bluuebunny/crossref_metadata_2025 huggingface dataset:
Saddle-point geometries and barriers to internal rotation of formamide : an ab initio study
Authors: Radom L , Riggs NV
Published: November 2006

By use of a direct transition-state
program and the STO-3G minimal basis set, two saddle-points are detected on the
energy surface for internal motion of formamide. These correspond mainly to
rotation about the C-N bond along with some lengthening of this bond and
increased pyramidal distortion at nitrogen as compared with that in the ground
state. The STO-3G estimates of the barrier height (34-39 kJ mol-1)
are in very poor agreement with experimental values (70-90 kJ mol-1),
but 4- 31G energy evaluations for the STO-3G-optimized structures give much better
estimates (62-80 kJ mol-1). Contrary to a previous report, use of
the 4-31G extended basis set for geometry optimization suggests that only the
lower-energy member (NH2 cis to CO) of the above pair is a true
transition state for internal motion of formamide; its energy relative to that
of the 4-31G-optimized ground state (planar) is 83.5 kJ mol-1, very
close to the midpoint of the experimental range. The transition state appears
to lie in a region of the 4-31G energy surface that is relatively flat with
respect to pyramidal distortion at nitrogen; constraining the amino group to
planarity raises the calculated energy by only 6.5kJmol-1.
Organophosphorus intermediates. VI. The acid-catalysed reaction of trialkyl orthoformates with phosphinic acid
Authors: Gallagher MJ , Honegger H
Published: November 2006

Trialkyl orthoformates
react with phosphinic acid to give the corresponding alkyl phosphinate and
alkyl mono- or bis- (dialkoxymethyl)phosphinates;
dialkyl phosphonites and phosphine, PH3, are also formed. The
formation of P-alkylated products is acid- catalysed and is believed to proceed
by alkylation of the trivalent tautomer of phosphinic acid (or its ester) by
the dialkoxymethyl carbonium ion arising from the ortho ester in the presence
of acid. A comparison with the corresponding reactions of phosphonic acid
suggests that the trivalent tautomer of phosphinic acid [HP(OH)2] is
formed much more readily than the trivalent form of phosphonic acid [P(OH)3]
and this is accounted for by proposing that the equilibria

RPH(O)OR′ +H+ ↔
RP+H(OH)OR' ↔ RP(OH)OR'+H+ (R = H, OH; R' = H,
alkyl)
lie further to the right
for R = H than for R = OH because of inductive effects. 31P and 1H
n.m.r. data are reported.
Crystal structures of some eriostyl/nitrobenzoate derivatives
Authors: Jefferies PR , Skelton BW , Walter B , White AH
Published: November 2006

Following the suggestion
made earlier, on the basis of solution spectroscopy, that a number
of eriostyl/nitrobenzoate compounds form charge-transfer self-complexes, a
number of these have been investigated structurally by single-crystal X-ray
diffraction methods in order to ascertain the presence or otherwise of such
interactions in the solid state. The substances thus studied were eriostyl
3,5-dinitrobenzoate (1), eriostyl p-nitrobenzoate (2), tetrahydroeriostyl 3,5-dinitrobenzoate
(3), and eriostemyl 3,5-dinitrobenzoate (4);* structure determinations in all
cases, although displaying the presence of strong charge-transfer interactions
from the two moieties of each molecule, show that the interactions in the solid
state are intermolecular in nature.
The Density, Viscosity and Transference Number of Aqueous Manganese Chloride at 298.15 K
Authors: Phang S
Published: November 2006

The density, viscosity and
transference number of aqueous manganese chloride have been determined over the
concentration range of 0.1-5.8 mol kg-1 at 298.15 K. The viscosity
data are compared with literature values and the transference numbers are used
to discuss chloro-complexformation.
Crystal structure of trans-chlorobis(ethane-l,2-diamine)sulfitocobalt(III) monohydrate
Authors: Raston CL , White AH , Yandell JK
Published: November 2006

The crystal structure of
the title compound, [Co(en)2ClSO3],H2O (en = ethane-1,2-diamine), has been
determined by single-crystal X-ray diffraction methods at 295(1) K and refined
by least squares to a residual of 0.050 for 3252 'observed' reflections. Crystals
are monoclinic, P21/c, a 9.862(4), b 15.897(8), c 16.936(7) Ǻ,
β 117.44(4)°, Z 8. The two independent molecules in the asymmetric unit
are pseudosymmetrically related. (Co-S) is 2.204
Ǻ, while (Co-Cl) is the longest six-coordinate
cobalt(III)-chloride distance observed, being 2.377 Ǻ.
Crystal structure of swainsonine diacetate
Authors: Skelton BW , White AH
Published: November 2006

The crystal structure of swainsonine diacetate, C12H19NO5,
has been determined at 295(1) K by single-crystal X-ray diffraction and refined
by least squares to a residual of 0.054 for 521 'observed' reflections.
Crystals are orthorhombic, P212121, a 18.783(9),
b 13.497(6), c 5.164(3) Ǻ, Z 4.
Carbon-13 N.M.R. spectra of 4-hydroxytetrahydroisoquinolinium chlorides
Authors: Baddeley GV , Quessy SN , Williams LR
Published: November 2006

