bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement of the GaSb surface band bending potential from the magnetotransport characteristics of GaSb–InAs–AlSb quantum wells
Authors: Folkes P. A. , Gumbs Godfrey , Xu Wen , Taysing-Lara M.
Published: November 2006

Low-temperature magnetotransport measurements on GaSb∕InAs∕AlSb coupled quantum well structures with a GaSb cap layer and self-consistent calculations of their electronic structure have led to the determination of the Fermi level at the surface, EFS, of undoped molecular-beam-epitaxy-grown GaSb. EFS is pinned around 0.2eV above the top of the GaSb valence band when the GaSb cap layer width is greater than around 900Å. For smaller GaSb cap widths, EFS decreases with the GaSb width. The undoped GaSb∕InAs∕AlSb heterostructure’s Fermi level is determined by bulk donor defects in the AlSb layer adjacent to the InAs quantum well.
Magnetoelectric exchange bias systems in spintronics
Authors: Chen Xi , Hochstrat Andreas , Borisov Pavel , Kleemann Wolfgang
Published: November 2006

Magnetoelectric switching of perpendicular exchange bias is observed in a Co∕Pt multilayer attached to single crystalline magnetoelectric antiferromagnetic Cr2O3(111). The exchange bias field HEB can be set to positive or negative values by applying an electric field Efr either parallel or antiparallel to the magnetic freezing field Hfr while cooling to below the Néel temperature. Based on this result, the antiferromagnetic spin state can be used as a medium for data storage. The authors propose magnetic random access memory cells and magnetic logic devices, which are purely voltage controlled.
The vibrational progressions of the N→V electronic transition of ethylene: A test case for the computation of Franck-Condon factors of highly flexible photoexcited molecules
Authors: Borrelli Raffaele , Peluso Andrea
Published: November 2006

The vibrational progressions of the N→V electronic transition of ethylene—a test case for the computation of Franck-Condon factors between electronic states exhibiting very different equilibrium geometries—have been calculated by using both the Cartesian and the curvilinear internal coordinate representations of the normal modes of vibration. The comparison of the theoretical spectra with the experimental one shows that the Cartesian representation yields vibrational progressions which are not observed in the experimental spectrum, whereas the curvilinear one gives a very satisfying agreement, even in harmonic approximation.
Morphologies of multicompartment micelles formed by triblock copolymers
Authors: Chou Shih-Hao , Tsao Heng-Kwong , Sheng Yu-Jane
Published: November 2006

Multicompartment micelles are desirable for advanced applications such as drug delivery. Recently, core-shell-corona (CSC) and segmented-worm (SW) micelles formed by ABC triblock terpolymers with three mutually immiscible blocks are observed in experiments. We have performed dissipative particle dynamics simulations to study the effects of molecular architecture, block length, and solution concentration on the morphologies of ABC triblock terpolymers. The formation of CSC and SW micelles for linear and miktoarm star ABC terpolymers is confirmed in this work. In addition, we predict that different multicompartment micellar morphologies (e.g., incomplete skin-layered micelles and segmented worms) can be formed by linear copolymer with different arrangements of the three blocks.
Pigments of Australasian Dermocybe Toadstools
Authors: Gill M
Published: November 2006

A number of new secondary metabolites, mostly pigments, which have been isolated from indigenous Australasian toadstools belonging to the genus Dermocybe, are described and discussed from structural, stereochemical and biosynthetic points of view. The potential for the discovery of new biologically active substances in the native fungal flora is demonstrated and a plea for greater taxonomic involvement is expressed.
The Chemistry of 5-Oxodihydroisoxazoles. XII. Trapping of Derived Ketenimines With Lithium Amides and Alkyllithiums
Authors: Ang KH , Prager RH , Williams CM
Published: November 2006

Isoxazolones unsubstituted at C3 react with lithium amides or alkyllithiums to give ketenimines . The presence of an ethoxycarbonyl group at C4 allows capture of this species by addition of a second equivalent of the lithiated species to give enolates which can be alkylated in situ. The presence of a phenyl group at C4 gives a ketenimine which reacts intramolecularly in the presence of lithium amides, whereas alkyllithiums undergo addition in synthetically useful processes.
Organoamido- and Aryloxo-Lanthanoids. XI. Syntheses and Crystal Structures of Nd(Odpp)3, Nd(Odpp)3(thf) and [Nd(Odpp)3(thf)2].2(thf) (Odpp-=2,6-Diphenylphenolate): Variations in Intramolecular π-Ph-Nd Interactions
Authors: Deacon GB , Feng TC , Skelton BW , White AH
Published: November 2006

