bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-term potentiation of exogenous glutamate responses at single dendritic spines
Authors: Bagal Ashish A. , Kao Joseph P. Y. , Tang Cha-Min , Thompson Scott M.
Published: September 2005

Long-term increases in the strength of excitatory transmission at Schaffer collateral-CA1 cell synapses of the hippocampus require the insertion of new α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors (AMPARs) into the synapse, but the kinetics of this process are not well established. Using microphotolysis of caged glutamate to activate receptors at single dendritic spines in hippocampal CA1 cells, we report the long-lasting potentiation of AMPAR-mediated currents with only a single pairing of photoreleased glutamate and brief postsynaptic depolarization. This potentiation was
N
-methyl-
d
-aspartate receptor (NMDAR)-dependent and was reversed with low-frequency photostimulation in an NMDAR-dependent manner, suggesting that it is mediated by the same mechanism(s) as conventional synaptic long-term potentiation. Potentiation of photolytic responses developed rapidly in a stepwise manner after a brief and variable delay (<60 s) at spines, but could not be induced at extrasynaptic sites on the dendritic shaft. Potentiation was accompanied by a concomitant decrease in postsynaptic, polyamine-dependent paired-pulse facilitation of the photolytic currents, indicating that a change in the subunit composition of the AMPARs underlying the response contributed to the potentiation. These changes are consistent with an increase in the proportion of GluR2-containing AMPARs in the spine head. These results demonstrate that activation of postsynaptic glutamate receptors by glutamate is not only necessary, but sufficient, for the induction of NMDAR-dependent long-term potentiation and reveal additional aspects of its expression.
Degassing Lakes Nyos and Monoun: Defusing certain disaster
Authors: Kling George W. , Evans William C. , Tanyileke Greg , Kusakabe Minoru , Ohba Takeshi , Yoshida Yutaka , Hell Joseph V.
Published: September 2005

Since the catastrophic releases of CO
2
in the 1980s, Lakes Nyos and Monoun in Cameroon experienced CO
2
recharge at alarming rates of up to 80 mol/m
2
per yr. Total gas pressures reached 8.3 and 15.6 bar in Monoun (2003) and Nyos (2001), respectively, resulting in gas saturation levels up to 97%. These natural hazards are distinguished by the potential for mitigation to prevent future disasters. Controlled degassing was initiated at Nyos (2001) and Monoun (2003) amid speculation it could inadvertently destabilize the lakes and trigger another gas burst. Our measurements indicate that water column structure has not been compromised by the degassing and local stability is increasing in the zones of degassing. Furthermore, gas content has been reduced in the lakes ≈12-14%. However, as gas is removed, the pressure at pipe inlets is reduced, and the removal rate will decrease over time. Based on 12 years of limnological measurements we developed a model of future removal rates and gas inventory, which predicts that in Monoun the current pipe will remove ≈30% of the gas remaining before the natural gas recharge balances the removal rate. In Nyos the single pipe will remove ≈25% of the gas remaining by 2015; this slow removal extends the present risk to local populations. More pipes and continued vigilance are required to reduce the risk of repeat disasters. Our model indicates that 75-99% of the gas remaining would be removed by 2010 with two pipes in Monoun and five pipes in Nyos, substantially reducing the risks.
The ryanodine receptor mediates early zymogen activation in pancreatitis
Authors: Husain Sohail Z. , Prasad Priyajit , Grant Wayne M. , Kolodecik Thomas R. , Nathanson Michael H. , Gorelick Fred S.
Published: September 2005

Acute pancreatitis is characterized by the pathologic activation of zymogens within pancreatic acinar cells. The process requires a rise in cytosolic Ca
2+
from undefined intracellular stores. We hypothesized that zymogen activation is mediated by ryanodine receptor (RYR)-regulated Ca
2+
release, because early zymogen activation takes place in a supranuclear compartment that overlaps in distribution with the RYR. Ca
2+
signals in the basolateral, but not apical, region of acinar cells observed during supraphysiologic agonist stimulation were dependent on RYR Ca
2+
release. Inhibition of RYR or depletion of RYR-sensitive Ca
2+
pools each reduced pathologic zymogen activation in isolated acinar cells, but neither treatment affected amylase secretion. Inhibition of RYR also inhibited zymogen activation
in vivo
. We propose that Ca
2+
release from the RYR mediates zymogen activation but not enzyme secretion. The findings imply a role for the RYR in acute pancreatitis.
Inhibiting farnesylation reverses the nuclear morphology defect in a HeLa cell model for Hutchinson-Gilford progeria syndrome
Authors: Mallampalli Monica P. , Huyer Gregory , Bendale Pravin , Gelb Michael H. , Michaelis Susan
Published: September 2005

