bluuebunny/crossref_metadata_2025 huggingface dataset:
Theory of the almost-highest wave: the inner solution
Authors: Longuet-Higgins M. S. , Fox M. J. H.
Published: April 2006

This paper investigates the flow near the summit of steep, progressive gravity wave when the crest is still rounded but the flow is approaching Stokes's corner flow. The natural length scale in the neighbourhood of the summit is seen to be l =q2/2g, where g denotes gravity and q is the particle speed at the crest in a reference frame moving with the wave speed. We show that a class of self-similar smooth local flows exists which satisfy the free-surface condition and which tend to Stokes's corner flow when the radial distance r becomes large compared withl. The behaviour of the solution at large values of r/l is shown to depend on the roots of the transcendental equation
\[
K \tan h K = \pi/2\surd{3}.
\]
The two real roots correspond to a damped oscillation of the free surface decaying like (l/r)½. The positive imaginary roots correspond to perturbations vanishing like higher negative powers of r.

The complete flow is calculated by transforming the domain onto the interior of a circle in the complex plane and expanding the potential at the surface in a Fourier series. The computation is checked by an independent method, based on approximating the flow by a sequence of dipoles. The profile of the surface is found to intersect its asymptote at large values of r/l. This implies that the maximum slope slightly exceeds 30°. The computed value 30·37° is in close agreement with that obtained by extrapolating the maximum slopes of steep gravity waves, as calculated by previous authors. The vertical acceleration of a particle at the crest is 0·388g. In the far field, however, the acceleration tends to the value ½g corresponding to the Stokes corner flow.
Numerical solutions of the nonlinear α-effect dynamo equations
Authors: Proctor Michael R. E.
Published: April 2006

An extension is made of the α-effect model of the earth's dynamo into the nonlinear regime following the prescription of Malkus & Proctor (1975). In this model, the effects of small-scale dynamics on the α-effect are suppressed, and the global effects of induced velocity fields examined in isolation. The equations are solved numerically using finite-difference methods, and it is shown that viscous and inertial forces are unimportant in the final equilibration, as suggested in the above paper.
Effect of external disturbances on the spreading rate of a plane turbulent jet
Authors: Bradshaw P.
Published: April 2006

The nonlinear growth of turbulent jets documented by Kotsovinos (1976) is tentatively attributed to draughts in the laboratory, caused principally by the jet itself.
Aspiration of peritonsillar abscess in severe trismus
Authors: Badran K H , Karkos P D
Published: April 2006

We present a novel method of aspirating a peritonsillar abscess in a patient with severe trismus. In our experience, this method is efficient, allows good access to the peritonsillar area and facilitates rapid resolution of the trismus before definitive drainage can be performed.
HYPO-ALLERGENIC INTERVENTIONS DURING PREGNANCY
Authors: SALVATORE S , KEYMOLEN K , HAUSER B , VANDENPLAS Y
Published: April 2006

Baron Clemens von Pirquet, an Austrian paediatrician, proposed in 1903 the terms allergy and allergen after observing that some of his patients had “altered responses” to certain substances. Allergic symptoms are not necessarily accompanied by sensitization or vice versa. Recently, nomenclature for allergy has been revised.
DIAGNOSIS AND MANAGEMENT OF NAUSEA AND VOMITING IN PREGNANCY
Authors: MAGEE LAURA , SHRIM ALON , KOREN GIDEON
Published: April 2006

Nausea and vomiting of pregnancy (NVP) is a term used to describe a wide spectrum of symptoms. At one end of the spectrum is the common, mild to moderate nausea and vomiting that is usually limited to the first trimester. At the other end of the spectrum are the intractable, severe symptoms of hyperemesis gravidarum (HG) that is associated with weight loss, dehydration, electrolyte imbalance and hospitalisation.
Methanotrophic microbial communities associated with bubble plumes above gas seeps in the Black Sea
Authors: Schubert Carsten J. , Durisch‐Kaiser Edith , Holzner Christian P. , Klauser Lucia , Wehrli Bernhard , Schmale Oliver , Greinert Jens , McGinnis Daniel F. , De Batist Marc , Kipfer Rolf
Published: April 2006

Bubbles evolving from active gas seeps can be traced by hydroacoustic imaging up to 1000 m high in the Black Sea water column. Although methane concentrations are not distinguishable between the water column above the deep seep and reference sites, atmospheric noble gas measurements clearly show the constant input of gases (mainly methane) via seepage into the Black Sea. Archaea (ANME‐1, ANME‐2) and methanotrophic bacteria detected with specific 16S rRNA‐targeted oligonucleotide probes are related to active gas seeps in the oxic and anoxic water column. It is suggested that methane seeps have a much greater influence on the Black Sea methane budget than previously acknowledged and that ANME‐1 and ANME‐2 are injected via gas bubbles from the sediment into the anoxic water column mediating methane oxidation. Our results show further that only minor amounts of methane evolving from Black Sea gas seeps reach the atmosphere due to the very effective microbial barrier. Hence only major thermodynamically and/or tectonically triggered gas hydrate dissociation has the potential to induce rapid climate changes as suggested by the “clathrate gun hypothesis.”
The40Ar/39Ar dating of the early Jehol Biota from Fengning, Hebei Province, northern China
Authors: He H. Y. , Wang X. L. , Jin F. , Zhou Z. H. , Wang F. , Yang L. K. , Ding X. , Boven A. , Zhu R. X.
Published: April 2006

