bluuebunny/crossref_metadata_2025 huggingface dataset:
Subjective report versus objective measurement of activities of daily living in Parkinson's disease
Authors: Shulman Lisa M. , Pretzer‐Aboff Ingrid , Anderson Karen E. , Stevenson Rashida , Vaughan Christopher G. , Gruber‐Baldini Ann L. , Reich Stephen G. , Weiner William J.
Published: February 2006

We compared subjective self‐reports with objective performance ratings of activities of daily living (ADLs) and instrumental ADLs (IADLs) in patients with Parkinson's disease (PD) and identified variables associated with discordance of ratings between these two methods. Seventy‐six PD patients completed a modified Older Americans Resources and Services scale, assessing ADLs and IADLs. These results were compared with structured performance tests of walking, eating, dressing, money, and medicine management administered in the clinic. Patient performance was rated on a five‐point Likert‐type scale, ranging from 1 = no difficulty to 5 = completely unable to perform task. Significant differences were found between patients and clinicians' ratings on all tasks except walking. On the other four tasks, paired group t tests showed that patients reported better function compared with the clinician rating of medication management (1.33 vs. 2.80), eating (1.53 vs. 1.76), dressing (1.64 vs. 1.86), and managing money (1.44 vs. 2.06). A discrepancy was found between patients subjective reporting of ADL and IADL function and objective ratings. Patients overestimated their function on four of five tasks. Further study is necessary to identify whether subjective or objective performance ratings are more reflective of actual daily function. © 2006 Movement Disorder Society
Schauder estimates for solutions to a mixed boundary value problem for the Stokes system in polyhedral domains
Authors: Maz'ya V. G. , Rossmann J.
Published: February 2006

A mixed boundary value problem for the Stokes system in a polyhedral domain is considered. The authors prove the existence of solutions in weighted and non‐weighted Hölder spaces and obtain regularity results for the solutions. The results are essentially based on estimates of the Green's matrix. Copyright © 2006 John Wiley & Sons, Ltd.
Characterization of linker histone H1FOO during bovine in vitro embryo development
Authors: McGraw Serge , Vigneault Christian , Tremblay Karine , Sirard Marc‐André
Published: February 2006

Linker histones H1 are involved in various mechanisms, such as chromatin organization and gene transcription. In different organisms, a unique subtype can be found in the oocyte, however its function remains unclear. To assess the potential involvement of this oocyte linker histone (H1FOO) in chromatin modulation, we have cloned and sequenced the bovine H1FOO cDNA and followed its mRNA profile by quantitative RT‐PCR in the oocyte and throughout bovine early embryo development. The highest level of mRNA was found in the germinal vesicle (GV) oocyte and diminished constantly throughout embryo development. In the 16‐cell embryo and blastocyst, respectively, the mRNA levels were 200 and 2,000 times lower than in the GV oocyte. A specific antibody raised against bovine H1FOO was used to establish protein distribution in the oocyte and preimplantation embryo by immunocytochemistry. In the GV and metaphase II (MII) oocyte, as well as in the 1‐, 2‐ and 4‐cell embryo, H1FOO was localized in the cytoplasm and nucleus. The protein was uniformly spread within the cytoplasm, while it was concentrated onto the chromatin in the nucleus. In the 8‐ to 16‐cell embryo, H1FOO's presence diminished in the cytoplasm, although it was still strongly expressed in nucleus. In the morula and blastocyst stages, the protein was totally lacking. By its position on chromatin, H1FOO could not only be involved in chromatin conformation but could also participate in activation or repression of genes during oogenesis and embryo development before embryonic genome activation. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Automated in vivo segmentation of carotid plaque MRI with Morphology‐Enhanced probability maps
Authors: Liu Fei , Xu Dongxiang , Ferguson Marina S. , Chu Baocheng , Saam Tobias , Takaya Norihide , Hatsukami Thomas S. , Yuan Chun , Kerwin William S.
Published: February 2006

MRI is a promising noninvasive technique for characterizing atherosclerotic plaque composition in vivo, with an end‐goal of assessing plaque vulnerability. Because of limitations arising from acquisition time, achievable resolution, contrast‐to‐noise ratio, patient motion, and the effects of blood flow, automatically identifying plaque composition remains a challenging task in vivo. In this article, a segmentation method using maximum a posteriori probability Bayesian theory is presented that divides axial, multi‐contrast‐weighted images into regions of necrotic core, calcification, loose matrix, and fibrous tissue. Key advantages of the method are that it utilizes morphologic information, such as local wall thickness, and coupled active contours to limit the impact from noise and artifacts associated with in vivo imaging. In experiments involving 142 sets of multi‐contrast images from 26 subjects undergoing carotid endarterectomy, segmented areas of each of these tissues per slice agreed with histologically confirmed areas with correlations (R2) of 0.78, 0.83, 0.41, and 0.82, respectively. In comparison, manually identifying areas blinded to histology yielded correlations of 0.71, 0.76, 0.33, and 0.78, respectively. These results show that in vivo automatic segmentation of carotid MRI is feasible and comparable to or possibly more accurate than manual review for quantifying plaque composition. Magn Reson Med, 2006. Published 2006 Wiley‐Liss, Inc.
Tissue specificity of nonlinear dynamics in baseline fMRI
Authors: Deshpande Gopikrishna , LaConte Stephen , Peltier Scott , Hu Xiaoping
Published: February 2006

