bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective activation around the left occipito‐temporal sulcus for words relative to pictures: Individual variability or false positives?
Authors: Wright Nicholas D. , Mechelli Andrea , Noppeney Uta , Veltman Dick J. , Rombouts Serge A.R.B. , Glensman Janice , Haynes John‐Dylan , Price Cathy J.
Published: August 2007

We used high‐resolution fMRI to investigate claims that learning to read results in greater left occipito‐temporal (OT) activation for written words relative to pictures of objects. In the first experiment, 9/16 subjects performing a one‐back task showed activation in ≥1 left OT voxel for words relative to pictures (P < 0.05 uncorrected). In a second experiment, another 9/15 subjects performing a semantic decision task activated ≥1 left OT voxel for words relative to pictures. However, at this low statistical threshold false positives need to be excluded. The semantic decision paradigm was therefore repeated, within subject, in two different scanners (1.5 and 3 T). Both scanners consistently localised left OT activation for words relative to fixation and pictures relative to words, but there were no consistent effects for words relative to pictures. Finally, in a third experiment, we minimised the voxel size (1.5 × 1.5 × 1.5 mm3) and demonstrated a striking concordance between the voxels activated for words and pictures, irrespective of task (naming vs. one‐back) or script (English vs. Hebrew). In summary, although we detected differential activation for words relative to pictures, these effects: (i) do not withstand statistical rigour; (ii) do not replicate within or between subjects; and (iii) are observed in voxels that also respond to pictures of objects. Our findings have implications for the role of left OT activation during reading. More generally, they show that studies using low statistical thresholds in single subject analyses should correct the statistical threshold for the number of comparisons made or replicate effects within subject. Hum Brain Mapp 2008. © 2007 Wiley‐Liss, Inc.
Noninvasive measurement of the cerebral blood flow response in human lateral geniculate nucleus with arterial spin labeling fMRI
Authors: Lu Kun , Perthen Joanna E. , Duncan Robert O. , Zangwill Linda M. , Liu Thomas T.
Published: August 2007

To date, functional magnetic resonance imaging (fMRI) studies of the lateral geniculate nucleus (LGN) have primarily focused on measures of the blood oxygenation level dependent (BOLD) signal. Arterial spin labeling (ASL) is an MRI method that can provide direct measures of functional cerebral blood flow (CBF) changes. Because CBF is a well‐defined physiological quantity that contributes to BOLD contrast, CBF measures can be used to improve the quantitative interpretation of fMRI studies. However, due in part to the low intrinsic signal‐to‐noise ratio of the ASL method, measures of functional CBF changes in the LGN are challenging and have not previously been reported. In this study, we demonstrate the feasibility of using ASL fMRI to measure the CBF response of the LGN to visual stimulation on a 3 T MRI system. The use of background suppression and physiological noise reduction techniques allowed reliable detection of LGN activation in all five subjects studied. The measured percent CBF response during activation ranged from 40 to 100%, assuming no interaction between the left and right LGN. Hum Brain Mapp 2008. © 2007 Wiley‐Liss, Inc.
Photocycloaddition of Six‐Membered Cyclic Enones to Propen‐2‐yl Isocyanate
Authors: Bahaji Maryam , Margaretha Paul
Published: August 2007

On irradiation in the presence of propen‐2‐yl isocyanate (4), six‐membered cyclic enones 3 are converted into regio‐ and stereoisomeric mixtures of [2+2] cycloadducts 5–10; the preferentially formed HT products, 5–8, can be converted into the corresponding bicyclic amines by acid hydrolysis, whereas, under these conditions, the regioisomeric HH‐isocyanato derivatives undergo a retro‐Mannich reaction.
Flabelliformides A and B, Two Novel Indole Alkaloids from Ervatamia flabelliformis
Authors: Liang Shuang , Chen Hai‐Sheng , Shen Yun‐Heng , Jin Li , Zhang Wei‐Dong
Published: August 2007

Flabelliformides A (1) and B (2), containing a novel C20 indole core, have been isolated from the stems of Ervatamia flabelliformis. The structures of 1 and 2 were elucidated on the basis of spectral analysis and X‐ray crystallography.
N‐Heterocyclic Carbene–Palladium Complexes as Efficient Catalysts for the Oxidative Carbonylation of Amines to Ureas
Authors: Zheng Shuzhan , Peng Xingao , Liu Jianming , Sun Wei , Xia Chungu
Published: August 2007

A highly efficient oxidative carbonylation reaction of amines to ureas was developed making use of carbene–palladium complexes in the absence of any promoter. Both aliphatic amines and aromatic amines were transformed in good to excellent yields to the expected ureas.
Chemical Constituents from Craibiodendron yunnanense
Authors: Yang Sheng‐Xiang , Gao Jin‐Ming , Qin Jian‐Chun , Zhou Lin , Chiu Ming‐Hua , Wang Lei
Published: August 2007