The bird fossil‐bearing deposits at the Jiecaigou section, correlative to the Dabeigou Formation, in Fengning, Hebei Province, northern China, is well known for yielding a fossil assemblage representing the earliest evolutionary stage of the Jehol Biota. The precise age of the fossil‐bearing deposits, however, is unknown. The40Ar/39Ar age spectrum obtained on bulk K‐feldspars from the tuff layer about 2 m below the bird fossil‐bearing layer gave a plateau age of 129.0 ± 1.3 Ma (2σ, full external error) and an isochron age of 132.3 ± 4.5 Ma (2σ, full external error). Seventeen total‐fusion40Ar/39Ar ages on K‐feldspars from the interbedded tuff about 6 m below the fossil‐bearing layer resulted in a weighted mean of 130.7 ± 1.4 Ma (2σ, full external error). These dates suggest an age of ∼131 Ma for the early Jehol Biota and combined with previous dating indicate that this biota lasted at least from 131 Ma to 120 Ma (Late Hauterivian to Aptian). These dates also represent the earliest absolute age for known enantiornithine birds in the world.
The location of lightning affecting the ionospheric sporadic‐E layer as evidence for multiple enhancement mechanisms
Authors: Johnson C. G. , Davis C. J.
Published: April 2006

We present a study of the geographic location of lightning affecting the ionospheric sporadic‐E (Es) layer over the ionospheric monitoring station at Chilton, UK. Data from the UK Met Office's Arrival Time Difference (ATD) lightning detection system were used to locate lightning strokes in the vicinity of the ionospheric monitoring station. A superposed epoch study of this data has previously revealed an enhancement in the Es layer caused by lightning within 200km of Chilton. In the current paper, we use the same data to investigate the location of the lightning strokes which have the largest effect on the Es layer above Chilton. We find that there are several locations where the effect of lightning on the ionosphere is most significant statistically, each producing different ionospheric responses. We interpret this as evidence that there is more than one mechanism combining to produce the previously observed enhancement in the ionosphere.
An assessment of radiation budget data provided by the ISCCP and GEWEX‐SRB
Authors: Raschke Ehrhard , Bakan Stephan , Kinne Stefan
Published: April 2006

The projects ISCCP and GEWEX‐SRB compute global data sets of radiation budget components at the top of the atmosphere and at the surface. Time series range from July 1983 to June 2001, and to October 1995, respectively. Comparing monthly averages over broader zones we find that the SRB underestimates the incident radiation at TOA by more than 2–5 Wm−2 over the tropics and up to 40 Wm−2 over polar regions. The ISCCP infrared radiation fluxes near the surface and at TOA, in particular over both polar zones, are higher than those of the SRB. Clouds in the ISCCP appear optically less effective than in the SRB. Interannual and month‐to‐month variations are observed indicating serious errors in ancillary data. Complete reprocessing is recommended. End products need validation within this large domain in space and time with correlated radiation budget measurements at TOA and at ground.
Analysis of Raman lidar and radiosonde measurements from the AWEX‐G field campaign and its relation to Aqua validation
Authors: Whiteman D. N. , Russo F. , Demoz B. , Miloshevich L. M. , Veselovskii I. , Hannon S. , Wang Z. , Vömel H. , Schmidlin F. , Lesht B. , Moore P. J. , Beebe A. S. , Gambacorta A. , Barnet C.
Published: April 2006

Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment–Ground (AWEX‐G) was held in October‐November 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolving the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX‐G field campaign permitted correction techniques to be validated for Raman lidar, Vaisala RS80‐H and RS90/92 that significantly improve the absolute accuracy of water vapor measurements from these systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.
The role of glutathione in disulphide bond formation and endoplasmic‐reticulum‐generated oxidative stress
Authors: Chakravarthi Seema , Jessop Catherine E , Bulleid Neil J
Published: April 2006

Glutathione is a ubiquitous molecule found in all parts of the cell where it fulfils a range of functions from detoxification to protection from oxidative damage. It provides the main redox buffer for cells and as such has been implicated in the formation of native disulphide bonds. However, the discovery of the enzyme Ero1 has called into question the exact role of glutathione in this process. In this review, we discuss the arguments for and against a role for glutathione in facilitating disulphide‐bond formation and consider its role in protecting the cell from endoplasmic‐reticulum‐generated oxidative stress.
Catalytic and mechanical cycles in F‐ATP synthases
Authors: Dimroth Peter , von Ballmoos Christoph , Meier T
Published: April 2006

