, and 604 μg per lung after 104 weeks’ exposure at 1, 4, and 16 mg/m3. The lung burdens were lower than have been reported in a similar study with a carbon-based toner. There were no significant effects on weight gain or food consumption in either study, or on clinical pathology parameters examined in the 13-week study. After 104 weeks’ exposure at 16 mg/m3, macroscopic examination revealed dark discoloration of the lungs and associated lymph nodes. Lung weights were significantly elevated by 21% and 14% for male and female rats, respectively. Microscopic findings indicative of a mild inflammatory response were similar in both studies, and included the presence of black-pigmented macrophages in the lungs and tracheobronchial and mediastinal lymph nodes; increased incidences of perivascular/peribronchiolar inflammatory cell infiltration; inflammation of the alveolar ducts (characterized by aggregations of black-pigmented alveolar macrophages and interstitial lymphocytic infiltration); increased cellularity of the bronchiole-associated lymphoid tissue; and a few instances of alveolar ciliated metaplasia. The 104-week study showed no increase in the incidence of pulmonary tumors.
Hen Egg Chorioallantoic Membrane Bioassay: An In Vitro Alternative to Draize Eye Irritation Test for Pesticide Screening
Authors: Kishore A. S. , Surekha P. A. , Sekhar P. V. R. , Srinivas A. , Murthy P. Balakrishna
Published: March 2009

As an alternative to the standard Draize eye irritation test, the potential irritancy of compounds was evaluated by observing adverse changes that occur in chorioallantoic membrane CAM) of the hen egg (HECAM) after exposure to a test chemical placed directly on the CAM. The occurrence of hemorrhage, coagulation, and lysis in response to a test compound is the basis for employing this technique to evaluate its potential for in vivo damage to mucous membrane, in particular the eye. Irritancy is scored according to the severity and speed at which damage occurs. In the present study, five different classes of pesticides were screened for irritation potential. There was good correlation between the HECAM assay and the in vivo Draize eye irritation test. The proposed HECAM assay, which reduces the requirement for laboratory animals, could be a painless alternative to the Draize test.
Self-antigen–specific CD8+ T cell precursor frequency determines the quality of the antitumor immune response
Authors: Rizzuto Gabrielle A. , Merghoub Taha , Hirschhorn-Cymerman Daniel , Liu Cailian , Lesokhin Alexander M. , Sahawneh Diana , Zhong Hong , Panageas Katherine S. , Perales Miguel-Angel , Altan-Bonnet Grégoire , Wolchok Jedd D. , Houghton Alan N.
Published: March 2009

A primary goal of cancer immunotherapy is to improve the naturally occurring, but weak, immune response to tumors. Ineffective responses to cancer vaccines may be caused, in part, by low numbers of self-reactive lymphocytes surviving negative selection. Here, we estimated the frequency of CD8+ T cells recognizing a self-antigen to be <0.0001% (∼1 in 1 million CD8+ T cells), which is so low as to preclude a strong immune response in some mice. Supplementing this repertoire with naive antigen-specific cells increased vaccine-elicited tumor immunity and autoimmunity, but a threshold was reached whereby the transfer of increased numbers of antigen-specific cells impaired functional benefit, most likely because of intraclonal competition in the irradiated host. We show that cells primed at precursor frequencies below this competitive threshold proliferate more, acquire polyfunctionality, and eradicate tumors more effectively. This work demonstrates the functional relevance of CD8+ T cell precursor frequency to tumor immunity and autoimmunity. Transferring optimized numbers of naive tumor-specific T cells, followed by in vivo activation, is a new approach that can be applied to human cancer immunotherapy. Further, precursor frequency as an isolated variable can be exploited to augment efficacy of clinical vaccine strategies designed to activate any antigen-specific CD8+ T cells.
Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652
Authors: Teras Riho , Jakovleva Julia , Kivisaar Maia
Published: March 2009