The X-ray crystal structure of Nd (Odpp)3 ( Odpp- = 2,6-diphenylphenolate), obtained by sublimation of Nd ( Odpp )3( thf )2 ( thf = tetrahydrofuran ) [triclinic, Pī , a 15.835(5), b 13.499(10), c 10.955(11) Ǻ, α 116.25(7), β 92.87(7), γ 101.66(6)°, V 2031 Ǻ3, Z2, No 5726 'observed' data (I > 3σ(I)) refined to conventional R 0.047 shows a near triangular array of oxygens surrounding neodymium { Nd -O} 2.169 Ǻ, ∑ O- Nd -O 353.2° with additional, intramolecular Nd-η6-Ph chelate interactions { Nd -C} 3.046 Ǻ and Nd-η1-Ph ( Nd -C 2.964(7)Ǻ). There is a pseudotrigonal bipyramidal arrangement of the oxygens, the centroid of the η6-Ph, and the η1-carbon. The complex Nd ( Odpp )3( thf ), obtained by crystallization of Nd ( Odpp )3( thf )2 from toluene (monoclinic, P21/c, a 12.213(4), b 21.447(4), c 17.744Ǻ, β 104.25(2)°, V 4505 Ǻ3, Z 4, R 0.042 for No 8014) also has pseudotrigonal bipyramidal stereochemistry, with a triangular equatorial array of aryl oxide oxygens { Nd -O} 2.193 Ǻ; ∑ O- Nd -O 358.7°, an apical thf oxygen (Nd -O 2.446(3)Ǻ), and an apical intramolecular chelating phenyl group. As the last has three Nd -C contacts (3.094(5), 3.144(5), 3.010(5)Ǻ) significantly shorter than the other three (3.300(5), 3.427(5), 3.377(5)Ǻ), an η3-Ph-Nd interaction seems likely. For [ Nd ( Odpp )3( thf )2].2( thf ), obtained by crystallization from tetrahydrofuran without drying of the crystals, the X-ray structure (monoclinic, P21, a 10.230(2), b 21.919(5), c 13.411(4) Ǻ, β 101.15(2)°, V 2950 A3, Z2, R 0.058 for No 3237) reveals a distorted trigonal bipyramidal arrangement of three aryl oxide oxygens (two equatorial 2.208(9), 2.16(1) Ǻ; one axial 2.203(9) Ǻ) and two thf oxygens (one equatorial 2.44(1) Ǻ; one axial (significantly distant) 2.62(1) Ǻ). The X-ray structure of [La( Odpp )3( thf )2].2( thf ) shows it to be isostructural with the neodymium analogue.
Metal-Directed Synthesis of Dithia Diaza Macrocycles Carrying Pendant Alcohol and Also Nitro or Carboxylate Groups
Authors: Wei G , Allen CC , Hambley TW , Lawrance GA , Maeder M
Published: November 2006

Copper(II)-directed condensation of 1,9-diamino-3,7-dithianonan-5-ol with nitroethane or di-ethyl malonate yields (6-methyl-6-nitro-1,11-dithia-4,8-diazacyclotetradecan-13-ol)copper(II) and (diethyl 13-hydroxy-1,11-dithia-4,8-diazacyclotetradecane-6,6-dicarboxylate)copper(II) respectively in good yields, with the latter readily converted by decarboxylation into the complex of ethyl 13-hydroxy-1,11-dithia-4,8-diazacyclotetradecane-6-carboxylate. Analogues without the alcohol group based on 3,7-dithianonane-1,9-diamine are also described. The pendant alcohol group fused directly to a macrocyclic ring carbon can act as an axial donor group, as illustrated in the X-ray crystal structure analysis of (diethyl 13-hydroxy-1,11-dithia-4,8-diazacyclotetradecane-6,6-dicarboxylate)copper(II) perchlorate . This complex crystallizes in the P21/c space group, a 12.650(3), b 8.620(1), c 24.382(4) Ǻ, β 96.10(2)°. The copper ion lies in a distorted square-based pyramidal environment of two sulfur donors (average Cu-S 2.338 A), two nitrogen donors (average Cu-N 2.035 Ǻ) and the pendant alcohol donor [Cu-O 2.319(6) Ǻ], with the copper ion displaced slightly (0.043 Ǻ) out of the macrocycle donor plane towards the pendant alcohol donor.
A Pyrolytic Approach to 2-Hydroxy-7-methoxy-5-methyl-1-naphthoic Acid
Authors: Brown RFC , Eastwood FW , Horvath JM
Published: November 2006

Condensation of 4-methoxy-2,6-dimethylbenzaldehyde with Meldrum's acid, and flash vacuum pyrolysis of the condensation product (12) gave in almost quantitative yield 7-methoxy-5-methyl-2-naphthol (9). This naphthol is a precursor of the title 1-carboxylic acid (6), an intercalating moiety of enediyne and other antibiotics.
Cyclodextrin and Termethylated Cyclodextrin Complexation of Aromatic Carboxylic Acids and Their Conjugate Bases in Aqueous Solution: the Effect of Size, Hydrophobicity and Charge
Authors: Hendrickson K , Easton CJ , Lincoln SF
Published: November 2006

For α- cyclodextrin ( αCD ), the complexation constants (K) for the formation of binary host-guest complexes ( HA.αCD ) are 750�60, 1070�60, 27�3 and 17�4 dm3 mol-1 when the guests (HA) are benzoic, 4-methylbenzoic and (R)- and (S)-2-phenylpropanoic acids, respectively, as determined by potentiometric titration in aqueous solution at 298.2 K and I = 0.10 mol dm-3 ( KCl ). For the analogous hexakis (2,3,6-tri-O-methyl)-α- cyclodextrin complexes ( HA.TMαCD ), K = 1580�150, 2890�130, 220�10 and 207�8 dm3 mol-1, and for the heptakis (2,3,6-tri-O-methyl)-β-cyclodextrin complexes ( HA.TMαCD ), K = 200�20, 340�30, 129�5 and 170�10 dm3 mol-1. The binary complexes formed by the corresponding carboxylates (A-) are much less stable. Ternary host-guest α- cyclodextrin complexes (HA.αCD2) are also formed. These data, together with literature data for β- cyclodextrin, are discussed in terms of the factors influencing complexation.
Molecular-Structure of bis(ethane-1,2-diolato)( tetraphenylporphyrinato )phosphorus(V) chloride: [P( tpp )(OCH2CH2OH)2]+Cl -
Authors: Lin YH , Lin YH , Tang SS , Tang SS , Lin CC , Lin CC , Chen JH , Chen JH , Zeng WF , Zeng WF , Wang SS , Wang SS , Lin HJ , Lin HJ
Published: November 2006