A new triterpene, (3β,12β)‐taraxast‐20(30)‐ene‐3,12‐diol (=(3β,12β,18α,19α)‐urs‐20(30)‐ene‐3,12‐diol; 1), together with the known compounds ursolic acid, α‐amyrin, β‐amyrin, (2α,3β)‐2,3‐dihydroxyursa‐5,12‐dien‐28‐oic acid, (2α,3β)‐2,3,23‐trihydroxyurs‐12‐en‐28‐oic acid, (2S,3S,4R,8Z)‐1‐O‐(β‐D‐glucopyranosyl)‐2‐{[(2R)‐2‐hydroxydocosanoyl]amino}octadec‐8‐ene‐1,3,4‐triol, and (2S,3S,4R,8Z)‐1‐O‐(β‐D‐glucopyranosyl)‐2‐[(palmitoyl)amino]octadec‐8‐ene‐1,3,4‐triol, and quercetin 3‐(β‐D‐glucopyranoside) were isolated from the leaves of Craibiodendron yunnanense. Their structures were established on the basis of spectral evidence. The last four compounds were identified for the first time in this plant.
Synthesis, Configuration, and Antimicrobial Properties of Novel Substituted and Cyclized ‘2′,3″‐Thiazachalcones’
Authors: Usta Asu , Yaşar Ahmet , Yılmaz Nagihan , Güleç Canan , Yaylı Nuran , Karaoğlu Şengül Alpay , Yaylı Nurettin
Published: August 2007

Nine new thiazachalcone‐based drugs, compounds 1–9, were prepared and fully characterized. The configurations of the photochemical‐dimerization products 7–9 were rationalized by semi‐empirical calculations. Both the experimental data and the theoretical calculations showed that the δ‐truxinic acid type dimer is the most stable isomer of all. All compounds were tested for their antibacterial and antifungal activities. The N‐alkylated congeners 4–6 showed strong antimicrobial activities against various bacteria and a yeast‐like fungus. The MIC and MBC values were as low as 0.1 μg/ml. All the compounds were active against the Gram‐positive bacterium Staphylococcus aureus.
Isolation and Structure Elucidation of Nortriterpenoids from Schisandra rubriflora
Authors: Xiao Wei‐Lie , Pu Jian‐Xin , Wang Rui‐Rui , Yang Liu‐Meng , Li Xiao‐Li , Li Sheng‐Hong , Li Rong‐Tao , Huang Sheng‐Xiong , Zheng Yong‐Tang , Sun Han‐Dong
Published: August 2007

Seven new highly oxygenated nortriterpenoids, rubriflorins D–J (1–7), were isolated from the leaves and stems of Schisandra rubriflora, and their structures were elucidated on the basis of extensive analysis of spectroscopic data. These new compounds feature the opening of ring A compared with related known nortriterpenoids isolated from the genus Schisandra and showed weak activity against HIV‐1.
Withanolide Compounds from the Flower of Datura metel L.
Authors: Yang Bingyou , Wang Qiuhong , Xia Yonggang , Feng Weisheng , Kuang Haixue
Published: August 2007

Three new withanolide compounds named baimantuoluoline A (1), B (2), and C (3) and the two known withanolides withafastuosin E (4) and withametelin C (5) were isolated from the fraction exhibiting activity for psoriasis in the flower of Datura metel L. The three new structures were determined as (5α,6α,7α,12β,15β,22R)‐6,7‐epoxy‐5,12,15‐trihydroxy‐1‐oxowitha‐2,24‐dienolide (1), (5α,6β,15β,22R)‐ 5,6,15,21‐tetrahydroxy‐1‐oxowith‐24‐enolide (2), and (5α,6β,12β,22R)‐5,6,12,21‐tetrahydroxy‐27‐methoxy‐1‐oxowitha‐2,24‐dienolide (3) on the basis of extensive spectroscopic data (HR‐ESI‐MS, 1H‐ and 13C‐NMR, 1H,1H‐COSY, HSQC, HMBC, and NOESY) (withanolide=22‐hydroxyergostan‐26‐oic acid δ‐lactone).
Kinetics and Mechanism of the Reaction between an Arenediazonium Ion and Methyl Gallate (=Methyl 3,4,5‐Trihydroxybenzoate) in Aqueous Solution: Evidence for Diazo Ether Formation through an O‐Coupling Reaction
Authors: Losada‐Barreiro Sonia , Sánchez‐Paz Verónica , Bravo‐Díaz Carlos
Published: August 2007

We have investigated the kinetics and mechanism of the reaction between 3‐methylbenzenediazonium ions (3MBD) and methyl gallate (=methyl 3,4,5‐trihydroxybenzoate; MG), in aqueous buffer solution by employing spectrophotometric (UV/VIS) and electrochemical (linear‐sweep voltammetry, LSV) techniques and computational methods. Because the absorption band of MG overlaps that of 3MBD, the reaction was monitored spectrophotometrically by measuring the changes in absorbance with time due to product formation, and biphasic kinetic profiles, indicative of accumulation of an intermediate in the course of the reaction, were obtained. The formation of an intermediate was confirmed by LSV. The observed rate constants kobs for 3MBD disappearance were obtained by fitting the decrease in the peak current of the first reduction peak of 3MBD with time to the integrated first‐order equation. The variation of kobs with [MG] was determined at different pH values and follows a saturation kinetic pattern. Alternatively, at a fixed [MG], kobs values show an inverse dependence on [H+], suggesting that the reactive species is the anion and not the neutral form of MG. To discern which of the three OH groups of MG is the first one undergoing deprotonation, the geometries of the resulting anions were optimized by using B3LYP hybrid density functional theory (DFT) and a 6‐31G(++d,p) basis set. The deprotonation energies suggest that the OH group at the 4‐position is first deprotonated. The kinetic results can be accommodated, therefore, by assuming two competitive mechanisms, the spontaneous DN+AN decomposition involving 3MBD, and a mechanism involving an electrophilic attack at the O‐atom at C(4) in a pre‐equilibrium step, leading to the formation of a transient diazo ether of the type ArNNOR which further decomposes. All attempts to isolate and characterize the diazo ether failed.
Further New Cembranoid Diterpenes from the Hainan Soft Coral Sarcophyton latum
Authors: Yan Xiao‐Hong , Li Zhen‐Yu , Guo Yue‐Wei
Published: August 2007