Transposition activity in bacteria is generally maintained at a low level. The activity of mobile DNA elements can be controlled by bacterially encoded global regulators. Regulation of transposition of Tn4652inPseudomonas putidais one such example. Activation of transposition of Tn4652in starving bacteria requires the stationary-phase sigma factor RpoS and integration host factor (IHF). IHF plays a dual role in Tn4652translocation by activating transcription of the transposase genetnpAof the transposon and facilitating TnpA binding to the inverted repeats of the transposon. Our previous results have indicated that besides IHF some otherP. putida-encoded global regulator(s) might bind to the ends of Tn4652and regulate transposition activity. In this study, employing a DNase I footprint assay we have identified a binding site ofP. putidaFis (factor for inversion stimulation) centred 135 bp inside the left end of Tn4652. Our results of gel mobility shift and DNase I footprint studies revealed that Fis out-competes IHF from the left end of Tn4652, thereby abolishing the binding of TnpA. Thus, the results obtained in this study indicate that the transposition of Tn4652is regulated by the cellular amount ofP. putidaglobal regulators Fis and IHF.
Bacterial variation, virulence and vaccines
Authors: Moxon E. Richard
Published: March 2009

Research into Haemophilus influenzae, a commensal and pathogen of humans, has resulted in major scientific contributions to biology. The first endonucleases (restriction enzymes), which paved the way for the new genetics, and the DNA used to obtain the first complete genome sequence of a free-living organism were obtained from H. influenzae. Prevention of invasive bacterial infections of infants, such as meningitis, has been achieved using a novel class of vaccines, of which the glycoconjugates of H. influenzae were the first to be licensed. Originally fallaciously proposed to be the aetiological agent of epidemic influenza, now known to be caused by a virus, H. influenzae is a pathogen of global public health importance. Research into the pathogenesis of the infections it causes (for example, meningitis, septicaemia, pneumonia and otitis media) are case studies in understanding the molecular basis of the variation in gene expression and gene sequences that are critical to its commensal and virulence behaviour and for the strategies that can be pursued to prevent H. influenzae diseases through vaccines.
M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target
Authors: Furmanek-Blaszk Beata , Boratynski Robert , Zolcinska Natalia , Sektas Marian
Published: March 2009

Methylation of a base in a specific DNA sequence protects the DNA from nucleolytic cleavage by restriction enzymes recognizing the same sequence. The MboII restriction–modification (R–M) system ofMoraxella bovisATCC 10900 consists of a restriction endonuclease gene and two methyltransferase genes. The enzymes encoded by this system recognize an asymmetrical sequence 5′-GAAGA-3′/3′-CTTCT-5′. M1.MboII modifies the last adenine in the recognition sequence 5′-GAAGA-3′ toN6-methyladenine. A second methylase, M2.MboII, was cloned and purified to electrophoretic homogeneity using a four-step chromatographic procedure. It was demonstrated that M2.MboII modifies the internal cytosine in the recognition sequence 3′-CTTCT-5′, yieldingN4-methylcytosine, and moreover is able to methylate single-stranded DNA. The protein exists in solution as a monomer of molecular mass 30 000±1000 Da under denaturing conditions. Divalent cations (Ca2+, Mg2+, Mn2+and Zn2+) inhibit M2.MboII methylation activity. It was found that the isomethylomer M2.NcuI fromNeisseria cuniculiATCC 14688 behaves in the same manner. Functional analysis showed that the complete MboII R–M system, consisting of two methyltransferases genes and themboIIRgene, is the most stable and the least harmful to bacterial cells.
Mutational analysis of genes implicated in LPS and capsular polysaccharide biosynthesis in the opportunistic pathogen Bacteroides fragilis
Authors: Patrick Sheila , Houston Simon , Thacker Zubin , Blakely Garry W.
Published: March 2009

The obligate anaerobe Bacteroides fragilis is a normal resident of the human gastrointestinal tract. The clinically derived B. fragilis strain NCTC 9343 produces an extensive array of extracellular polysaccharides (EPS), including antigenically distinct large, small and micro- capsules. The genome of NCTC 9343 encodes multiple gene clusters potentially involved in the biosynthesis of EPS, eight of which are implicated in production of the antigenically variable micro-capsule. We have developed a rapid and robust method for generating marked and markerless deletions, together with efficient electroporation using unmodified plasmid DNA to enable complementation of mutations. We show that deletion of a putative wzz homologue prevents production of high-molecular-mass polysaccharides (HMMPS), which form the micro-capsule. This observation suggests that micro-capsule HMMPS constitute the distal component of LPS in B. fragilis. The long chain length of this polysaccharide is strikingly different from classical enteric O-antigen, which consists of short-chain polysaccharides. We also demonstrate that deletion of a putative wbaP homologue prevents expression of the phase-variable large capsule and that expression can be restored by complementation. This suggests that synthesis of the large capsule is mechanistically equivalent to production of Escherichia coli group 1 and 4 capsules.
Novel subfamily of mitochondrial HMG box-containing proteins: functional analysis of Gcf1p from Candida albicans
Authors: Visacka Katarina , Gerhold Joachim M. , Petrovicova Jana , Kinsky Slavomir , Jõers Priit , Nosek Jozef , Sedman Juhan , Tomaska Lubomir
Published: March 2009