Hutchinson-Gilford progeria syndrome (HGPS) is a devastating premature aging disease resulting from a mutation in theLMNAgene, which encodes nuclear lamins A and C. Lamin A is synthesized as a precursor (prelamin A) with a C-terminal CaaX motif that undergoes farnesylation, endoproteolytic cleavage, and carboxylmethylation. Prelamin A is subsequently internally cleaved by the zinc metalloprotease Ste24 (Zmpste24) protease, which removes the 15 C-terminal amino acids, including the CaaX modifications, to yield mature lamin A. HGPS results from a dominant mutant form of prelamin A (progerin) that has an internal deletion of 50 aa near the C terminus that includes the Zmpste24 cleavage site and blocks removal of the CaaX-modified C terminus. Fibroblasts from HGPS patients have aberrant nuclei with irregular shapes, which we hypothesize result from the abnormal persistence of the farnesyl and/or carboxylmethyl CaaX modifications on progerin. If this hypothesis is correct, inhibition of CaaX modification by mutation or pharmacological treatment should alleviate the nuclear morphology defect. Consistent with our hypothesis, we find that expression in HeLa cells of GFP-progerin or an uncleavable form of prelamin A with a Zmpste24 cleavage site mutation induces the formation of abnormal nuclei similar to those in HGPS fibroblasts. Strikingly, inhibition of farnesylation pharmacologically with the farnesyl transferase inhibitorrac-R115777 or mutationally by alteration of the CaaX motif dramatically reverses the abnormal nuclear morphology. These results suggest that farnesyl transferase inhibitors represent a possible therapeutic option for individuals with HGPS and/or other laminopathies due to Zmpste24 processing defects.
Human airway epithelial cell determinants of survival and functional phenotype for primary human mast cells
Authors: Hsieh F. H. , Sharma P. , Gibbons A. , Goggans T. , Erzurum S. C. , Haque S. J.
Published: September 2005

Mast cells (MCs) are found in increased numbers at airway mucosal surfaces in asthmatic patients. Because human airway epithelial cells (HAECs) actively participate in airway inflammatory responses and are in direct contact with MCs in the mucosa, we hypothesized that HAEC-MC interactions may contribute to the differentiation and survival of MCs in the airway mucosa. Here, we show that HAECs express mRNA and protein for soluble and membrane-bound stem cell factor, releasing soluble stem cell factor into the cell culture supernatant at a concentration of 5.9 ± 0.1 ng per 106HAEC. HAECs were able to support MC survival in coculture in the absence of any exogenous cytokines for at least 4 d. Before the initiation of coculture, MCs were uniformly tryptase and chymase (MCTC) double positive, but by 2 d of coculture the majority of MCs expressed tryptase (MCT) alone. MCs supported in coculture generated low amounts of cysteinyl-leukotrienes (cys-LT) after FcεRI-dependent activation (0.2 ± 0.1 ng of cys-LT per 106cells) and required priming with IL-4 and IL-3 during coculture to achieve a quantity of cys-LT generation within the range expected for human lung mucosal MC (26.5 ± 16 ng of cys-LT per 106cells). In these culture conditions, HAECs were able to direct mucosal MC protease phenotype, but T cell-derived Th2 cytokines were required for the expression of a functional airway MC eicosanoid phenotype. Thus, distinct cell types may direct unique aspects of reactive mucosal MC phenotype in the airways.
Shape transitions of fluid vesicles and red blood cells in capillary flows
Authors: Noguchi Hiroshi , Gompper Gerhard
Published: September 2005

The dynamics of fluid vesicles and red blood cells (RBCs) in cylindrical capillary flow is studied by using a three-dimensional mesoscopic simulation approach. As flow velocity increases, a model RBC is found to transit from a nonaxisymmetric discocyteto an axisymmetric parachute shape (coaxial with the flow axis), while a fluid vesicle is found to transit from a discocyte to a prolate ellipsoid. Both shape transitions reduce the flow resistance. The critical velocities of the shape transitions are linearly dependent on the bending rigidity and on the shear modulus of the membrane. Slipper-like shapes of the RBC model are observed around the transition velocities. Our results are in good agreement with experiments on RBCs.
Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane
Authors: Ye Yihong , Shibata Yoko , Kikkert Marjolein , van Voorden Sjaak , Wiertz Emmanuel , Rapoport Tom A.
Published: September 2005

Misfolded proteins are eliminated from the endoplasmic reticulum (ER) by retrotranslocation into the cytosol, a pathway hijacked by certain viruses to destroy MHC class I heavy chains. The translocation of polypeptides across the ER membrane requires their polyubiquitination and subsequent extraction from the membrane by the p97 ATPase [also called valosin-containing protein (VCP) or, in yeast, Cdc48]. In higher eukaryotes, p97 is bound to the ER membrane by a membrane protein complex containing Derlin-1 and VCP-interacting membrane protein (VIMP). How the ubiquitination machinery is recruited to the p97/Derlin/VIMP complex is unclear. Here, we report that p97 interacts directly with several ubiquitin ligases and facilitates their recruitment to Derlin-1. During retrotranslocation, a substrate first interacts with Derlin-1 before p97 and other factors join the complex. These data, together with the fact that Derlin-1 is a multispanning membrane protein forming homo-oligomers, support the idea that Derlin-1 is part of a retrotranslocation channel that is associated with both the polyubiquitination and p97-ATPase machineries.
Multiprotein complexes that link dislocation, ubiquitination, and extraction of misfolded proteins from the endoplasmic reticulum membrane
Authors: Lilley Brendan N. , Ploegh Hidde L.
Published: September 2005

Polypeptides that fail to pass quality control in the endoplasmic reticulum (ER) are dislocated from the ER membrane to the cytosol where they are degraded by the proteasome. Derlin-1, a member of a family of proteins that bears homology to yeast Der1p, was identified as a factor that is required for the human cytomegalovirus US11-mediated dislocation of class I MHC heavy chains from the ER membrane to the cytosol. Derlin-1 acts in concert with the AAA ATPase p97 to remove dislocation substrate proteins from the ER membrane, but it is unknown whether other factors aid Derlin-1 in its function. Mammalian genomes encode two additional, related proteins (Derlin-2 and Derlin-3). The similarity of the mammalian Derlin-2 and Derlin-3 proteins to yeast Der1p suggested that these as-yet-uncharacterized Derlins also may play a role in ER protein degradation. We demonstrate here that Derlin-2 is an ER-resident protein that, similar to Derlin-1, participates in the degradation of proteins from the ER. Furthermore, we show that Derlin-2 forms a robust multiprotein complex with the p97 AAA ATPase as well as the mammalian orthologs of the yeast Hrd1p/Hrd3p ubiquitin-ligase complex. The data presented here define a set of interactions between proteins involved in dislocation of misfolded polypeptides from the ER.
Revision of T cell receptor α chain genes is required for normal T lymphocyte development
Authors: Huang Ching-Yu , Sleckman Barry P. , Kanagawa Osami
Published: September 2005