Four new cembranoid diterpenes, sarcophytonolides I–L (1–4), were isolated from the Hainan soft coral Sarcophyton latum. Their structures were established by detailed analysis of 1D and 2D NMR spectra and by comparison with related model compounds.
Efficient Synthesis of Oxazolidin‐2‐one via (Chitosan‐Schiff Base)cobalt(II)‐Catalyzed Oxidative Carbonylation of 2‐Aminoalkan‐1‐ols
Authors: Liu Jianming , Sun Wei , Zheng Shuzhan , Xia Chungu
Published: August 2007

The (chitosan‐Schiff base)cobalt(II) complex was found to be an efficient catalyst for the oxidative carbonylation (CO/O2) of 2‐aminoalkan‐1‐ols 1 to give oxazolidin‐2‐ones 2, in the presence of NaI. The effects of promoters, temperature, solvents, and other reaction conditions were investigated in this study.
Spatial sampling requirements for monitoring upper‐air climate change with radiosondes
Authors: McCarthy Mark P.
Published: August 2007

The global climate observing system upper air network (GUAN) was established to provide a network of high quality radiosonde stations with sufficient historical data records, and a commitment to future observing, in support of the needs of the climate research community. An assessment of the spatial sampling requirements for such a network in order to monitor large‐scale climate changes has been conducted.

The GUAN provides adequate coverage for monitoring global, tropical and hemispheric mean climate. Priority stations within the GUAN have been identified based upon their unique contribution to the network. Further sampling improvements to the GUAN may be possible by utilizing radiosonde stations located in India, Africa and northern polar regions. To keep sampling‐related trend error below 0.05 K/decade in the troposphere, and 0.1 K/decade in the stratosphere, requires a radiosonde station to be located approximately every 30° longitude and 15° latitude north of 30°N. The inhomogeneous distribution of radiosonde stations in the tropics and southern hemisphere place a stronger requirement of 20° longitude and 10° latitude south of 30°N. The radiosonde network is inadequate for monitoring humidity except in the northern mid‐latitudes. © Crown Copyright 2007. Reproduced with the permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd
1H and 23Na MRI studies of Atlantic salmon (Salmo salar) and Atlantic cod (Gadus morhua) fillet pieces salted in different brine concentrations
Authors: Veliyulin Emil , Aursand Ida G
Published: August 2007

BACKGROUND: Applicability of magnetic resonance imaging (MRI) to quantitative analysis of sodium in salted fish products is usually impaired by the partial 23Na MRI ‘invisibility’ phenomena as well as high investment costs of the MRI equipment.

RESULTS: Salmon and cod fillet pieces, unsalted and brine salted (50, 100, 150, 200 and 250 g kg−1 NaCl) for 48 h, were studied using 1H and 23Na MRI. Based on MRI results, T1 and T2 relaxation times were calculated for 1H and the T2 time for 23Na nuclei. In addition, water diffusion images for all fillet samples and reference brine solutions were obtained. Variation of the nuclear magnetic resonance relaxation times and water diffusion constants with brine concentration is discussed in terms of the muscle structural changes. Sodium MRI visibility factors for the MRI method used were determined for all fish samples.

CONCLUSION: Observed changes in proton and sodium NMR relaxation times with the salt content reflect complex counteraction of several factors related to the muscle structural changes. Sodium MRI visibility factors appear to be dependent on a number of experimental factors in a complex matter, making quantitative sodium analysis by the MRI technique used non‐trivial. Copyright © 2007 Society of Chemical Industry
Processing and Characterization of Waxy Maize Starch Films Plasticized by Sorbitol and Reinforced with Starch Nanocrystals
Authors: Viguié Jérémie , Molina‐Boisseau Sonia , Dufresne Alain
Published: August 2007

Nanocomposites films have been processed from a filler and a matrix having the same nature, i.e. waxy maize starch. The filler consists of nanoplatelet‐like starch particles obtained as an aqueous suspension by acid hydrolysis of starch granules and the matrix was prepared by plasticization and disruption of starch granules with water and sorbitol. Nanocomposite films were obtained by casting and evaporating the mixture of the aqueous suspension of starch nanocrystals with the gelatinized starch. The resulting films were conditioned before testing and the effect of accelerated ageing in moist atmosphere was investigated. The thermal properties of the nanocomposite films were determined from DSC measurements and the mechanical characterization was performed in both the linear and nonlinear range.

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Micellization of Poly(2‐oxazoline)‐Based Quasi‐Diblock Copolymers on Surfaces
Authors: Fustin Charles‐André , Lefèvre Nathalie , Hoogenboom Richard , Schubert Ulrich S. , Gohy Jean‐François
Published: August 2007

The micellization on surfaces of two series of quasi‐diblock copoly(2‐oxazoline)s consisting of 2‐phenyl‐2‐oxazoline (PhOx) segments linked to either 2‐methyl‐2‐oxazoline (MeOx) or 2‐ethyl‐2‐oxazoline (EtOx) segments is investigated in detail. Those micelles are not pre‐existing in the initial ethanol solution but are formed during the spin‐coating process by the evaporation of the solvent inducing the precipitation of the less soluble PhOx segments. The morphology and size of the surface micelles vary according to the fraction of PhOx in the copolymers. Moreover, it is demonstrated that the chemical nature of the more soluble MeOx or EtOx segments also has an influence on the morphology of the resulting surface micelles.

