bluuebunny/crossref_metadata_2025_split huggingface dataset:
Car–Parrinello Molecular Dynamics Study of DCl Hydrate Crystals
Authors: Sillanpää Atte , Laasonen Kari 
Published: August 2005

AbstractThree DCl hydrates have been studied using Car–Parrinello (CP) molecular dynamics. The structural results at low temperatures (T<350 K) agree with experiment and previously published CP results. The monohydrate has been shown to be built from D3O+ and Cl− ions. The dihydrate is built exclusively from D5O2+ and Cl− ions. The trihydrate consists of D2O, D5O2+, and Cl− ions. Thus, the DCl hydrates are excellent systems for studying ideal D3O+ and D5O2+ ions. The data from these ideal structures can be compared to high‐concentration acid–liquid simulations. [ClD⋅⋅⋅Cl]− ions were detected at amorphous and fluid conditions after melting the di‐ and trihydrate crystals. The experimentally observed spectral continuum can be explained by combining the Eigen and Zundel spectra, and interpolating between the shared deuterium frequencies of the latter and the stretching band of the former.
Improvement of detection specificity of Plasmodium‐infected murine erythrocytes by flow cytometry using autofluorescence and YOYO‐1
Authors: Jiménez‐Díaz María Belén , Rullas Joaquín , Mulet Teresa , Fernández Laura , Bravo Carmen , Gargallo‐Viola Domingo , Angulo‐Barturen Iñigo 
Published: August 2005

AbstractBackgroundMicroscopic analysis of blood smears is currently the most frequently used method to measure parasitemias in experiments of drug efficacy in murine models of malaria. However, it is subjective and labour intensive, which preclude its utilization in large‐scale evaluation programs. Flow cytometry is an alternative method, but due to the limited specificity achieved with the currently available techniques, it has not been widely used in murine models of malaria during preclinical evaluation. We describe a new flow cytometric method based on the differences of autofluorescence and DNA content measured after staining with YOYO‐1 that are observed in infected erythrocytes compared with noninfected erythrocytes.MethodsSamples of blood from Plasmodium yoelii–infected animals were fixed with glutaraldehyde, incubated with RNAase, and stained with YOYO‐1 in 96‐well plate format. After acquisition, erythrocytes gated in logarithmic side/scatter plots were analyzed in bidimensional FL‐2/YOYO‐1 plots in comparison with unidimensional YOYO‐1 analysis.ResultsThe infected erythrocytes showed a characteristic pattern of staining different from that of noninfected erythrocytes. In routine evaluation, the limit of sensitivity was 0.01% and the measurements of parasitemia were linear at parasitemias above 0.1%. Interestingly, using this approach, infected reticulocytes could be differentiated from infected normocytes.ConclusionsThe method described is robust, increases the specificity and sensitivity of detection in routine testing, and is especially well suited for detection of low parasitemias in murine models of malaria. © 2005 Wiley‐Liss, Inc.
Smart 3D‐fish: Automation of distance analysis in nuclei of interphase cells by image processing
Authors: Gué Michael , Messaoudi Cédric , Sun Jian Sheng , Boudier Thomas 
Published: August 2005

AbstractBackgroundDetection of fluorescent probes by fluorescence in situ hybridization in cells with preserved three‐dimensional nuclear structures (3D‐FISH) is useful for studying the organization of chromatin and localization of genes in interphase nuclei. Fast and reliable measurements of the relative positioning of fluorescent spots specific to subchromosomal regions and genes would improve understanding of cell structure and function.Methods3D‐FISH protocol, confocal microscopy, and digital image analysis were used.ResultsNew software (Smart 3D‐FISH) has been developed to automate the process of spot segmentation and distance measurements in images from 3D‐FISH experiments. It can handle any number of fluorescent spots and incorporate images of 4′,6‐diamino‐2‐phenylindole counterstained nuclei to measure the relative positioning of spot loci in the nucleus and inter‐spot distance. Results from a pilot experiment using Smart 3D‐FISH on ENL, MLL, and AF4 genes in two lymphoblastic cell lines were satisfactory and consistent with data published in the literature.ConclusionSmart 3D‐FISH should greatly facilitate image processing and analysis of 3D‐FISH images by providing a useful tool to overcome the laborious task of image segmentation based on user‐defined parameters and decrease subjectivity in data analysis. It is available as a set of plugins for ImageJ software. © 2005 Wiley‐Liss, Inc.
Small‐volume rapid‐mix device for subsecond kinetic analysis in flow cytometry
Authors: Wu Yang , Zwartz Gordon , Lopez Gabriel P. , Sklar Larry A. , Buranda Tione 
Published: August 2005