Mitochondria of eukaryotic organisms contain populations of DNA molecules that are packed into higher-order structures called mitochondrial nucleoids (mt-nucleoids). InSaccharomyces cerevisiae, the compaction of mitochondrial DNA (mtDNA) into mt-nucleoids is mediated primarily by the high-mobility group (HMG) box-containing protein Abf2, which is an important player in stabilization and metabolism of mtDNA. Although it is evident that analogous proteins must exist in other yeast species, an apparently fast divergence rate has precluded their identification, characterization and comparative analysis. Usingin silicoanalysis of the complete genome sequence of the pathogenic yeastCandida albicanswe predicted that the ORF 19.400/19.8030 assigned asGCF1encodes a putative mitochondrial HMG box-containing protein. In contrast to Abf2p, which contains two HMG boxes, Gcf1p contains only one C-terminal HMG box. In addition, it contains one putative coiled-coil domain with a potential role in protein dimerization. Fluorescence microscopy analysis of a C-terminally tagged Gcf1p with green fluorescent protein (GFP) revealed its mitochondrial localization in both heterologous (S. cerevisiae) and native (C. albicans) hosts. Biochemical analyses of DNA-binding properties indicate that Gcf1p is, similarly to Abf2p, a non-specific DNA-binding protein. To analyse the role of Gcf1p in mtDNA metabolism, we constructed strains lacking one functional allele of theGCF1gene and carrying oneGCF1allele under the control of theMET3promoter. Under repressible conditions this strain exhibited a more than 3000-fold decrease in levels ofGCF1mRNA, which was correlated with a substantial decrease in the number of mtDNA copies as well as recombination intermediates. The dramatic effect of reduced levels of Gcf1p on mtDNA metabolism indicates that the protein is involved in essential molecular transactions that relate to the mitochondrial genome.
The effects of metformin on endogenous androgens and SHBG in women: a systematic review and meta‐analysis
Authors: Barba Maddalena , Schünemann Holger J. , Sperati Francesca , Akl Elie A. , Musicco Felice , Guyatt Gordon , Muti Paola
Published: March 2009

Objectives  Elevated circulating androgens are risk factors for several chronic, metabolic and reproductive disorders. Metformin is an insulin‐sensitizing agent that may lower androgen levels. To evaluate the effects of metformin on endogenous androgens and SHBG levels in women, we conducted a systematic review and meta‐analysis of randomized controlled trials (RCTs) comparing metformin with placebo or no treatment.

Data source  We used OVID to search MEDLINE, EMBASE and CENTRAL until March 2007.

Review methods  Two reviewers independently extracted data on methodological quality, participants, interventions and outcomes of interest. Our a priori primary outcome was post‐treatment measurements. In a secondary analysis, we evaluated the difference between the pre‐ and post‐treatment levels. We computed the weighted mean difference (WMD) as a measure of effect for each outcome using the DerSimonian–Laird random effects method. We used the I2 statistic to assess heterogeneity and explored its causes in subgroup analyses of features related to participants’ characteristics and study design. Based on a regression model, we conducted sensitivity analyses by investigating the use of placebo as a predictor of effect size.