The natural abundance
carbon-13 n.m.r. spectra of several tetrahydroisoquinolinium salts are reported
and discussed in terms of the substitution profile and stereochemistry of the
salts.
The reaction of propene with iodine bromide
Authors: Alberts V , Carman RM
Published: November 2006

Iodobromination of propene gives a mixture (c. 60 : 40) of
2-bromo-1-iodopropane and 1-bromo-2-iodopropane. This mixture of kinetic
control converts into an equilibrium (c. 70 : 30) mixture with heat. The
addition to the double bond is postulated to occur through a bridged iodonium
ion rather than through a simple carbocation, and hence Markownikoff's
rule need not apply to this system.
Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX
Authors: Thibault Guillaume , Yudin Jovana , Wong Philip , Tsitrin Vladimir , Sprangers Remco , Zhao Rongmin , Houry Walid A.
Published: November 2006

Clp ATPases are a unique group of ATP-dependent chaperones supporting targeted protein unfolding and degradation in concert with their respective proteases. ClpX is a representative member of these ATPases; it consists of two domains, a zinc-binding domain (ZBD) that forms dimers and a AAA
+
ATP-binding domain that arranges into a hexamer. Analysis of the binding preferences of these two domains in ClpX revealed that both domains preferentially bind to hydrophobic residues but have different sequence preferences, with the AAA
+
domain preferentially recognizing a wider range of specific sequences than ZBD. As part of this analysis, the binding site of the ClpX dimeric cofactor, SspB
2
, on ZBD in ClpX was determined by NMR and mutational analysis. The SspB C terminus was found to interact with a hydrophobic patch on the surface of ZBD. The affinity of SspB
2
toward ZBD
2
and the geometry of the SspB
2
–ZBD
2
complex were investigated by using the newly developed quantitative optical biosensor method of dual polarization interferometry. The data suggest a model for the interaction between SspB
2
and the ClpX hexamer.
Developmental switch of mouse hematopoietic stem cells from fetal to adult type occurs in bone marrow after birth
Authors: Kikuchi Kazu , Kondo Motonari
Published: November 2006

Hematopoiesis originated by hematopoietic stem cells (HSCs) is distinguishable between fetal and adult mice. However, it is not clear whether the altered mode of differentiation is due to the change of properties of HSCs or different microenvironments in fetuses and adults. Here we show that fetal HSCs are fully capable of giving rise to all classes of B cells in the adult microenvironment. HSCs that are derived from fetal liver but not adult bone marrow (BM) of IL-7 receptor α chain (IL-7Rα)-deficient mice can also differentiate into B cells, suggesting that both IL-7 and thymic stromal-derived lymphopoietin (TSLP) are dispensable for fetal B cell development, because IL-7Rα is commonly used as a subunit of functional receptor complexes for IL-7 and TSLP. Similar IL-7/TSLP independent B cell potential is maintained by BM HSCs until 1 week after birth. In contrast, BM HSCs in mice older than 2 weeks of age absolutely requires IL-7Rα for B lymphopoiesis. These results demonstrate that fetal HSCs acquired adult characteristics between 1 and 2 weeks after birth in mouse BM.
Self-organization of nano-lines and dots triggered by a local mechanical stimulus
Authors: Biscarini Fabio , Cavallini Massimiliano , Kshirsagar Rajendra , Bottari Giovanni , Leigh David A. , León Salvador , Zerbetto Francesco
Published: November 2006

When a local mechanical perturbation is applied to the surface of a thin film of a mechanically interlocked molecule (a rotaxane), the molecules self-organize into periodic arrays of discrete dots or lines. The dimensionality of the nanostructures depends on whether the mechanical stimulus acts along a 1D line or over a 2D area. The size (50–500 nm) and periodicity (100–600 nm) of the patterns are controlled solely by the film thickness. This self-organization at the mesoscopic scale occurs via a nucleation-ripening mechanism eased by the relatively low energy barriers of the intramolecular rearrangement introduced by the mechanical bond. The phenomenon can be exploited as a bottom-up nanofabrication method.
Angiotensin II causes hypertension and cardiac hypertrophy through its receptors in the kidney
Authors: Crowley Steven D. , Gurley Susan B. , Herrera Maria J. , Ruiz Phillip , Griffiths Robert , Kumar Anil P. , Kim Hyung-Suk , Smithies Oliver , Le Thu H. , Coffman Thomas M.
Published: November 2006