AbstractBackgroundRapid‐mix flow cytometry has emerged as a powerful tool for mechanistic analysis of ligand binding, cell response, and molecular assembly. Although progress has come from improving sample delivery capabilities, little attention has been paid to the volumetric requirements associated with precious biological reagents.MethodsBy using programmable syringes, valves, and other fluidic components, we created a modular, precisely regulated rapid‐mix device for the delivery of small‐volume samples to the flow cytometer. The device was tested using a bead‐based assay in which the binding kinetics between native biotin and fluorescein biotin‐bearing beads were characterized.ResultsBead suspensions and reagents paired in 35‐ to 45‐μl aliquots were efficiently mixed by the device and delivered to the flow cytometer. Kinetic data associated with the fluorescein biotin beads were analyzed and used to calibrate the performance characteristics of the device in terms of sample delivery and mixing efficiency.ConclusionThe rapid‐mix device is capable of detecting subsecond kinetics of biological reactions using microliter volume of samples. Dimensions of the device have been minimized, and the quantitative aspects of sample delivery and analysis have been optimized. Further, the modular design has been optimized for adaptation to a variety of experimental protocols. © 2005 Wiley‐Liss, Inc.
Synthesis, Electronic Characterisation and Significant Second‐Order Non‐Linear Optical Responses of meso‐Tetraphenylporphyrins and Their ZnII Complexes Carrying a Push or Pull Group in the β Pyrrolic Position
Authors: Annoni Elisabetta , Pizzotti Maddalena , Ugo Renato , Quici Silvio , Morotti Tamara , Bruschi Maurizio , Mussini Patrizia 
Published: August 2005

AbstractThis work describes the synthesis and characterisation by electronic absorption spectroscopy, cyclic voltammetry and by a solvatochromic investigation of meso‐tetraphenylporphyrins and their ZnII complexes substituted at the β pyrrolic position by a pseudo‐linear, π‐delocalised organic linker carrying either an electron‐withdrawing (pull) or electron‐donating (push) group. The second‐order NLO response of these push‐pull porphyrinic chromophores has been investigated by the EFISH technique working with a non‐resonant incident wavelength of 1.907 µ;m. The porphyrin ring substituted at the β pyrrolic position by an electron‐acceptor π‐system behaves as a significant donor group, comparable to a ferrocenyl group or to a phthalocyanine. Unexpectedly, the porphyrin ring substituted at the β pyrrolic position with an electron‐donor π‐system shows a larger and significant second‐order NLO response. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
The Design and Synthesis of New Steroidal Compounds as Potential Mimics of Taxoids
Authors: Roussi Fanny , Ngo Quoc Anh , Thoret Sylviane , Guéritte Françoise , Guénard Daniel 
Published: August 2005

AbstractEight new steroidal compounds bearing the phenylisoserine and benzoate side‐chains of docetaxel were synthesised as potential mimics of antitumour taxoids. They were readily obtained either from cholic acid or from 4‐androstene‐3,17‐dione by a reductive Tsuji–Trost/reduction one‐pot reaction. Two compounds showed an unexpected inhibitory activity of tubulin assembly. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
NMR Study of the (Z)‐Phenylhydrazones of 5‐Alkyl‐ and 5‐Aryl‐3‐benzoyl‐1,2,4‐oxadiazoles: Support for the Interpretation of Kinetic Results on the Rearrangement of 1,2,4‐Oxadiazoles to 1,2,3‐Triazoles
Authors: Mezzina Elisabetta , Spinelli Domenico , Lamartina Liliana , D’Anna Francesca , Frenna Vincenzo , Macaluso Gabriella 
Published: August 2005