In this work, recent advances in the field of nonlinear dynamics (NLD) were applied to fMRI data to examine the spatio‐temporal properties of BOLD resting state fluctuations. Five human subjects were imaged during resting state (visual fixation) at 3T using single‐shot gradient echo planar imaging (EPI). Respiration and cardiac signals were concurrently recorded for retrospectively removing fluctuations due to these physiologic activities. Patterns of singularity in the complex plane (PSC) and Lempel‐Ziv complexity (LZ) were used to study the deterministic nonlinearity in resting state fMRI data. The results show that there is greater nonlinearity (higher PSC) and determinism (lower LZ) in gray matter compared to white matter and CSF. In addition, the removal of respiratory and cardiac pulsations decreases the nonlinearity and determinism but does not alter the relative difference between gray matter and white matter. Therefore, our results demonstrate that determinism and nonlinearity in the fMRI data are tissue‐specific, suggesting that they reflect native physiologic and metabolic fluctuations and are not a result of physiologic artifacts due to respiration and cardiac pulsation. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Frequency‐dependent conduction block in carpal tunnel syndrome
Authors: Watson Bradley V. , Brown William F. , Doherty Timothy J.
Published: February 2006

Frequency‐dependent conduction block (FDB) across segments of demyelination in response to high‐frequency nerve stimulation has been well demonstrated in animals and has been explored in humans. However, attempts to demonstrate this phenomenon in sensory fibers involved in entrapment neuropathies have been unsuccessful. Therefore, we investigated the effects of high‐frequency nerve stimulation in the median motor nerve in patients with carpal tunnel syndrome (CTS) with moderate to severely increased distal motor terminal latencies (MTL). As a group, the mean decrease in negative peak amplitude (npAmp) during 20 stimuli at 30‐HZ frequency was significantly greater in CTS subjects (−11.3%) than in controls (+7.9%). The degree of FDB was greater when MTL was more prolonged (i.e., −4.9% at 5.0 ms and −25.3% at 9.4 ms) and FDB was more pronounced at higher stimulation frequencies (20 and 30 HZ). Our results suggest that the safety margin for impulse transmission is impaired in the motor axons of patients with a focal demyelinating lesion. These findings may correlate with the observation of weakness in the absence of conduction block in patients with entrapment neuropathies. Muscle Nerve, 2006
Efficacy of botulinum‐A toxin bladder injections for the treatment of neurogenic detrusor overactivity in multiple sclerosis patients: An objective and subjective analysis
Authors: Schulte‐Baukloh H. , Schobert J. , Stolze T. , Stürzebecher B. , Weiß C. , Knispel H.H.
Published: February 2006

Aims

We studied the use of botulinum‐a toxin (BTX‐A) injections into the bladder as an alternative approach in patients with neurogenic detrusor overactivity due to multiple sclerosis (MS) with drug‐refractory overactive bladder (OAB) symptoms.

Methods

Sixteen MS patients—11 women, 5 men; mean age 48.6 years—with refractory OAB symptoms were included in a one‐center prospective study. For outcome analysis, we used a bladder diary, a complete urodynamic study, and validated questionnaires for subjective assessment. We injected 300 U of BTX‐A (Botox®) into the bladder and into the external sphincter muscle to reduce the probability of posttreatment urine retention.

Results

There was an increase in residual volume from 81.3 ± 23.8 to 126.3 ± 32.9 ml after 4 weeks. In one woman, transient self‐catheterization was unavoidable. Four weeks and 3 and 6 months after BTX‐A injection, the significant results were as follows: daytime frequency was reduced by 29%, 44%, and 30%, respectively. Nocturia diminished by 33%, 72%, and 40%. Use of pads was be reduced by 38% after 4 weeks and by 64% after 3 months. Urodynamically, reflex volume and maximal cystometric bladder capacity increased by 73%, 77%, and 58% (at 6 months, the increase was not significant) and by 36%, 27%, and 36% (not significant). Maximal detrusor pressure decreased by 35%, 22%, and 57%. Subjective outcome indicated significant improvement of symptoms at 4 weeks and 3 months, but not at 6 months. Patient satisfaction with the therapy was very high.

Conclusions

BTX‐A detrusor injections are very effective in the treatment of drug‐resistant OAB symptoms in MS patients as reflected in urodynamic measurements and in patient satisfaction. Build up of residual urine remains a problem of which patients must be informed. Neurourol. Urodynam. © 2006 Wiley‐Liss, Inc.
Proton MRS of early post‐natal mouse brain modifications in vivo
Authors: Larvaron Pierre , Bielicki Guy , Boespflug‐Tanguy Odile , Renou Jean‐Pierre
Published: February 2006