Results  Twenty RCTs fulfilled the inclusion criteria. Pooled WMDs in post‐treatment levels between the metformin and control group were –0·31 nmol/l (95% CI –0·65 to 0·03) for total testosterone (TT), 0·10 pmol/l (95% CI –0·89 to 1·10) for free testosterone (FT), 0·14 µmol/l (95% CI –0·34 to 0·62) for dehydroepiandrosteronesulfate (DHEAS), –0·60 nmol/l (95% CI –1·67 to 0·46) for androstenedione (AND) and 5·88 nmol/l (95% CI 2·01–9·75) for SHBG. Pooled WMDs of the pre‐ to post‐treatment differences (i.e. with adjustment for baseline hormone levels) were –0·38 (95% CI –0·51 to –0·25) for TT, –2·71 (95% CI –10·35 to 4·93) for FT, –0·50 (95% CI –0·83 to –0·16) for DHEAS, –1·39 (95% CI –2·30 to –0·49) for AND and 6·63 (95% CI 2·32–10·94) for SHBG. In subgroup analyses, features related to the administered treatment (i.e. metformin as a single agent or as part of combined regimens) partly explained the heterogeneity. Sensitivity analyses of studies using placebo showed similar results to those not using placebo.

Conclusions  Our systematic review and meta‐analysis provides evidence of metformin‐induced changes in circulating androgens and SHBG levels in women but the quality of evidence is not high. However, there are no data from RCTs regarding these effects in postmenopausal women or healthy premenopausal women. High‐quality RCTs are required to evaluate whether metformin has effects on surrogate markers and patient‐important outcomes in these patient groups.
Community concordance between bryophyte and insect assemblages in boreal springs: a broad‐scale study in isolated habitats
Authors: VIRTANEN RISTO , ILMONEN JARI , PAASIVIRTA LAURI , MUOTKA TIMO
Published: March 2009

1. We examined species–environment relationships and community concordance between aquatic bryophytes and insects in boreal springs. We sampled bryophytes (Marchantiophyta and Bryophyta), benthic macroinvertebrates and environmental variables in 138 springs in Finland, spanning a latitudinal gradient of 1000 km. Macroinvertebrates were subdivided into two groups: Ephemeroptera, Plecoptera, Trichoptera and Coleoptera (EPTC taxa) and chironomid midges (Diptera; Chironomidae). Our aim was to test whether EPTC taxa could be used as surrogates in biodiversity surveys and bioassessment for the two less‐well known organism groups, chironomids and bryophytes.

2. Bryophyte assemblages were clearly differentiated along gradients in thermal conditions and water chemistry (pH, conductivity). Chironomids and EPTC were also differentiated in relation to thermal conditions and, to a lesser extent, physical habitat variables, but were only weakly associated to spring water chemistry. Chironomid and EPTC assemblages were more concordant with each other than with bryophytes, but all concordances were relatively weak.

3. Our results suggest that even if the overall compositional patterns of the three taxonomic groups were significantly concordant, the relative importance of environmental drivers underlying their community compositions differed strongly. The results thus imply that spring bryophytes and insects are relatively poor surrogates for each other. The proportion of spring specialists was highest in bryophytes, promoting their primacy for spring bioassessment and biodiversity conservation. We suggest that adequate variation in water chemistry be assured to protect spring bryophyte biodiversity, whereas preserving the physical variation of springs is more important for macroinvertebrates.
High variation in frequency of infection by endophytes in cultivars of meadow fescue in Finland
Authors: Saari S. , Lehtonen P. , Helander M. , Saikkonen K.
Published: March 2009

Systemic and asymptomatic Neotyphodium fungal endophytes infect numerous species of the Poaceae. The frequencies of Neotyphodium endophyte infection in Finland were investigated among and within seven Nordic cultivars of meadow fescue, Schedonorus pratensis (Huds.) P. Beauv., which is a widely grown pasture and forage grass species in Scandinavia. The cultivars were Kasper, Salten, Antti, Fure, Ilmari, Inkeri and Kalevi. Frequencies of infection of cultivars varied from endophyte‐free cultivar Fure to highly infected cultivar Inkeri [mean (standard deviation of mean) of 0·95 (0·023)]. Mean frequencies of infection of three cultivars remained lower than 0·10, and two of the cultivars, Kasper and Salten, were intermediately infected. In most of the cultivars, frequencies of infection varied only slightly among seed lots. In cultivar Kasper, however, the frequency of endophyte infection was highly variable (0–0·96) among the 45 seed lots examined. The relative importance of cultivar, seed lot and infection by Neotyphodium endophyte to the aphid Rhopalosiphum padi L. was studied experimentally, using both endophyte‐free and endophyte‐infected plants of four seed lots of the two intermediately infected cultivars. Endophyte infection increased plant resistance to R. padi, overriding the influences of seed lot and cultivar. It is proposed that variation caused by endophyte infections in cultivars of meadow fescue should be taken into account in assessing plant breeding programmes in Europe.
Individual‐level diet variation in four species of Brazilian frogs
Authors: Araújo M. S. , Bolnick D. I. , Martinelli L. A. , Giaretta A. A. , Dos Reis S. F.
Published: March 2009

