bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of GFP spectral properties using artificial neural network
Authors: Nantasenamat Chanin , Isarankura‐Na‐Ayudhya Chartchalerm , Tansila Natta , Naenna Thanakorn , Prachayasittikul Virapong 
Published: February 2007

AbstractThe prediction of the excitation and the emission maxima of green fluorescent protein (GFP) chromophores were investigated by a quantitative structure‐property relationship study. A data set of 19 GFP color variants and an additional data set consisting of 29 synthetic GFP chromophores were collected from the literature. Artificial neural network implementing the back‐propagation algorithm was employed. The proposed computational approach reliably predicted the excitation and the emission maxima of GFP chromophores with correlation coefficient exceeding 0.9. The usefulness of quantum chemical descriptors was revealed by a comparative study with other molecular descriptors. Assignment of appropriate protonation state of the chromophore for the GFP color variants data set was shown to be necessary for good predictive performance. Results suggest that the confinement of the GFP chromophore has no significant influence on the predictive performance of the data set used. A comparative investigation with the traditional modeling methods, particularly multiple linear regression and partial least squares, reveals that artificial neural network is the most suitable modeling approach for the GFP spectral properties. It is anticipated that this methodology has great potential in accelerating the design and engineering of novel GFP color variants of scientific or industrial interest. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
QSAR models based on isomorphic and nonisomorphic data fusion for predicting the blood brain barrier permeability
Authors: Cuadrado Manuel Urbano , Ruiz Irene Luque , Gómez‐Nieto Miguel Ángel 
Published: February 2007

AbstractA QSAR model for predicting the blood brain barrier permeability (BBBP) in a large and heterogeneous variety of compounds (136 compounds) has been developed using approximate similarity (AS) matrices as predictors and PLS as multivariate regression technique. AS values fuse information of both the isomorphic similarity and nonisomorphic dissimilarity with the purpose of achieving an accurate predictive space. In addition to the fact of applying AS values to heterogeneous data sets, a new concept on graph isomorphism based on the extended maximum common subgraph (EMCS) is defined for the building of AS spaces considering the atoms and bonds, which are bridges between the isomorphic and nonisomorphic substructures. This new isomorphism detection has as objective to take into account the position and nature of the nucleus substituents, thus allowing the development of accurate models for large and diverse sets of compounds. After an outliers study, the training and test stages were made and the results obtained using several AS approaches were compared. Several validation processes were carried out by means of employing several test sets, and high predictive ability was obtained for all the cases (Q2 = 0.81 and standard error in prediction, SEP = 0.29). © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Quantification of red myotomal muscle volume and geometry in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis) using T1‐weighted magnetic resonance imaging
Authors: Perry Cameron N. , Cartamil Daniel P. , Bernal Diego , Sepulveda Chugey A. , Theilmann Rebecca J. , Graham Jeffrey B. , Frank Lawrence R. 
Published: February 2007

AbstractT1‐weighted magnetic resonance imaging (MRI) in conjunction with image and segmentation analysis (i.e., the process of digitally partitioning tissues based on specified MR image characteristics) was evaluated as a noninvasive alternative for differentiating muscle fiber types and quantifying the amounts of slow, red aerobic muscle in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis). MRI‐determinations of red muscle quantity and position made for the mid‐body sections of three mako sharks (73.5–110 cm fork length, FL) are in close agreement (within the 95% confidence intervals) with data obtained for the same sections by the conventional dissection method involving serial cross‐sectioning and volumetric analyses, and with previously reported findings for this species. The overall distribution of salmon shark red muscle as a function of body fork length was also found to be consistent with previously acquired serial dissection data for this species; however, MR imaging revealed an anterior shift in peak red muscle cross‐sectional area corresponding to an increase in body mass. Moreover, MRI facilitated visualization of the intact and anatomically correct relationship of tendon linking the red muscle and the caudal peduncle. This study thus demonstrates that MRI is effective in acquiring high‐resolution three‐dimensional digital data with high contrast between different fish tissue types. Relative to serial dissection, MRI allows more precise quantification of the position, volume, and other details about the types of muscle within the fish myotome, while conserving specimen structural integrity. J. Morphol., 2007. © 2007 Wiley‐Liss, Inc.
Plasticity of mandibular biomineralization in myostatin‐deficient mice
Authors: Ravosa Matthew J. , Klopp Emily B. , Pinchoff Jessie , Stock Stuart R. , Hamrick Mark W. 
Published: February 2007