NMR provides a non‐invasive tool for the phenotypic characterisation of mouse models. The aim of the present study was to apply reliable in vivo MRS techniques for non‐invasive investigations of brain development in normal and transgenic mice, by monitoring metabolite concentrations in different brain regions. The conditions of anaesthesia, immobilisation and respiratory monitoring were optimized to carry out in vivo MRS studies in young mice. All the experiments were performed in normal mice, at 9.4 T, applying a point‐resolved spectroscopy (PRESS) sequence (TR = 2000 ms; TE = 130 ms). We obtained reproducible in vivo 1H NMR spectra of wild‐type mouse brains as early as post‐natal day 5, which allowed us to follow brain maturation variations from post‐natal days 5 to 21. The survival rate of animals was between 66 and 90% at post‐natal days 5 and 21, respectively. Developmental changes of metabolite concentrations were measured in three brain regions: the thalamus, a region rich in cell bodies, the olfactory bulb, rich in fibre tracts actively myelinated during brain maturation, and the cerebellum. The voxel size varied from 2 to 8 µL according to the size of the brain structure analysed. The absolute concentrations of the total creatine, taurine, total choline, N‐acetylaspartate and of the glutamate/glutamine pool were determined from 1H NMR spectra obtained in the different brain regions at post‐natal day 5, 10, 15 and 21. Variations observed during brain development were in accordance with those previously reported in mice using ex vivo MRS studies, and also in rats and humans in vivo. Possibilities of longitudinal MRS analysis in maturing mice brains provide new perspectives to characterise better the tremendous number of transgenic mutant mice generated with the aim of decrypting the complexity of brain development and neurodegenerative diseases but also to follow the impact of environmental and therapeutic factors. Copyright © 2006 John Wiley & Sons, Ltd.
On algebraic multigrid methods derived from partition of unity nodal prolongators
Authors: Boonen Tim , Deliége Geoffrey , Vandewalle Stefan
Published: February 2006

This paper is concerned with algebraic multigrid for finite element discretizations of the divgrad, curlcurl and graddiv equations on tetrahedral meshes with piecewise linear shape functions. First, an edge, face and volume prolongator are derived from an arbitrary partition of unity nodal prolongator for a tetrahedral fine mesh, using the formulas for edge, face and volume elements. This procedure can be repeated recursively. The implied coarse topology and the normalization of the prolongators are analysed. It is proved that the range spaces of the nodal prolongator and of the derived edge, face and volume prolongators form a discrete de Rham complex if these prolongators have full rank. It is shown that on simplicial meshes, the constructed edge prolongator is a generalization of the Reitzinger–Schöberl prolongator. The derived edge and face prolongators are applied in an algebraic multigrid method for the curlcurl and graddiv equations, and numerical results are presented. Copyright © 2006 John Wiley & Sons, Ltd.
A cache‐oblivious self‐adaptive full multigrid method
Authors: Mehl M. , Weinzierl T. , Zenger Chr.
Published: February 2006

This paper presents a new efficient way to implement multigrid algorithms on adaptively refined grids. To cope with todays demands in high‐performance computing, we cannot do without such highly sophisticated numerical methods. But if we do not implement them very carefully, we lose a lot of efficiency in terms of memory usage: using trees for the storage of hierarchical multilevel data causes a large amount of non‐local (in terms of the physical memory space) data accesses, and often requires the storage of pointers to neighbours to allow the evaluation of discrete operators (difference stencils, restrictions, interpolations, etc.). The importance of this problem becomes clear if we remember that storage and not the CPUs is the bottleneck on modern computers.

We established a cache‐oblivious and storage‐minimizing algorithm based on the concept of space‐tree grids combined with a cell‐oriented operator evaluation, a linear ordering of grid cells along a space‐filling curve, and a sophisticated construction of linearly processed data structures for vertex data. In this context, we could show that the implementation of a dynamically adaptiveF‐cycle is, first, very natural and, second, does not cause any overhead in terms of storage usage and access as adaptivity and multilevel data do not disturb the linear processing order of our data structures. Copyright © 2006 John Wiley & Sons, Ltd.
The effects of polyelectrolytes on the inhibition and aggregation of calcium oxalate crystallization
Authors: Akyol Emel , Bozkurt Ayhan , Öner Mualla
Published: February 2006

The influence of polyelectrolytes with different architecture on spontaneous batch crystallization of calcium oxalate was investigated. A series of acidic acrylate block copolymers were been made, by radical polymerization, with defined molecular weight and structure. Radical polymerization of acrylic acid (AA) was carried out in the presence of α‐thiopolyethylene glycol monomethylether as a chain transfer agent to produce poly(ethylene glycolblockacrylic acid) copolymers. Poly(ethylene glycol) (PEG) block length in the copolymers was controlled by using three different molecular weight chain transfer agents (Mn = 350, 750 and 2000 g/mol). The presence of copolymers inhibited the crystal growth of calcium oxalate possibly through adsorption onto the active growth sites for crystal growth due to the charge and hydrophilic effects. Copyright © 2006 John Wiley & Sons, Ltd.
A second leiomyosarcoma in the urinary bladder of a child with a history of retinoblastoma 12 years following partial cystectomy
Authors: Brucker Benjamin , Ernst Linda , Meadows Anna , Zderic Stephen
Published: February 2006