To become mature αβ T cells, developing thymocytes must first assemble a T cell receptor (TCR) β chain gene encoding a TCRβ chain that forms a pre-TCR. These cells then need to generate a TCRα chain gene encoding a TCRα chain, which, when paired with the TCRβ chain, forms a selectable αβ TCR. Newly generated VJα rearrangements that do not encode TCRα chains capable of forming selectable αβ TCRs can be excised from the chromosome and replaced with new VJα rearrangements. Such replacement occurs through the process of TCRα chain gene revision whereby a Vα gene segment upstream of the VJα rearrangement is appended to a downstream Jα gene segment. A multistep, gene-targeting approach was used to generate a modified TCRα locus (TCRα
sJ
) with a limited capacity to undergo revision of TCRα chain genes. Thymocytes from mice homozygous for the TCRα
sJ
allele are defective in their ability to generate an αβ TCR. Furthermore, those thymocytes that do generate an αβ TCR have a diminished capacity to be positively selected, and TCRα
sJ/sJ
mice have significantly reduced numbers of mature αβ T cells. Together, these findings demonstrate that normal T cell development relies on the ability of developing thymocytes to revise their TCRα chain genes.
Surface-mounted altitudinal molecular rotors in alternating electric field: Single-molecule parametric oscillator molecular dynamics
Authors: Horinek Dominik , Michl Josef
Published: September 2005

Molecular dynamics simulations of the response to oscillating electric field elicited from an altitudinal dipolar molecular rotor mounted on the Au(111) surface and previously studied experimentally in static fields show unidirectional rotation in one of the three pairs of conformational enantiomers. The simulations are based on the universal force field and take into account electronic friction in the metal through its effect on the image charges. The rotor consists of two cobalt sandwich posts whose upper decks carry a biphenyl-like rotator with a dipole moment perpendicular to the rotation axle, mounted parallel to the surface. A phase diagram of rotor performance at 10 K as a function of field frequency and amplitude contains five unidirectional rotation regions: synchronous, half-synchronous (every other cycle skipped), quarter-synchronous (only indistinctly), asynchronous, and essentially no response. The nature of the subharmonic “single-molecule parametric oscillator” behavior is understood in mechanistic detail. Simulations at higher temperatures distinguish the thermal (“Brownian”) and driven regimes of rotation, elucidated in terms of time-dependent potential energy surfaces for the rotation.
Innate signals compensate for the absence of PKC-θ duringin vivoCD8+ T cell effector and memory responses
Authors: Marsland Benjamin J. , Nembrini Chiara , Schmitz Nicole , Abel Brian , Krautwald Stefan , Bachmann Martin F. , Kopf Manfred
Published: September 2005

PKC-θ is central to T-helper (Th) 2 cell differentiation and effector function; however, its importance for antiviral effector, and in particular memory CD8+ T cell responses, remains unclear. We have investigated the role of PKC-θ duringin vivoandin vitroresponses against influenza virus, lymphocytic choriomeningitis virus, vaccinia virus, and replication-deficient virus-like particles. In the absence of PKC-θ, antiviral CD8+ T cells presented an unresponsive phenotypein vitro, which could be restored with exogenous IL-2 or by Toll-like receptor ligand-activated dendritic cells. In striking contrast, PKC-θ appeared to be superfluous forin vivoantiviral responses irrespective of whether the virus infected systemically, was localized to the lung, or did not replicate. In addition, CD8+ CCR7-effector memory responses were normal in PKC-θ-deficient mice, both in lymphoid and peripheral tissues. Our data show that increased activation signals deliveredin vivoby highly activated dendritic cells, as present during viral infections, overcome the requirement for PKC-θ during CD8+ T cell antiviral responses.
Involvement of β-catenin and unusual behavior of CBP and p300 in glucocorticosteroid signaling in Schwann cells
Authors: Fonte Cosima , Grenier Julien , Trousson Amalia , Chauchereau Anne , Lahuna Olivier , Baulieu Etienne-Emile , Schumacher Michael , Massaad Charbel
Published: September 2005

In the nervous system, glucocorticosteroid hormones play a major role during development and adult life. Myelin-forming cells are among the targets of glucocorticosteroids, which have been shown to promote myelination both in the central and peripheral nervous system. Glucocorticosteroid-stimulated gene transcription is mediated by the glucocorticosteroid receptor (GR) that recruits coactivators of the p160 family, forming a docking platform for secondary coactivators, such as cAMP-response element binding protein (CREB)-binding protein (CBP) or its close homologue, p300. Here, we investigated the role of CBP and p300 in mouse Schwann cells (MSC80). We show that, although the CBP/p300 binding domain of steroid receptor coactivator-1 is crucial for GR transactivation, neither CBP nor p300 enhanced GR transcriptional activation, as shown by overexpression and small interfering RNA (siRNA) knocking-down experiments. Unexpectedly, overexpression of p300, considered as a coactivator of the GR, resulted in inhibition of GR transcriptional activity. Studies with p300 deletion mutants demonstrated that p300-dependent repression is related to its acetyltransferase activity. Functional and pull-down assays showed that β-catenin may be the coactivator replacing CBP in the GR transcriptional complex. Our results suggest the formation of a GR-coactivator complex within Schwann cells, indicating that glucocorticosteroids may act by means of unusual partners in the nervous system, and we show a repressive effect of p300 on nuclear receptors.
A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels
Authors: Hickman Jason W. , Tifrea Delia F. , Harwood Caroline S.
Published: September 2005