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A Mechanistic and Characteristic Investigation of Electrooxidation of 2‐Amino‐3‐cyano‐4‐methylthiophene
Authors: Pak Faruk , Ekinci Duygu , Tümer Ferhan , Demir Ümit
Published: August 2007

The electrochemical oligomerization of 2‐amino‐3‐cyano‐4‐methylthiophene (ACMT) has been studied by cyclic voltammetry, potential controlled electrolysis and digital simulation. The product analysis after preparative electrolysis was carried out by UV‐vis‐NIR, 1H and 13C NMR and FT‐IR spectroscopic techniques. The kinetic data were estimated using the results of fitting the digitally simulated voltammograms to the experimentally obtained cyclic voltammograms. The oligomerization proceeds according to an ECE mechanism resulting in the formation of an oligomeric mixture containing dimer and tetramer. UV‐vis‐NIR and fluorescence measurements indicated that the isolated dimer and tetramer showed higher conjugation than the monomer unit and the conjugation increased with an increase in the number of monomer units.

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Piezoelectric Ink‐Jet Printing of Horseradish Peroxidase: Effect of Ink Viscosity Modifiers on Activity
Authors: Di Risio Sabina , Yan Ning
Published: August 2007

In this study a bioink containing the horseradish peroxidase (HRP) enzyme was formulated and jetted with a piezoelectric‐based ink‐jet deposition system. A number of polymers with different molecular weights, functional groups and electric charge were tested as viscosity modifiers. The impact of viscosity modifiers on HRP activity was systematically studied. It was found that viscosity modifiers typically used in commercial ink formulations significantly impaired HRP activity possibly due to limitations in diffusion. In contrast, carboxymethyl cellulose increased viscosity to the desired range for piezoelectric jetting without negatively affecting the HRP activity. Good jettability was obtained for the HRP bioink by adding a suitable surfactant, a viscosity modifier and a humectant.

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Energy Transfer Between a Cationic‐Conjugated Poly(fluorene‐co‐phenylene) and Thiazole Orange for DNA Hybridization Detection Involving G‐Rich Sequences
Authors: Liu Bin , Bazan Guillermo C.
Published: August 2007

Efficient energy transfer between a cationic poly(fluorene‐co‐phenylene) and thiazole orange mediated by a G‐rich oligonucleotide provided sensitized TO emission over 25 000‐fold more intense than that from free TO. Higher energy transfer efficiency to ssDNA/TO relative to dsDNA/TO leads to an improved sensitivity and selectivity in G‐rich DNA hybridization detection as compared to the direct use of TO as the signal reporter. The signal amplification provided by conjugated polymers is useful to amplify the response from other TO‐based detection protocols.

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Reliability and validity of ICARS in focal cerebellar lesions
Authors: Schoch Beate , Regel Jens Peter , Frings Markus , Gerwig Marcus , Maschke Matthias , Neuhäuser Markus , Timmann Dagmar
Published: August 2007

To evaluate the therapies for cerebellar diseases appropriate neurological assessment methods to measure severity of ataxia are required. Reliability and validity of the semiquantitative International Cooperative Ataxia Rating Scale (ICARS) has recently been examined in patients with degenerative ataxias. We evaluated reliability (internal consistency), criterion‐related validity and internal construct validity of ICARS for the first time in patients with focal cerebellar lesions (68 patients with surgical lesions and 68 patients with ischemic lesions). For comparison 45 patients with degenerative cerebellar ataxia were included. We found an excellent Cronbach's α as a measurement for internal consistency which was independent from underlying disease. Criterion‐related validity was high. Total ICARS score mirrored clearly the immediate postsurgical worsening and the improvement during the first 3 months after focal surgical and ischemic lesions, whereas in chronic state of focal and degenerative cerebellar disorders ICARS score remained nearly unchanged. Principal component analysis in patients with focal lesions revealed five distinct and clinically meaningful factors which corresponded to the four ICARS subscores and reflected the laterality of kinetic functions. In degenerative disorders, however, the items for the subscore “kinetic function” loaded to more than one factor. Total ICARS score seems to be a useful and valid measurement to describe the time course of ataxia in patients with focal and degenerative disorders affecting primarily the cerebellum. Validity of subscores however is good in focal, but not in degenerative disorders. © 2007 Movement Disorder Society
Different cerebral cortical areas influence the effect of subthalamic nucleus stimulation on parkinsonian motor deficits and freezing of gait
Authors: Lyoo Chul Hyoung , Aalto Sargo , Rinne Juha O , Lee Ki Ook , Oh Seung Hun , Chang Jin Woo , Lee Myung Sik
Published: August 2007

Inconsistent response in freezing of gait (FOG) with levodopa treatment or STN DBS makes the pathogenesis difficult to understand. We studied brain areas associated with the expression of STN DBS effect on parkinsonian motor deficits and FOG. Ten Parkinson's disease patients with typical FOG were included. One month before STN DBS, we performed [18F]‐deoxyglucose PET scans and measured the UPDRS motor and modified FOG (mFOG) scores during levodopa off and on periods. At two months after STN DBS, same rating scores were measured. The percentage improvement of mFOG and UPDRS motor scores by STN DBS during levodopa off period was calculated. We searched for brain areas in which glucose metabolism correlated with the improvement of mFOG and UPDRS motor scores by DBS. During levodopa off period, STN DBS improved the UPDRS motor scores by 32.3% and the mFOG scores by 56.6%. There was no correlation between the improvements of both scores. The improvement of UPDRS motor score by DBS correlated with the metabolic activities of rostral supplementary motor area (Brodmann's area 8; BA8), anterior cingulate cortex (BA32), and prefrontal cortex (BA9). On the other hand, there was a positive correlation between the improvement of mFOG score by DBS and the metabolic activity of the parietal, occipital, and temporal sensory association cortices. In conclusion, dysfunction of different cerebral cortical areas limits the beneficial effects of DBS on parkinsonian motor deficits and FOG. © 2007 Movement Disorder Society
Cause of death in Wilson disease
Authors: Walshe John M.
Published: August 2007

