bluuebunny/crossref_metadata_2025 huggingface dataset:
Production and properties of micro‐porous glas bubble zinc and aluminium composites
Authors: Weise J. , Yezerska O. , Busse M. , Haesche M. , Zanetti‐Bueckmann V. , Schmitt M.
Published: November 2007

Micro‐porous syntactic foams were produced by means of integration of glass bubbles into aluminium and zinc matrices. Preforms of glass bubbles were pressure infiltrated with the alloys AlSi9Cu9 ans ZnAl4Cu using squeeze casting. The preforms were sintered thermically without the use of bonding agents. Using the combination of different sintering steps syntactic foams with locally different densities could be produced. The mechanical properties of the foams were tested indicating a high compression strength of the foams and a very good compression energy absorption. Furthermore, corrosion behaviour and behaviour at higher temperatures were investigated.
Modifizierung des ABSE‐Polycarbosilazans mit Multi‐Walled Carbon Nanotubes zur Herstellung spinnfähiger Massen
Authors: Kokott S. , Motz G.
Published: November 2007

In den letzten 10 Jahren wurde eine preisgünstige Herstellungsmethode für keramische SiCN‐Fasern über die Precursorroute gefunden, welche die fünf Prozessschritte Polymersynthese, Herstellung der Spinnmasse, Schmelzspinnen, Härtung mittels Elektronenbestrahlung und kontinuierliche Pyrolyse bei 1100 °C unter Stickstoffatmosphäre beinhaltet. Für diese Anwendung wurde am Lehrstuhl Keramische Werkstoffe der Universität Bayreuth ein festes und schmelzbares Polymer (ABSE) entwickelt, das sich besonders zur Faserherstellung eignet. Auf Grund seines relativ niedrigen Molekulargewichts ist jedoch eine angepasste katalytische und thermische Nachbehandlung nötig, um einen stabilen Schmelzspinnprozess zu gewährleisten. Dieser Artikel stellt eine alternative Herstellungsmethode geeigneter Spinnmassen über die Einbringung von Multi‐Walled Carbon Nanotubes (MWCNTs) in die ABSE‐Schmelze vor. Für diese Anwendung ist eine homogene Einbringung der MWCNTs in die ABSE‐Matrix notwendig. Durch optische Analyse und Vergleich des Dispergiergrades in auf verschiedene Art und Weise hergestellten Spinnmassen wurde ein optimiertes Dispergierverfahren für MWCNTs im ABSE gefunden. Ebenso wurde der Einfluss eines Dispergators auf den Grad der Dispergierung untersucht. Während durch Zugabe eines Dispergator die Homogenität der MWCNTs in der ABSE‐Matrix deutlich ansteigt, werden die Wechselwirkungen zwischen den MWCNTs und dem Polymer herabgesetzt. In ersten Spinnversuchen konnte eine gute Verspinnbarkeit der MWCNT‐versetzten Massen festgestellt werden. Damit stellt die Zugabe von MWCNTs eine neue Methode dar, den ABSE‐Precursor in geeigneter Weise für den Schmelzspinnprozess zu modifizieren.
Bilateral effects of unilateral thalamic deep brain stimulation: A case report
Authors: Kovacs Norbert , Pal Endre , Merkli Hajnalka , Kellenyi Lorant , Nagy Ferenc , Janszky Jozsef , Balas Istvan
Published: November 2007

A recent study has proved that unilateral deep brain stimulation (DBS) of the subthalamic nucleus has bilateral effects. However, it is still unclear whether unilateral ventral intermediate thalamic nucleus (Vim) DBS exerts exclusively contralateral or bilateral effects on tremor. Previous studies demonstrated a clinically irrelevant improvement on the nontarget side after thalamic stimulator implantation, which was considered to be solely the result of mechanical effects. We report here the case of a 55‐year‐old woman in whom unilateral thalamic DBS can stop the disabling postural‐kinetic tremor in both hands. Simultaneous surface electromyography (sEMG), accelerometry, and video recordings were obtained to evaluate the underlying mechanism. After the right Vim DBS was turned off, moderate rest tremor appeared in both hands accompanied by bilateral bursts on sEMG. Because right hand tremor cannot simply reflect the mechanical overflow of the left side, the bilateral improvement caused by right Vim DBS is probably due to an active tremor reduction in this particular case. © 2007 Movement Disorder Society
Macrophages: An elusive yet emerging therapeutic target of atherosclerosis
Authors: Tiwari R.L. , Singh V. , Barthwal M.K.
Published: November 2007