Pseudomonas aeruginosa
causes chronic biofilm infections, and its ability to attach to surfaces and other cells is important for biofilm formation and maintenance. Mutations in a gene called
wspF
, part of a putative chemosensory signal-transduction operon, have been shown to result in cell aggregation and altered colony morphology. The WspF phenotypes depend on the presence of WspR, which is a member of a family of signal transduction proteins known as response regulators. It is likely that the effect of the
wspF
mutation is to cause constitutive activation of WspR by phosphorylation. WspR contains a GGDEF domain known to catalyze formation of a cytoplasmic signaling molecule cyclic diguanylate (c-diGMP). We determined that purified WspR catalyzed the formation of c-diGMP
in vitro
and phosphorylation stimulated this activity. We observed increased cellular levels of c-diGMP and increased biofilm formation in a
wspF
mutant. Expression of a protein predicted to catalyze degradation of c-diGMP reversed the phenotypes of a
wspF
mutant and inhibited biofilm initiation by wild-type cells, indicating that the presence of c-diGMP is necessary for biofilm formation. A transcriptome analysis showed that expression levels of at least 560 genes were affected by a
wspF
deletion. The
psl
and
pel
operons, which are involved in exopolysaccharide production and biofilm formation, were expressed at high levels in a
wspF
mutant. Together, the data suggest that the
wsp
signal transduction pathway regulates biofilm formation through modulation of cyclic diguanylate levels.
Role for macrophage migration inhibitory factor in asthma
Authors: Mizue Y. , Ghani S. , Leng L. , McDonald C. , Kong P. , Baugh J. , Lane S. J. , Craft J. , Nishihira J. , Donnelly S. C. , Zhu Z. , Bucala R.
Published: September 2005

Macrophage migration inhibitory factor (MIF) is an immunologic regulator that is expressed in inflammatory and autoimmune disorders. We investigated MIF's role in asthma using genetic approaches in a mouse model and in a cohort of asthma patients. Mice genetically deficient in MIF that were primed and aerosol-challenged with ovalbumin showed less pulmonary inflammation and lower airway hyperresponsiveness than genetically matched, wild-type controls. MIF deficiency also resulted in lower titers of specific IgE, IgG
1
, and IgG
2a
, and decreased pulmonary, T
H
2 cytokine levels. IL-5 concentrations were lower and corresponded to decreased eosinophil numbers in bronchoalveolar lavage fluid. T cell studies also showed a lower level of antigen-specific responses in MIF-KO versus wild-type mice. In an analysis of 151 white patients with mild, moderate, or severe asthma (Global Initiative for Asthma criteria), a significant association was found between mild asthma and the low-expression, 5-CATT
MIF
allele. Pharmacologic inhibition of MIF may be beneficial and could be guided by the
MIF
genotype of affected individuals.
In vitro
assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation
Authors: Glover Kerney Jebrell , Weerapana Eranthie , Imperiali Barbara
Published: September 2005

Campylobacter jejuni
has a general N-linked glycosylation pathway (encoded by the
pgl
gene cluster), which culminates in the transfer of a heptasaccharide: GalNAc-α1,4-GalNAc-α1,4-(Glcβ1,3)-GalNAc-α1,4-GalNAc-α1,4-GalNAc-α1,3-Bac [where Bac is bacillosamine (2,4-diacetamido-2,4,6-trideoxyglucose)] from a membrane-anchored undecaprenylpyrophosphate (Und-PP)-linked donor to the asparagine side chain of proteins at the Asn-X-Ser/Thr motif. Herein we report, the cloning, overexpression, and purification of four of the glycosyltransferases (PglA, PglH, PglI, and PglJ) responsible for the biosynthesis of the Und-PP-linked heptasaccharide. Starting with chemically synthesized Und-PP-linked Bac and various combinations of enzymes, we have deduced the precise functions of these glycosyltransferases. PglA and PglJ add the first two GalNAc residues on to the isoprenoid-linked Bac carrier, respectively. Elongation of the trisaccharide with PglH results in a hexasaccharide revealing the polymerase activity of PglH. The final branching glucose is then added by PglI, which prefers native lipids for optimal activity. The sequential activities of the glycosyl transferases in the pathway can be reconstituted
in vitro
. This pathway represents an ideal venue for investigating the integrated functions of a series of enzymatic processes that occur at a membrane interface.
Tumor cells convert immature myeloid dendritic cells into TGF-β–secreting cells inducing CD4+CD25+ regulatory T cell proliferation
Authors: Ghiringhelli François , Puig Pierre E. , Roux Stephan , Parcellier Arnaud , Schmitt Elise , Solary Eric , Kroemer Guido , Martin François , Chauffert Bruno , Zitvogel Laurence
Published: September 2005