Essential hypertension is a common disease, yet its pathogenesis is not well understood. Altered control of sodium excretion in the kidney may be a key causative feature, but this has been difficult to test experimentally, and recent studies have challenged this hypothesis. Based on the critical role of the renin-angiotensin system (RAS) and the type I (AT
1
) angiotensin receptor in essential hypertension, we developed an experimental model to separate AT
1
receptor pools in the kidney from those in all other tissues. Although actions of the RAS in a variety of target organs have the potential to promote high blood pressure and end-organ damage, we show here that angiotensin II causes hypertension primarily through effects on AT
1
receptors in the kidney. We find that renal AT
1
receptors are absolutely required for the development of angiotensin II-dependent hypertension and cardiac hypertrophy. When AT
1
receptors are eliminated from the kidney, the residual repertoire of systemic, extrarenal AT
1
receptors is not sufficient to induce hypertension or cardiac hypertrophy. Our findings demonstrate the critical role of the kidney in the pathogenesis of hypertension and its cardiovascular complications. Further, they suggest that the major mechanism of action of RAS inhibitors in hypertension is attenuation of angiotensin II effects in the kidney.
Evidence that the adaptive allele of the brain size gene
microcephalin
introgressed into
Homo sapiens
from an archaic
Homo
lineage
Authors: Evans Patrick D. , Mekel-Bobrov Nitzan , Vallender Eric J. , Hudson Richard R. , Lahn Bruce T.
Published: November 2006

At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic
Homo
lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene
microcephalin
(
MCPH1
) regulates brain size during development and has experienced positive selection in the lineage leading to
Homo sapiens
. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy ≈37,000 years ago and swept to exceptionally high frequency (≈70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans ≈1.1 million years ago and introgressed into humans by ≈37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic
Homo
populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.
Gene transfer in humans using a conditionally replicating lentiviral vector
Authors: Levine Bruce L. , Humeau Laurent M. , Boyer Jean , MacGregor Rob-Roy , Rebello Tessio , Lu Xiaobin , Binder Gwendolyn K. , Slepushkin Vladimir , Lemiale Franck , Mascola John R. , Bushman Frederic D. , Dropulic Boro , June Carl H.
Published: November 2006

We report findings from a clinical evaluation of lentiviral vectors in a phase I open-label nonrandomized clinical trial for HIV. This trial evaluated the safety of a conditionally replicating HIV-1-derived vector expressing an antisense gene against the HIV envelope. Five subjects with chronic HIV infection who had failed to respond to at least two antiviral regimens were enrolled. A single i.v. infusion of gene-modified autologous CD4 T cells was well tolerated in all patients. Viral loads were stable, and one subject exhibited a sustained decrease in viral load. CD4 counts remained steady or increased in four subjects, and sustained gene transfer was observed. Self-limiting mobilization of the vector was observed in four of five patients. There is no evidence for insertional mutagenesis after 21–36 months of observation. Immune function improved in four subjects. Lentiviral vectors appear promising for gene transfer to humans.
Development of 17-allylamino-17-demethoxygeldanamycin hydroquinone hydrochloride (IPI-504), an anti-cancer agent directed against Hsp90
Authors: Sydor Jens R. , Normant Emmanuel , Pien Christine S. , Porter James R. , Ge Jie , Grenier Louis , Pak Roger H. , Ali Janid A. , Dembski Marlene S. , Hudak Jebecka , Patterson Jon , Penders Courtney , Pink Melissa , Read Margaret A. , Sang Jim , Woodward Caroline , Zhang Yilong , Grayzel David S. , Wright Jim , Barrett John A. , Palombella Vito J. , Adams Julian , Tong Jeffrey K.
Published: November 2006

Heat shock protein 90 (Hsp90) is an emerging therapeutic target of interest for the treatment of cancer. Its role in protein homeostasis and the selective chaperoning of key signaling proteins in cancer survival and proliferation pathways has made it an attractive target of small molecule therapeutic intervention. 17-Allylamino-17-demethoxygeldanamycin (17-AAG), the most studied agent directed against Hsp90, suffers from poor physical-chemical properties that limit its clinical potential. Therefore, there exists a need for novel, patient-friendly Hsp90-directed agents for clinical investigation. IPI-504, the highly soluble hydroquinone hydrochloride derivative of 17-AAG, was synthesized as an Hsp90 inhibitor with favorable pharmaceutical properties. Its biochemical and biological activity was profiled in an Hsp90-binding assay, as well as in cancer-cell assays. Furthermore, the metabolic profile of IPI-504 was compared with that of 17-AAG, a geldanamycin analog currently in clinical trials. The anti-tumor activity of IPI-504 was tested as both a single agent as well as in combination with bortezomib in myeloma cell lines andin vivoxenograft models, and the retention of IPI-504 in tumor tissue was determined. In conclusion, IPI-504, a potent inhibitor of Hsp90, is efficacious in cellular and animal models of myeloma. It is synergistically efficacious with the proteasome inhibitor bortezomib and is preferentially retained in tumor tissues relative to plasma. Importantly, it was observed that IPI-504 interconverts with the known agent 17-AAGin vitroandin vivovia an oxidation-reduction equilibrium, and we demonstrate that IPI-504 is the slightly more potent inhibitor of Hsp90.
Fabrication of a nanocrystalline Ni–Co/CoO functionally graded layer with excellent electrochemical corrosion and tribological performance
Authors: Liping Wang  , Junyan Zhang  , Zhixiang Zeng  , Yiming Lin  , Litian Hu
Published: November 2006

The authors regret that the data in table 1 contained some errors. The correct table 1 is shown below.

Table 1.Corrosion potential (Ecorr), corrosion current (icorr) and polarization resistance (Rp) of nancorystalline Ni–Co graded deposits measured in different solutions.