Cycles have a profound role in cellular life at all levels of organization. Well‐known cycles in cell metabolism include the tricarboxylic acid and the urea cycle, in which a specific carrier substrate undergoes a sequence of chemical transformations and is regenerated at the end. Other examples include the interconversions of cofactors, such as NADH or ATP, which are present in the cell in limiting amounts and have to be recycled effectively for metabolism to continue. Every living cell performs a rapid turnover of ATP to ADP to fulfil various energetic demands and effectively regenerates the ATP from ADP in an energy‐consuming process. The turnover of the ATP cycle is impressive; a human uses about its body weight in ATP per day. Enzymes perform catalytic reaction cycles in which they undergo several chemical and physical transformations before they are converted back to their original states. The ubiquitous F1Fo ATP synthase is of particular interest not only because of its biological importance, but also owing to its unique rotational mechanism. Here, we give an overview of the membrane‐embedded Fo sector, particularly with respect to the recent crystal structure of the c ring from Ilyobacter tartaricus, and summarize current hypotheses for the mechanism by which rotation of the c ring is generated.
Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation
Authors: Zheng Zhong-liang , Ye Mao-qing , Zuo Zhen-yu , Liu Zhi-gang , Tai Keng-chang , Zou Guo-lin
Published: April 2006

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Ala60, Ser62→Ala62, and Thr220→Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (ΔΔGT). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the Km values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.
Mapping and conformational characterization of the DNA-binding region of the breast cancer susceptibility protein BRCA1
Authors: Naseem Riffat , Sturdy Alice , Finch David , Jowitt Thomas , Webb Michelle
Published: April 2006

The breast cancer susceptibility gene, BRCA1, encodes a large nuclear phosphoprotein, the major isoform of which is 1863 amino acids in size. Structure–function studies have been largely restricted to the only two domains identified by homology searches: the RING (really interesting new gene) and BRCT (BRCA1 C-terminus) domains. However, we have recently reported the identification of a large central soluble region of BRCA1 (residues 230–534) that binds specifically to four-way junction DNA, a property that potentially facilitates its role in the repair of DNA lesions by homologous recombination. We have now used a combination of limited proteolysis and extension cloning to identify more accurately the DNA-binding region of BRCA1. Limited trypsinolysis of BRCA1-(230–534) resulted in the production of a soluble domain identified as residues 230–339. However, after cloning, expression and purification of this region, studies revealed that it was unable to bind to four-way junctions, suggesting that the DNA-binding activity, in part, resides within residues 340–534. A series of fragments extending from residue 340 were produced, and each was tested for its ability to bind to four-way junction DNA in gel retardation assays. In these experiments, residues 340–554 of BRCA1 were identified as the minimal DNA-binding region. We then went on to characterize the conformation of this region using CD spectroscopy and analytical centrifugation.
Inefficient coupling between proton transport and ATP synthesis may be the pathogenic mechanism for NARP and Leigh syndrome resulting from the T8993G mutation in mtDNA
Authors: Sgarbi Gianluca , Baracca Alessandra , Lenaz Giorgio , Valentino Lucia M. , Carelli Valerio , Solaini Giancarlo
Published: April 2006

Mutations in the ATP6 gene of mtDNA (mitochondrial DNA) have been shown to cause several different neurological disorders. The product of this gene is ATPase 6, an essential component of the F1F0-ATPase. In the present study we show that the function of the F1F0-ATPase is impaired in lymphocytes from ten individuals harbouring the mtDNA T8993G point mutation associated with NARP (neuropathy, ataxia and retinitis pigmentosa) and Leigh syndrome. We show that the impaired function of both the ATP synthase and the proton transport activity of the enzyme correlates with the amount of the mtDNA that is mutated, ranging from 13–94%. The fluorescent dye RH-123 (Rhodamine-123) was used as a probe to determine whether or not passive proton flux (i.e. from the intermembrane space to the matrix) is affected by the mutation. Under state 3 respiratory conditions, a slight difference in RH-123 fluorescence quenching kinetics was observed between mutant and control mitochondria that suggests a marginally lower F0 proton flux capacity in cells from patients. Moreover, independent of the cellular mutant load the specific inhibitor oligomycin induced a marked enhancement of the RH-123 quenching rate, which is associated with a block in proton conductivity through F0 [Linnett and Beechey (1979) Inhibitors of the ATP synthethase system. Methods Enzymol. 55, 472–518]. Overall, the results rule out the previously proposed proton block as the basis of the pathogenicity of the mtDNA T8993G mutation. Since the ATP synthesis rate was decreased by 70% in NARP patients compared with controls, we suggest that the T8993G mutation affects the coupling between proton translocation through F0 and ATP synthesis on F1. We discuss our findings in view of the current knowledge regarding the rotary mechanism of catalysis of the enzyme.
Characterization of the amino acid response element within the human sodium-coupled neutral amino acid transporter 2 (SNAT2) System A transporter gene
Authors: Palii Stela S. , Thiaville Michelle M. , Pan Yuan-Xiang , Zhong Can , Kilberg Michael S.
Published: April 2006