AbstractAn analysis of the 1H, 13C, and 15N NMR substituent chemical shifts (SCSs) of the title compounds in CDCl3 solution has been carried out by using the SCSs of other classes of compounds (arenes, methyl esters or amides), Hammett substituent constants or kinetic data. The results obtained provide information concerning the ground‐state electronic distribution of the compounds examined. The results relevant to the carbon and nitrogen atoms of the 1,2,4‐oxadiazole ring can be considered of special interest, as the effects of the substituents on the chemical shifts of N‐4 and C‐5 appear in line with kinetic results collected in the study of the rearrangement (Boulton–Katritzky reaction) of the title compounds into the relevant 1,2,3‐triazoles, thereby strongly supporting the importance of the leaving‐group ability of the N‐4/C‐5/O‐1 system. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
C‐3′‐Cyclopropanated Taxol Analogs: Synthesis, Bioassay and Biostructural Analysis
Authors: Liu Changhui , Tamm Markus , Nötzel Marcus W. , Rauch Karsten , de Meijere Armin , Schilling Jennifer K. , Lakdawala Ami , Snyder James P. , Bane Susan L. , Shanker Natasha , Ravindra Rudravajhala , Kingston David G. I. 
Published: August 2005

AbstractTen taxoids with a cyclopropanated side chain were synthesized by coupling a spirocyclopropanated oxazoline‐5‐carboxylic acid with 7‐(triethylsilyl)baccatin III, followed by hydrolytic ring opening and benzoyl migration. The absolute configuration of the 2′‐position was determined by NMR analysis of the corresponding Mosher esters. These paclitaxel analogs were active in A2780 mammalian and PC‐3 prostate cancer cell lines, and also in a tubulin‐assembly assay, but all the analogs were less active than paclitaxel itself. To probe the basis for the uniform potency reduction shown by the cyclopropanated taxoid series, we have examined the conformational properties of compound 3b alone by molecular mechanics and in complex with tubulin by molecular dynamics. In addition, we have performed an NMR/NAMFIS conformer deconvolution analysis for compound 3b. Both modeling and NAMFIS approaches provide a satisfying understanding of the biological behavior of the series of cyclopropanated taxoids and provide further, though indirect, support for the T‐form as characteristic of taxoids bound to β‐tubulin. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
N‐Confused Porphine
Authors: Morimoto Tatsuki , Taniguchi Shozo , Osuka Atsuhiro , Furuta Hiroyuki 
Published: August 2005

AbstractA skeleton of N‐confused porphyrin (NC‐porphine) has been synthesized for the first time, through a [3+1] coupling reaction. A completely planar inner 3H tautomeric form was found in the crystals, and the molecular packing shows a sandwich herringbone structure similar to that of normal porphine, whilst some of the spectroscopic properties demonstrate systematic substituent effects by the meso‐phenyl groups on the N‐confused porphyrin. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Separation and determination of toxic pyrrolizidine alkaloids in traditional Chinese herbal medicines by micellar electrokinetic chromatography with organic modifier
Authors: Yu Lijun , Xu Yan , Feng Huatao , Li Sam Fong Yau 
Published: August 2005

AbstractA simple and rapid micellar electrokinetic chromatography (MEKC) method was developed for the separation and determination of four toxic pyrrolizidine alkaloids (PAs) (senkirkine, senecionine, retrorsine, and seneciphylline) in two traditional Chinese herbal medicines (Qian liguang and Kuan donghua). Separation was performed in the running buffer consisting of 20 mM borate, 30 mM SDS, and 20% methanol at pH 9.1. With the optimized separation conditions, four PAs were separated in 17 min by a single run. The calibration curves showed good linearity with correlation efficiencies (R2) between 0.9940 and 0.9988. RSDs in migration time and peak area were 0.31, 0.40, 0.39, 0.48% and 3.28, 3.48, 4.16, 3.42% for senkirkine, senecionine, retrorsine, and seneciphylline, respectively. Limits of detection (S/N = 3) varied from 1.19 to 2.70 μg/mL. The proposed method was applied to determine the PAs extracted from Chinese herbal medicines (Qian liguang and Kuan donghua). PA of senkirkine in Kuan donghua was detected and the amount was found to be 79.1 μg/g. The results obtained indicate that the proposed MEKC method could potentially become an effective alternative tool for qualification control and quantitative analysis of herbal medicines in pharmaceutical industry.
Analysis of neutral nitromusks in incenses by capillary electrophoresis in organic solvents and gas chromatography‐mass spectrometry
Authors: Gotti Roberto , Fiori Jessica , Mancini Francesca , Cavrini Vanni 
Published: August 2005