Macrophages are central to the initiation and progression of atherosclerosis and thus can be very appropriate targets for therapy. Cell adhesion molecules mediating monocytes recruitment to the endothelium are attractive therapy targets and their inhibitors are in clinical trials. Macrophage scavenger receptors like SR‐A and CD‐36 mediate foam cell formation by facilitating the uptake of modified lipids. Peroxisome proliferator‐activated receptors (PPAR), liver X receptor (LXR)‐mediated signaling, mitogen‐activated protein kinase (MAPK) induced phosphorylation events seem to play an important role in this phenomenon. Proteins affecting macrophage cholesterol metabolism and transport, including ATP‐binding cassette (ABC) A1, ABCG1, acyl‐CoA:cholesterol acyltransferase (ACAT), apolipoprotein A‐1 (ApoA‐1), neutral cholesteryl ester hydrolase (NCEH) also regulate foam cell formation and are being developed as therapeutic targets by many pharmaceutical companies. Macrophage proliferation and apoptosis are important events controlling inflammatory response, plaque vulnerability, and destabilization. Free cholesterol (FC) activates the macrophage endoplasmic reticulum (ER) stress pathway and apoptosis. Free radicals and nitric oxide also modulate macrophage foam cell formation and apoptosis. Various antioxidants like AGI‐1067 and BO‐653 are in clinical trials for atherosclerosis treatment. Macrophage matrix metalloproteinase's (MMP's) play a significant role in weakening and rupture of plaques. Efforts are on to develop isoform specific MMP inhibitor. CD‐14, MMP‐3, ABCA1, Toll‐like receptor‐4 (TLR‐4), lectin‐like oxidized low‐density lipoprotein receptor‐1 (LOX‐1), arachidonate lipoxygenase‐15 (ALOX‐15), and Connexin37 polymorphisms and macrophage dysfunction signify their importance in atherosclerosis. Deciphering the role of macrophages in regulating dyslipidemia and inflammation during atherosclerosis is important for developing them as therapeutic targets. © 2007 Wiley Periodicals, Inc. Med Res Rev, 28, No. 4, 483–544, 2008
CpG Island hypermethylation in cell‐free serum DNA identifies patients with localized prostate cancer
Authors: Ellinger Jörg , Haan Kim , Heukamp Lukas C. , Kahl Philip , Büttner Reinhard , Müller Stefan C. , von Ruecker Alexander , Bastian Patrick J.
Published: November 2007

BACKGROUND

One of the earliest and most common epigenetic events in prostate carcinogenesis is DNA CpG island (CGI) hypermethylation. Our aim was to analyze the diagnostic and prognostic possibilities of multigene methylation analysis in cell‐free serum DNA of prostate cancer (PCA) patients.

METHODS

We analyzed serum samples from 226 consecutive patients (168 PCA; 42 benign prostatic hyperplasia (BPH); 5 incidental PCA; 11 healthy individuals). Cell‐free DNA was digested with methylation‐sensitive restriction endonucleases (HpaII and HinP1I). Subsequently, CGI hypermethylation at GSTP1, PTGS2, Reprimo, and TIG1 was assessed using real‐time PCR.

RESULTS

CGI hypermethylation at GSTP1, TIG1, PTGS2, and Reprimo was more frequent in PCA (42.3%, 9.5%, 2.4%, and 1.2%, respectively) compared to BPH (7.7%, 0%, 0%, and 0%, respectively) and healthy individuals (all 0%) with a statistical significant difference of GSTP1 (P < 0.0001) and TIG1 (P = 0.038). GSTP1 hypermethylation was also detected in four patients with incidental PCA. Hypermethylation in serum DNA at GSTP1 and hypermethylation at any gene site distinguished between PCA and BPH patients in a highly specific (92%) but less sensitive (42–47%) manner. Neither CGI hypermethylation at a single gene loci nor the combination of multiple gene sites was correlated to the pathological stage, grade or biochemical recurrence following radical prostatectomy.

CONCLUSIONS

The detection of aberrant hypermethylation in cell‐free serum DNA allows the highly specific diagnosis of PCA. A test based on GSTP1 hypermethylation in serum samples of patients with suspected PCA may help to identify men with increased risk of harboring PCA despite negative prostate biopsy. Prostate 68: 42–49, 2008. © 2007 Wiley‐Liss, Inc.
Molecular imaging of NF‐kappaB in prostate tissue after systemic administration of IL‐1β
Authors: Vykhovanets Eugene V. , Shukla Sanjeev , MacLennan Gregory T. , Resnick Martin I. , Carlsen Harald , Blomhoff Rune , Gupta Sanjay
Published: November 2007

BACKGROUND

Activation of nuclear‐factor kappaB (NF‐κB) influences the transcription of number of genes, many of which participate in inflammatory responses and tumor development. A wide range of human cancers and inflammatory disorders express inappropriate regulation of NF‐κB. The role of NF‐κB in intraprostatic inflammation has not been elucidated.