This case describes a twin with bilateral retinoblastoma who developed leiomyosarcoma of the bladder at age 17 and again at 39. At 17‐years of age she was diagnosed with a leiomyosarcoma of the bladder after presenting with recurrent urinary tract infections, hematuria, and dysuria. She was treated with partial cystectomy. After a 12‐year disease‐free interval, she was diagnosed with a second leiomyosarcoma of the bladder. This case supports the relationship between the genetic form of retinoblastoma and leiomyosarcoma and illustrates the necessity for extensive follow‐up and well‐defined treatment of secondary neoplasms. © 2006 Wiley‐Liss, Inc.
Proteomic analysis in human breast cancer: Identification of a characteristic protein expression profile of malignant breast epithelium
Authors: Hudelist Gernot , Singer Christian F. , Pischinger Kerstin I. D. , Kaserer Klaus , Manavi Mahmood , Kubista Ernst , Czerwenka Klaus F.
Published: February 2006

Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Surprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow proteins of interest to be identified by their expression and/or modification pattern in 2‐DE rather than using the traditional approach of translating gene expression data. To identify a proteomic pattern that is characteristic for malignant breast epithelium, we performed differential 2‐DE analysis in sets of microdissected malignant breast epithelia and corresponding adjacent normal breast epithelia from five patients with invasive breast carcinoma. Thirty‐two protein spots were found to be selectively regulated in malignant epithelium, and were subjected to MALDI‐TOF and/or immunoblotting for protein identification. Thirteen of the identified proteins had previously not been associated with breast cancer. The validity of these findings was confirmed by literature review and immunohistochemistry for identified proteins in an independent cohort of 50 breast cancer specimens. We here describe, for the first time, a proteomic analysis of matched normal and malignant epithelia from invasive breast carcinomas. This strategy leads to a better understanding of oncogenesis at an operational level and helps to characterize the malignant phenotype of individual tumors, and thereby to identify novel targets for antineoplastic therapy.
Identification of novel phosphoproteins in signaling pathways triggered by latent membrane protein 1 using functional proteomics technology
Authors: Yan Guangrong , Li Lili , Tao Yongguang , Liu Sufang , Liu Yiping , Luo Wei , Wu Yong , Tang Min , Dong Zigang , Cao Ya
Published: February 2006

Previous studies have shown that the Epstein–Barr virus‐encoded latent membrane protein1 (LMP1) could activate nuclear factor kappa B, activator protein‐1, and Janus kinases/signal transducer and activation of transcription factors pathways. However, many signaling molecules and downstream target proteins triggered by LMP1 have not been identified. To determine the functional components in signaling pathways triggered by LMP1, we combined the novel strategy of phosphoprotein enrichment with proteomics technology to elucidate the signaling cascade activated by LMP1. We found that LMP1 could increase the quantity of total phosphoproteins by 18.03%, and 43 proteins showed significant changes in the degree of phosphorylation when LMP1 was expressed. Twenty‐five signaling molecules or downstream targets of signaling pathways triggered by LMP1 were identified, several of which had previously been implicated in LMP1 signal pathways. The other proteins, including annexin A2, heat shock protein 27, stathmin, annexin I, basic transcription factor 3, and porin, were novel signaling molecules or targets with no previously known function in LMP1 signal transduction. The method used here has proven to be suitable for the identification of molecules involved in various signaling pathways.
Proteomic characterization of the effects of clofibrate on protein expression in rat liver
Authors: Léonard Jean‐François , Courcol Martine , Mariet Claire , Charbonnier Aurore , Boitier Eric , Duchesne Marc , Parker Fabienne , Genet Bruno , Supatto Françoise , Roberts Ruth , Gautier Jean‐Charles
Published: February 2006

Clofibrate is a peroxisome proliferator known to induce liver tumours in rats. A proteomics study was conducted to provide new insights into the molecular mechanisms of clofibrate‐induced non‐genotoxic hepatocarcinogenesis. Rats were treated with 250 mg/kg day clofibrate orally and sacrificed after 7 days. Proteins extracted from the liver were analysed by 2‐DE using DIGE technology. The protein identification performed by MS showed that clofibrate induced up‐regulation of 77 proteins and down‐regulation of 27 proteins. The highest expression ratios corresponded to proteins involved in a series of biochemical pathways such as lipid metabolism, fatty acid metabolism, amino acid metabolism, protein metabolism, citric acid cycle, xenobiotic detoxification and oxidative stress. Proteins implicated in cell proliferation and apoptosis, such as prohibitin, 10‐formyl tetrahydrofolate dehydrogenase, senescence marker protein‐30, pyridoxine 5'‐phosphate oxidase and vimentin, were also identified as being regulated. These results provide leads for further investigations into the molecular mechanisms of liver tumours induced by clofibrate. In addition, MS results showed that a series of regulated proteins were detected as several spots corresponding to different pI and/or Mr. Differential effects on those variants could result from specific PTM and could be a specific molecular signature of the clofibrate‐induced protein expression modulation in rat liver.
Surface‐enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node‐negative breast cancer tumors
Authors: Ricolleau Gabriel , Charbonnel Catherine , Lodé Laurence , Loussouarn Delphine , Joalland Marie‐Pierre , Bogumil Ralf , Jourdain Sabine , Minvielle Stéphane , Campone Mario , Déporte‐Fety Régine , Campion Loïc , Jézéquel Pascal
Published: February 2006