The neutral amino acid transport activity, System A, is enhanced by amino acid limitation of mammalian cells. Of the three gene products that encode System A activity, the one that exhibits this regulation is SNAT2 (sodium-coupled neutral amino acid transporter 2). Fibroblasts that are deficient in the amino acid response pathway exhibited little or no induction of SNAT2 mRNA. Synthesis of SNAT2 mRNA increased within 1–2 h after amino acid removal from HepG2 human hepatoma cells. The amino acid responsive SNAT2 genomic element that mediates the regulation has been localized to the first intron. Increased binding of selected members of the ATF (activating transcription factor) and C/EBP (CCAAT/enhancer-binding protein) families to the intronic enhancer was established both in vitro and in vivo. In contrast, there was no significant association of these factors with the SNAT2 promoter. Expression of exogenous individual ATF and C/EBP proteins documented that specific family members are associated with either activation or repression of SNAT2 transcription. Chromatin immunoprecipitation analysis established in vivo that amino acid deprivation led to increased RNA polymerase II recruitment to the SNAT2 promoter.
Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases
Authors: Eswaran Jeyanthy , von Kries Jens Peter , Marsden Brian , Longman Emma , Debreczeni Judit É. , Ugochukwu Emilie , Turnbull Andrew , Lee Wen Hwa , Knapp Stefan , Barr Alastair J.
Published: April 2006

Protein tyrosine phosphatases PTPN5, PTPRR and PTPN7 comprise a family of phosphatases that specifically inactivate MAPKs (mitogen-activated protein kinases). We have determined high-resolution structures of all of the human family members, screened them against a library of 24000 compounds and identified two classes of inhibitors, cyclopenta[c]quinolinecarboxylic acids and 2,5-dimethylpyrrolyl benzoic acids. Comparative structural analysis revealed significant differences within this conserved family that could be explored for the design of selective inhibitors. PTPN5 crystallized, in two distinct crystal forms, with a sulphate ion in close proximity to the active site and the WPD (Trp-Pro-Asp) loop in a unique conformation, not seen in other PTPs, ending in a 310-helix. In the PTPN7 structure, the WPD loop was in the closed conformation and part of the KIM (kinase-interaction motif) was visible, which forms an N-terminal aliphatic helix with the phosphorylation site Thr66 in an accessible position. The WPD loop of PTPRR was open; however, in contrast with the structure of its mouse homologue, PTPSL, a salt bridge between the conserved lysine and aspartate residues, which has been postulated to confer a more rigid loop structure, thereby modulating activity in PTPSL, does not form in PTPRR. One of the identified inhibitor scaffolds, cyclopenta[c]quinoline, was docked successfully into PTPRR, suggesting several possibilities for hit expansion. The determined structures together with the established SAR (structure–activity relationship) propose new avenues for the development of selective inhibitors that may have therapeutic potential for treating neurodegenerative diseases in the case of PTPRR or acute myeloblastic leukaemia targeting PTPN7.
Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose
Authors: Alberto François , Jordi Emmanuelle , Henrissat Bernard , Czjzek Mirjam
Published: April 2006

Thermotoga maritima invertase (β-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases β-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves β-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed β-propeller catalytic domain linked to a β-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule α-D-galactopyranosyl-(1,6)-α-D-glucopyranosyl-β-D-fructofuranoside (raffinose) at 1.87 Å (1 Å=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.
A proprotein convertase-inhibiting serpin with an endoplasmic reticulum targeting signal from Branchiostoma lanceolatum, a close relative of vertebrates
Authors: Bentele Caterina , Krüger Olaf , Tödtmann Ulf , Oley Mareke , Ragg Hermann
Published: April 2006

Lancelets are considered to take a key position in the evolution of lineages leading to vertebrates. Herein, a serpin from the lancelet Branchiostoma lanceolatum, Bl-Spn1, was identified that inhibits the PCs (proprotein convertases) PC1/3 and furin. The inhibitor forms SDS-stable complexes with either of its targets. Analysis of the inhibitor/furin reaction products by mass spectroscopy assigns the enzyme's cleavage position C-terminally to Met-Met-Lys-Arg↓ in the reactive site loop of Spn1, in concordance with the classical recognition/cleavage site of the principal vertebrate PCs. The inhibitor is equipped with a canonical ER (endoplasmic reticulum) retrieval signal, Lys-Asp-Glu-Leu (KDEL), marking the inhibitor as a guardian of the cellular secretory routes. Deletion of the ER retrieval signal results in the export of the inhibitor into the medium of transfected COS-7 cells, consistent with the assigned intracellular location. These results identify Bl-Spn1 as the first serpin that may inhibit PC1/3-like subtilases at their natural sites of action. Phylogenetic comparisons support a concept implying a general role for ER-residing serpins in the surveillance of subtilase-like enzymes along the constitutive and regulated secretory pathways of metazoans including a role in the defence of intruders that turn PCs to their propagation.
Tissue-specific expression of ferritin H regulates cellular iron homoeostasis in vivo
Authors: Wilkinson John , Di Xiumin , Schönig Kai , Buss Joan L. , Kock Nancy D. , Cline J. Mark , Saunders Thomas L. , Bujard Hermann , Torti Suzy V. , Torti Frank M.
Published: April 2006