METHODS

Using transgenic NF‐κB‐Luciferase Tag mice coupled to the luciferase reporter gene, we performed serial, noninvasive in vivo and ex vivo molecular imaging of NF‐κB activation in the mouse body after systemic administration of mouse pro‐inflammatory cytokines: TNF‐α, IL‐6, and IL‐1β at 10 µg/kg body weights. In some experiments, pretreatment with dexamethasone (10 mg/kg) was used to modulate the cytokine‐induced NF‐κB‐dependent luminescence in vivo.

RESULTS

Treatment of NF‐κB‐Luc mice with cytokines increased luminescence in a time‐ and organ‐ specific manner. Highest levels of NF‐κB‐dependent luminescence were observed approximately 3–4 hr after IL‐1β administration. An important finding was the cumulative effect of IL‐1β to activate NF‐κB in the prostate during chronic administration.

CONCLUSIONS

The molecular imaging of NF‐κB activity might be an attractive approach to distinguish the role of cytokine‐induced NF‐κB signaling in intraprostatic inflammation and prostate cancer development. Since dexamethasone, a known NF‐κB inhibitor, could reduce the IL‐1β‐induced NF‐κB‐dependent luminescence in the prostate, NF‐κB‐Luc mice might be useful tool to screen potential candidate drugs for treatment of inflammation and tumor associated with aberrant NF‐κB activity. Prostate 68: 34–41, 2008. © 2007 Wiley‐Liss, Inc.
Evolution of binding sites for zinc and calcium ions playing structural roles
Authors: Torrance James W. , MacArthur Malcolm W. , Thornton Janet M.
Published: November 2007

The geometry of metal coordination by proteins is well understood, but the evolution of metal binding sites has been less studied. Here we present a study on a small number of well‐documented structural calcium and zinc binding sites, concerning how the geometry diverges between relatives, how often nonrelatives converge towards the same structure, and how often these metal binding sites are lost in the course of evolution. Both calcium and zinc binding site structure is observed to be conserved; structural differences between those atoms directly involved in metal binding in related proteins are typically less than 0.5 Å root mean square deviation, even in distant relatives. Structural templates representing these conserved calcium and zinc binding sites were used to search the Protein Data Bank for cases where unrelated proteins have converged upon the same residue selection and geometry for metal binding. This allowed us to identify six “archetypal” metal binding site structures: two archetypal zinc binding sites, both of which had independently evolved on a large number of occasions, and four diverse archetypal calcium binding sites, where each had evolved independently on only a handful of occasions. We found that it was common for distant relatives of metal‐binding proteins to lack metal‐binding capacity. This occurred for 13 of the 18 metal binding sites we studied, even though in some of these cases the original metal had been classified as “essential for protein folding.” For most of the calcium binding sites studied (seven out of eleven cases), the lack of metal binding in relatives was due to point mutation of the metal‐binding residues, whilst for zinc binding sites, lack of metal binding in relatives always involved more extensive changes, with loss of secondary structural elements or loops around the binding site. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Effects of glycerol on the compaction and stability of the wild type and mutated rabbit muscle creatine kinase
Authors: Feng Shan , Yan Yong‐Bin
Published: November 2007

All organisms have developed detect, repair, regulation, and stabilization mechanisms to survive from cellular and molecular damage induced by diverse stresses. Among them, the accumulation of osmolytes is a common mechanism evolved by cells to maintain cell volume and stabilize macromolecules against various environmental stresses. The molecular mechanisms by which osmolytes stabilize proteins and prevent aggregation have been well‐established. However, little is known about the effects of osmolytes on mutated or damaged proteins. In this research, we investigated the effects of glycerol on the activity, structure, and stability of the wild type (WT) and D54G CK under normal and extreme (high temperature) conditions. It was found that glycerol had similar effects on the suppression of the aggregation during the refolding of both proteins. Under native conditions, the effect of glycerol on the mutated protein was more obvious than on the WT protein. Glycerol could efficiently force the mutated protein to fold to a state close to the WT protein, and thus stabilize the native state of the mutated protein. Glycerol could also protect both the WT and mutated proteins against heat‐induced denaturation. However, the change in the transition free energy of heat‐induced inactivation of the WT protein was larger than that of the mutated protein. These results suggested that glycerol might have differential effects on the changes of the chemical potential and the transition free energy of the WT and mutated proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structure–function relationships in the 2‐oxo acid dehydrogenase family: Substrate‐specific signatures and functional predictions for the 2‐oxoglutarate dehydrogenase‐like proteins
Authors: Bunik Victoria I. , Degtyarev Dmitry
Published: November 2007