SolutionSampleEcorr(mV)icorr(A cm-2)Rp(k Ω cm2)NaOHAs-deposited Ni–Co FGDs−6244.53 E −60.67NC Ni–Co/CoO LGMs−2693.66 E −76.96NaClAs-deposited Ni–Co FGDs−5393.38 E −60.93NC Ni–Co/CoO LGMs−2018.12 E −73.53

We apologise for any inconvenience caused.
In silicogrouping of peptide/HLA class I complexes using structural interaction characteristics
Authors: Tong Joo Chuan , Tan Tin Wee , Ranganathan Shoba
Published: November 2006

Motivation: Classification of human leukocyte antigen (HLA) proteins into supertypes underpins the development of epitope-based vaccines with wide population coverage. Current methods for HLA supertype definition, based on common structural features of HLA proteins and/or their functional binding specificities, leave structural interaction characteristics among different HLA supertypes with antigenic peptides unexplored.

Methods: We describe the use of structural interaction descriptors for the analysis of 68 peptide/HLA class I crystallographic structures. Interaction parameters computed include the number of intermolecular hydrogen bonds between each HLA protein and its corresponding bound peptide, solvent accessibility, gap volume and gap index.

Results: The structural interactions patterns of peptide/HLA class I complexes investigated herein vary among individual alleles and may be grouped in a supertype dependent manner. Using the proposed methodology, eight HLA class I supertypes were defined based on existing experimental crystallographic structures which largely overlaps (77% consensus) with the definitions by binding motifs. This mode of classification, which considers conformational information of both peptide and HLA proteins, provides an alternative to the characterization of supertypes using either peptide or HLA protein information alone.

Contact:  shoba@els.mq.edu
The nested structure of marine cleaning symbiosis: is it like flowers and bees?
Authors: Guimarães Paulo R , Sazima Cristina , Reis Sérgio Furtado dos , Sazima Ivan
Published: November 2006

In a given area, plant–animal mutualistic interactions form complex networks that often display nestedness, a particular type of asymmetry in interactions. Simple ecological and evolutionary factors have been hypothesized to lead to nested networks. Therefore, nestedness is expected to occur in other types of mutualisms as well. We tested the above prediction with the network structure of interactions in cleaning symbiosis at three reef assemblages. In this type of interaction, shrimps and fishes forage on ectoparasites and injured tissues from the body surface of fish species. Cleaning networks show strong patterns of nestedness. In fact, after controlling for species richness, cleaning networks are even more nested than plant–animal mutualisms. Our results support the notion that mutualisms evolve to a predictable community-level structure, be it in terrestrial or marine communities.
Harvesting of males delays female breeding in a socially monogamous mammal; the beaver
Authors: Parker Howard , Rosell Frank , Mysterud Atle
Published: November 2006

Human exploitation may skew adult sex ratios in vertebrate populations to the extent that males become limiting for normal reproduction. In polygynous ungulates, females delay breeding in heavily harvested populations, but effects are often fairly small. We would expect a stronger effect of male harvesting in species with a monogamous mating system, but no such study has been performed. We analysed the effect of harvesting males on the timing of reproduction in the obligate monogamous beaver (
Castor fiber
). We found a negative impact of harvesting of adult males on the timing of parturition in female beavers. The proportion of normal breeders sank from over 80%, when no males had been shot in the territories of pregnant females, to under 20%, when three males had been shot. Harvesting of males in monogamous mammals can apparently affect their normal reproductive cycle.
A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
Authors: Didelot Xavier , Achtman Mark , Parkhill Julian , Thomson Nicholas R. , Falush Daniel
Published: November 2006

All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for ∼600,000 deaths per annum. We developed a Bayesian changepoint model that uses variation in the degree of nucleotide divergence along two genomes to detect homologous recombination between these strains, and with other lineages of Salmonella enterica. Paratyphi A and Typhi showed an atypical and surprising pattern. For three quarters of their genomes, they appear to be distantly related members of the species S. enterica, both in their gene content and nucleotide divergence. However, the remaining quarter is much more similar in both aspects, with average nucleotide divergence of 0.18% instead of 1.2%. We describe two different scenarios that could have led to this pattern, convergence and divergence, and conclude that the former is more likely based on a variety of criteria. The convergence scenario implies that, although Paratyphi A and Typhi were not especially close relatives within S. enterica, they have gone through a burst of recombination involving more than 100 recombination events. Several of the recombination events transferred novel genes in addition to homologous sequences, resulting in similar gene content in the two lineages. We propose that recombination between Typhi and Paratyphi A has allowed the exchange of gene variants that are important for their adaptation to their common ecological niche, the human host.
Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots
Authors: Gomes João P. , Bruno William J. , Nunes Alexandra , Santos Nicole , Florindo Carlos , Borrego Maria J. , Dean Deborah
Published: November 2006