Before 1948, all patients with Wilson disease died shortly after diagnosis. In 1948, BAL (dimercaprol) was introduced as a possible effective treatment, to be followed by penicillamine (1955), zinc salts (1961), trientine (1969), liver transplantation (1982), and tetrathiomolybdate (1984). Despite this wide range of therapeutic options, patients still die. This article examines the cause of death in 67 patients (33 men, 34 women) out of a series of 300 seen between 1948 and 2000. Patients were classified according to their presentation as neurological, 32 patients, hepatic 11, mixed hepatic/neurological 10, hemolytic, 6, and “sibling biopsy ” 8. Diagnostic failure was the principal cause of death but there were multiple other causes of which the principal was poor compliance and the development of malignant disease after 10 years of follow‐up. The development of new symptoms should alert the physician to the possibility of a new pathology. © 2007 Movement Disorder Society
Pure akinesia with gait freezing: A third clinical phenotype of progressive supranuclear palsy
Authors: Williams David R. , Holton Janice L. , Strand Kate , Revesz Tamas , Lees Andrew J.
Published: August 2007

The clinical syndrome of pure akinesia has most often been associated with progressive supranuclear palsy (PSP) and is characterized by difficulty initiating gait and “freezing” during walking, writing and speaking. Similar syndromes have been described under the rubrics of primary progressive freezing gait and primary gait ignition failure. We investigated the specificity of the clinical syndrome of pure akinesia with gait freezing (PAGF) for PSP‐tau pathology. Among 749 patients archived at the QSBB, only 7 fulfilled proposed diagnostic criteria of: gradual onset of freezing of gait or speech; absent limb rigidity and tremor; no sustained response to levodopa; and no dementia or ophthalmoplegia in the first 5 years of disease. In these cases detailed pathological examination was performed. PSP was the pathological diagnosis in six patients, and Parkinson's disease (PD) in the seventh. As defined, this syndrome had a positive predictive value of 86% for PSP‐tau pathology. In the cases with PSP there were no additional features of coexistent vascular or PD and the median PSP‐tau score was 3, reflecting relative mild tau load. The clinical syndrome of PAGF appears to have a high specificity for PSP‐tau pathology. This relatively uncommon presentation of PSP‐tau pathology has less severe tau accumulation than in the more common, “classic” PSP clinical phenotype: Richardson's disease. © 2007 Movement Disorder Society
CD44‐positive colorectal adenoma cells express the potential stem cell markers musashi antigen (msi1) and ephrin B2 receptor (EphB2)
Authors: Schulenburg A , Cech P , Herbacek I , Marian B , Wrba F , Valent P , Ulrich‐Pur H
Published: August 2007

The majority of colorectal adenomas contain a mutation in the APC gene activating the wnt pathway. As wnt signalling preserves stem cell functions, it would be expected that stem cells would be enriched in adenomas. We have shown expression of the wnt target gene CD44, which may characterize the expanded stem cell compartment, in colorectal tumours. To investigate this possibility, we performed an immunohistological survey of CD44 expression in relation to the proliferation marker Ki67 and apoptosis in colorectal tumour tissue, and have isolated a CD44‐positive subpopulation of the human colorectal adenoma cell line LT97 for cell biological analysis. In tissues, CD44 expression was not related to Ki67, but was associated with lower apoptosis in the CD44‐positive areas. CD44‐positive and ‐negative populations isolated from LT97 cultures were identical in their Ki‐ras and p53 status but differed in their growth and survival characteristics. While CD44‐positive cells attached and grew to reconstitute the original culture, the CD44‐negative cells rapidly underwent apoptosis and were unable to resume growth. In comparison to unsorted growing LT97 cells, the CD44‐positive cells had shifted ß‐catenin into the nucleus and expressed ß‐catenin target genes, such as ephrin B receptor (ephB2) and musashi antigen (msi1). By contrast, CD44‐negative cultures contained no cells with nuclear β‐catenin. In summary, the CD44‐positive cells accumulating in colorectal tumours have increased survival capacity both in vivo and in vitro. They also express markers typical of colorectal progenitor cells, msi1 and ephB2, in the premalignant progenitor population. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A serial lectin approach to the mucin‐type O‐glycoproteome of Drosophila melanogaster S2 cells
Authors: Schwientek Tilo , Mandel Ulla , Roth Udo , Müller Stefan , Hanisch Franz‐Georg
Published: August 2007