Many natural populations exploiting a wide range of resources are actually composed of relatively specialized individuals.

This interindividual variation is thought to be a consequence of the invasion of ‘empty’ niches in depauperate communities, generally in temperate regions. If individual niches are constrained by functional trade‐offs, the expansion of the population niche is only achieved by an increase in interindividual variation, consistent with the ‘niche variation hypothesis’.

According to this hypothesis, we should not expect interindividual variation in species belonging to highly diverse, packed communities.

In the present study, we measured the degree of interindividual diet variation in four species of frogs of the highly diverse Brazilian Cerrado, using both gut contents and δ13C stable isotopes.

We found evidence of significant diet variation in the four species, indicating that this phenomenon is not restricted to depauperate communities in temperate regions.

The lack of correlations between the frogs’ morphology and diet indicate that trade‐offs do not depend on the morphological characters measured here and are probably not biomechanical. The nature of the trade‐offs remains unknown, but are likely to be cognitive or physiological.

Finally, we found a positive correlation between the population niche width and the degree of diet variation, but a null model showed that this correlation can be generated by individuals sampling randomly from a common set of resources. Therefore, albeit consistent with, our results cannot be taken as evidence in favour of the niche variation hypothesis.
fMRI study of brain activity elicited by oral parafunctional movements
Authors: BYRD K. E. , ROMITO L. M. , DZEMIDZIC M. , WONG D. , TALAVAGE T. M.
Published: March 2009

Summary  Parafunctional masticatory activity, such as the tooth clenching and grinding that is associated with bruxism, is encountered by clinicians in many disciplines, including dentistry, neurology and psychiatry. Despite this, little is known about the neurological basis for these activities. To identify the brain network engaged in such complex oromotor activity, functional magnetic resonance imaging (fMRI) was used to elucidate the brain activation patterns of 20 individuals (10 males and 10 females, mean ± s.d. age of 26·3 ± 4·1 years) with (parafunctional, PFx group, 5M/5F) and without (normal functional, NFx group, 5 M/5F) self‐reported parafunctional grinding and clenching habits during clenching and grinding tasks. Subject group classification was based on: (i) self‐reported history, (ii) clinical examination, (iii) evaluation of dental casts and (iv) positive responses to the temporomandibular disorder (TMD) History Questionnaire [Dworkin and LeResche, Journal of Craniomandibular Disorders, (1992) 6:301]. While subjects performed these oromotor tasks, each wore a custom‐designed oral appliance minimizing head motion during imaging. Mean per cent signal changes showed significant between group differences in motor cortical (supplementary motor area, sensorimotor cortex and rolandic operculum) and subcortical (caudate) regions. Supplementary motor area data suggest that motor planning and initiation, particularly during the act of clenching, are less prominent in individuals with oromotor parafunctional behaviours. The overall extent of activated areas was reduced in subjects with self‐reported parafunctional masticatory activity compared with the controls. This study’s methodology and findings provide an initial step in understanding the neurological basis of parafunctional masticatory activities that are relevant for therapeutic research applications of temporomandibular joint and muscle disorders and associated comorbidities.
Pleistocene population expansions of Antarctic seals
Authors: CURTIS CAITLIN , STEWART BRENT S. , KARL STEPHEN A.
Published: March 2009