The structure of bis(ethane-1,2-diolato)( tetraphenylporphyrinato )phosphorus(V) chloride, [P( tpp )(OCH2CH2OH)2]+Cl -, has been confirmed by X-ray diffraction. The cation displays an octahedral coordination about the phosphorus atom and exhibits a ruffled porphyrin geometry with a core size of 1.841 Ǻ. It crystallizes in the orthorhombic space group P212121, with a 12.524(3), b 25.177(5), c 14.275(3) Ǻ, and Z = 4. Refinement based on 4194 observed reflections led to a final R value of 5.1%. The displacement of the phosphorus atom from the porphyrin mean plane is 0.014 Ǻ. The geometry around the phosphorus centre of the [P( tpp )(OCH2CH2OH)2]+Cl- molecule has P-O(1) 1.643(4), P-O(3) 1.642(4) and P- Np 1.841(4) Ǻ. n.m.r. spectroscopy provides a complementary method for the investigation of the ethane-1,2-diolate ligand. The 13C resonances (24°C) of this axial ligand were observed at 62.9 [P-O-C-C-OH, with 2J(P,C) 16.1 Hz] and 57.8 ppm [P-O-C-C-OH with 3J(P,C) 19.1 Hz].
Mechanism and Models for Collisional Energy Transfer in Highly Excited Large Polyatomic Molecules
Authors: Gilbert RG
Published: November 2006

Collisional energy transfer in highly excited molecules (say, 200-500 kJ mol-1 above the zero-point energy of reactant, or of product, for a recombination reaction) is reviewed. An understanding of this energy transfer is important in predicting and interpreting the pressure dependence of gas-phase rate coefficients for
unimolecular and recombination reactions. For many years it was thought that
this pressure dependence could be calculated from a single energy-transfer
quantity, such as the average energy transferred per collision. However, the
discovery of 'supercollisions' (a small but significant fraction of collisions
which transfer abnormally large amounts of energy) means that this simplistic
approach needs some revision. The 'ordinary' (non-super) component of the
distribution function for collisional energy transfer can be quantified either
by empirical models (e.g., an exponential-down functional form) or by models
with a physical basis, such as biased random walk (applicable to monatomic or
diatomic collision partners) or ergodic (for polyatomic collision partners)
treatments. The latter two models enable approximate expressions for the
average energy transfer to be estimated from readily available molecular
parameters. Rotational energy transfer, important for finding the pressure
dependence for recombination reactions, can for these purposes usually be taken
as transferring sufficient energy so that the explicit functional form is not
required to predict the pressure dependence. The mechanism of 'ordinary' energy
transfer seems to be dominated by low-frequency modes of the substrate, whereby
there is sufficient time during a vibrational period for significant energy
flow between the collision partners. Supercollisions may involve sudden energy
flow as an outer atom of the substrate is squashed between the substrate and
the bath gas, and then is moved away from the interaction by large-amplitude
motion such as a ring vibration or a rotation; improved experimental and
theoretical understanding of this phenomenon is seen as an important area for
future development.
Binding of the Immunosuppressant Peptide Cyclosporine A to Calcium, Zinc and Copper. Is Cyclosporine A an Ionophore?
Authors: Dancer RJ , Jones A , Fairlie DP
Published: November 2006

Cyclosporin A is an immunosuppressant drug that has made organ transplantation possible during the past decade. This conformationally flexible peptide, which interferes in an unknown way with calcium-dependent intracellular signalling events, has now been examined in aqueous and acetone solutions containing metal ions. By using electrospray mass spectrometry and nuclear magnetic resonance spectroscopy, cyclosporin A was found to bind directly to endogenous metal ions Ca2+, Zn2+ and Cu2+, with the highest affinity being for Ca2+. These observations raise the possibility that cyclosporins might directly regulate local concentrations of metal ions associated with intracellular signal transduction. This may be an important clue to the mechanism of immunoregulation by this and structurally related drugs.
The Chemistry of 5-Oxodihydroisoxasoles. XIV. Synthesis of 2-(1-Aryltetrazol-5-yl)propanoic Acids
Authors: Caiazza D , Prager RH , Schafer K
Published: November 2006

A number of N-arylisoxazol-5(2H)-ones (aryl = phenyl, isoquinolin-1-yl, quinolin-2-yl, 2-phenylquinazolin-4-yl and benzothiazol-2-yl) have been reacted with lithium azide to give 2-(1-aryltetrazol-5-yl)acetic esters, which have been C- methylated and hydrolysed. The resulting 2-(1-aryltetrazol-5-yl) propanoic acids had low antiinflammatory activity, as judged by inhibition of synthesis of prostaglandin PGE2 or tumour necrosis factor α.
A Synthesis of (Z)-Octadec-9-enedioic Acid
Authors: Brunow G , Stick RV , Syrjanen K , Tilbrook DMG , Williams SJ
Published: November 2006

The monomethyl ester of azelaic acid was transformed into two fragments, namely [8-( methoxy -carbonyl) octyl ] triphenylphosphonium bromide and methyl 9-oxononanoate. A Wittig reaction between these two fragments produced dimethyl (Z)-octadec-9-enedioate and subsequent hydrolysis gave the title diacid. Interestingly, the same diacid was available directly from oleic acid in a published procedure which utilized a mutant strain of Candida tropicalis.
Organoamido- and Aryloxo-lanthanoids. XII. The Coordination Chemistry of Bis(2-phenylindol-1-yl)ytterbium(II), and the X-Ray Crystal Structures of Yb(pin)2(diglyme)(thf) and [Yb(pin)2(dme)]2 (pin = 2-Phenylindol-1-yl, diglyme = Bis(2-methoxyethyl) Ether, thf Equals Tetrahydrofuran, dme = 1,2-Dimethoxyethane)
Authors: Abrahams CT , Deacon GB , Forsyth CM , Patalinghug WC , Skelton BW , White AH
Published: November 2006