Identification of mucin‐type O‐glycosylated proteins with known functions in model organisms like Drosophila could provide keys to elucidate functions of the O‐glycan moiety and proteomic analyses of O‐glycoproteins in higher eukaryotes remain a challenge due to structural heterogeneity and a lack of efficient tools for their specific isolation. Here we report a strategy to evaluate the O‐glycosylation potential of the embryonal hemocyte‐like Drosophila Schneider 2 (S2) cell line by expression of recombinant glycosylation probes derived from tandem repeats of the human mucin MUC1 or of the Drosophila salivary gland protein Sgs1. We obtained evidence that mucin‐type O‐glycosylation in S2 cells grown under serum‐free conditions is restricted to the Tn‐antigen (GalNAcα‐Ser/Thr) and the T‐antigen (Galβ1‐3GalNAcα‐Ser/Thr) and this structural homogeneity enables unique glycoproteomic strategies. We present a label‐free strategy for the isolation, profiling and analysis of O‐glycosylated proteins consisting of serial lectin affinity capture, 2‐DE‐based glycoprotein analysis by O‐glycan specific mAbs and protein identification by MALDI‐MS. Protein identity and O‐glycosylation was confirmed by ESI‐MS/MS with detection of diagnostic sugar oxonium‐ion fragments. Using this strategy, we established 2‐D reference maps and identified 21 secreted and intracellular mucin‐type O‐glycoproteins. Our results show that Drosophila S2 cells express O‐glycoproteins involved in a wide range of biological functions including proteins of the extracellular matrix (Laminin γ‐chain, Peroxidasin and Glutactin), pathogen recognition proteins (Gnbp1), stress response proteins (Glycoprotein 93), secreted proteases (Matrix‐metalloprotease 1 and various trypsin‐like serine proteases), protease inhibitors (Serpin 27A) and proteins of unknown function.
Implementation and application of a versatile clustering tool for tandem mass spectrometry data
Authors: Flikka Kristian , Meukens Jeroen , Helsens Kenny , Vandekerckhove Joël , Eidhammer Ingvar , Gevaert Kris , Martens Lennart
Published: August 2007

High‐throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant spectra to turn this redundancy into a useful property of the dataset. To this end, we have created the first general‐purpose, freely available open‐source software application for clustering and merging MS/MS spectra. The application also introduces a novel approach to calculating the similarity of fragmentation mass spectra that takes into account the increased precision of modern mass spectrometers, and we suggest a simple but effective improvement to single‐linkage clustering. The application and the novel algorithms are applied to several real‐life proteomic datasets and the results are discussed. An analysis of the influence of the different algorithms available and their parameters is given, as well as a number of important applications of the overall approach.
Phosphorylation of human eukaryotic elongation factor 1Bγ is regulated by paclitaxel
Authors: Prado Miguel A. , Casado Pedro , Zuazua‐Villar Pedro , del Valle Eva , Artime Noelia , Cabal‐Hierro Lucía , Martínez‐Campa Carlos M. , Lazo Pedro S. , Ramos Sofía
Published: August 2007

Paclitaxel (Ptx) is an antitumoural drug that inhibits microtubule dynamics, causes G2/M arrest and induces cell death. 2‐D PAGE and MALDI‐TOF‐MS analysis of HeLa cells extracts revealed that Ptx up‐regulates a form of the eukaryotic elongation factor 1Bγ (eEF1Bγ) and down‐regulates another one. This event, linked to the lack of Ptx effect over eEF1Bγ mRNA or protein levels suggested a PTM of this elongation factor. Further 2‐D PAGE analysis followed by a phosphospecific staining with PRO‐Q Diamond showed the staining of the Ptx up‐regulated form only. Moreover, this Ptx up‐regulated form of eEF1Bγ disappears upon treatment with protein phosphatase. Thus, we demonstrate that human eEF1Bγ phosphorylation is regulated by Ptx.
Combination of peptide OFFGEL fractionation and label‐free quantitation facilitated proteomics profiling of extraocular muscle
Authors: Fraterman Sven , Zeiger Ulrike , Khurana Tejvir S. , Rubinstein Neal A. , Wilm Matthias
Published: August 2007

Several label‐free quantitation strategies have been introduced that obliterate the need for expensive isotopically labeled molecules. However label‐free approaches have considerably higher demands in respect of repeatability of sample preparation and fractionation than multiplexing isotope labeling‐based strategies. OFFGEL fractionation promises the necessary separation efficiency and repeatability. To test this platform, 12‐fraction peptide OFFGEL electrophoresis and online reversed‐phase LC connected to a quadrupole TOF mass spectrometer were used to determine differences of the physiological, pathological and biochemical distinct extraocular muscle allotype in comparison to hind‐limb muscle. Close to 70% of the peptides separated by OFFGEL electrophoresis were detected only in a single fraction. To determine the separation repeatability of four samples, we compared the ion volumes of multiple peptides deriving from the thick filament‐associated protein titin over several fractions and determined a coefficient of variation below 20%. Of the 474 proteins identified, 61 proteins were differently expressed between the two muscle allotypes and were involved in metabolism, muscle contraction, stress response, or gene expression. Several expression differences were validated using immunohistochemistry and Western blot analysis. We therefore consider peptide OFFGEL fractionation an effective and efficient addition to our label‐free quantitative proteomics workflow.
Exactness of simplified scalar optical approaches in modelling a threshold operation of possible nitride vertical‐cavity surface‐emitting diode lasers
Authors: Czyszanowski Tomasz , Wasiak Michał , Sarzała Robert P. , Nakwaski Włodzimierz
Published: August 2007

Modern small‐size vertical‐cavity surface‐emitting diode lasers (VCSELs) require principally fully vectorial optical modelling because their cavity sizes are of the order of the wavelength of emitted radiation. However, much simpler scalar approaches are often surprisingly exact even beyond the limits of their confirmed validity. Therefore, in the present paper, reasonable limits of an application of simplified scalar optical approaches (instead of more exact but also much more involved and time‐consuming rigorous vectorial ones) are determined to model threshold operation of possible nitride VCSELs equipped with tunnel junctions with the aid of a comparison of results of the scalar effective frequency method with those obtained using the fully vectorial three‐dimensional plane wave admittance method. Both these optical methods have been found to give usually quite close results for the fundamental transverse mode. Larger discrepancies between the results of both approaches have been found for first‐order transverse modes (and even larger are expected for higher‐order ones) and for larger (or very small) active regions. Some structural modifications of nitride VCSELs, which may enable their low‐threshold single‐fundamental‐mode room‐temperature continuous‐wave operation, are proposed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of activation energies from thermally stimulated currents: application to the CdS crystal containing cupric ions
Authors: Salehi S. M. A.
Published: August 2007