Ferritin is a ubiquitously distributed iron-binding protein. Cell culture studies have demonstrated that ferritin plays a role in maintenance of iron homoeostasis and in the protection against cytokine- and oxidant-induced stress. To test whether FerH (ferritin H) can regulate tissue iron homoeostasis in vivo, we prepared transgenic mice that conditionally express FerH and EGFP (enhanced green fluorescent protein) from a bicistronic tetracycline-inducible promoter. Two transgenic models were explored. In the first, the FerH and EGFP transgenes were controlled by the tTACMV (Tet-OFF) (where tTA and CMV are tet transactivator protein and cytomegalovirus respectively). In skeletal muscle of mice bearing the FerH/EGFP and tTACMV transgenes, FerH expression was increased 6.0±1.1-fold (mean±S.D.) compared with controls. In the second model, the FerH/EGFP transgenes were controlled by an optimized Tet-ON transactivator, rtTA2S-S2LAP (where rtTA is reverse tTA and LAP is liver activator protein), resulting in expression predominantly in the kidney and liver. In mice expressing these transgenes, doxycycline induced FerH in the kidney by 14.2±4.8-fold (mean±S.D.). Notably, increases in ferritin in overexpressers versus control littermates were accompanied by an elevation of IRP (iron regulatory protein) activity of 2.3±0.9-fold (mean±S.D.), concurrent with a 4.5±2.1-fold (mean±S.D.) increase in transferrin receptor, indicating that overexpression of FerH is sufficient to elicit a phenotype of iron depletion. These results demonstrate that FerH not only responds to changes in tissue iron (its classic role), but can actively regulate overall tissue iron balance.
Differential gene and protein expression in abluminal sprouting and intraluminal splitting forms of angiogenesis
Authors: Williams James L. , Weichert Alexander , Zakrzewicz Andreas , Da Silva-Azevedo Luis , Pries Axel R. , Baum Oliver , Egginton Stuart
Published: April 2006

In adult skeletal muscle, abluminal sprouting or longitudinal splitting of capillaries can be initiated separately by muscle overload and elevated microcirculation shear stress respectively. In the present study, gene and protein expression patterns associated with the different forms of angiogenesis were examined using a targeted gene array (Superarray), validated by quantitative RT (reverse transcription)-PCR and immunoblots. Sprouting angiogenesis induced large changes in expression levels in genes associated with extracellular matrix remodelling, such as MMP-2 (matrix metalloproteinase-2), TIMP (tissue inhibitor of metalloproteinases), SPARC (secreted protein, acidic and rich in cysteine) and thrombospondin. Changes in neuropilin, midkine and restin levels, which may underpin changes in endothelial morphology, were seen during splitting angiogenesis. Up-regulation of VEGF (vascular endothelial growth factor), Flk-1, angiopoietin-2 and PECAM-1 (platelet/endothelial cell adhesion molecule-1) was seen in both forms of angiogenesis, representing a common angiogenic response of endothelial cells. In conclusion, the present study demonstrates that general angiogenic signals from growth factors can be influenced by the local microenvironment resulting in differing forms of capillary growth to produce a co-ordinated expansion of the vascular bed.
Iron and infection: effects of host iron status and the iron-regulatory genes haptoglobin and NRAMP1 (SLC11A1) on host–pathogen interactions in tuberculosis and HIV
Authors: McDermid Joann M. , Prentice Andrew M.
Published: April 2006

There are many lines of evidence illustrating that iron plays a pivotal role in modulating the battle for survival between mammalian hosts and their pathogens. Each displays considerable genetic investment in a wide range of mechanisms for acquiring and maintaining iron. These competitive mechanisms are highly complex, existing within an interacting matrix of absorption, transport, storage and detoxification systems, each of which are iron-responsive and thus able to adapt to the different phases of infection. Considerable genetic polymorphism in some of these systems, with signals of geographic selection in the hosts, and niche selection in the pathogens, indicates that they are critical for species survival. In this review we briefly summarize the role of iron in host immune function before reviewing the available evidence that iron modulates susceptibility and disease outcomes in HIV and TB (tuberculosis). We then examine the putative role of iron-related host genes by focussing on two candidate genes, haptoglobin and NRAMP1, for which there are common polymorphic variants in humans with strong evidence of functionally distinct biochemical phenotypes that would be predicted to influence the course of HIV and TB infections. Finally, we examine the limited evidence so far available that nutrient–gene interactions are likely to influence the way in which gene variants can protect against infection. We conclude that there is a wealth of evidence associating alterations in iron balance and in iron-regulatory systems with disease progression, but that many issues related to the direction of causality, mechanisms of action and sensitivity to pharmacological intervention remain to be elucidated. Since iron is probably the most widely prescribed compound throughout the world, used in both preventative and treatment regimens, a deeper understanding of the host–pathogen interactions relating to iron constitutes an important area for both basic and clinical research.
Status report of the radioactive ion beam production at TRIUMF (invited)
Authors: Bricault Pierre
Published: April 2006