Novel prognostic biomarkers are imperatively needed to help direct treatment decisions by typing subgroups of node‐negative breast cancer patients. The current study has used a proteomic approach of SELDI‐TOF‐MS screening to identify differentially cytosolic expressed proteins with a prognostic impact in 30 node‐negative breast cancer patients with no relapse versus 30 patients with metastatic relapse. The data analysis took into account 73 peaks, among which 2 proved, by means of univariate Cox regression, to have a good cumulative prognostic‐informative power. Repeated random sampling (n = 500) was performed to ensure the reliability of the peaks. Optimized thresholds were then computed to use both peaks as risk factors and, adding them to the St. Gallen ones, improve the prognostic classification of node‐negative breast cancer patients. Identification of ubiquitin and ferritin light chain (FLC), corresponding to the two peaks of interest, was obtained using ProteinChip LDI‐Qq‐TOF‐MS. Differential expression of the two proteins was further confirmed by Western blotting analyses and immunohistochemistry. SELDI‐TOF‐MS protein profiling clearly showed that a high level of cytosolic ubiquitin and/or a low level of FLC were associated with a good prognosis in breast cancer.
Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source
Authors: Athenstaedt Karin , Jolivet Pascale , Boulard Céline , Zivy Michel , Negroni Luc , Nicaud Jean‐Marc , Chardot Thierry
Published: February 2006

Lipid particles (LP) of all types of cells are a depot of neutral lipids. The present investigation deals with the isolation of LP from the yeast Yarrowia lipolytica and the characterization of their lipid and protein composition. Properties of LP varied depending on the carbon source. LP from glucose‐grown cells revealed a mean diameter of 650 nm with a hydrophobic core mainly formed of triacylglycerols (TAG) and a minor amount of steryl esters (SE). Oleic acid was the major fatty acid species esterified in LP. When cells were grown on oleic acid, LP size increased 3.8‐fold, the particles exhibited a significantly lower ratio of TAG to SE, and the relative amount of oleic acid in LP lipids increased compared to cells grown on glucose. Analysis of LP proteins revealed an increasing number of polypeptides when cells were shifted from glucose‐ to oleic acid‐containing medium. Twenty‐one major LP proteins were identified under both growth conditions, and additional nine polypeptides were specific for growth on oleic acid. Identification of these proteins by MS and comparison of the deduced ORFs to those from Saccharomyces cerevisiae revealed that most proteins of Y. lipolytica LP are involved in lipid metabolism. LP proteins specific for growth on oleic acid are also enzymes involved in lipid metabolism, but some of them are also components of the intracellular traffic machinery. Thus, proteom analysis of LP proteins suggests involvement of this compartment in different cell biological processes.
Disease Biomarker Discovery in Korea
Authors: Paik Young‐Ki
Published: February 2006

No abstracts.
Phosphopeptide detection using automated online IMAC‐capillary LC‐ESI‐MS/MS
Authors: Wang Jinglan , Zhang Yangjun , Jiang Hong , Cai Yun , Qian Xiaohong
Published: February 2006

No abstracts.
Synthesis and chiroptical properties of L‐valine‐containing poly(phenylacetylene)s with (a)chiral pendant terminal groups
Authors: Lai Lo Ming , Lam Jacky W. Y. , Tang Ben Zhong
Published: February 2006

Poly(phenylacetylene)s containing L‐valine residues (P1) with (a)chiral pendant terminal groups R(*) [−(HCC{C6H4CONHCH[CH(CH3)2]COOR(*)})n−]; R(*) = 1‐octyl (P1o), (1S,2R,5S)‐(+)‐menthyl [P1(+)], (1R,2S,5R)‐(−)‐menthyl [P1(−)] are designed and synthesized. The polymers are prepared by organorhodium catalysts in high yields (yield up to 88%) with high molecular weights (Mw up to ˜6.4 × 105). Their structures and properties are characterized by NMR, IR, TGA, UV, and circular dichroism analyses. All the polymers are thermally fairly stable (Td ≥ 320 °C). The chiral moieties induce the poly(phenylacetylene) chains to helically rotate in a preferred direction. The chirality of the pendant terminal groups affects little the helicity of the polymers but their bulkiness stabilizes the helical conformation against solvent perturbation. The backbone conjugation and chain helicity of the polymers can be modulated continuously and reversibly by acid. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2117–2129, 2006
Rapid Holocene chemical weathering on a calcitic lake shoreline in an alpine periglacial environment: Attgløyma, Sognefjell, southern Norway
Authors: Owen Geraint , Matthews John A. , Shakesby Richard A.
Published: February 2006