AbstractNitromusks used as fragrances in a variety of personal‐care products, cleansers, and domestic deodorants, including incense sticks, are neutral nitro aromatic compounds; some of these have been reported as photosensitizers. In this work, their analysis was performed by capillary electrophoresis (CE) in a methanol‐based background electrolyte (BGE). In particular, a 10 mM solution of citric acid in methanol was used; under these conditions the strong suppression of the electroosmotic flow favored the use of negatively charged surfactants as additives for the anodic migration of the studied analytes. To this end, sodium taurodeoxycholate (TDC) was supplemented at high concentration (190 mM) to the organic background electrolyte (BGE), showing strong indication of the ability to give micelle‐like aggregates. Since nitromusks are characterized by the presence of a nitroaromatic ring with low charge density, their association with TDC aggregates can be ascribed to donor–acceptor interactions. Separation of musk xylene, musk ketone, and the banned musk moskene and musk ambrette was obtained under full nonaqueous BGE; the addition of relatively small water percentages (15% v/v) was found to be useful in improving the separation of pairs of adjacent peaks. Under optimized conditions (190 mM sodium TDC in methanol–water, 85–15 v/v containing citric acid 10 mM) the system was applied to the analysis of nitromusks in incense sticks extracted with methanol. The results were compared with those obtained by the analysis of the same samples using gas chromatography with mass detector. The expected different selectivity of separation obtained using the two techniques can be useful in the unambiguous determination of the analytes; furthermore, a substantial accord of the preliminary quantitative results achieved with the two methods was assumed as the confirmation of the potential reliability of CE performed with high percentage of organic solvent.
Distributed current estimates using cortical orientation constraints
Authors: Lin Fa‐Hsuan , Belliveau John W. , Dale Anders M. , Hämäläinen Matti S. 
Published: August 2005

AbstractDistributed source models of magnetoencephalographic (MEG) and electroencephalographic (EEG) data employ dense distributions of current sources in a volume or on a surface. Previously, anatomical magnetic resonance imaging (MRI) data have been used to constrain locations and orientations based on cortical geometry extracted from anatomical MRI data. We extended this approach by first calculating cortical patch statistics (CPS), which for each patch corresponding to a current source location on the cortex comprise the area of the patch, the average normal direction, and the average deviation of the surface normal from its average. The patch areas were then incorporated in the forward model to yield estimates of the surface current density instead of dipole amplitudes at the current locations. The surface normal data were employed in a loose orientation constraint (LOC), which allows some variation of the current direction from the average normal. We employed this approach both in the ℓ2 minimum‐norm estimates (MNE) and in the more focal ℓ1 minimum‐norm solutions, the minimum‐current estimate (MCE). Simulations in auditory and somatosensory areas with current dipoles and 10‐ or 20‐mm diameter cortical patches as test sources showed that applying the LOC can increase localization accuracy. We also applied the method to in vivo auditory and somatosensory data. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
Bilateral activation of the prefrontal cortex after strategic semantic cognitive training
Authors: Miotto Eliane C. , Savage Cary R. , Evans Jonathan J. , Wilson Barbara A. , Martins M.G.M. , Iaki Suzan , Amaro Edson 
Published: August 2005

AbstractThe prefrontal cortex (PFC) has been implicated in the ability to apply semantic organizational strategies during verbal encoding and episodic learning. However, there has been no direct evidence demonstrating which specific areas in the PFC are engaged after cognitive training using semantic organizational strategies in healthy adult human subjects. In this study, we investigated the effects of semantic strategic training on brain activity and changes in behavioral performance, after cognitive training, using functional MRI (fMRI). There was a significant activation in bilateral dorsolateral prefrontal (DLPF) and orbitofrontal (OFC) areas after cognitive training. These results demonstrate the engagement of bilateral DLPF and OFC cortex during strategic memory processes, particularly when mobilization and effort of effective use of strategies are required. The functional adaptations observed here may also shed light on some of the processes underlying recovery with cognitive rehabilitation in patient populations with brain injury. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
Proteomic analysis of protein adsorption: Serum amyloid P adsorbs to materials and promotes leukocyte adhesion
Authors: Kim Jin‐Ku , Scott Evan A. , Elbert Donald L. 
Published: August 2005

AbstractSerum and plasma protein adsorption on materials was analyzed using gel electrophoresis and ion trap mass spectrometry. Following incubation of polypropylene, polyethylene terephthalate (PET), or polydimethylsiloxane (PDMS) with 5% serum for longer than 4 h, we found unexpectedly high amounts of the pentraxin serum amyloid P. It was previously shown that serum amyloid P is constitutively expressed in humans, functions as an opsonin, and interacts with the Fcγ receptors on leukocytes. We demonstrate that serum amyloid P adsorbed to tissue culture polystyrene, PDMS, and PET promotes the adhesion of granulocytes and monocytes in the presence of calcium. The methods developed for these studies may be useful for the large‐scale study of protein adsorption and do not rely on radiolabeling or the availability of antibodies. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
Excretion of resorption products from bioactive glass implanted in rabbit muscle
Authors: Lai William , Garino Jonathan , Flaitz Catherine , Ducheyne Paul 
Published: August 2005