AbstractCompared with the normal or wild‐type condition, knockout mice lacking myostatin (Mstn), a negative regulator of skeletal muscle growth, develop significant increases in relative masticatory muscle mass as well as the ability to generate higher maximal muscle forces. Wild‐type and myostatin‐deficient mice were compared to assess the postweaning influence of elevated masticatory loads because of increased jaw‐adductor muscle and bite forces on the biomineralization of mandibular cortical bone and dental tissues. Microcomputed tomography (microCT) was used to quantify bone density at a series of equidistant external and internal sites in coronal sections for two symphysis and two corpus locations. Discriminant function analyses and nonparametric ANOVAs were used to characterize variation in biomineralization within and between loading cohorts. Multivariate analyses indicated that 95% of the myostatin‐deficient mice and 95% of the normal mice could be distinguished based on biomineralization values at both symphysis and corpus sections. At the corpus, ANOVAs suggest that between‐group differences are due to the tendency for cortical bone mineralization to be higher in myostatin‐deficient mice, coupled with higher levels of dental biomineralization in normal mice. At the symphysis, ANOVAs indicate that between‐group differences are related to significantly elevated bone‐density levels along the articular surface and external cortical bone in the knockout mice. Both patterns, especially those for the symphysis, appear because of the postweaning effects of increased masticatory stresses in the knockout mice versus normal mice. The greater number of symphyseal differences suggest that bone along this jaw joint may be characterized by elevated plasticity. Significant differences in bone‐density levels between normal and myostatin‐deficient mice, coupled with the multivariate differences in patterns of plasticity between the corpus and symphysis, underscore the need for a comprehensive analysis of the plasticity of masticatory tissues vis‐à‐vis altered mechanical loads. J. Morphol., 2007. © 2007 Wiley‐Liss, Inc.
Disulfide bond cleavages observed in SORI‐CID of three nonapeptides complexed with divalent transition‐metal cations
Authors: Mihalca Romulus , van der Burgt Yuri E. M. , Heck Albert J. R. , Heeren Ron M. A. 
Published: February 2007

AbstractTandem MS sequencing of peptides that contain a disulfide bond is often hampered when using a slow heating technique. We show that complexation of a transition‐metal ion with a disulfide‐bridge‐containing nonapeptide yields very rich tandem mass spectra, including fragments that involve the cleavage of the disulfide bond up to 56% of the total product ion intensity. On the contrary, MS/MS of the corresponding protonated nonapeptides results predominantly in fragments from the region that is not involved in the disulfide bond. Eleven different combinations of three nonapeptides and three metal ions were measured using Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS) combined with sustained off‐resonance irradiation collision induced dissociation (SORI‐CID). All observed fragments are discussed with respect to four different types of product ions: neutral losses, b/y‐fragmentation with and without the disulfide bond cleavage, and losses of internal amino acids without rupture of the disulfide bridge. Furthermore, it is shown that the observed complementary fragment pairs obtained from peptide–metal complexes can be used to determine the region of the binding site of the metal ion. This approach offers an efficient way to cleave disulfide‐bridged structures using low energy MS/MS, which leads to increased sequence coverage and more confidence in peptide or protein assignments. Copyright © 2007 John Wiley & Sons, Ltd.
Applications of LC/MS in structure identifications of small molecules and proteins in drug discovery
Authors: Chen Guodong , Pramanik Birendra N. , Liu Yan‐Hui , Mirza Urooj A. 
Published: February 2007

AbstractWith advancements in ionization methods and instrumentation, liquid chromatography/mass spectrometry (LC/MS) has become a powerful technology for the characterization of small molecules and proteins. This article will illustrate the role of LC/MS analysis in drug discovery process. Examples will be given on high‐throughput analysis, structural analysis of trace level impurities in drug substances, identification of metabolites, and characterization of therapeutic protein products for process improvement. Some unique MS techniques will also be discussed to demonstrate their effectiveness in facilitating structural identifications. Copyright © 2007 John Wiley & Sons, Ltd.
LC‐MS ion maps for the characterization of aniline derivatives of fatty acids and triglycerides in laboratory‐denatured rapeseed oil
Authors: Reig Natalia , Calaf Rosa E. , Messeguer Angel , Morató Anna , Escabros Jordi , Gelpí Emilio , Abian Joaquín 
Published: February 2007