A small lake (Attgløyma) at an altitude of about 1220 m in the low‐alpine zone, southern Norway, has a shore platform in calcitic and quartzitic muscovite‐chlorite schists. The platform has recently been exposed by a fall in lake level due to upstream dam construction and exhibits micro‐landforms ranging from pits and grooves to upstanding crenulate ridges produced by differential chemical weathering under relatively constant conditions over the last ca. 10 000 years. The maximum surface lowering rate of the calcitic layers estimated from differential weathering is 35 mm ka−1, which is about an order of magnitude greater than most previous estimates from alpine and polar periglacial environments. Average bedrock surface lowering across the whole platform reached a maximum of 15.5 ± 2.2 mm ka−1 in a vertical zone corresponding with the former lake level, declining to negligible values around 0.7 m below lake level. Differential weathering and bedrock surface lowering were also negligible immediately above lake level. Correspondence of maximum surface lowering rates with the former lake level and a shoreline notch at the back of a platform suggest that the effects of solutional weathering of the calcite have been enhanced by water movement generated by small lake‐surface waves. Copyright © 2006 John Wiley & Sons, Ltd.
Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes
Authors: Bordner Andrew J. , Abagyan Ruben
Published: February 2006

Since determining the crystallographic structure of all peptide‐MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T‐cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased‐Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all‐atom MHC model. Our method was tested by a comparison of the results of cross‐docking 14 peptides into HLA‐A*0201 and 9 peptides into H‐2Kb as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 Å backbone RMSD) for cross‐docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 Å illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA‐A*0201 binders or nonbinders. In contrast with sequence‐based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H‐2Kb), not used for training, with comparable prediction accuracy. Proteins 2006. © 2006 Wiley‐Liss, Inc.
What determines the spectrum of protein native state structures?
Authors: Lezon Timothy R. , Banavar Jayanth R. , Lesk Arthur M. , Maritan Amos
Published: February 2006

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focusses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. Proteins 2006. © 2006 Wiley‐Liss, Inc.
RIP death domain structural interactions implicated in TNF‐mediated proliferation and survival
Authors: Thakar Juilee , Schleinkofer Karin , Borner Christoph , Dandekar Thomas
Published: February 2006

Death domain (DD)–containing proteins are involved in both apoptosis and survival/proliferation signaling induced by activated death receptors. Here, a phylogenetic and structural analysis was performed to highlight differences in DD domains and their key regulatory interaction sites. The phylogenetic analysis shows that receptor DDs are more conserved than DDs in adaptors. Adaptor DDs can be subdivided into those that activate or inhibit apoptosis. Modeling of six homotypic DD interactions involved in the TNF signaling pathway implicates that the DD of RIP (Receptor interacting protein kinase 1) is capable of interacting with the DD of TRADD (TNFR1‐associated death domain protein) in two different, exclusive ways: one that subsequently recruits CRADD (apoptosis/inflammation) and another that recruits NFκB (survival/proliferation). Proteins 2006. © 2006 Wiley‐Liss, Inc.
Involvement of disulfide bonds and histidine 172 in a unique β‐sheet to α‐helix transition of α1‐acid glycoprotein at the biomembrane interface
Authors: Nishi Koji , Komine Yoshio , Fukunaga Naoko , Maruyama Toru , Suenaga Ayaka , Otagiri Masaki
Published: February 2006

Human α1‐acid glycoprotein (AGP), which is comprised of 183 amino acid residues and 5 carbohydrate chains, is a major plasma protein that binds to basic and neutral drugs as well as to steroid hormones. It has a β‐sheet–rich structure in aqueous solution. Our previous findings suggest that AGP forms an α‐helix structure through an interaction with biomembranes. We report herein on a study of the mechanism of α‐helix formation in AGP using various modified AGPs. The disulfide reduced AGP (R‐AGP) was extensively unfolded, whereas asialylated AGP (A‐AGP) maintained the native structure. Intriguingly, reduced and asialylated AGP (RA‐AGP) increased the α‐helix content as observed in the presence of biomembrane models, and showed a significant decrease in ligand binding capacity. This suggests that AGP has an innate tendency to form an α‐helix structure, and disulfide bonds are a key factor in the conformational transition between the β‐sheet and α‐helix structures. However, RA‐AGP with all histidine residues chemically modified (HRA‐AGP) was found to lose the intrinsic ability to form an α‐helix structure. Furthermore, disulfide reduction of the H172A mutant expressed in Pichia pastoris also caused a similar loss of folding ability. The present results indicate that disulfide bonds and the C‐terminal region, including H172 of AGP, play important roles in α‐helix formation in the interaction of the protein with biomembranes. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Identification of a high‐affinity binding site for dinotefuran in the nerve cord of the American cockroach
Authors: Miyagi Satoshi , Komaki Iori , Ozoe Yoshihisa
Published: February 2006

The binding of the neonicotinoid insecticide dinotefuran to insect nicotinic acetylcholine receptors (nAChRs) was examined by a centrifugation method using the nerve cord membranes of American cockroaches and [3H]dinotefuran (78 Ci mmol−1). The Kd and Bmax values of [3H]dinotefuran binding were estimated to be 13.7 nM and 14.8 fmol 40 µg−1 protein respectively by Scatchard analysis. Epibatidine, an nAChR agonist, showed a rather lower affinity to the dinotefuran binding site (IC50 = 991 nM) than dinotefuran (IC50 = 5.02 nM). Imidacloprid and nereistoxin displayed lower potencies than dinotefuran but higher potencies than epibatidine. The potencies of five dinotefuran analogues in inhibiting the specific binding of [3H]dinotefuran to nerve cord membranes were determined. A good correlation (r2 = 0.970) was observed between the −log IC50 values of the tested compounds and their piperonyl butoxide‐synergised insecticidal activities (−log LD50 values) against German cockroaches. The results indicate that a high‐affinity binding site for dinotefuran is present in the nerve cord of the American cockroach and that the binding of ligands to the site leads to the manifestation of insecticidal activity. Copyright © 2006 Society of Chemical Industry
Comparative toxicity of Rosmarinus officinalis L. essential oil and blends of its major constituents against Tetranychus urticae Koch (Acari: Tetranychidae) on two different host plants
Authors: Miresmailli Saber , Bradbury Rod , Isman Murray B
Published: February 2006