We sequenced a portion (c. 475 bp) of the mitochondrial control region of three species of Antarctic phocid carnivores (Weddell seal, Leptonychotes weddellii, N = 181; crabeater seal, Lobodon carcinophaga, N = 143; and Ross seal, Ommatophoca rossii, N = 41) that live seasonally or permanently in the fast ice and seasonal pack ice of the western Amundsen and Ross seas of western Antarctica. We resolved 251 haplotypes with a haplotype diversity of 0.98 to 0.99. Bayesian estimates of Θ from the program LAMARC ranged from 0.075 for Weddell seals to 0.576 for crabeater seals. We used the values of theta to estimate female effective population sizes (NEF), which were 40 700 to 63 000 for Weddell seals, 44 400 to 97 800 for Ross seals, and 358 500 to 531 900 for crabeater seals. We used mismatch distributions to test for historical population size expansions. Weddell seals and crabeater seals had significant, unimodal mean pairwise difference distributions (P = 0.56 and 0.36, respectively), suggesting that their populations expanded suddenly around 731 000 years ago (Weddell seals) and around 1.6 million years ago (crabeater seals). Both of these expansions occurred during times of intensified glaciations and may have been fostered by expanding pack ice habitat.
Phylogeography of the common ragworm Hediste diversicolor (Polychaeta: Nereididae) reveals cryptic diversity and multiple colonization events across its distribution
Authors: VIRGILIO M. , FAUVELOT C. , COSTANTINI F. , ABBIATI M. , BACKELJAU T.
Published: March 2009

Previous studies on the common ragworm Hediste diversicolor (Polychaeta: Nereididae) revealed a marked genetic fragmentation across its distribution and the occurrence of sibling taxa in the Baltic Sea. These results suggested that the phylogeographic patterns of H. diversicolor could reflect interactions between cryptic differentiation and multiple colonization events. This study aims to describe the large‐scale genetic structuring of H. diversicolor and to trace the phylogeographic origins of the genetic types described in the Baltic Sea. Samples of H. diversicolor (2 < n < 28) were collected at 16 locations across the NE Atlantic coasts of Europe and Morocco and in the Mediterranean, Black and Caspian Seas and sequenced at two mitochondrial gene fragments (COI and cytb, 345 and 290 bp, respectively). Bayesian analyses revealed deep phylogeographic splits yielding three main clades corresponding to populations (i) from the NE Atlantic coasts (from Germany to Morocco) and from part of the Western Mediterranean, (ii) from the Mediterranean Sea, and (iii) from the Black and Caspian Seas. These clades are further divided in well‐supported subclades including populations from different regions of NE Atlantic and Mediterranean (i.e. Portugal/Morocco, Western Mediterranean, Adriatic Sea). The Baltic Sea comprises three sympatric lineages sharing a common evolutionary history with populations from NE Atlantic, Western Mediterranean and Black/Caspian Seas, respectively. Hence, the current patterns of genetic structuring of H. diversicolor appear as the result of allopatric isolation, multiple colonization events and possible adaptation to local environmental conditions.
Management of neonatal cow’s milk allergy in high‐risk neonates
Authors: Miyazawa Tokuo , Itahashi Kazuo , Imai Takanori
Published: March 2009

Background:  We conducted a multicenter clinical survey to clarify the current attitudes to diagnosis or treatment of neonatal milk allergy (NMA) in institutions providing medical care for high‐risk neonates in Japan.

Methods:  Questionnaires were distributed to 263 institutions that provide medical care for high‐risk infants. Information was requested on the number of hospitalized neonates between January 2004 and December 2005, the number of neonates diagnosed with milk allergy, frequent clinical symptoms, and clinical tests performed routinely when NMA was suspected.

Results:  Responses were received from 145 institutions (55.1%). Of 69 796 hospitalized neonates, a diagnosis of cow's milk allergy was made in 0.21%. The incidence in infants with birthweight <1000 g was 0.35%. Gastrointestinal symptoms were identified as the most frequent symptoms that suggested NMA by 80% of institutions. A challenge test in each suspected case was performed in only 15% of institutions, even though it was considered to be the most significant test for diagnosis. Most institutions considered a specific immunoglobulin E test in cases of suspected NMA, but only one‐third agreed on its diagnostic significance. A lymphocyte stimulation test was performed in only 5.5% of institutions.

Conclusions:  This study is the first to show the incidence of NMA in institutions providing medical care for high‐risk neonates in Japan. Current clinical tests may be insufficient for diagnosis of NMA in which non‐immunoglobulin‐E‐mediated delayed allergic reactions are involved. Therefore, awareness of the clinical features of this disorder is required among neonatologists and allergists.