Theoretical calculations which take into account thermally stimulated conductivity are presented. The model used has been established for the case of a single type of electron trap, a single type of recombination centre and in the presence of thermally disconnected deep traps. The conductivity relation has been derived and solved numerically in order to determine electron trap depths. It was then tested in the case of CdS single crystals doped with copper ions. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of hydrogenation, low energy ion irradiation and annealing on hydrogen bonding to polycrystalline diamond surface studied by high resolution electron energy loss spectroscopy
Authors: Michaelson Sh. , Ternyak O. , Akhvlediani R. , Lafosse A. , Bertin M. , Azria R. , Hoffman A.
Published: August 2007

The effects of different processes of hydrogenation, thermal treatment and ion irradiation of hydrogenated polycrystalline diamond surface have been investigated by means of high resolution electron energy loss spectroscopy (HR‐EELS). Analysis of the different contributions in the CH stretching, overtones and combination modes, as well as changes in relative intensities of the diamond CC and CHx related vibrations allowed us to identify the CHx adsorbed species on the diamond surface following the different treatments. Ex‐situ hydrogenation of diamond surface by means of exposure to H‐MW plasma results in a fully hydrogenated well‐ordered diamond surface and etching of the amorphous phase located on the grain boundaries present on the sample after CVD‐deposition. Annealing this surface to 600 °C results in some subtle changes in the HR‐EELS, probably associated with decomposition of CHx (x = 2, 3) adsorbed species. Ion irradiation on the surface induces partial desorption of hydrogen from the diamond phase and a large amount of amorphous defects, some of them of sp and the most of them of sp2 character. Annealing to 600–700 °C of the irradiated surface leads to hydrogen desorption. In‐situ hydrogenation of the irradiated and annealed sample does not restore the diamond structure, and results in hydrogenated amorphous surface, unstable with thermal annealing above 600–700 °C. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A theoretical study of Li as n‐type dopants for diamond: the role of aggregation
Authors: Goss J. P. , Eyre R. J. , Briddon P. R.
Published: August 2007

The formation of n‐type diamond has proved highly challenging, with the best species to date being the relatively deep phosphorus donor. Theory suggests that interstitial Li may be a superior donor species. In this paper we report the first principles modelling of Li as a donor, and report on the highly energetically favourable aggregation process that limits the likely success for Li‐based n‐type material. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and optical properties of multivacancy centres in diamond
Authors: Jones Robert , Hounsome Luke S. , Fujita Naomi , Öberg Sven , Briddon Patrick R.
Published: August 2007

Recent experiments have shown that vacancy clusters are common defects in all types of monocrystalline brown diamond. This is believed to be due to an enhanced stability of the bounding 〈111〉 or 〈110〉 surfaces, arising from the formation of π‐bonded chains. These chains lead to broad bands of gap states with acceptor and donor levels around Ev + 2 eV. They also are likely to be responsible for the broad absorption continuum extending from the NIR through the visible and into the UV region which is characteristic of brown diamonds. High temperature treatment removes or transforms the clusters in CVD and type IIa diamonds leaving the diamond colourless. In type Ia brown diamonds, heat treatments up to 2500 °C lead to the breakup of the clusters and the formation of specific vacancy‐nitrogen defects. We show that ab initio modelling of the interaction of nitrogen with the chains open a gap and leads to a threshold absorption energy in the 1–2 eV range. Finally, the calculations shed light on the identity of the vacancy‐nitrogen defects observed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Differential theory of diffraction in cylindrical coordinates
Authors: Popov E. , Bonod N.
Published: August 2007

The principles of the differential theory of light diffraction are presented in cylindrical coordinates. Special attention is played to the factorisation rules necessary to obtain faster convergence with respect to the number of basic functions used in the field representation. A detailed description is given for diffracting objects having rotational symmetry and finite cylindrical length. Some properties of light diffracted by a single circular aperture piereced in a finitely conducting screen are discussed, including the excitation of surface plasmon wave and the enhanced beaming. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Light–matter interaction in photonic crystal slabs
Authors: Andreani Lucio Claudio , Gerace Dario
Published: August 2007

A theoretical treatment of waveguide‐embedded photonic crystals based on a guided‐mode expansion method is reviewed. The following issues are discussed: (i) a formulation of the method for calculating photonic‐mode dispersion and intrinsic losses due to out‐of‐plane diffraction, (ii) modelling of disorder‐induced losses due to fabrication imperfections, and (iii) a quantum‐mechanical treatment of radiation‐matter interaction, with application to exciton‐polaritons in photonic crystal slabs. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Unusual temperature dependence of the positron lifetime in a polymer of intrinsic microporosity
Authors: Lima de Miranda Rodrigo , Kruse Jan , Rätzke Klaus , Faupel Franz , Fritsch Detlev , Abetz Volker , Budd Peter M. , Selbie James D. , McKeown Neil B. , Ghanem Bader S.
Published: August 2007

The performance of polymeric membranes for gas separation is mainly determined by the free volume. Polymers of intrinsic microporosity are interesting due to the high abundance of accessible free volume. We performed measurements of the temperature dependence of the positron lifetime, generally accepted for investigation of free volume, in two polymers of intrinsic microporosity (PIM‐1 and PIM‐7) in the range from 143 to 523 K. The mean value of the free volume calculated from the ortho‐positronium lifetime is in the range of typical values for high free volume polymers. However, the temperature dependence of the local free volume is non‐monotonous in contrast to the macroscopic thermal expansion. The explanation is linked to the spirocenters in the polymer. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction of a two‐level cyclic XY n‐spin model with a two‐mode cavity field in off‐resonant states
Authors: Grinberg Horacio
Published: August 2007