Bioassays of Rosmarinus officinalis L. essential oil and blends of its major constituents were conducted using host‐specific strains of the two‐spotted spider mite, Tetranychus urticae Koch, on bean and tomato plants. Two constituents tested individually against a bean host strain and five constituents tested individually against a tomato host strain accounted for most of the toxicity of the natural oil. Other constituents were relatively inactive when tested individually. Toxicity of blends of selected constituents indicated a synergistic effect among the active and inactive constituents, with the presence of all constituents necessary to equal the toxicity of the natural oil. Copyright © 2006 Society of Chemical Industry
Application of linear fracture mechanics to notched timber elements
Authors: Leicester R H
Published: February 2006

The application of linear elastic fracture mechanics is ideally suited to estimating the strength of notched timber elements because wood is quite brittle with respect to tension across the grain. Elements with notches more than a few millimetres deep behave in a brittle manner. Some of the early research in developing this practical application of linear elastic fracture mechanics is presented.

In mathematical terms the stress field in the vicinity of a notch contains at least one and sometimes two stress singularities. The magnitudes of these singularities are defined by stress intensity factors. Crack initiation, associated with a predictable size effect, occurs when these factors reach critical values.

This paper gives equations for the stress fields around an orthotropic notch root. It also provides a simple method for computing stress intensity factors and size effects in notched structural elements. Some examples of stress intensity factors for timber elements containing zero and non‐zero angle notches are listed. Critical stress intensity factors for timber, related to density, are given for a series of notch types. Measured effects on strength arising from interactions between loading configurations are also presented. Copyright © 2006 John Wiley & Sons, Ltd.
Silicon‐based light emitters
Authors: Kittler M. , Reiche M. , Arguirov T. , Seifert W. , Yu X.
Published: February 2006

A new concept for a Si light emitting diode (LED) capable of emitting efficiently at 1.55 µm or at 1.3 µm, respectively, is proposed. It utilizes radiation from a well‐defined dislocation network created in a reproducible manner by direct Si wafer bonding. The wavelength of the light emitted from the network can be tailored by adjusting the misorientation between the Si wafers. That way dominance of radiation at 1.55 µm (D1 line) or at 1.3 µm (D3 line) was achieved. There are hints that decoration of the dislocations by oxygen enhances the intensity of the D1 radiation. A critical analysis of the light emitter proposed by W. L. Ng et al. [Nature 410, 192 (2001)] using band‐to‐band emission is given. Its application at the above wavelengths would require a few microns thick SiGe layer on top of the Si substrate. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Decrease of dielectric loss in CaCu3Ti4O12 ceramics by La doping
Authors: Feng Lixin , Tang Xiaoming , Yan Yueyue , Chen Xuezhi , Jiao Zhengkuan , Cao Guanghan
Published: February 2006

We have developed a novel route to reduce the dielectric loss of CaCu3Ti4O12 (CCTO) material based on the internal‐barrier‐layer‐capacitance (IBLC) model. By the partial La‐for‐Ca substitution the dielectric loss was suppressed re‐markably while the giant dielectric constant still remains. The sample of Ca0.8La0.2Cu3Ti4O12 exhibits a high dielectric con‐ stant over 3000 and a low dissipation factor below 0.015 at 10 kHz from 180 K to 300 K. The impedance spectroscopy analysis confirms that the decrease of dielectric loss is mainly due to the increase of conductivity in the CCTO grain/subgrain. Our result is expected to be able to promote practical applications. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum transport through finite length double‐walled carbon nanotubes
Authors: Yang Linfeng , Chen Jiangwei , Zhang Jizhou , Zhang Jingchang
Published: February 2006

Using tight binding‐based Green's function approach, we studied the quantum transport property of double‐walled carbon nanotubes (DWNTs). Our calculations show that the transport property is mainly determined by the outer wall; the effect of inter‐wall interaction on quantum conductance is quite different for commensurate and incommensurate DWNTs in ideal contacts case: the conductance oscillations vs. Fermi energy only exist in commensurate DWNTs, the quantum conductance step still exists in incommensurate DWNTs except for few deep dips, which result from the antiresonance with edge states in inner tube. In the nonideal electrical contacts cases, however, the conductance oscillations can be induced in both the commensurate and incommensurate DWNTs. The slow background oscillation of the fast conductance oscillations can also be seen if the outer wall is not zigzag type. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic structure of Sb monolayers on the Mo(110) surface
Authors: Proskurin D. , Nikolaychik A. , Koval I. F. , Yakovkin I. N.
Published: February 2006