Chlamydia trachomatisis an obligate intracellular bacterium of major public health significance, infecting over one-tenth of the world’s population and causing blindness and infertility in millions. Mounting evidence supports recombination as a key source of genetic diversity among free-living bacteria. Previous research shows that intracellular bacteria such asChlamydiaceaemay also undergo recombination but whether this plays a significant evolutionary role has not been determined. Here, we examine multiple loci dispersed throughout the chromosome to determine the extent and significance of recombination among 19 laboratory reference strains and 10 present-day ocular and urogenital clinical isolates using phylogenetic reconstructions, compatibility matrices, and statistically based recombination programs. Recombination is widespread; all clinical isolates are recombinant at multiple loci with no two belonging to the same clonal lineage. Several reference strains show nonconcordant phylogenies across loci; one strain is unambiguously identified as recombinantly derived from other reference strain lineages. Frequent recombination contrasts with a low level of point substitution; novel substitutions relative to reference strains occur less than one per kilobase. Hotspots for recombination are identified downstream fromompA, which encodes the major outer membrane protein. This widespread recombination, unexpected for an intracellular bacterium, explains why strain-typing using one or two genes, such asompA, does not correlate with clinical phenotypes. Our results do not point to specific events that are responsible for different pathogenicities but, instead, suggest a new approach to dissect the genetic basis for clinical strain pathology with implications for evolution, host cell adaptation, and emergence of new chlamydial diseases.
Influence of plastic deformation and prolonged ageing time on microstructure of a Haynes 242 alloy
Authors: DYMEK S. , WRÓBEL M. , DOLLAR M. , BLICHARSKI M.
Published: November 2006

The material used in this study was a commercial HAYNES® alloy 242™ with a nominal composition of Ni‐25% Mo‐8% Cr (in wt.%). In the standard heat treatment, the 242 alloy is annealed at a temperature between 1065 and 1095 °C and then water quenched. The ageing treatment is carried out at 650 °C for 24 h in order to develop the long‐range‐order strengthening. The alloy in the conventionally aged condition was additionally cold rolled to 50% reduction in thickness and subsequently subjected to prolonged ageing at 650 °C for 4000 h. The enhanced diffusion resulted in the decomposition of the Ni2(Mo,Cr) metastable phase into the stable Ni3Mo‐based phase. The presence of the new stable phase increased the yield and tensile strengths but deteriorated the ductility of the alloy at both room and 650 °C temperatures.
Transmission electron microscopy study of crystallization in Fe‐Si–B–Cr–C amorphous alloy
Authors: KOZIEŁ T. , ZIELIŃSKA‐LIPIEC A. , KEDZIERSKI Z. , CZEPPE T.
Published: November 2006

The crystallization behaviour of Fe72Si9.1B14.8Cr2.2C1.9 alloy was studied. Three forms of the examined alloy were studied: water‐atomized powder, as‐spun ribbon and fully crystallized ribbon. Transmission electron microscopy studies of the examined alloy in the form of powder revealed partial crystallization of Fe2B. The as‐spun ribbon was found to be fully amorphous, and no evidence of any crystalline phases was detected. Formation of metastable phases in the fully devitrificated ribbon was observed. The examined alloy, heated to above its crystallization temperature, consisted of α‐Fe3(Si), Fe23(C,B)6, Fe3B and Fe2B crystalline phases.
Influence of Ca content and oxygen partial pressure on microstructural evolution of (Co,Ca)O at elevated temperatures
Authors: KUSINSKI J. , CIENIEK L. , PETOT‐ERVAS G. , PETOT C. , BALDINOZZI G.
Published: November 2006

Ca‐doped (1, 1.7, 5 and 10 mol% CaO) cobalt oxide single‐crystal samples, with an [001] orientation, were annealed at elevated temperatures of 1000–1200 °C for different times and at different oxygen partial pressures. The microstructure was examined by means of transmission light and electron microscopy. High‐temperature X‐ray diffractometry was used, with the aim of determining the temperature of the CoO ⇔ Co3O4 transition in these materials. Extensive precipitation of Ca‐free Co3O4 spinel crystals was observed with increasing Ca content and oxygen activity. It is suggested that the electrical conductivity changes in this material may be related to this precipitation, because it changes the electronic state of cobalt cations.
Cathodoluminescence studies of nanostructured semiconductors
Authors: GUSTAFSSON A.
Published: November 2006

Spatially and spectrally resolved cathodoluminescence in the scanning electron microscope is a very powerful technique for studying the optical properties of semiconductor structures, especially low‐dimensional structures (structures with nanometre‐sized features). The technique is generally nondestructive and can be combined with the normal imaging capabilities and analysis possibilities of the scanning electron microscope. This article gives an introduction to the technique and a number of examples of the possibilities of the technique.
New system for secondary electron detection in variable‐pressure scanning electron microscopy
Authors: SLÓWKO W.
Published: November 2006

A novel secondary electron detection system combining a two‐stage detector head and a differential pumping system is presented. The detector head consisted of a scintillation Everhart‐Thornley detector and a microsphere plate, separating it from the lower vacuum in the intermediate chamber (below 0.1 mbar). The system was arranged asymmetrically, which should contribute to a lower gas leakage through the plate and a longer life span of the plate. The system offered all the advantages of the scintillator detector in a wide range of gas pressures, from high vacuum to those of the order of 10 mbar, typical of high‐pressure scanning electron microscopy.
The effect of coarse intermetallic particles on the fracture process in forged 7000 alloys
Authors: VRATNICA M. , CVIJOVIĆ Z. , DEGISCHER H. P. , REQUENA G. C.
Published: November 2006