With the facile displacement being utilized of thf from Yb(pin)2(thf)4 (pin = 2-phenylindol-1-yl, thf = tetrahydrofuran) in toluene solution, the complexes Yb(pin)2(dme)2 (dme = 1,2- dimethoxyethane), Yb(pin)2 (tmen)(tmen = N,N,N′,N′-tetramethylethane-1,2-diamine) and Yb(pin)2(diglyme)(thf) (diglyme = bis(2-methoxyethyl) ether) have been prepared from the respective ligands and Yb(pin)2(thf)4. Yb(pin)2 (diglyme) (thf) [monoclinic, space group P 21 /c, a 15.35(1), b 16.179(5), c 14.45(2) Ǻ, β 107.51(8)°, Z 4, R 0.044 for 2956 (I > 3σ(I)) 'observed' reflections] has a monomeric six-coordinate structure with transoid nitrogen donor atoms, N-Yb-N 143.6(4)° and an irregular coordination polyhedron described as either a distorted trigonal prism or a monocapped square pyramid. Attempted crystallization of Yb(pin)2 (thf) by partial desolvation of Yb(pin)2(thf)4 in hot toluene, containing a trace of dme, gave a mixture of red Yb(pin)2(thf) and orange [Yb(pin)2(dme)]2. The latter was independently synthesized by partial desolvation of Yb(pin)2(dme)2 in toluene. An X-ray crystal structure showed [Yb(pin)2(dme)]2 [monoclinic, space group P 21/c, a 11 .614(2), b 15.945(7), c 15.327(4) Ǻ, β 110.19(2)°, Z 2 dimers, R 0.070 for 2314 (I ≥ 3σ(I)) 'observed' reflections] to be a dimer with two bridging pin ligands, coordinated through nitrogen only. There is an approximately square pyramidal five-coordinate ytterbium environment with an apical dme oxygen, and with two bridging nitrogens, a terminal nitrogen, and a dme oxygen in the basal plane.
Substituent-Dependent Nitration of 9-Substituted 9,10-Dihydro-9,10-ethanoanthracenes
Authors: Harsanyi MC , Norris RK , Sze G , Witting PK
Published: November 2006

Mononitration of 9-substituted ethanoanthracenes, bearing Me, But, F, Br, I, OMe , NO2, CN, CHO or CO2Me substituents at the bridgehead carbon, was found to occur exclusively at the β-positions of the aromatic ring. The mononitro products were isolated, identified by 1H n.m.r. spectroscopy, and their relative proportions were estimated by quantitative g.l.c . and/or by 1H n.m.r. spectroscopy. For all the above substrates the proportion of nitration at the β-position meta to the bridgehead carbon bearing the substituent [to give compounds of the general form (4)] was greater than the proportion of nitration at the corresponding β-position para to the bridgehead substituent [to give compounds of the general form (3)]. Whilst the preferential nitration at the β-positions of the aromatic rings is consistent with the previously reported nitration of 9,10-dihydro-9,10-ethanoanthracene (2a) itself, no observations of this preferential meta attack have been made previously. No correlation could be made of this behaviour with available substituent parameters for the widely sterically and electronically disparate set of substituents used in this study, and the origin of this preferential attack remains unclear. Dinitration in this system was studied only superficially. The influence of the bridgehead substituent together with that of the nitro group already present on one aromatic ring appear to combine with quite unpredictable results in orienting the position of attack of the incoming nitro group onto the other (non-nitrated) aromatic ring.
Enhanced anxiety and stress-induced corticosterone release are associated with increased
Crh
expression in a mouse model of Rett syndrome
Authors: McGill Bryan E. , Bundle Sharyl F. , Yaylaoglu Murat B. , Carson James P. , Thaller Christina , Zoghbi Huda Y.
Published: November 2006

Rett syndrome (RTT), a postnatal neurodevelopmental disorder, is caused by mutations in the methyl-CpG-binding protein 2 (
MECP2
) gene. Children with RTT display cognitive and motor abnormalities as well as autistic features. We studied mice bearing a truncated
Mecp2
allele (

Mecp2
308/Y

mice) and found evidence of increased anxiety-like behavior and an abnormal stress response as evidenced by elevated serum corticosterone levels. We found increased corticotropin-releasing hormone (
Crh
) gene expression in the paraventricular nucleus of the hypothalamus, the central amygdala, and the bed nucleus of the stria terminalis. Finally, we discovered that MeCP2 binds the
Crh
promoter, which is enriched for methylated CpG dinucleotides. In contrast, the MeCP2
308
protein was not detected at the
Crh
promoter. This study identifies
Crh
as a target of MeCP2 and implicates
Crh
overexpression in the development of specific features of the

Mecp2
308/Y

mouse, thereby providing opportunities for clinical investigation and therapeutic intervention in RTT.
A Conserved Dileucine Motif Mediates Clathrin and AP-2–dependent Endocytosis of the HIV-1 Envelope Protein
Authors: Byland Rahel , Vance Patricia J. , Hoxie James A. , Marsh Mark
Published: November 2006