Structural relationship within the family of the thiamine diphosphate‐dependent 2‐oxo acid dehydrogenases was analyzed by combining different methods of sequence alignment with crystallographic and enzymological studies of the family members. For the first time, the sequence similarity of the homodimeric 2‐oxoglutarate dehydrogenase to heterotetrameric 2‐oxo acid dehydrogenases is established. The presented alignment of the catalytic domains of the dehydrogenases of pyruvate, branched‐chain 2‐oxo acids and 2‐oxoglutarate unravels the sequence markers of the substrate specificity and the essential residues of the family members without the 3D structures resolved. Predicted dual substrate specificity of some of the 2‐oxo acid dehydrogenases was confirmed experimentally. The results were used to decipher functions of the two hypothetical proteins of animal genomes, OGDHL and DHTKD1, similar to the 2‐oxoglutarate dehydrogenase. Conservation of all the essential residues confirmed their catalytic competence. Sequence analysis indicated that OGDHL represents a previously unknown isoform of the 2‐oxoglutarate dehydrogenase, whereas DHTKD1 differs from the homologs at the N‐terminus and substrate binding pocket. The differences suggest changes in heterologous protein interactions and accommodation of more polar and/or bulkier structural analogs of 2‐oxoglutarate, such as 2‐oxoadipate, 2‐oxo‐4‐hydroxyglutarate, or products of the carboligase reaction between a 2‐oxodicarboxylate and glyoxylate or acetaldehyde. The signatures of the Ca2+‐binding sites were found in the Ca2+‐activated 2‐oxoglutarate dehydrogenase and OGDHL, but not in DHTKD1. Mitochondrial localization was predicted for OGDHL and DHTKD1, with DHTKD1 probably localized also to nuclei. Medical implications of the obtained results are discussed in view of the possible associations of the 2‐oxo acid dehydrogenases and DHTKD1 with neurodegeneration and cancer. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Sequence‐similar, structure‐dissimilar protein pairs in the PDB
Authors: Kosloff Mickey , Kolodny Rachel
Published: November 2007

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which “redundant” structures have been removed, based on a sequence‐based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence‐similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence‐based structural superpositions and geometry‐based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence‐based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry‐based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence‐based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry‐based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence‐similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm). Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structural disorder serves as a weak signal for intracellular protein degradation
Authors: Tompa P. , Prilusky J. , Silman I. , Sussman J. L.
Published: November 2007

Targeted turnover of proteins is a key element in the regulation of practically all basic cellular processes. The underlying physicochemical and/or sequential signals, however, are not fully understood. This issue is particularly pertinent in light of the recent recognition that intrinsically unstructured/disordered proteins, common in eukaryotic cells, are extremely susceptible to proteolytic degradation in vitro. The in vivo half‐lives of proteins were determined recently in a high‐throughput study encompassing the entire yeast proteome; here we examine whether these half‐lives correlate with the presence of classical degradation motifs (PEST region, destruction‐box, KEN‐box, or the N‐terminal residue) or with various physicochemical characteristics, such as the size of the protein, the degree of structural disorder, or the presence of low‐complexity regions. Our principal finding is that, in general, the half‐life of a protein does not depend on the presence of degradation signals within its sequence, even of ubiquitination sites, but correlates mainly with the length of its polypeptide chain and with various measures of structural disorder. Two distinct modes of involvement of disorder in degradation are proposed. Susceptibility to degradation of longer proteins, containing larger numbers of residues in conformational disorder, suggests an extensive function, whereby the effect of disorder can be ascribed to its mere physical presence. However, after normalization for protein length, the only signal that correlates with half‐life is disorder, which indicates that it also acts in an intensive manner, that is, as a specific signal, perhaps in conjunction with the recognition of classical degradation motifs. The significance of correlation is rather low; thus protein degradation is not determined by a single characteristic, but is a multi‐factorial process that shows large protein‐to‐protein variations. Protein disorder, nevertheless, plays a key signalling role in many cases. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Protein structure mining using a structural alphabet
Authors: Tyagi M. , de Brevern A. G. , Srinivasan N. , Offmann B.
Published: November 2007

We present a comprehensive evaluation of a new structure mining method called PB‐ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB‐ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super‐family members. On comparison to 13 existing structure comparison/mining methods, PB‐ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut‐off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB‐ALIGN is freely available on web server called Protein Block Expert (PBE) athttp://bioinformatics.univ‐reunion.fr/PBE/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Binding similarity network of ligand
Authors: Park Keunwan , Kim Dongsup
Published: November 2007