The effect of coarse intermetallic particles on the fracture process in 7000 alloy forgings was investigated using three alloys with different (Fe + Si) impurity levels. The intermetallic particles were identified by selective etching and energy dispersive spectroscopy analysis conducted on a scanning electron microscope. Their geometrical parameters were estimated by image analysis and then correlated with area fractions of different fracture modes on the broken fracture toughness test specimens. It was found that the dominant fracture mode varies with the (Fe + Si) content. The coarse voiding at large intermetallic particles increases systematically with an increase of the impurity level, which in turn increases the amount and size of particles containing Fe and Si while decreasing their spacing. That the crack nucleation and propagation are accelerated by these particles was revealed by in situ scanning electron microscopy observation of the fracture process.
A sharper view of the outer Galaxy at 1420 and 408 MHz from the Canadian Galactic Plane Survey – I. Revisiting the KR catalogue and new Gigahertz Peaked Spectrum sources
Authors: Kerton C. R.
Published: November 2006

Arcminute-resolution radio continuum images at 408 and 1420 MHz from the Canadian Galactic Plane Survey (CGPS) have been used to re-examine radio sources listed in the Kallas & Reich catalogue. This catalogue is of particular interest to Galactic studies as it lists both extended and compact radio sources found in the second Galactic quadrant. We have determined the nature (extended versus compact, Galactic versus extragalactic) of all of these bright radio sources. A number of large H ii regions with no optical counterparts are highlighted along with a sample of large radio galaxies. Many sources previously thought to be extended Galactic objects are shown to be point sources. A sample of point sources with flat or rising spectra between 408 and 1420 MHz has been compiled, and within this sample likely Gigahertz Peaked Spectrum sources have been identified.
Association of Arabidopsis topoisomerase IIA cleavage sites with functional genomic elements and T‐DNA loci
Authors: Makarevitch Irina , Somers David A.
Published: November 2006

Topoisomerase IIA (Topo IIA) is an essential ubiquitous enzyme involved in controlling DNA topology during multiple processes of genome function, and has been implicated in the generation of double‐stranded breaks (DSB) in genomic DNA prior to DNA integration in plant genomes. Despite extensive characterization of type II topoisomerases from bacteria, viruses and animals, no studies on the specificity of plant Topo IIA‐mediated DNA cleavage have been reported. We mapped and characterized Arabidopsis thaliana Topo IIA (AtTopoIIA) cleavage sites and demonstrated that they were cleaved in vivo. The consensus for the AtTopoIIA cleavage sites (ANNNRN↓GTACNTNNNY) was significantly different from recognition sequences reported for Topo IIA from other organisms. The mapped cleavage sites were abundant in the Arabidopsis genome, exhibited a weak consensus, and were cleaved with relatively low efficiency. Use of the systematic evolution of ligands by exponential enrichment (SELEX) protocol identified a single, efficiently cleaved sequence TATATATATGTATATATATA that was over‐represented in the genome. The mapped AtTopoIIA cleavage sites and the SELEX sites differed in their genomic distribution and associations with gene regulatory elements, matrix attachment regions, stress‐induced DNA duplex destabilization sequences and T‐DNA loci, suggesting different genome functions. Mapped AtTopoIIA sites but not SELEX sites were strongly associated with T‐DNA integration sites, providing evidence for the involvement of AtTopoIIA‐mediated DSB formation in T‐DNA integration.
The rice HIGH‐TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds
Authors: Zou Junhuang , Zhang Shuying , Zhang Weiping , Li Gang , Chen Zongxiang , Zhai Wenxue , Zhao Xianfeng , Pan Xuebiao , Xie Qi , Zhu Lihuang
Published: November 2006

Rice tillering is an important agronomic trait for grain production. The HIGH‐TILLERING DWARF1 (HTD1) gene encodes an ortholog of Arabidopsis MAX3. Complementation analyses for HTD1 confirm that the defect in HTD1 is responsible for both high‐tillering and dwarf phenotypes in the htd1 mutant. The rescue of the Arabidopsis max3 mutant phenotype by the introduction of Pro35S:HTD1 indicates HTD1 is a carotenoid cleavage dioxygenase that has the same function as MAX3 in synthesis of a carotenoid‐derived signal molecule. The HTD1 gene is expressed in both shoot and root tissues. By evaluating ProHTD1:GUS expression, we found that the HTD1 gene is mainly expressed in vascular bundle tissues throughout the plant. Auxin induction of HTD1 expression suggests that auxin may regulate rice tillering partly through upregulation of HTD1 gene transcription. Restoration of dwarf phenotype after the removal of axillary buds indicates that the dwarfism of the htd1 mutant may be a consequence of excessive tiller production. In addition, the expression of HTD1, D3 and OsCCD8a in the htd1 and d3 mutants suggests a feedback mechanism may exist for the synthesis and perception of the carotenoid‐derived signal in rice. Characterization of MAX genes in Arabidopsis, and identification of their orthologs in pea, petunia and rice indicates the existence of a conserved mechanism for shoot‐branching regulation in both monocots and dicots.
UPSC‐BASE –Populus transcriptomics online
Authors: Sjödin Andreas , Bylesjö Max , Skogström Oskar , Eriksson Daniel , Nilsson Peter , Rydén Patrik , Jansson Stefan , Karlsson Jan
Published: November 2006