The mechanisms through which regulatory T cells accumulate in lymphoid organs of tumor-bearing hosts remain elusive. Our experiments indicate that the accumulation of CD4+CD25+ regulatory T cells (T reg cells) expressing FoxP3 and exhibiting immunosuppressive function originates from the proliferation of naturally occurring CD25+ T cells and requires signaling through transforming growth factor (TGF)–β receptor II. During tumor progression, a subset of dendritic cells (DCs) exhibiting a myeloid immature phenotype is recruited to draining lymph nodes. This DC subset selectively promotes the proliferation of T reg cells in a TGF-β–dependent manner in mice and rats. Tumor cells are necessary and sufficient to convert DCs into regulatory cells that secrete bioactive TGF-β and stimulate T reg cell proliferation. In conclusion, tumor expansion can stimulate T reg cells via a specific DC subset.
Treatment of advanced tumors with agonistic anti-GITR mAb and its effects on tumor-infiltrating Foxp3+CD25+CD4+regulatory T cells
Authors: Ko Kuibeom , Yamazaki Sayuri , Nakamura Kyoko , Nishioka Tomohisa , Hirota Keiji , Yamaguchi Tomoyuki , Shimizu Jun , Nomura Takashi , Chiba Tsutomu , Sakaguchi Shimon
Published: September 2005

T cell stimulation via glucocorticoid-induced tumor necrosis factor receptor family–related protein (GITR) can evoke effective tumor immunity. A single administration of agonistic anti-GITR monoclonal antibody (mAb) to tumor-bearing mice intravenously or directly into tumors provoked potent tumor-specific immunity and eradicated established tumors without eliciting overt autoimmune disease. A large number of CD4+ and CD8+ T cells, including interferon (IFN)-γ–secreting cells, infiltrated regressing tumors. Tumor-specific IFN-γ–secreting CD4+ and CD8+ T cells also increased in the spleen. The treatment led to tumor rejection in IFN-γ–intact mice but not IFN-γ–deficient mice. Furthermore, coadministration of anti-GITR and anti–CTLA-4 mAbs had a synergistic effect, leading to eradication of more advanced tumors. In contrast, coadministration of anti-CD25 and anti-GITR mAbs was less effective than anti-GITR treatment alone, because anti-CD25 depleted both CD25+-activated effector T cells and CD25+CD4+ naturally occurring regulatory T (T reg) cells. Importantly, CD4+ T cells expressing the T reg–specific transcription factor Foxp3 predominantly infiltrated growing tumors in control mice, indicating that tumor-infiltrating natural Foxp3+CD25+CD4+ T reg cells may hamper the development of effective tumor immunity. Taken together, T cell stimulation through GITR attenuates T reg–mediated suppression or enhances tumor-killing by CD4+ and CD8+ effector T cells, including those secreting IFN-γ, or both. Agonistic anti-GITR mAb is therefore instrumental in treating advanced cancers.
Stability, energetic particles, waves and current drive summary
Authors: Stambaugh R.D.
Published: September 2005

This is the summary paper for the subjects of plasma stability, energetic particles, waves and current drive at the 20th IAEA Fusion Energy Conference, Vilamoura, Portugal, 1–6 November 2004. Material summarized herein was drawn from 65 contributed papers and 21 overview papers. The subject-wise distribution of contributed papers is shown in the following table:

Subject
Papers

Resistive wall modes
7

Disruptions
6

Neoclassical tearing modes
6

Edge localized modes and the edge pedestal   
13

Other stability topics
9

Alfvén modes
9

Wave physics
10

Current drive
5

Total
65

Significant advances have been reported on the principal instabilities in magnetically confined plasmas, even extending to the burning plasma state. Wave-plasma physics is maturing and novel methods of current drive and non-inductive current generation are being developed.
Comparing community structure identification
Authors: Danon Leon , Díaz-Guilera Albert , Duch Jordi , Arenas Alex
Published: September 2005

We compare recent approaches to community structure identification in terms of sensitivity
and computational cost. The recently proposed modularity measure is revisited and the
performance of the methods as applied to ad hoc networks with known community
structure, is compared. We find that the most accurate methods tend to be more
computationally expensive, and that both aspects need to be considered when choosing a
method for practical purposes. The work is intended as an introduction as well
as a proposal for a standard benchmark test of community detection methods.
A third blind test of crystal structure prediction
Authors: Day G. M. , Motherwell W. D. S. , Ammon H. L. , Boerrigter S. X. M. , Della Valle R. G. , Venuti E. , Dzyabchenko A. , Dunitz J. D. , Schweizer B. , van Eijck B. P. , Erk P. , Facelli J. C. , Bazterra V. E. , Ferraro M. B. , Hofmann D. W. M. , Leusen F. J. J. , Liang C. , Pantelides C. C. , Karamertzanis P. G. , Price S. L. , Lewis T. C. , Nowell H. , Torrisi A. , Scheraga H. A. , Arnautova Y. A. , Schmidt M. U. , Verwer P.
Published: September 2005

Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in searching for and ranking the likelihood of predicted crystal structures is represented amongst the 18 participating research groups, although most are based on the global minimization of the lattice energy. Initially the participants were given molecular diagrams of three molecules and asked to submit three predictions for the most likely crystal structure of each. Unlike earlier blind tests, no restriction was placed on the possible space group of the target crystal structures. Furthermore, Z′ = 2 structures were allowed. Part-way through the test, a partial structure report was discovered for one of the molecules, which could no longer be considered a blind test. Hence, a second molecule from the same category (small, rigid with common atom types) was offered to the participants as a replacement. Success rates within the three submitted predictions were lower than in the previous tests – there was only one successful prediction for any of the three `blind' molecules. For the `simplest' rigid molecule, this lack of success is partly due to the observed structure crystallizing with two molecules in the asymmetric unit. As in the 2001 blind test, there was no success in predicting the structure of the flexible molecule. The results highlight the necessity for better energy models, capable of simultaneously describing conformational and packing energies with high accuracy. There is also a need for improvements in search procedures for crystals with more than one independent molecule, as well as for molecules with conformational flexibility. These are necessary requirements for the prediction of possible thermodynamically favoured polymorphs. Which of these are actually realised is also influenced by as yet insufficiently understood processes of nucleation and crystal growth.
Evidence for differentiation in the iron-helicoidal chain in GdFe3(BO3)4
Authors: Klimin S. A. , Fausti D. , Meetsma A. , Bezmaternykh L. N. , van Loosdrecht P. H. M. , Palstra T. T. M.
Published: September 2005