During the assembly of enveloped viruses viral and cellular components essential for infectious particles must colocalize at specific membrane locations. For the human and simian immunodeficiency viruses (HIV and SIV), sorting of the viral envelope proteins (Env) to assembly sites is directed by trafficking signals located in the cytoplasmic domain of the transmembrane protein gp41 (TM). A membrane proximal conserved GYxxØ motif mediates endocytosis through interaction with the clathrin adaptor AP-2. However, experiments with SIVmac239Env indicate the presence of additional signals. Here we show that a conserved C-terminal dileucine in HIVHxB2also mediates endocytosis. Biochemical and morphological assays demonstrate that the C-terminal dileucine motif mediates internalization as efficiently as the GYxxØ motif and that both must be removed to prevent Env internalization. RNAi experiments show that depletion of the clathrin adaptor AP-2 leads to increased plasma membrane expression of HIV Env and that this adaptor is required for efficient internalization mediated by both signals. The redundancy of conserved endocytosis signals and the role of the SIVmac239Env GYxxØ motif in SIV pathogenesis, suggest that these motifs have functions in addition to endocytosis, possibly related to Env delivery to the site of viral assembly and/or incorporation into budding virions.
A novel real-time PCR to detect Chlamydia trachomatis in first-void urine or genital swabs
Authors: Jaton Katia , Bille Jacques , Greub Gilbert
Published: November 2006

Screening for Chlamydia trachomatis infections can be performed on urine samples and genital swabs using molecular techniques. A novel approach was developed that combined an automated extraction procedure, an automated liquid-handling system and real-time PCR to detect C. trachomatis from urine or swabs. This novel real-time PCR approach was compared to the commercial Cobas Amplicor system on 628 specimens. In a retrospective analysis, 51 samples that tested positive using the Cobas assay were also positive with the real-time PCR, whereas the 49 samples negative with Cobas were also negative with the real-time PCR, for an overall agreement of 100 %. Among 528 prospective samples consecutively received at the authors' laboratory with a request for C. trachomatis PCR, five PCR reactions were inhibited when tested with Cobas. These five inhibited samples were found negative with the real-time PCR. Among the remaining 523 samples, 45 (8.6 %) were positive with both methods, 476 (91 %) were negative with both methods, and 2 (0.4 %) were positive with Cobas but negative with the real-time PCR. Thus, when considering Cobas as the gold standard, the overall agreement was 99.6 %, the sensitivity of the real-time PCR was 95.7 % and the specificity was 100 %. The two discrepant samples were retested in parallel and were found negative with both methods. When testing a batch of 25 samples, both reagent costs and laboratory technician time were reduced with the new technique (7.30 euros per sample and 134 min) compared to Cobas (11.20 euros per sample and 232 min). Moreover, due to reduced organizational constraints, the median time from sample reception to result was only 24 h using the automated platform. Overall, this novel real-time PCR approach exhibited an excellent specificity and a sensitivity similar to that of Cobas Amplicor PCR for the detection of C. trachomatis. Given its high throughput potential and low costs/laboratory technician time requirement, it may be useful for future use in large C. trachomatis screening programs.
emm typing of invasive T28 group A streptococci, 1995–2004, Finland
Authors: Siljander Tuula , Toropainen Maija , Muotiala Anna , Hoe Nancy P. , Musser James M. , Vuopio-Varkila Jaana
Published: November 2006

A total of 985 group A streptococcus (GAS) bacteraemia isolates collected in Finland during 1995–2004 were T-serotyped, and of these, 336 isolates of serotype T28 were subjected to furtheremmtyping. The total number of isolates referred per year showed an increase within the study period, from 43 in 1995 to 130 in 2004. The annual incidence of invasive GAS (iGAS) bacteraemia showed a general increase during the study period, from 1.1 to 2.5 per 100 000 population. Serotype T28 remained among the most common serotypes, in addition to serotypes TB3264 and T1. The serotype T28 isolates were found to be distributed across six distinctemmtypes:emm28,emm77,emm53 (including subtypes 53.2 and 53.4),emm87,emm2 andemm4. The serotype distribution and theemmtype distribution of serotype T28 fluctuated over time. Within the study period, the proportion of T28/emm28 isolates became the most prominent. During periods of lowemm28 incidence,emmtypes 77 and 53 seemed to show a resurgence.emmtyping revealed T28 isolates to be a genetically heterogeneous group harbouring a variety of distinct M proteins. This study confirms that T serotyping alone is not a sufficient method for epidemiological surveillance of iGAS.
Isolation of Salmonella enterica subspecies enterica serovar Paratyphi B dT+, or Salmonella Java, from Indonesia and alteration of the d-tartrate fermentation phenotype by disrupting the ORF STM 3356
Authors: Han Kyung Ho , Choi Seon Young , Lee Je Hee , Lee Hyejon , Shin Eun Hee , Agtini Magdarina D. , von Seidlein Lorenz , Ochiai R. Leon , Clemens John D. , Wain John , Hahn Ji-Sook , Lee Bok Kwon , Song Manki , Chun Jongsik , Kim Dong Wook
Published: November 2006

Salmonella enterica subspecies enterica serovar Paratyphi B [O1,4,(5),12 : Hb : 1,2] can cause either an enteric fever (paratyphoid fever) or self-limiting gastroenteritis in humans. The d-tartrate non-fermenting variant S. enterica subsp. enterica serovar Paratyphi B dT− (S. Paratyphi B) is the causative agent of paratyphoid fever, and the d-tartrate fermenting variant S. enterica subsp. enterica serovar Paratyphi B dT+ (S. Paratyphi B dT+; formerly called Salmonella Java) causes gastroenteritis. S. Java is currently recognized as an emerging problem worldwide. Twelve dT+
S. Java isolates were collected in Indonesia between 2000 and 2002. One-third of them contained Salmonella genomic island 1 (SGI1), which gives the multidrug-resistant phenotype to the bacteria. In this study, a PCR-based method to detect a single nucleotide difference responsible for the inability to ferment d-tartrate, reported elsewhere, was validated. The d-tartrate fermenting phenotype of S. Java was converted to the non-fermenting phenotype by the disruption of the ORF STM 3356, and the d-tartrate non-fermenting phenotype of the ORF STM 3356-disrupted strain and the dT− reference strain was changed to the dT+ phenotype by complementing ORF STM 3356 in trans. The results show that the dT+ phenotype requires a functional product encoded by STM 3356, and support the use of the PCR-based discrimination method for S. Paratyphi B and S. Java as the standard differentiation method.
Characterization of intron loss events in mammals
Authors: Coulombe-Huntington Jasmin , Majewski Jacek
Published: November 2006