The ISAC radioactive ion beam (RIB) facility has been operational since November 1998. The ISAC Facility at TRIUMF utilizes up to 100μA proton intensity at 500MeV from the existing H− cyclotron to produce RIB using the isotopic separation on-line (ISOL) method. The science programs at ISAC range from nuclear astrophysics to fundamental symmetry. The facility can deliver RIB to the low energy area and a linear accelerator composed of a four-rod radio frequency quadrupole and a linear accelerator can provide beam from A=3to30amu with an energy range from 0.15to1.5AMeV. An accelerator upgrade is underway and will allow us to extend the mass range to A=150amu and the energy up to 6.5AMeV. The target/ion source assembly and heavy-ion optics components are located in a shield canyon under 2m of steel shielding allowing high proton beam intensity on a thick target. At the beginning the production target was operating at 2–5μA but rapidly the proton beam intensity was raised to 40μA. Now, we operate up to nearly 100μA proton beam using the new high power target design equipped with radial fins. While the production target capabilities have improved quite a lot, from 2to100μA, the ion sources development have not followed the same trend. Since the beginning of ISAC most of the RIB production is done using the surface ion source. A 2.45GHz electron cyclotron resonance ion source (ECRIS) was built and used on line with moderate success.
The melting point of ice Ih for common water models calculated from direct coexistence of the solid-liquid interface
Authors: García Fernández Ramón , Abascal José L. F. , Vega Carlos
Published: April 2006

In this work we present an implementation for the calculation of the melting point of ice Ih from direct coexistence of the solid-liquid interface. We use molecular dynamics simulations of boxes containing liquid water and ice in contact. The implementation is based on the analysis of the evolution of the total energy along NpT simulations at different temperatures. We report the calculation of the melting point of ice Ih at 1bar for seven water models: SPC/E, TIP4P, TIP4P-Ew, TIP4P/ice, TIP4P/2005, TIP5P, and TIP5P-E. The results for the melting temperature from the direct coexistence simulations of this work are in agreement (within the statistical uncertainty) with those obtained previously by us from free energy calculations. By taking into account the results of this work and those of our free energy calculations, recommended values of the melting point of ice Ih at 1bar for the above mentioned water models are provided.
Pretransitional behavior in the isotropic phase of a nematic liquid crystal with the transverse permanent dipole moment
Authors: Janik Malgorzata , Rzoska Sylwester J. , Drozd-Rzoska Aleksandra , Zioło J. , Janik Pawel , Maslanka Slawomir , Czupryński Krzysztof
Published: April 2006

The results presented give the evidence for the quasicritical, pretransitional behavior of dielectric properties in the isotropic phase of a rodlike nematic liquid crystal with the transverse permanent dipole moment. Studies were conducted in 2-cyano-4-pentylbiphenyl 4-(trans-4-pentylcyclohexyl) benzoate, focusing on the static-and ionic-dominated low-frequency (LF) regions. For the static dielectric permittivity [ε′(T)] the application of the derivative analysis revealed the pretransitional anomaly associated with the specific heat exponent α≈0.5. For the LF domain the contribution to ε′(T) from residual ionic impurities follows a linear temperature dependence on approaching the isotropic-nematic (I-N) transition. This dependence and pretransitional anomalies of electric conductivity and dielectric modulus can be associated with the influence of prenematic fluctuations. “Linear” dielectric studies were supported by the static nonlinear dielectric effect measurements, which delivered reliable estimations of the temperature of the hypothetical continuous phase transition T* and the discontinuity of the I-N transition ΔT≈1.7K.
Optimal control of ultrafast laser driven many-electron dynamics in a polyatomic molecule: N-methyl-6-quinolone
Authors: Klamroth Tillmann
Published: April 2006

We report time-dependent configuration interaction singles calculations for the ultrafast laser driven many-electron dynamics in a polyatomic molecule, N-methyl-6-quinolone. We employ optimal control theory to achieve a nearly state-selective excitation from the S0 to the S1 state, on a time scale of a few (≈6) femtoseconds. The optimal control scheme is shown to correct for effects opposing a state-selective transition, such as multiphoton transitions and other, nonlinear phenomena, which are induced by the ultrashort and intense laser fields. In contrast, simple two-level π pulses are not effective in state-selective excitations when very short pulses are used. Also, the dependence of multiphoton and nonlinear effects on the number of states included in the dynamical simulations is investigated.
Femtosecond degenerate four-wave mixing of carbon disulfide: High-accuracy rotational constants
Authors: Kummli Dominique S. , Frey Hans M. , Leutwyler Samuel
Published: April 2006

Femtosecond degenerate four-wave mixing (fs-DFWM) rotational coherence spectroscopy (RCS) has been used to determine the rotational and centrifugal distortion constants of the 0000 ground and 0101 vibrationally excited states of gas-phase CS2. RCS transients were recorded over the 0–3300ps optical delay range, allowing the observation of 87 recurrences. The fits yield rotational constants B0000=3.2715492(18)GHz for C12S232 and B0000=3.17506(21)GHz for the C12S32S34 isotopomer. The rotational constants of the degenerate 0101 bending level of C12S232 are B0101=3.27672(40) and 3.27903(40)GHz for the e and f substrates, respectively. These fs-DFWM rotational constants are ten times more accurate than those obtained by CO2 laser/microwave heterodyne measurements and are comparable to those obtained by high-resolution Fourier transform infrared spectroscopy. Ab initio calculations were performed at two levels, second-order Møller-Plesset theory and coupled-cluster singles, doubles, and iterative triples [CCSD(T)]. The equilibrium and vibrationally averaged CS distances were calculated using large Dunning basis sets. An extrapolation procedure combining the ab initio rotational constants with the experiment yields an equilibrium CS bond length of 155.448pm to an accuracy of ±20fm. The theoretical CS bond length obtained by a complete basis set extrapolation at the CCSD(T) level is re(CS)=155.579pm, or 0.13pm longer than that in the experiment.
Pulse shaping for optimal control of molecular processes
Authors: Cheng Taiwang , Brown Alex
Published: April 2006