A single-crystal X-ray structure study of gadolinium triiron tetraborate, GdFe_3(BO_3)_4, at room temperature and at 90 K is reported. At room temperature GdFe_3(BO_3)_4 crystallizes in a trigonal space group, R32 (No. 155), the same as found for other members of the iron borate family RFe_3(BO_3)_4. At 90 K the structure of GdFe_3(BO_3)_4 transforms to the space group P3_{1}21 (No. 152). The low-temperature structure determination gives new insight into the weakly first-order structural phase transition at 156 K and into the related Raman phonon anomalies. The presence of two inequivalent iron chains in the low-temperature structure provides a new perspective on the interpretation of the low-temperature magnetic properties.
In situ high-pressure crystallization and compression of halogen contacts in dichloromethane
Authors: Podsiadło Marcin , Dziubek Kamil , Katrusiak Andrzej
Published: September 2005

The structure of dichloromethane, CH2Cl2, crystallized in situ in a diamond–anvil cell, has been determined by single-crystal X-ray diffraction at 1.33 and 1.63 GPa. The pressure-frozen crystal was determined to be orthorhombic, with the space group Pbcn, and isostructural with the low-temperature phase at 0.1 MPa. The CH2Cl2 molecules are located on one set of crystallographic twofold axes. The characteristics determined for the CH2Cl2 crystal (compression of the close intermolecular contacts, molecular association and the crystal habit of dichloromethane) suggest that the crystal cohesion forces are dominated by H...Cl interactions rather than by Cl...Cl attractions.
Extremely long period-stacking structure in the Sb–Te binary system
Authors: Kifune Kouichi , Kubota Yoshiki , Matsunaga Toshiyuki , Yamada Noboru
Published: September 2005

The crystal structure of the δ-phase in the Sb–Te binary system has been determined by synchrotron powder diffraction. It is clearly shown that many intermetallic compounds, which have different stacking periods depending on compound composition, exist in this phase. These structures are based on the cubic ABC stacking structure, and two kinds of fundamental structural units form an intergrowth along the stacking direction at the atomic level. The chemical formulae of these compounds are expressed as Sb2n
Te3, where n is an integer and the number of stacking layers is 2n + 3. There is a relationship of inverse proportionality between the stacking period and the Te concentration.
Searching the Cambridge Structural Database for polymorphs
Authors: van de Streek Jacco , Motherwell Sam
Published: September 2005

In order to identify all pairs of polymorphs in the Cambridge Structural Database (CSD), a method was devised to automatically compare two crystal structures. The comparison is based on simulated powder diffraction patterns, but with special provisions to deal with differences in unit-cell volumes caused by temperature or pressure. Among the 325 000 crystal structures in the Cambridge Structural Database, 35 000 pairs of crystal structures of the same chemical compound were identified and compared. A total of 7300 pairs of polymorphs were identified, of which 154 previously were unknown.
Pseudoepitaxial transrotational structures in 14 nm-thick NiSi layers on [001] silicon
Authors: Alberti Alessandra , Bongiorno Corrado , Cafra Brunella , Mannino Giovanni , Rimini Emanuele , Metzger Till , Mocuta Cristian , Kammler Thorsten , Feudel Thomas
Published: September 2005

In a system consisting of two different lattices, structural stability is ensured when an epitaxial relationship occurs between them and allows the system to retain the stress whilst avoiding the formation of a polycrystalline film. The phenomenon occurs if the film thickness does not exceed a critical value. Here we show that in spite of its orthorhombic structure, a 14 nm-thick NiSi layer can three-dimensionally adapt to the cubic Si lattice by forming transrotational domains. Each domain arises by the continuous bending of the NiSi lattice, maintaining a close relationship with the substrate structure. The presence of transrotational domains does not cause a roughening of the layer, but instead it improves the structural and electrical stability of the silicide in comparison with a 24 nm-thick layer formed using the same annealing process. These results have relevant implications for the thickness scaling of NiSi layers which are currently used as metallizations of electronic devices.
Energetic materials: α-NTO crystallizes as a four-component triclinic twin
Authors: Bolotina Nadezhda , Kirschbaum Kristin , Pinkerton A. Alan
Published: September 2005

The prevalent polymorph of the energetic material 5-nitro-2,4-dihydro-1,2,4,-triazol-3-one, α-NTO, crystallizes as a four-component twin with triclinic symmetry (space group P\bar 1). All crystals under investigation were fourlings, i.e. they contained each of the four possible twin components. Complete data sets were collected for two crystals, one with a predominant amount of one individual component (55%) and one with approximately equal volumes of each component. In both cases the fourling components are related by the twofold axes inherent in the holohedral symmetry of a pseudo-orthorhombic superlattice with a

o
= a

t
, b

o
= b

t
and c

o
= a

t
+ b

t
+ 2c

t
. The triclinic unit cell contains four crystallographically independent planar molecules in the asymmetric unit, each of which forms a hydrogen-bonded flat chain parallel to a

t
. Pairs of chains are combined into planar ribbons by additional hydrogen bonds. Thus, two independent ribbons extend parallel to a

t
, creating a dihedral angle of ∼ 70°. The origin of the twinning is derived from consideration of the crystal packing and the hydrogen-bonding scheme.
Comparing hypothetical structures generated in the third Cambridge blind test of crystal structure prediction
Authors: van Eijck Bouke P.
Published: September 2005