The exon/intron structure of eukaryotic genes differs extensively across species, but the mechanisms and relative rates of intron loss and gain are still poorly understood. Here, we used whole-genome sequence alignments of human, mouse, rat, and dog to perform a genome-wide analysis of intron loss and gain events in >17,000 mammalian genes. We found no evidence for intron gain and 122 cases of intron loss, most of which occurred within the rodent lineage. The majority (68%) of the deleted introns were extremely small (<150 bp), significantly smaller than average. The intron losses occurred almost exclusively within highly expressed, housekeeping genes, supporting the hypothesis that intron loss is mediated via germline recombination of genomic DNA with intronless cDNA. This study constitutes the largest scale analysis for intron dynamics in vertebrates to date and allows us to confirm and extend several hypotheses previously based on much smaller samples. Our results in mammals show that intron gain has not been a factor in the evolution of gene structure during the past 95 Myr and has likely been restricted to more ancient history.
An instrument for time-resolved and anomalous simultaneous small- and wide-angle X-ray scattering (SWAXS) at NSRRC
Authors: Lai Ying-Huang , Sun Ya-Sen , Jeng U-Ser , Lin Jhih-Min , Lin Tsang-Lang , Sheu Hwo-Sheunn , Chuang Wei-Tsung , Huang Yu-Shan , Hsu Chia-Hung , Lee Ming-Tao , Lee Hsin-Yi , Liang Keng S. , Gabriel Andre , Koch Michel H. J.
Published: November 2006

A SWAXS (small- and wide-angle X-ray scattering) instrument was recently installed at the wiggler beamline BL17B3 of the National Synchrotron Radiation Research Center (NSRRC), Taiwan. The instrument, which is designed for studies of static and dynamic nanostructures and correlations between the nano (ormeso) structure (SAXS) and crystalline structure (WAXS), provides a flux of 1010–1011photon s−1at the sample at energies between 5 and 14 keV. With a SAXS area detector and a WAXS linear detector connected to two data acquisition systems operated in master–slave mode, the instrument allows one to perform time-resolved as well as anomalous scattering measurements. Data reduction algorithms have been developed for rapid processing of the large SWAXS data sets collected during time-resolved measurements. The performance of the instrument is illustrated by examples taken from different classes of ongoing projects: (i) time-resolved SAXS/WAXS/differential scanning calorimetry (DSC) with a time resolution of 10 s on a semicrystalline poly(hexamethylene terephthalate) sample, (ii) anomalous SAXS/WAXS measurements on a nanoparticulate PtRu catalyst, and (iii) grazing-incidence SAXS of a monolayer of oriented semiconductor quantum wires, and humidity-controlled ordering of Alamethicin peptides embedded in an oriented lipid membrane.
Application of Bayesian analysis to indirect Fourier transformation in small-angle scattering
Authors: Vestergaard Bente , Hansen Steen
Published: November 2006

Using Bayesian analysis for indirect Fourier transformation (IFT) of data from small-angle scattering (SAS) leads to probability distributions for parameters describing the experimental data. This quantification may provide extra information about the scattering system. The shape of the probability distribution for the maximum diameter of the scatterer may contain information aboute.g.the heterogeneity of the scattering sample. The information content in the experimental data can be quantified as an `effective number of parameters' which can be determined from the data. The applicability of the Bayesian approach to IFT in SAS is demonstrated using simulated as well as experimental data.
Fortran90 sources of the subroutines ofUMWEG. I. The subroutineUPFORMfor the determination of dispersion corrections and scattering-factors for free atoms and ions
Authors: Rossmanith Elisabeth
Published: November 2006

The Fortran90 source of the subroutineUPFORM, which provides dispersion corrections and scattering factors for all free atoms and ions in the range 0 ≤ sinθ/λ ≤ 6 Å−1, has been deposited in the IUCr electronic archives.
An automated platform for parallel crystallization of small organic molecules
Authors: Florence Alastair J. , Johnston Andrea , Fernandes Philippe , Shankland Norman , Shankland Kenneth
Published: November 2006

An automated platform for parallel crystallization of small organic molecules from solution is described. The principal gain over manual crystallization lies in the automated sequencing of crystallization steps, including computer-controlled dosing of liquids and solids. The platform is designed to conduct 32 crystallizations per day, from solution volumes up to 10 ml, allowing a search for physical forms to be conducted over a finer grid than might be accessible manually and thereby increasing the probability of success.
A simple method for motorized alignment of Osmic confocal optics
Authors: Ruble John R. , Wang Bi-Cheng , Rose John P.
Published: November 2006

A system for the remote alignment of X-ray optics has been designed to address safety considerations related to manual optic adjustment. The described system also addresses some of the common problems associated with the alignment process, such as binding of components and the effects of external forces due to user contact that lead to irreproducibility of the process. The system as described should be applicable to most home laboratories.
Structure of strontium barium niobate Sr
x
Ba1 − x
Nb2O6 (SBN) in the composition range 0.32 ≤ x ≤ 0.82
Authors: Podlozhenov Sergey , Graetsch Heribert A. , Schneider Julius , Ulex Michael , Wöhlecke Manfred , Betzler Klaus
Published: November 2006