The protein and ligand interaction takes an important part in protein function. Both ligand and its binding site are essential components for understanding how the protein–ligand complex functions. Until now, there have been many studies about protein function and evolution, but they usually lacked ligand information. Accordingly, in this study, we tried to answer the following questions: how much ligand and binding site are associated with protein function, and how ligands themselves are related to each other in terms of binding site. To answer the questions, we presented binding similarity network of ligand. Through the network analysis, we attempted to reveal systematic relationship between the ligand and binding site. The results showed that ligand binding site and function were closely related (conservation ratio, 81%). We also showed conservative tendency of function in line with ligand structure similarity with some exceptional cases. In addition, the binding similarity network of ligand revealed scale‐free property to some degree like other biological networks. Since most nodes formed highly connected cluster, a clustering coefficient was very high compared with random. All the highly connected ligands (hubs) were involved in various functions forming large cluster and tended to act as a bridge between modular clusters in the network. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Modeling ensembles of transmembrane β‐barrel proteins
Authors: Waldispühl Jérôme , O'Donnell Charles W. , Devadas Srinivas , Clote Peter , Berger Bonnie
Published: November 2007

Transmembrane β‐barrel (TMB) proteins are embedded in the outer membrane of Gram‐negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few nonhomologous TMB structures have been determined by X‐ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. We introduce the program partiFold to investigate the folding landscape of TMBs. By computing the Boltzmann partition function, partiFold estimates inter‐β‐strand residue interaction probabilities, predicts contacts and per‐residue X‐ray crystal structure B‐values, and samples conformations from the Boltzmann low energy ensemble. This broad range of predictive capabilities is achieved using a single, parameterizable grammatical model to describe potential β‐barrel supersecondary structures, combined with a novel energy function of stacked amino acid pair statistical potentials. PartiFold outperforms existing programs for inter‐β‐strand residue contact prediction on TMB proteins, offering both higher average predictive accuracy as well as more consistent results. Moreover, the integration of these contact probabilities inside a stochastic contact map can be used to infer a more meaningful picture of the TMB folding landscape, which cannot be achieved with other methods. Partifold's predictions of B‐values are competitive with recent methods specifically designed for this problem. Finally, we show that sampling TMBs from the Boltzmann ensemble matches the X‐ray crystal structure better than single structure prediction methods. A webserver running partiFold is available at http://partiFold.csail.mit.edu/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Intrinsically disordered protein from a pathogenic mesophile Mycobacterium tuberculosis adopts structured conformation at high temperature
Authors: Kumar Niti , Shukla Swati , Kumar Sanjiv , Suryawanshi Anju , Chaudhry Uma , Ramachandran Srinivasan , Maiti Souvik
Published: November 2007

Compared to eukaryotes, the occurrence of “intrinsically disordered” or “natively unfolded” proteins in prokaryotes has not been explored extensively. Here, we report the occurrence of an intrinsically disordered protein from the mesophilic human pathogen Mycobacterium tuberculosis. The Histidine‐tagged recombinant Rv3221c biotin‐binding protein is intrinsically disordered at ambient and physiological growth temperatures as revealed by circular dichroism and Fourier transform infrared (FTIR) spectroscopic studies. However, an increase in temperature induces a transition from disordered to structured state with a folding temperature of ≈53°C. Addition of a structure inducing solvent trifluoroethanol (TFE) causes the protein to fold at lower temperatures suggesting that TFE fosters hydrophobic interactions, which drives protein folding. Differential Scanning Calorimetry studies revealed that folding is endothermic and the transition from a disordered to structured state is continuous (higher‐order), implying existence of intermediates during folding process. Secondary structure analysis revealed that the protein has propensity to form β‐sheets. This is in conformity with FTIR spectrum that showed an absorption peak at wave number of 1636 cm−1, indicative of disordered β‐sheet conformation in the native state. These data suggest that although Rv3221c may be disordered under ambient or optimal growth temperature conditions, it has the potential to fold into ordered structure at high temperature driven by increased hydrophobic interactions. In contrast to the generally known behavior of other intrinsically disordered proteins folding at high temperature, Rv3221c does not appear to oligomerize or aggregate as revealed through numerous experiments including Congo red binding, Thioflavin T‐binding, turbidity measurements, and examining molar ellipticity as a function of protein concentration. The amino acid composition of Rv3221c reveals that it has 24% charged and 54.9% hydrophobic amino acid residues. In this respect, this protein, although belonging to the class of intrinsically disordered proteins, has distinct features. The intrinsically disordered state and the biotin‐binding feature of this protein suggest that it may participate in many biochemical processes requiring biotin as a cofactor and adopt suitable conformations upon binding other folded targets. Proteins 2008. © 2007 Wiley‐Liss, Inc.
X‐ray analysis of phosphoglycerate kinase 2, a sperm‐specific isoform from Mus musculus
Authors: Sawyer Gregory M. , Monzingo Arthur F. , Poteet Ethan C. , O'Brien Deborah A. , Robertus Jon D.
Published: November 2007

Phosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X‐linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3‐phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 Å resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the “open” form; that is the N‐terminal domain that can bind 3PG and the C‐terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13° rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C‐terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Ranking predicted protein structures with support vector regression
Authors: Qiu Jian , Sheffler Will , Baker David , Noble William Stafford
Published: November 2007

Protein structure prediction is an important problem of both intellectual and practical interest. Most protein structure prediction approaches generate multiple candidate models first, and then use a scoring function to select the best model among these candidates. In this work, we develop a scoring function using support vector regression (SVR). Both consensus‐based features and features from individual structures are extracted from a training data set containing native protein structures and predicted structural models submitted to CASP5 and CASP6. The SVR learns a scoring function that is a linear combination of these features. We test this scoring function on two data sets. First, when used to rank server models submitted to CASP7, the SVR score selects predictions that are comparable to the best performing server in CASP7, Zhang‐Server, and significantly better than all the other servers. Even if the SVR score is not allowed to select Zhang‐Server models, the SVR score still selects predictions that are significantly better than all the other servers. In addition, the SVR is able to select significantly better models and yield significantly better Pearson correlation coefficients than the two best Quality Assessment groups in CASP7, QA556 (LEE), and QA634 (Pcons). Second, this work aims to improve the ability of the Robetta server to select best models, and hence we evaluate the performance of the SVR score on ranking the Robetta server template‐based models for the CASP7 targets. The SVR selects significantly better models than the Robetta K*Sync consensus alignment score. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Photosensitized luminescent lanthanide (III) clusters encapsulated with polyphenylsilsesquioxane
Authors: Manseki Kazuhiro , Yanagida Shozo
Published: November 2007

An inorganic–organic lanthanide (III) cluster encapsulated with polyphenylsilsesquioxane (PPSQ), which would be a suitable luminescent material for violet LEDs excitation will be reported. The cluster with adjacent 9 terbium (III) ions in close proximity (3.6 ∼ 3.7 Å), in which lanthanide (III) ions are stabilized with organic photosensitizing compounds, 16 hexylsalicylates, has been successfully introduced. The terbium (III) cluster was highly soluble in PPSQ and had high thermostability. By the ligand excitation of the cluster‐doped PPSQ at around near‐UV light region (e.g., 360–380 nm), the terbium (III) cluster displayed strong green luminescence with a maximum intensity at 547 nm (intra‐4f transition of terbium (III) ion: 5D4 → 7F5). It was likely that energy transfer from excited hexylsalicylates to terbium (III) ions mediated sensitized emission of Tb (III) ions in PPSQ. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A comparative investigation of the damage build‐up in GaN and Si during rare earth ion implantation
Authors: Gloux Florence , Ruterana Pierre , Lorenz K. , Alves E.
Published: November 2007

The medium range implantation of rare earth ions at room temperature in GaN layers leads to the formation of point defect clusters, basal and prismatic stacking faults from the lowest fluence. When a threshold fluence of about 3 × 1015 at/cm2 is reached, a highly disordered ‘nanocrystalline layer’ (NL) is observed to form at the surface. This layer is made of a mixture of misoriented nanocrystallites and voids. Beyond this NL, I1, I2 and E basal stacking faults (BSFs) have been identified, as well as in GaN implanted at lower fluences than the threshold. Prismatic stacking faults (PSFs) with Drum atomic configuration connect the I1 BSFs. A similar investigation of the damage in Eu implanted Si shows a completely different behaviour; in this case, from the relatively low fluence 1 × 1014 at/cm2, amorphization starts in patches at the projected range and extends very rapidly towards the surface and the bulk, to form a uniform amorphous layer already at 2 × 1014 at/cm2. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gallium nitride and GaN:Eu nanocrystalline luminescent powders
Authors: Flores G. A. Hirata
Published: November 2007

In this study, we report on the fabrication and luminescent properties of pure and europium‐doped gallium nitride (GaN) powders obtained by means of two different chemical methods. Firstly, GaN and GaN:Eu microcrystalline powders were successfully prepared by using the combustion synthesis of metallic nitrates as the precursors (method A). By using a second processing route, GaN and (Ga1–x Eux )N powders are synthesized from metallic oxides (method B) yielding directly nanocrystalline‐phase gallium nitride and Eu‐doped gallium nitride luminescent materials. In the present work, we report two excellent methods to produce nanocrystalline or microcrystalline gallium nitride (GaN) and Eu‐doped GaN powders with different Eu concentrations. The GaN:Eu materials were characterized by photoluminescence and cathodoluminescence measurements showing strong luminescence due to f–f transition lines within Eu3+(4f6) electron emission configuration. Furthermore we present a crystallographic characterization conducted by X‐ray diffraction (XRD), luminescence properties including photoluminescence and local cathodoluminescence spectra and monochromatic imaging at low‐temperature to detect the areas from where the emission is originated within the GaN:Eu grains.