AbstractBioactive glass granules were implanted in the paraspinal muscle of rabbits to determine the pathway of the silicon released from bioactive glass in vivo. We traced and quantified the silicon released by obtaining 24‐h urine and blood samples for up to 6 months after implantation. Furthermore, local muscle tissue as well as the following organs were resected for chemical and histopathological analyses: brain, heart, kidney, liver, lung, lymph nodes, spleen, and thymus. The urinary silicon of the group with implanted granules was significantly higher than in the sham‐operated, control group. The average excretion rate was 2.4 mg/day, and as such, 100% of the implanted silicon was excreted in 19 weeks. No elevated concentrations of silicon were found at the implant sites or in the other organs at sacrifice, that is, 24 weeks. The histological appearance of all organs was normal throughout. The concentrations of silicon measured in the urine were well below saturation and because no significant increase in silicon was found in any organ, including kidney, the increased silicon excretion rate was within the physiological capacity of rabbits. Therefore, it can be concluded that the resorbed silica gel is harmlessly excreted in soluble form through the urine. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
A joint study based on the electron localization function and catastrophe theory of the chameleonic and centauric models for the Cope rearrangement of 1,5‐hexadiene and its cyano derivatives
Authors: Polo Victor , Andrés Juan 
Published: August 2005

AbstractA novel interpretation of the chameleonic and centauric models for the Cope rearrangements of 1,5‐hexadiene (A) and different cyano derivatives (B: 2,5‐dicyano, C: 1,3,4,6‐tetracyano, and D: 1,3,5‐tricyano) is presented by using the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT) on the reaction paths calculated at the B3LYP/6‐31G(d,p) level. The progress of the reaction is monitorized by the changes of the ELF structural stability domains (SSD), each being change controlled by a turning point derived from CT. The reaction mechanism of the parent reaction A is characterized by nine ELF SSDs. All processes occur in the vicinity of the transition structure and corresponding to a concerted formation/breaking of C1C6 and C3C4 bonds, respectively, together with an accumulation of charge density onto C2 and C5 atoms. Reaction B presents the same number of ELF SSDs as A, but a different order appears; the presence of 2,5‐dicyano substituents favors the formation of C1C6 bonds over the breaking of C3C4 bond process, changing the reaction mechanism from a concerted towards a stepwise, via a cyclohexane biradical intermediate. On the other side, reaction C presents the same type of turning points but two ELF SSD less than A or B; there is an enhancement of the C3C4 bond breaking process at an earlier stage of the reaction by delocalizing the electrons from the C3C4 bond among the cyano groups. In the case of competitive effects of cyano subsituents on each moiety, as it is for reaction D, seven different ELF SSDs have been identified separated by eight turning points (two of them occur simultaneously). Both processes, formation/breaking of C1C6 and C3C4 bonds, are slightly favored with respect to the parent reaction (A), and the TS presents mixed electronic features of both B and C. The employed methodology provides theoretical support for the centauric nature (half‐allyl, half‐radical) for the TS of D. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1427–1437, 2005
Mechanical Aspects of Clathrin Cage Formation
Authors: Nossal Ralph 
Published: August 2005

AbstractThe principal component of the coats of endocytic vesicles involved in the receptor‐mediated uptake of materials from the surfaces of eucaryotic cells is a protein known as clathrin. Clathrin normally appears as a three‐legged trimer joined at a common hub (a ‘triskelion’) which, under appropriate conditions, co‐assembles with other triskelia to form variably‐sized polyhedra (‘cages’, or ‘baskets’) that contain pentagonal and hexagonal faces. The size distribution of the cages can be described by a simple energetic model which contains, as a parameter, the flexural rigidity, EI, of the edges (struts) of the baskets. By comparing the values of EI thus obtained with similar quantities determined by analyzing electron micrographs of isolated triskelia (A. J. Jin, R. Nossal, Biophys. J. 2000, 78, 1183), we infer that one role of clathrin‐associated proteins known as ‘assembly proteins’ is to link the intertwined legs of neighboring triskelia to prevent slippage when the cages are stressed.