The structure of strontium barium niobate crystals Sr
x
Ba1 − x
Nb2O6 is comprehensively studied in the whole range of the tetragonal tungsten bronze phase (x = 0.32–0.82) using both powder and single-crystal X-ray diffraction measurements. Unit-cell parameters, density, site-occupancy factors and interionic distances show an explicit composition dependence which can be consistently explained using simple model calculations. The temperature dependence of the unit-cell parameters exhibits a remarkable anisotropy in a broad temperature region below the phase transition temperature. This proves that the electrostrictive contribution to the thermal expansion plays an important role in strontium barium niobate.
6q deletion in Waldenström macroglobulinemia is associated with features of adverse prognosis
Authors: Ocio E. M. , Schop R. F. J. , Gonzalez B. , Van Wier S. A. , Hernandez‐Rivas J. M. , Gutierrez N. C. , Garcia‐Sanz R. , Moro M. J. , Aguilera C. , Hernandez J. , Xu R. , Greipp P. R. , Dispenzieri A. , Jalal S. M. , Lacy M. Q. , Gonzalez‐Paz N. , Gertz M. A. , San Miguel J. F. , Fonseca R.
Published: November 2006

Fluorescence in situ hybridisation (FISH) is an effective technique for the cytogenetic analysis of Waldenström macroglobulinemia (WM), but the potential impact of molecular cytogenetics on disease evolution and as a prognostic marker is still unknown. Deletion of the long arm of chromosome 6 (6q−) is the most frequent cytogenetic abnormality in WM. This study analysed the prevalence of this aberration in 102 WM patients, and correlated it with disease characteristics. The incidence of 6q21 deletion was 7% by conventional cytogenetics and 34% when analysed by FISH (54% when cytoplasmic immunoglobulin M‐FISH was used). Patients with deletion of 6q displayed features of adverse prognosis, such as higher levels of β2‐microglobulin and monoclonal paraprotein and a greater tendency to display anaemia and hypoalbuminemia. Interestingly, there was a correlation between the presence of 6q deletion and the International Staging System prognostic index (incidence of 6q− among patients stratified in stages 1, 2 and 3 was 24%, 42% and 67% respectively). Those patients diagnosed with smouldering WM who displayed the abnormality showed a trend to an earlier requirement of treatment. Finally, the survival analysis did not show differences between the two groups of patients, probably due to the short follow up of our series.
Possibility of selection of chondrogenic progenitor cells by telomere length in FGF‐2‐expanded mesenchymal stromal cells
Authors: Yanada S. , Ochi M. , Kojima K. , Sharman P. , Yasunaga Y. , Hiyama E.
Published: November 2006

Abstract.  Telomere length plays an important role in regulating the proliferative capacity of cells, and serves as a marker for cell cycle history and also for their remaining replicative potential. Mesenchymal stromal cells (MSC) are known to be a significant cell source for therapeutic intervention and tissue engineering. To investigate any possible limitations in the replicative potential and chondrogenic differentiation potential of fibroblast growth factor‐2‐expanded MSCs (FGF(+)MSC), these cells were differentiated at various population doublings (PDs), and telomere length and telomerase activity were measured before and after differentiation. FGF(+)MSC cultured at a relatively low density maintained proliferation capability past more than 80 PD and maintained chondrogenic differentiation potential up to at least 46 PD and long telomeres up to 105 PD, despite expressing low levels of telomerase activity. Interestingly, upon chondrogenic differentiation of these cells, telomeres showed a remarkable reduction in length. This shortening was more extensive when FGF(+)MSC of higher PD levels were differentiated. These findings suggest that telomere length may be a useful genetic marker for chondrogenic progenitor cells.
Assessment of pluripotency and multilineage differentiation potential of NTERA‐2 cells as a model for studying human embryonic stem cells
Authors: Pal Rajarshi , Ravindran Geeta
Published: November 2006

Abstract.  Embryonal carcinoma cells are pluripotent stem cells derived from teratocarcinomas and are considered to be the malignant counterparts of human embryonic stem cells. As there are few reliable experimental systems available to study the molecular mechanisms governing normal embryogenesis, well‐characterized human embryonal carcinoma stem cell lines may provide a robust and simple model to study certain aspects of pluripotency and cellular differentiation. Here, we have analysed NTERA‐2 cL.D1 cells at molecular and cellular levels during expansion and differentiation, via formation of cell aggregates similar to embryoid bodies in embryonic stem cells. Thus, human embryonal carcinoma cells may provide a valuable insight into cell fate determination, into the embryonic ectoderm, mesoderm and endoderm and their downstream derivatives.
Targeting adenosine receptors in the treatment of allergic rhinitis: a randomized, double‐blind, placebo‐controlled study
Authors: Rimmer J. , Peake H. L. , Santos C. M.C. , Lean M. , Bardin P. , Robson R. , Haumann B. , Loehrer F. , Handel M. L.
Published: November 2006

Background
There is evidence that adenosine plays a role in the pathogenesis of asthma and rhinitis; however, it is currently unclear whether adenosine receptors are useful therapeutic targets in the treatment of allergic airway diseases.

Objective
The study evaluated the efficacy of intranasal treatment with an adenosine A2A receptor agonist/adenosine A3 receptor antagonist (50 μg), administered twice daily for 7 days, to reduce nasal symptoms and release of inflammatory mediators following intranasal allergen challenge in patients with allergic rhinitis (AR). The compound was compared with twice‐daily treatment with intranasal fluticasone proprionate nasal spray (FPANS) for 7 days.

Methods
A randomized, double‐blind, double‐dummy, placebo‐controlled, three‐way balanced, incomplete block, crossover study was conducted on 48 males with verified AR. Following intranasal challenge with either an extract from the house dust mite (HDM), Dermatophagoides pteronyssinus, rye grass or cat dander, nasal responses and the concentrations of albumin, tryptase, myeloperoxidase, eosinophilic cationic protein, epithelial neutrophil‐activating protein‐78 (ENA‐78), IL‐5 and IL‐8 in nasal secretions were measured and treatment groups were compared.