Our results show that (Ga0.95Eu0.05)N powders are cathodoluminescent with the main emission occurring at λ = 611 nm which is originated from the 5D0 → 7F2 transitions within the Eu3+ electronic levels. Low‐temperature monochromatic cathodoluminescence images taken on microcrystalline powders (produced by method A), indicate that the main emission at λ = 611 nm is originated within nanocrystalline areas of the GaN:Eu3+ microcrystalline grains. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Well‐Defined Poly(N‐glycosyl 1,2,3‐triazole) Multivalent Ligands: Design, Synthesis and Lectin Binding Studies
Authors: Geng Jin , Lindqvist Josefina , Mantovani Giuseppe , Chen Gaojian , Sayers Claire T. , Clarkson Guy J. , Haddleton David M.
Published: November 2007

Glycopolymers have been synthesised by post‐functionalisation of well‐defined alkyne‐functional polymers with sugar azides to yield N‐glycosyl 1,2,3‐triazole functional polymers. The Cu(I)‐catalysed Huisgen cycloaddition was used to attach α‐mannoside, β‐galactoside and β‐lactoside derivatives via an azide functionality bound directly to the sugar anomeric carbon. Three different catalytic systems were investigated for the click reactions; [(PPh3)3Cu(I)Br], TBTA/Cu(I)Br and bathophenanthrolinedisulphonic acid disodium salt/Cu(I)Br. The latter of these was found to be the most efficient for the attachment of the larger/more sterically hindered disaccharide lactose moiety. The interaction of the lactose‐ and galactose‐bearing glycopolymers with Ricinus Communis Agglutinin (RCA I) lectin was investigated by affinity HPLC analysis. The rate of the interaction between mannose polymer and concanavalin A (Con A) lectin was assessed by turbidimetry. The results from the lectin conjugation studies indicate that the glycopolymers prepared in this work are able to function as multivalent ligands, further suggesting that the attachment of the triazole directly to the sugar anomeric carbon has no significant effect on the interaction of these glycopolymers with Con A and RCA I.
Desorption electrospray ionization of aerosol particles
Authors: Dong Jianan , Rezenom Yohannes H. , Murray Kermit K.
Published: November 2007

We have applied desorption electrospray ionization to aerosol particles. Ions were formed from aerosols by merging suspended dry particles with an electrospray of solvent in a modified ion trap mass spectrometer. Dry aerosol particles were generated using a fluidized bed powder disperser and directed toward the inlet of the mass spectrometer. A nanospray source was used to create a spray of solvent droplets directed at the inlet and at a right angle with respect to the aerosol. Ions generated by the interaction of the particles and electrospray were transferred into the ion trap mass spectrometer. Using this method, pure samples of caffeine and erythromycin A were analyzed. In addition, commonly available food and drug powders including instant cocoa powder, artificial sweetener and ibuprofen were analyzed. Copyright © 2007 John Wiley & Sons, Ltd.
An environment for dataflow program development of parallel processing system‐harray
Authors: Yatnana Hayato , Kohdate Jun , Members Toshiaki Yasue, Associate , Muraoka Yoichi
Published: November 2007

This paper considers the dataflow program development environment for the system programmer who develops the compiler and proposes a method to improve the debugging efficiency. The conventional debugging methods are either: (1) to monitor the packet in the dataflow ring, or (2) to specify the function containing a bug. The former contains unsolved problems such as the determination of start timing for the data monitoring and the presentation of a large amount of information to the user. The latter contains a problem in that the debugging is impossible at the dataflow level.

This paper aims at the solution of those problems, and the detailed debugging is executed on the software, not on the real machine. The information presentation on a dataflow graph is considered for systematic presentation of the debugging information. As the development environment, the parallel processing system Harray proposed by the authors is considered. In the proposed system, a two‐stage process is employed in which the first step is to specify the macro‐block (which is a task unit in Harray) containing the bug, and the second step is the detailed debugging of the specified macro‐block. The debugging within the macroblock is executed on the software, and the debugging efficiency is improved by: (1) diagram representation for easier visual recognition, and (2) backward tracing function.
Edge surface detection with subvoxel accuracy from 3‐d images
Authors: Kimura Shigeru , Ozawa Shinji
Published: November 2007

A method is described for edge surface detection with subvoxel accuracy for three‐dimensional (3‐D) images. Direct extension of the subpixel edge detection method for 2‐D images into 3‐D applications has to deal with an explosion of operational combinations that make the method impractical. To overcome such a shortcoming, this paper proposes a practical approach consisting of two major steps: (1) extraction of local edge information; and (2) estimation of global edge surface from local edge information.