In this paper, a new method is proposed to design optimized control fields with desired temporal and/or spectral properties. The method is based on penalizing the difference between an optimized field obtained from an iterative scheme and a reference field with desired temporal and/or spectral properties. Compared with the standard optimal control theory, the current method allows a simple, experimentally accessible field be found on the fly; while compared with parameter space searching optimization, the iterative nature of this method allows automatic exploration of the intrinsic mechanism of the population transfer. The method is illustrated by examing the optimal control of vibrational excitation of the Cl–O bond with both temporally and spectrally restricted pulses.
Highly accurate ignition delay apparatus for hypergolic fuel research
Authors: Alfano Angelo J. , Mills Jeffrey D. , Vaghjiani Ghanshyam L.
Published: April 2006

The efficient development of hypergolic fuels requires an interdisciplinary approach involving ab initio modeling, synthesis, and experimental physical chemistry. Candidate molecules must exhibit hypergolic ignition delay times that are fast enough to warrant further testing for safety and performance criteria. Hypergolic ignition delay apparatus has been mentioned in the open literature for six decades, but accurate, detailed, modern ignition delay hardware that uses inexpensive laboratory building blocks and a minimum of custom circuitry is still needed. This article details line-of-sight electro-optical circuitry with direct digital readout and additional oscilloscope recording that can be used to measure total ignition and chemical delay times for screening candidate fuels. We also illustrate the value of high speed video and quantum chemical calculations to supplement the ignition delay measurements for a comprehensive approach to hypergolic fuel research.
Loss of chlorine in mass spectra of DCl picked up by water clusters in a beam
Authors: Moro Ramiro , Rabinovitch Roman , Kresin Vitaly V.
Published: April 2006

Water clusters (H2O)n, n⩽16, are produced by supersonic expansion of water vapor into vacuum, and then pick up a DCl molecule. The resulting mixed clusters are analyzed by electron bombardment ionization mass spectrometry. In all cases observed, the chlorine atom is lost in the ionization process, producing a deuterated water cluster cation [(H2O)nD+]. This suggests that the chlorine atom stays on the surface and has a weaker bond to the host cluster.
Electronic structures and spectroscopic properties of nitrido-osmium(VI) complexes with acetylide ligands [OsN(CCR)4]− RH, CH3, and Ph by density functional theory calculation
Authors: Zhang Yu-Hua , Xia Bao-Hui , Pan Qing-Jiang , Zhang Hong-Xing
Published: April 2006

Electronic structures and spectroscopic properties of a series of nitrido-osmium (VI) complex ions with acetylide ligands, [OsN(CCR)4]− (RH, (1), CH3 (2), and Ph (3)) were investigated theoretically. The structures of the complexes were fully optimized at the B3LYP and CIS level for the ground states and excited states, respectively. The calculated bond lengths of OsN (1.639Å in 1, 1.642Å in 2, and 1.643Å in 3) and Os–C (2.040Å in 1, 2.043Å in 2, and 2.042Å in 3) in ground state agree well with the experimental results. The bond length of OsN bond is lengthened by ca. 0.13Å in the AB23 excited state compared to the A11 ground state, which is consistent with the lower vibration frequency of ν(Os–N) (∼780cm−1) in the excited state than that (∼1175cm−1) in the ground state. Among the calculated dipole-allowed absorptions at λ>250nm, the intense absorption at 261nm for 1, 266nm for 2, and 300nm for 3 were attributed to the [π(CC)]1→[π*(NOs)+π*(CC)]1, [π(CC)]1→[π*(NOs)+π*(CC)]1, and [π(CCPh)]1→[π*(NOs)+π*(CCPh)]1, respectively. The lowest energy absorption at λmax=393nm for 1, 400nm for 2, and 400nm for 3 were assigned as [dxy(Os)+π(CC)]1→[π*(NOs)+π*(CC)]1, [dxy(Os)+π(CC)]1→[π*(NOs)+π*(CC)]1, and [dxy(Os)+π(CCPh)]1→[π*(NOs)+π*(CCPh)]1, respectively. The calculated phosphorescence emission at λmax=581nm for 1, 588nm for 2, and 609nm for 3 were originated from [(π*(NOs)+π*(CC))1(dxy(Os)+π(CC))1]3, [(π*(NOs)+π*(CC))1(dxy(Os)+π(CC))1]3, and [(π*(NOs)+π*(CCPh))1(dxy(Os)+π(CCPh))1]3 excited state, respectively.
Influence of trap states on dynamic properties of single grain silicon thin film transistors
Authors: Yan F. , Migliorato P. , Ishihara R.
Published: April 2006