The interaction of the XY n‐spin cyclic model with a two‐mode cavity field in the rotating‐wave approximation is investigated in the framework of a generalized Jaynes–Cummings two‐level system consisting of the vacuum state and a thermally averaged manifold of excited sates. Computation of the energy of this manifold allows this interaction to be examined in off‐resonant states. Time evolution of the population inversion, photon distribution, and temperature distribution for an excited initial state are computed via second‐ and third‐order perturbation expansion of the time evolution operator matrix elements for the excited and ground states, respectively and for an ideal squeezed initial coherent state of the cavity field. It was assumed that the two modes have initially the same photon distribution. The pattern of the spin population inversion appears as a manifestation of multiple and complicated inerferences, which is mathematically reflected in a double discrete summation that appears in the calculation of the dynamics. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
3D‐quantitative structure activity analysis and quantum chemical analysis of pyrido‐di‐indoles
Authors: Pasha Farhan A. , Chung Hwan W. , Kang Soon B. , Cho Seung J.
Published: August 2007

The computational analyses of pyrido‐di‐indoles have been performed with various methods such as quantum mechanical studies (AM1, PM3, and DFT) and 3D‐QSAR analyses (CoMFA and CoMSIA). The electrophilicity index along with some other properties has been related with biological activities. Electrostatic field has been identified as an important descriptor from the 3D‐QSAR analyses. The AM1 geometry and Gasteiger–Marsili charged base CoMFA (r = 0.75) and CoMSIA (r = 0.62) give strong correlation and indicate that a substitution at sites 2 and 3 of Ring A might affect the activity. In addition, a plausible statistical model has been found with DFT‐based local philicity and negative Fukui function with a value of r2 = 0.82 and rcv2 = 0.60. The DFT analysis indicates that electron density of nitrogen atom of Ring B significantly contributes to activity. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Riccati differential equation for quantum mechanical bound states: Comparison of numerical integrators
Authors: Chou Chia‐Chun , Wyatt Robert E.
Published: August 2007

Computational comparison is presented of several integrators for the Riccati differential equation for the one‐dimensional quantum mechanical bound state problem. The computational method for the quantum Hamilton‐Jacobi equation for stationary states is briefly reviewed. An interpolation formula for the quantum momentum function is proposed for the evaluation of the phase integral. The Möbius integrator, the R‐matrix propagation method, the log derivative method, and the symplectic integrator can accurately pass through singularities in the solution. These four integrators are actually Möbius transformations with different coefficients. Analytical analysis and numerical results demonstrate that the classical momentum is a good choice for the initial condition to obtain the bound state solution of the Riccati differential equation as long as the starting point of the propagation is far enough from the origin. The computational comparison is demonstrated for the harmonic oscillator. The numerical results indicate that the symplectic integrators achieve highest accuracy, and the simplicity of these algorithms shows an advantage over the other methods. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Many‐body Brillouin–Wigner second‐order perturbation theory: A robust and efficient approach to the multireference correlation problem
Authors: Papp P. , Mach P. , Hubač I. , Wilson S.
Published: August 2007

The multireference, state‐specific, second‐order, Brillouin–Wigner perturbation theory is presented as a robust approach to the electron correlation problem for systems demanding the use of a multireference function. A posteriori modifications are made which, in the case of a single reference function, recover the well known formula of second‐order many‐body perturbation theory (MBPT2), i.e. Møller–Plesset (MP2) theory, and in the multireference case can be shown to be equivalent to state‐specific multireference Rayleigh–Schrödinger‐like perturbation theory. It is shown that multireference many‐body Brillouin–Wigner perturbation theory when restricted to second‐order is a true many‐body theory, that is, it is a theory, which has the property of extensivity. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Single drop microextraction as a concentrating probe for rapid screening of low molecular weight drugs from human urine in atmospheric‐pressure matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Shrivas Kamlesh , Wu Hui‐Fen
Published: August 2007

The present work reports the development of a new analytical procedure for simple and rapid screening of low molecular weight drugs (<500 Da) from human urine samples by atmospheric‐pressure matrix‐assisted laser desorption/ionization mass spectrometry (AP‐MALDI‐MS) combined with single drop microextraction (SDME). The success of the proposed method is due to the use of methyltrioctylammonium chloride (MTOAC) as additive to avoid the noise arising from the matrix ions (α‐cyano‐4‐hydroxycinnamic acid (CHCA)). SDME also aided in alleviating the interferences arising from other matrix ions present in the urine samples prior to AP‐MALDI‐MS analysis. Factors affecting the extraction efficiency of drugs, such as selection of solvent, stirring speed, extraction time, exposure volume of extraction phase and salt addition, have been optimized. The optimum molar ratio of CHCA/MTOAC that gave the minimum background noise of CHCA ions was 700:1. The limit of detection (LOD) and relative standard deviation (RSD) of the method were in the ranges 0.3–1.6 µM and 7.8–11.4%, respectively. The SDME method was compared with liquid‐liquid extraction (LLE) and hollow fiber liquid‐phase microextraction (HF‐LPME) to evaluate the compatibility of the present method in the extraction of drugs from urine samples. The role of MTOAC as matrix ion signal suppressor and SDME as analyte‐separating device in the rapid screening of low molecular weight drugs from human urine samples using AP‐MALDI/MS has been reported. Copyright © 2007 John Wiley & Sons, Ltd.