To extract the candidate edge points as local edge information, we make use of the connected three voxels located on the straight lines referred to as the edge estimation axes. The coordinates of candidate edge points are derived from intensity gradients of three neighboring voxels along the edge estimation axis. Then, a planar fitting is performed on a set of candidate edge points to estimate a global edge surface in 3‐D.

The key points of the method directly affecting the accuracy are the selection of the edge estimation axis and the weighting of the candidate edge points. The implementation reflecting these points is described.
Word spotting system based on stochastic models of phonemic segments
Authors: Okada Michio , Kohda Masaki
Published: November 2007

This paper presents a new architecture for word spotting, one of the most important technologies in continuous speech recognition. If the word spotting algorithm can automatically create standard word and phrase models from phonemic segment models smaller than single words, it is able to facilitate large vocabulary spotting. It is also flexible in accommodating acoustic variation in phonetic units within continuously spoken speech.

The word spotting algorithm proposed here has the following features: (1) Local spectrum sequence in speech are referred to as “acoustic events,” and each phonetic segment is represented as a sequence of these events. Local spectrum variations are accommodated in terms of probabilistic models, and variations in the temporal structure of phonemic segments are handled by using dynamic time warping matching method for event sequences. (2) In continuous speech used for learning, the event sequence that make up the phonemic segment are automatically learned through an iterative process of altering the boundaries of phonemic segments. (3) Phonetic strings in phonetic orthography may be joined into phonemic segments appropriate to the phonemic environment, automatically creating any desired standard patterns for words or phrases. The performance of this algorithm is demonstrated in phoneme recognition, word spotting and phrase spotting.
Improved reslicing by voxel‐project‐method
Authors: Nakanishi Mamoru
Published: November 2007

The projection processing has frequently been applied in recent years, where the three‐dimensional image composed of a large number slices, such as X‐ray CT and MRI, is used as the input. In such processings, the cross section is produced with arbitrary position and inclination, or the three‐dimensional image is reprojected on an arbitrary plane. In the generation of the cross section especially, the highspeed processing is required as a pre‐processing for the image understanding. The voxel‐search method and the voxel‐projection method have been employed as the methods for projection. The voxel‐search method has been used widely because of the better image quality, but has a problem in that the speed improvement by parallel structure is difficult. The voxel‐projection method, on the other hand, can easily be implemented on a parallel system, but the deterioration of the image quality has been a problem.

This paper aims at the method to generate cross section which can realize the same image quality as in the conventional voxel‐search method while maintaining the parallelism of the voxel‐projection method. The image deterioration, such as the missing of the image data and the striped pattern of intensities on the image, are remedied. The scanning place determination is proposed for the former problem, which can determine the object of projection according to the inclination of the cross section. The average distribution technique is proposed for the latter problem, and it is shown that the cross section with a satisfactory image quality can be generated. Thus, it is shown that the voxel‐projection method can be applied to the cross section generation, paving the way to the realization of the cross section generation system with the speed improved by the parallel processing.
Bidirectional learning for neural network having butterfly structure
Authors: Morita Tatsuya , Nakajima Kazuyoshi
Published: November 2007

The number of interconnections between cells in a neural network, which is proportional to square of the number, causes a problem in the structure of the network when the number is large. The fast Fourier transform is a method to speed up matrix operation by using a butterfly operation.

This paper proposes a method of reducing the number of connections between cells in a neural network by using a multilayer structure which is based on a butterfly operation. Since the neural network inevitably a multilayer structure, it is necessary to employ a new learning method which replaces the conventional backpropagation method.

To satisfy this condition, this paper proposes an inverse function method which generates an intermediate target of learning in an inverse direction from a teacher signal at the last stage, and a bidirectional learning method which is an improvement of the inverse function method. The bidirectional learning method improves the learning effect, since the learning process is more stable than the inverse function method, and intermediate targets are generated taking into account the state of the output of each step. This is demonstrated by using a two‐dimensional pattern transform problem.
A unified theory of the family of projection filters for signal and image estimation
Authors: Koide Yuji , Yamashita Yukihiko , Ogawa Hidemitsu
Published: November 2007

In an image restoration problem, there are many problems involved in accurate estimation of the original form from the restricted form. The family of projection filters, comprising the projection filter, the partial projection filter, and the averaged projection filter, has a good performance in such estimation problems. To construct these filters, we have to solve a system of operator equations. These operator equations have been solved in several ways and there were subtle differences between each expression of the form of solution. Besides, there were some properties already known for one filter, while not known for another filter. If we can discuss these three filters together, we can clarify unknown properties at the same time and give the unified form for each filter. One of authors has in fact had some success in this regard. However, the filter forms obtained there were more complicated than the original forms obtained respectively. To solve this problem, we propose another system of operator equations which can give almost the same form as the original and discuss the unified theory of the family of projection filter.