We compare theory and experimental (LEED and EELS) studies of the atomic and electronic structure of adsorbed Sb layers on Mo(110). At half a monolayer coverage, Sb atoms occupy the “long‐bridge” (hollow) sites forming the (1 × 2) film structure. At this coverage, a dramatic decrease of surface density of states in vicinity of Fermi level results in a quasi dielectric state of the surface. With increasing coverage, direct lateral interaction between Sb atoms becomes increasingly important and leads to push‐out of some Sb atoms in the (2 × 3/2) surface unit cell from the adsorption sites that are favorable at lower coverages. Substantial overlap of orbitals of neighboring adatoms results in metallic state of adsorbed Sb film, as suggested from significant increase of DOS at Fermi level. In EEL spectra, the nonmetal to metal transition reveals itself also by appearance of the –7.8 eV peak, which may be explained by the interband transition from Sb s band to unoccupied p states above EF. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of surface piezoelectricity on the electromechanical behaviour of a piezoelectric ring
Authors: Huang Gan‐Yun , Yu Shou‐Wen
Published: February 2006

A relation on electric field dependent surface stress, or alternatively surface piezoelectricity, is proposed in this paper. Based on such relation, a piezoelectric ring under prescribed potential has been studied and the results show that the surface piezoelectricity may play an important role in the electromechanical behavior of piezoelectric nanostructures. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Double‐pole approximation in time‐dependent density functional theory
Authors: Appel H. , Gross E. K. U. , Burke K.
Published: February 2006

A simple approximate solution to the linear response equations of time‐dependent density functional theory (TDDFT) is given. This extends the single‐pole approximation (SPA) to two strongly coupled poles.The analysis provides both an illustration of how TDDFT works when strong exchange‐correlation effects are present and insight into such corrections.For example, interaction can cause a transition to vanish entirely from the optical spectrum. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Host‐defence skin peptides of the Australian Streambank Froglet Crinia riparia: isolation and sequence determination by positive and negative ion electrospray mass spectrometry
Authors: Maselli Vita M. , Bilusich Daniel , Bowie John H. , Tyler Michael J.
Published: February 2006

A combination of positive and negative ion electrospray mass spectrometry (ES‐MS) together with automated Edman sequencing has been used to determine the amino acid sequences of the host‐defence peptides from the skin glands of the froglet Crinia riparia. The peptides are called riparins. Of the eight peptides isolated, five are neuropeptides containing intramolecular disulfide linkages; e.g. the major peptide riparin 1.4 (FFLPPCAYKGTC‐OH). Positive ion ES‐MS identifies the five residues of riparin 1.4 outside the disulfide moiety, but provides no information on the sequence within the disulfide ring. In contrast, the negative ion dissociations of the [M–H]− ion of riparin 1.4 identify the S‐S link by loss of H2S2 from the [M–H]− ion, and also provide the sequence within the disulfide unit. Other peptides are riparin 2.1 [(IIEKLVNTALGLLSGL‐NH2), a narrow‐spectrum antibiotic], signiferin 3.1 [(GIAEFLNYIKSKA‐NH2), an nNOS inhibitor] and riparin 5.1 [IVSYPDDAGEHAHKMG‐NH2], which shows no neuropeptide, antibiotic or nNOS activity. Copyright © 2006 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry with size‐exclusion chromatographic fractionation for structural characterization of synthetic aliphatic copolyesters
Authors: Adamus Grażyna , Rizzarelli Paola , Montaudo Maurizio S. , Kowalczuk Marek , Montaudo Giorgio
Published: February 2006

We report matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) and off‐line coupling of size‐exclusion chromatography with MALDI‐TOFMS analysis (SEC/MALDI‐TOFMS) methods for the detailed characterization of poly[(R,S)‐3‐hydroxybutyrate‐co‐L‐lactic acid], P[(R,S)‐3HB‐co‐LA], and poly[(R,S)‐3‐hydroxybutyrate‐co‐ε‐caprolactone], P[(R,S)‐3HB‐co‐CL], copolymer samples which are expected to be used in special medical application as scaffolds for cartilage and soft tissue engineering. The novel copolyesters contained randomly distributed (R,S)‐3‐hydroxybutyrate structural units, were synthesized by transesterification of the corresponding homopolymers, i.e. atactic poly[(R,S)‐3‐hydroxybutyrate], a‐PHB, and poly(L‐Lactide) (PLLA) or poly(ε‐caprolactone) (PCL), respectively. The MS methods used for the characterization of the resulting polydisperse copolyester samples were supported by classical methods (NMR, SEC). The structures of individual copolyester macromolecules, including end‐group chemical structures, were established using initially MALDI‐TOFMS and then SEC/MALDI‐TOFMS. The compositions of the copolyesters were determined by two methods, namely based on 1H NMR and MALDI‐TOF spectra. The two sets of values showed good agreement. The sequence distribution was determined using the signal intensities of individual copolyester macromolecules, which appeared in MALDI‐TOF mass spectra. Furthermore, sequence analysis gave information about the degree of transesterification. The copolyesters synthesized, with only one exception, were demonstrated to be almost random, which implies that the ester‐ester exchange was close to completion. Copyright © 2006 John Wiley & Sons, Ltd.