The transient properties of single grain–thin film transistors (SG-TFTs) with high electron mobility have been studied. Overshoot current induced by trap states has been observed in most of the devices. A method of ac measurements has been used to investigate the trap processes. Both transient and ac measurements show that the response of some SG-TFTs with high field effect mobility is dominated by a single trap level. Bias stressing on SG-TFT can induce more trap states and thus change the ac response of the device.
Work function and implications of doped poly(3,4-ethylenedioxythiophene)-co-poly(ethylene glycol)
Authors: Sapp Shawn , Luebben Silvia , Losovyj Ya. B. , Jeppson P. , Schulz D. L. , Caruso A. N.
Published: April 2006

We report work function and conductivity measurements of the block copolymer poly(3,4-ethylenedioxythiophene)-co-poly(ethylene glycol) (PEDOT-PEG) doped with perchlorate or para-toluenesulfonate anions. The electronic and chemical properties of doped PEDOT-PEG are discussed in the context of the hole injection for organic light emitting diodes. We show that different dopants can result in significant differences in conductivity with only small alterations to the work function.
Convergence study of bispectral analysis in experiments of high temperature plasmas
Authors: Nagashima Y. , Itoh S.-I. , Yagi M. , Itoh K. , Fujisawa A. , Hoshino K. , Shinohara K. , Uehara K. , Kusama Y. , Ejiri A. , Takase Y.
Published: April 2006

A convergence study of bispectral analysis on toroidal plasma turbulence is presented with a theoretical estimate of bicoherence for the system of the drift wave and zonal flow. Examples are chosen from the analysis of floating potential fluctuation in the edge region of the JFT-2M tokamak. The convergence properties of the bispectral functions are clarified for an oscillatory branch of zonal flow (or geodesic acoustic mode) and drift waves. The total squared bicoherence or the biphase converges inversely proportional to the realization number or to the square root of the realization number, respectively. The numbers of realizations to qualitatively converge and obtain a quantitatively significant value of bicoherence are discussed for the drift wave fluctuations and for the zonal flow.
Measurements of groove density for concave gratings with the long trace profiler
Authors: Liu Bin , Wang Qiuping , Xu Xiangdong , Fu Shaojun
Published: April 2006

A long trace profiler method has been developed to measure the groove density of concave gratings in National Synchrotron Radiation Laboratory recently. With the aid of large angular acceptance (35mrad), it is suitable for precise measurement of concave or convex gratings with high curvatures. The effects of the slope variations along its substrate are discussed in detail. To eliminate the off-axis errors, which are the essential error sources in the measuring system based on rotating mounts of gratings, an error-reduced method is introduced consequently. A commercially available concave grating with a curvature radius of 998mm is measured and the relative groove density error δN∕N is about 4×10−5 rms.
Ferromagnetic metal to cluster-glass insulator transition induced by A-site disorder in manganites
Authors: Wang K. F. , Wang Y. , Wang L. F. , Dong S. , Yu H. , Li Q. C. , Liu J.-M. , Ren Z. F.
Published: April 2006

The magnetotransport behaviors of a series of rare earth manganites with the same A-site cational mean radius and different A-site ionic radii variance (A-site disorder) are investigated. It is found that the system’s ground state transforms from ferromagnetic metal to cluster-glass insulator with increasing A-site disorder. In the cluster-glass state, the magnetization shows the steplike behavior, indicating the existence of short-range magnetically ordered clusters. The significant effect of the A-site disorder on the electronic phase separation is revealed by detecting the cluster-glass ground state at low temperature.
Beam patterns of terahertz quantum cascade lasers with subwavelength cavity dimensions
Authors: Adam A. J. L. , Kašalynas I. , Hovenier J. N. , Klaassen T. O. , Gao J. R. , Orlova E. E. , Williams B. S. , Kumar S. , Hu Q. , Reno J. L.
Published: April 2006

The need to reach single-mode lasing and minimize at the same time the electrical dissipation of cryogenically operated terahertz quantum cascade lasers may result in small and subwavelength cavity dimensions. To assess the influence of such dimensions on the shape of the laser emission, we have measured the beam pattern of two metal-metal cavity quantum cascade lasers. The patterns show regular angular intensity variations which depend on the length of the laser cavity. The physical origin of these features is discussed in terms of interference of the coherent radiation emitted by end and side facets of the laser bar.
Measurement of Young’s modulus of carbon nanotubes by nanoprobe manipulation in a transmission electron microscope
Authors: Enomoto Kazuki , Kitakata Shintaro , Yasuhara Toshiyuki , Ohtake Naoto , Kuzumaki Toru , Mitsuda Yoshitaka
Published: April 2006

A method for quantifying the nanomechanics of nanomaterials was developed using a nanoprobe manipulator fitted into a transmission electron microscope. Apparent Young’s moduli of various carbon nanotubes (CNTs) were measured using this method. The apparent Young’s modulus of an arc-grown CNT is as large as approximately 3.3TPa, which is close to the theoretical Young’s modulus (5.5TPa) of the single-walled CNT simulated using molecular dynamics. The relationship between the apparent Young’s modulus and the crystallinity of CNTs is demonstrated using the crystallinity parameter ID∕IG derived by Raman spectroscopic analysis. The apparent Young’s modulus is higher for better crystallinity of CNT.