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose‐designed storage and analysis tools. Here we present UPSC‐BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC‐BASE, researchers can perform standard and advanced microarray analysis procedures in a user‐friendly environment. Background corrections, normalizations, quality‐control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert‐level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC‐BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.
Investigation of prion removal/inactivation from chromatographic gel
Authors: Thyer J. , Unal A. , Hartel G. , Middleton D. , Bingham J. , Braun M. , Uren E. , Maher D.
Published: November 2006

Background and Objectives  Concerns about the potential for prions to be retained on chromatography gels during the manufacture of plasma products prompted development of an investigational strategy for detecting infectious prions bound to gels. The objective was to firstly examine methods of implanting gels intracerebrally (IC) in mice, then to examine prion cleaning from a scaled‐down version of the DEAE Sepharose column used in a production process to fractionate immunoglobulins and albumin from human plasma.

Materials and Methods  The study consisted of two parts: (i) the pathophysiological impact by IC inoculation of ground gel beads was compared to whole gel beads; (ii) the feedstreams to two DEAE Sepharose columns were spiked with scrapie ME7. One column was subjected to the protein loading and elution portions of the chromatography cycle. The other column was subjected to the full cycle of protein loading and elution, followed by regeneration with 0·5 m NaCl, 1 m NaOH and solvent/detergent washes. The gels were unpacked and bioassayed by IC implantation in mice to quantify infectivity.

Results  IC inoculation of ground gel beads resulted in unacceptably high pathological impact in the mice whereas whole gel bead inoculation resulted in a reduced affect. Accordingly, the whole bead model system was used to assess prion removal/inactivation from chromatography gels at the pre‐ and postcleaning stage of the chromatography cycle. Infectious prions were detected on the DEAE Sepharose prior to the cleaning step; however, the gel cleaning cycle reduced infectivity by a log reduction factor (LRF) of ≥ 2·75, thus reducing infectivity by bioassay to below detectable limits.

Conclusions  A model system for assessment of prion inactivation/removal from chromatography gels has been established. Spiked prion infectivity does bind to DEAE Sepharose gel; however, the cleaning cycle removed infectivity to levels below that detectable by bioassay.
Value of a negative colonoscopy in patients with non‐specific gastrointestinal symptoms
Authors: Esfandyari Tuba , Harewood Gavin C
Published: November 2006

Background:  The yield of colonoscopy for neoplasia among patients aged <50 years with non‐specific gastrointestinal symptoms is very low. However, a negative colonoscopy may benefit these patients by decreasing anxiety and thereby reducing subsequent health resource utilization. This study sought to characterize the effect of a negative colonoscopy in terms of: (i) reassurance value; and (ii) decreasing health resource utilization, in patients under 50 years of age with non‐specific gastrointestinal symptoms (abdominal pain, diarrhea, constipation).

Methods:  Consecutive patients, aged 18‐49 years, undergoing their first colonoscopy for evaluation of non‐specific gastrointestinal symptoms (abdominal pain, diarrhea, constipation) were prospectively enrolled. Health‐related anxiety was evaluated before and immediately after disclosure of the negative result of colonoscopy using a validated questionnaire and at 1‐, 2‐ and 6‐month intervals postcolonoscopy by telephone follow‐up. Symptom scores and health resource utilization were assessed prior to colonoscopy and at 2 and 6 months postcolonoscopy.

Results:  Fifty‐nine patients were prospectively enrolled. Mean health anxiety score declined immediately after colonoscopy from 20.6 to 17.8. Sustained improvement was seen in anxiety scores at 1, 2 and 6 months. Symptom scores also decreased at 6 months for abdominal pain (2.3 to 1.5), diarrhea (2.3 to 1.6) and constipation (1.9 to 1.6). There was a significant decrease in all four measures of health resource utilization at 6 months postcolonoscopy.

Conclusions:  Despite minimal diagnostic yield, colonoscopy for non‐specific gastrointestinal symptoms in patients <50 years of age is associated with a decline in health‐related anxiety and symptom scores. These effects appear to translate into reductions in health resource utilization.
Elevated plasma resistin concentrations in patients with liver cirrhosis
Authors: Kakizaki Satoru , Sohara Naondo , Yamazaki Yuichi , Horiguchi Norio , Kanda Daisuke , Kabeya Kenji , Katakai Kenji , Sato Ken , Takagi Hitoshi , Mori Masatomo
Published: November 2006

Background:  Resistin, an adipose‐derived polypeptide hormone, has been proposed to be a candidate in insulin resistance, although its role in humans remains controversial. Liver cirrhosis (LC) is characterized by an elevated number of circulating proinflammatory cytokines, hyperinsulinemia and insulin resistance. The aim of this study was to determine the plasma resistin levels in patients with LC.