In the third Cambridge blind test of crystal structure prediction, participants submitted extended lists of up to 100 hypothetical structures. In this paper these lists are analyzed for the two small semi-rigid molecules, hydantoin and azetidine, by performing a new energy minimization using an accurate force field, and grouping these newly minimized structures into clusters of equivalent structures. Many participants found the same low-energy structures, but no list appeared to be complete even for the structures with one independent molecule in the asymmetric unit. This may well be due to the fact that a cutoff at even 100 structures cannot ensure the presence of a structure that has a relatively high ranking in another force field. Moreover, some structures should have possibly been discarded because they correspond to transition states rather than true energy minima. The r.m.s. deviation between energies in corresponding clusters was calculated to compare the reported relative crystal energies for each pair of participants. Some groups of force fields show a reasonably good correspondence, yet the order of magnitude of their discrepancies is comparable to the energy differences between, say, the first ten structures of lowest energy. Therefore, even if we assume that energy is a sufficient criterion, it is not surprising that crystal structure predictions are still inconsistent and unreliable.
Effect of IL‐2‐Bax, a novel interleukin‐2‐receptor‐targeted chimeric protein, on bleomycin lung injury1
Authors: Segel Michael J. , Aqeilan Rami , Zilka Keren , Lorberboum‐Galski Haya , Wallach‐Dayan Shulamit B. , Conner Michael W. , Christensen Thomas G. , Breuer Raphael
Published: September 2005

The role of lymphocytes in the pathogenesis of lung fibrosis is not clear, but the weight of the evidence supports a pro‐fibrotic effect for lymphocytes. The high‐affinity interleukin‐2 receptor (haIL‐2R) is expressed on activated, but not quiescent, T lymphocytes. This selective expression of haIL‐2R provides the basis for therapeutic strategies that target IL‐2R‐expressing cells. We hypothesized that elimination of activated lymphocytes by IL‐2R‐targeted chimeric proteins might ameliorate lung fibrosis. We investigated the effects of IL‐2‐Bax, a novel apoptosis‐inducing IL‐2R‐targeted chimeric protein, on bleomycin‐induced lung injury in mice. Treatment groups included (i) a single intratracheal instillation of bleomycin and twice‐daily intraperitoneal injections of IL‐2‐Bax; (ii) intratracheal bleomycin and intraperitoneal IL‐2‐PE664Glu, an older‐generation chimeric protein; (iii) intratracheal bleomycin/intraperitoneal PBS; (iv) intratracheal saline/intraperitoneal PBS. Lung injury was evaluated 14 days after intratracheal instillation by cell count in bronchoalveolar lavage (BAL) fluid, semi‐quantitative and quantitative histomorphological measurements and by biochemical analysis of lung hydroxyproline. Bleomycin induced a BAL lymphocytosis that was significantly attenuated by IL‐2‐Bax and IL‐2‐PE664Glu. However, morphometric parameters and lung hydroxyproline were unaffected by the chimeric proteins. These results show that IL‐2‐Bax reduces the lymphocytic infiltration of the lungs in response to bleomycin, but this effect is not accompanied by a decrease in lung fibrosis.
Evaluation of human knee meniscus biopsies with near‐infrared, reflectance confocal microscopy. A pilot study
Authors: Campo‐Ruiz Vanessa , Patel Dinesh , Anderson R. Rox , Delgado‐Baeza Emilio , González Salvador
Published: September 2005

Knee cartilage biopsy is used to confirm the pathology in both clinical and experimental conditions and often guides diagnosis and therapeutic strategies. Current histopathological techniques are time consuming, induce tissue artefacts and often prevent further evaluation, once the tissue has been fixed. Hence, there is a potential need for a fast and nondestructive imaging technique for unfixed tissue. Near‐infrared, reflectance confocal microscopy (CM) allows real‐time, virtual sectioning of unstained, bulk tissue samples. This pilot study evaluates the use of CM in the assessment of meniscus histopathology in a series of 26 freshly‐excised human meniscus samples compared to standard light microscopy of stained sections. CM images of the meniscus show cell and matrix detail, depicting morphologic features of collagen and elastic fibres, vessels and nerve endings. In addition, crystal deposits of gout and pseudogout are also demonstrable. Thus, CM is a novel imaging technique that could enable the pathologist to make a rapid microscopic evaluation of cartilage in a fresh and unfixed fashion.
Analysing the effect of novel therapies on cytokine expression in experimental arthritis
Authors: Williams Richard O. , Inglis Julia J. , Simelyte Egle , Criado Gabriel , Sumariwalla Percy F.
Published: September 2005