Results
Drug improved nasal blockage but had no significant effect on rhinorrhoea, number of sneezes or peak nasal inspiratory flow measurements when compared with placebo. Drug reduced tryptase release after EAR but did not significantly reduce the levels of other mediators.

Conclusion
A novel agonist/antagonist of adenosine A2A and A3 receptors appears to have limited clinical benefit in both the early‐phase and the late‐phase response to intranasal allergen challenge. However, reduction of some pro‐inflammatory mediators suggests that comparable, more selective compounds may have additional benefits meriting further investigation.
Effects of elevated O3, alone and in combination with elevated CO2, on tree leaf chemistry and insect herbivore performance: a meta‐analysis
Authors: VALKAMA ELENA , KORICHEVA JULIA , OKSANEN ELINA
Published: November 2006

We reviewed the effects of elevated ozone (O3), alone and in combination with elevated carbon dioxide (CO2) on primary and secondary metabolites of trees and performance of insect herbivores by means of meta‐analysis. Our database consisted of 63 studies conducted on 22 species of trees and published between 1990 and 2005. Ozone alone had no overall effect on concentrations of carbohydrates or nutrients, whereas in combination with CO2, elevated O3 reduced nutrient concentrations and increased carbohydrate concentrations. In contrast to primary metabolites, concentrations of phenolics and terpenes were significantly increased by 16% and 8%, respectively, in response to elevated O3. Effects of ozone in combination with elevated CO2 were weaker than those of ozone alone on phenolics, but stronger than those of ozone alone on terpenes. The magnitude of secondary metabolite responses depended on the type of ozone exposure facility and increased in the following order: indoor growth chamber <open‐top chamber <free‐air ozone exposure. The results of meta‐analysis demonstrated that, in terms of leaf chemistry, angiosperms are more responsive to elevated O3 than gymnosperms, as shifts in concentrations of carbohydrate and phenolics were observed in the former, but not in the latter. Elevated O3 had positive effects on some indices of insect performance: pupal mass increased and larval development time shortened, but these effects were counteracted by elevated CO2. Therefore, despite the observed increase in secondary metabolites, elevated O3 tends to increase tree foliage quality for herbivores, but elevated CO2 may alleviate these effects. Our meta‐analysis clearly demonstrated that effects of elevated O3 alone on leaf chemistry and some indices of insect performance differed from those of O3+CO2, and therefore, it is important to study effects of several factors of global climate change simultaneously.
Durum wheat quality: II. The relationship of kernel physicochemical composition to semolina quality and end product utilisation
Authors: Samaan Jihad , El‐Khayat Ghassan H. , Manthey Frank A. , Fuller Mick P. , Brennan Charles S.
Published: November 2006

Kernel quality characteristics, semolina milling potential, dough rheology and pasta making properties of kernels from nine fully irrigated Syrian durum wheat genotypes were observed. Protein content of the kernels exerted a significant affect on the physical characteristics hardness and the degree of kernel vitreousness, both of which were highly correlated with superior end‐use product. Gluten composition of semolina appeared as significant as overall protein content in determining the optimum end‐use product cooking quality (cooking time and pasta texture). The final viscosity of durum flour exhibited positive correlations with semolina recovery, protein content, gluten content, vitreousness, the optimum‐cooking time of pasta and pasta firmness. This indicates the relevance of using the rapid visco analyser technique in evaluating the durum wheat and pasta qualities. Dough rheology measurements confirmed that farinograph and extensograph are useful indicators of the cooking properties of pasta. The research also illustrates that although variability between Syrian durum wheat genotypes were observed, their milling and processing parameters were similar to those previously reported for Canadian and American durum wheats, indicating the potential to use these lines in mainstream pasta production.
Textural characterisation of lasagna made from organic whole wheat
Authors: Olivera Daniela F. , Salvadori Viviana O.
Published: November 2006

In the last years, trade of organic foods has risen significantly. Relevant quality studies for organic foods are generally related to environmental and health attributes/considerations. However, very few studies that analyse the traditional characteristics of food quality have been carried out. The importance of these studies is that they enable us to compare them with conventional food. Therefore, the objective of this article is to study the quality (texture and sensory properties) of lasagna prepared only with organic ingredients, without additives and through standard procedures of manufacture. Organic lasagna characteristics are compared with conventional white and whole wheat ones. The analysis of variance indicates the existence of significant differences in all the texture parameters, except for the cohesiveness. These differences show a possible interaction between the fibre and the gluten network. The relaxation curves show that conventional dough is more elastic than both the whole wheat samples; on the contrary, the viscous components are higher in whole wheat doughs, indicating the fibre–protein interaction. From the sensory analysis, the only parameter in which the organic pasta differed significantly from the conventional one was appearance. On the whole, these differences did not affect the acceptability of the product.
Influence of growing conditions on the technological performance of bread wheat (Triticum aestivum L.)
Authors: Carcea Marina , Salvatorelli Simona , Turfani Valeria , Mellara Francesco
Published: November 2006

Six bread wheat cultivars were grown in the same environment according to a conventional and an organic agricultural protocol. Hardness, moisture, test weight, protein and ash content and falling number were determined on kernels. Flour yield, particle size distribution and damaged starch were determined on flours together with farinograph and alveograph parameters. Loaves of bread were also baked following a straight dough standardised recipe. Results indicated that protein content was the quality parameter which was negatively influenced by organic farming. Hardness was also negatively influenced in four out of six cultivars, whereas the other technological parameters did not show the same trend for all the cultivars. The milling performance was similar between organic and conventional samples, whereas the differences in protein contents were clearly responsible for differences in rheological properties. As expected, volumes of the organic loaves of breads were significantly lower than those of the corresponding conventional ones.