Methods:  Resistin levels were determined in 79 patients with LC and in 31 healthy controls. Patients included 34 with Child–Pugh grade A, 30 with Child's B and 15 with Child's C LC. Fasting plasma glucose, fasting plasma insulin, adiponectin, the homeostatic model assessment insulin resistance (HOMA‐IR) index, quantitative insulin sensitivity check index (QUICKI) and biochemical parameters were also determined.

Results:  Plasma resistin levels were 7.61 ± 6.70 ng/mL in the LC patients and 3.38 ± 1.68 ng/mL in the controls, respectively. The plasma resistin levels were significantly elevated in patients with LC in comparison to the controls (P < 0.01). The plasma resistin levels increased in a stepwise fashion in line with a higher grade according to Child–Pugh classification. Fasting plasma insulin, adiponectin and HOMA‐IR index were also significantly elevated in patients with LC in comparison to controls. Inversely, QUICKI significantly decreased in patients with LC. According to Spearman's rank correlation, log resistin showed significantly positive correlation with fasting plasma insulin, log adiponectin, HOMA‐IR index, and a negative correlation with QUICKI (P < 0.01). The plasma resistin levels did not correlate with sex, body mass index and fasting plasma glucose levels.

Conclusion:  The plasma resistin levels increased in patients with LC, thus showing a positive correlation with fasting plasma insulin, adiponectin, HOMA‐IR index, and a negative correlation with QUICKI. Although a decreased extraction of resistin due to reduced liver function cannot be ruled out, resistin may contribute to insulin resistance in patients with LC. The pathophysiological roles of resistin in LC still require further investigation.
What You See Is What You Get
Authors: Lleras Alejandro , Moore Cathleen M.
Published: November 2006

A perceptually filled-in surface, such as occurs during sustained attention to a peripheral stimulus (Troxler fading), can be functionally equivalent to a physically presented stimulus. Observers failed to detect probes that were presented in the location of a filled-in surface that had the same surface attributes as the probes; this was true even though, physically, the probes contrasted with the background. Probe stimuli with surface characteristics different from those of the filled-in surface were detected more often, though not quite as often as when there was no filled-in surface. Together, these findings support the idea that there are two components in perceptual filling: a neural filling-in component and a sustained-attention component, which actively suppresses perceptual processing at the filled-in location. More broadly, they illustrate the interplay of basic visual mechanisms in the creation and representation of visual surfaces and in the coding and detection of changes to these surfaces.
The Prepared Mind
Authors: Kounios John , Frymiare Jennifer L. , Bowden Edward M. , Fleck Jessica I. , Subramaniam Karuna , Parrish Todd B. , Jung-Beeman Mark
Published: November 2006

Insight occurs when problem solutions arise suddenly and seem obviously correct, and is associated with an “Aha!” experience. Prior theorizing concerning preparation that facilitates insight focused on solvers' problem-specific knowledge. We hypothesized that a distinct type of mental preparation, manifested in a distinct brain state, would facilitate insight problem solving independently of problem-specific knowledge. Consistent with this hypothesis, neural activity during a preparatory interval before subjects saw verbal problems predicted which problems they would subsequently solve with, versus without, self-reported insight. Specifically, electroenceph-alographic topography and frequency (Experiment 1) and functional magnetic resonance imaging signal (Experiment 2) both suggest that mental preparation leading to insight involves heightened activity in medial frontal areas associated with cognitive control and in temporal areas associated with semantic processing. The results for electroencephalographic topography suggest that non-insight preparation, in contrast, involves increased occipital activity consistent with an increase in externally directed visual attention. Thus, general preparatory mechanisms modulate problem-solving strategy.
Sleep Facilitates Consolidation of Emotional Declarative Memory
Authors: Hu Peter , Stylos-Allan Melinda , Walker Matthew P.
Published: November 2006

Both sleep and emotion are known to modulate processes of memory consolidation, yet their interaction is poorly understood. We examined the influence of sleep on consolidation of emotionally arousing and neutral declarative memory. Subjects completed an initial study session involving arousing and neutral pictures, either in the evening or in the morning. Twelve hours later, after sleeping or staying awake, subjects performed a recognition test requiring them to discriminate between these original pictures and novel pictures by responding “remember,” “know” (familiar), or “new.” Selective sleep effects were observed for consolidation of emotional memory: Recognition accuracy for know judgments of arousing stimuli improved by 42% after sleep relative to wake, and recognition bias for remember judgments of these stimuli increased by 58% after sleep relative to wake (resulting in more conservative responding). These findings hold important implications for understanding of human memory processing, suggesting that the facilitation of memory for emotionally salient information may preferentially develop during sleep.
Black Americans Reduce the Racial IQ Gap
Authors: Dickens William T. , Flynn James R.
Published: November 2006

It is often asserted that Black Americans have made no IQ gains on White Americans. Until recently, there have been no adequate data to measure trends in Black IQ. We analyzed data from nine standardization samples for four major tests of cognitive ability. These data suggest that Blacks gained 4 to 7 IQ points on non-Hispanic Whites between 1972 and 2002. Gains have been fairly uniform across the entire range of Black cognitive ability.