Type II collagen‐induced arthritis (CIA) is an animal model of rheumatoid arthritis that has been used extensively to address questions of disease pathogenesis and to validate novel therapeutic targets. Susceptibility to CIA is strongly associated with major histocompatibility complex class II genes, and the development of arthritis is accompanied by a robust T‐ and B‐cell response to type II collagen. The main pathological features of CIA include proliferative synovitis with infiltration of inflammatory cells, pannus formation, cartilage degradation, erosion of bone and fibrosis. Pro‐inflammatory cytokines, such as tumour necrosis factor α and interleukin‐1β, are expressed in the arthritic joints in both murine CIA and human rheumatoid arthritis, and blockade of these molecules results in amelioration of disease. Hence, there is a great deal of interest in the development of small‐molecular‐weight inhibitors of pro‐inflammatory cytokines. There is also interest in the development and testing of drugs with the capacity to modulate the immune pathways involved in driving the inflammatory response in arthritis. For these reasons, there is a need to monitor the effect of novel treatments on cytokine expression in vivo. In this review, we outline the various techniques used to detect cytokines in experimental arthritis and describe how these techniques have been used to quantify changes in cytokine expression following therapeutic intervention.
Sintering Behavior of Doped Lanthanum and Yttrium Manganite
Authors: Stevenson Jeffry W. , Hallman Paul F. , Armstrong Timothy R. , Chick Larry A.
Published: September 2005

The sintering behavior of doped manganite powders was found to be highly dependent on changes in calcination conditions and A/B cation ratio. Coarsening of combustion synthesized powders by calcination allowed for higher green densities in dry‐pressed compacts, which resulted in higher sintered densities for powders calcined in the temperature range 800°‐1200°C. Sintered densities decreased for calcination temperatures greater than 1200°C. Preparation of manganites with a deficiency of A‐site cations improved the densification behavior substantially. This effect was attributed to an increased concentration of A‐site vacancies which enhanced the diffusion of A‐site cations during sintering. Modification of doped manganites by alteration of composition and calcination conditions allowed their sintering shrinkage to be “tailored” to more closely match the shrinkage of yttria‐stabilized zirconia.
Viscosities and Sintering Rates of Composite Packings of Spheres
Authors: Jagota Anand , Scherer George W.
Published: September 2005

The effective sintering rates and viscosities of three‐dimensional composite packings have been studied using a discrete numerical model. The packings consist of random mixtures of hard and soft spheres of the same size. With increasing substitution of hard particles for soft particles in the packing, the viscosity increases and the sintering rate decreases. This is particularly abrupt at well‐defined rigidity thresholds where there is a transition from softlike to hardlike behavior. The site fraction of hard particles at which the transition occurs depends on the nature of the interaction between hard particles. When the contact between hard particles resists all six relative degrees of freedom (relative velocities and spins), the bonded case, the rigidity threshold coincides with the percolation threshold (site fraction ∼0.32). When the contact between hard particles resists only interpenetration, the sliding case, the threshold occurs at a site fraction of hard particles very close to unity. Results for the variation of effective properties with site fraction of hard particles are presented for these and other cases. These results can also be applied to the study of elastic percolating networks.
Group II Tris(glycolato)silicates as Precursors to Silicate Glasses and Ceramics
Authors: Kansal Pallavi , Laine Richard M.
Published: September 2005

Group II tris(glycolato)silicates, MSi(OCH2CH2O)3 (where M = Ba, Ca, Mg), can be synthesized directly by reaction of silica with ethylene glycol and alkaline‐earth (group II) oxides at 200°C. These hexa‐alkoxy silicates serve as precursors to silicate glass and ceramic powders. They are readily modified by exchange with longer‐chain diols into processable polymer precursors. These Theologically useful precursors may provide access to silicate or aluminosilicate powders, thin fllms, fibers, and coatings. Thus, we have examined the utility of hexacoordinate glycolatosilicates as model precursors. Pyrolysis of the compounds, MSi(OCH2‐CH2O)3, in air transforms them to their anticipated ceramic products, MO‐SiO2. The phase transformations and chemical changes that occur during pyrolysis were characterized using X‐ray powder diffractometry (XRD), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), thermal gravimetric analysis (TGA), differential thermal analysis (DTA), and scanning electron microscopy (SEM). The hexacoordinate glycolatosilicates oxidatively decompose at ∼300°C to form amorphous materials. Moderate to significant quantities of the group II carbonates, MCO3 (15–50 wt%), form coincidentally as the amorphous intermediates trap CO2 generated by ligand oxidation. At ∼900°C, the amorphous materials crystallize into the expected, phase‐pure, MO‐SiO2.
Reaction Densification of α′‐SiAION: II, Densification Behavior
Authors: Menon Mohan , Chen I‐Wei
Published: September 2005

Reaction hot‐pressing behavior of α‐Si3N4, Al2O3, A1N, and M2OZ powder mixtures (M = Li, Mg, Ca, Y, Nd, Sm, Gd, Dy, Er, and Yb) forming α′‐SiAlON has been studied. Five characteristic temperatures are found to control the densification behavior of these materials. The densification proceeded in three major stages. The first two stages were formation of ternary oxide eutectic and wetting of majority nitride powder. The third stage involved dissolution/melting of intermediate phase. Variation from this behavior sometimes occurs due to localization of wetting liquid at A1N, extremely high melting/dissolution temperature of Mg2Al4SisO18 and Nd and Sm melilite, and secondary precipitation of Dy‐α′‐SiAlON. The dominant densification mechanism was found to be massive particle rearrangement, irrespective of the wetting and dissolution/melting behavior. The efficiency of this mechanism is mostly affected by the amount of available liquid and less by its viscosity. Fully dense, single‐phase ceramics were obtained in all cases except Mg when hot‐pressed at a constant heating rate to 1750°C, and considerably lower temperatures for Li, Ca, Gd, Dy, Er, and Yb‐SiAlON when held isothermally.