AbstractIn 1981 Spain went through a unique epidemic associated with a food‐borne vector, affecting more than 20 000 people with over 800 deaths, which came to be known as the Toxic Oil Syndrome (TOS). Early epidemiological studies showed a link between this illness and the ingestion of rapeseed oil denatured with 2% aniline. This oil, originally aniline‐denatured for industrial use, was fraudulently processed in an attempt to remove free aniline, and marketed as edible oil. Fatty acid anilides (FAA), monoesters and diesters of 3‐(N‐phenylamino)‐1,2‐propanediol (PAP) are present in oil samples as they arise in the refining process from reactions of aniline with constituent fatty acids and triglycerides of the oil matrix and are the only extraneous compounds found in these samples. To expand the search for the causative agents in TOS‐associated oils and to look for new aniline‐related compounds, an exhaustive characterization of laboratory‐processed oils was undertaken. These oils, in the presence of aniline doped with 14C labelled aniline, were submitted to the laboratory conditions required for the generation of PAPs and FAAs. Laboratory‐generated oil samples were submitted to a liquid‐liquid extraction procedure to remove the unreacted aniline. The extract was processed by double solid‐phase extraction to improve detection limits for minor amine‐containing compounds in oils. The extracts enriched in aniline derivatives were submitted to on‐line HPLC‐UV‐APCI‐MS. Using two‐dimensional ion maps, the components of several families of derivatives were readily identified. Additionally, the extracts were also fractionated by HPLC‐UV and the fractions were analyzed by HPLC‐APCI‐MS/MS to obtain structural information. Standards of some of these compounds were synthesized and analyzed to confirm the results. A total of 115 aniline derivatives from 9 aniline‐related families were identified in these oil samples. These included fatty acid anilides and an extensive array of phenylaminopropanediol esters distributed in eight major compound classes. Copyright © 2007 John Wiley & Sons, Ltd.
Simple and rapid characterization of soybean cultivars by perfusion reversed‐phase HPLC: Application to the estimation of the 11S and 7S globulin contents
Authors: García María Concepción , Heras José María , Marina María Luisa 
Published: February 2007

AbstractA perfusion RP HPLC method enabling the separation of soybean proteins in an analysis time lower than 3 min has been used to obtain the chromatographic profiles of different soybean cultivars. The chromatograms obtained for each soybean variety presented clear differences that justified the potential use of this method for cultivar characterization. The area percentages obtained were employed as variables for cluster and principal components analysis of these soybeans. The application of these multivariate methods enabled the grouping of the soybeans in different categories. The protein fractions obtained from these soybeans by the application of a fractionation method were also analyzed. The chromatographic profiles obtained enabled the assignment of peaks to the main soybean proteins (7S and 11S globulins). These data were used for the estimation, for the first time, of the 7S and 11S globulin contents in soybean cultivars.
Online preconcentration of arsenic compounds by dynamic pH junction‐capillary electrophoresis
Authors: Jaafar Jafariah , Irwan Zildawarni , Ahamad Rahmalan , Terabe Shigeru , Ikegami Tohru , Tanaka Nobuo 
Published: February 2007

AbstractAn online preconcentration technique by dynamic pH junction was studied to improve the detection limit for anionic arsenic compounds by CE. The main target compound is roxarsone, or 3‐nitro‐4‐hydroxyphenylarsonic acid, which is being used as an animal feed additive. The other inorganic and organoarsenic compounds studied are the possible biotransformation products of roxarsone. The arsenic species were separated by a dynamic pH junction in a fused‐silica capillary using 15 mM phosphate buffer (pH 10.6) as the BGE and 15 mM acetic acid as the sample matrix. CE with UV detection was monitored at a wavelength of 192 nm. The influence of buffer pH and concentration on dynamic pH junction were investigated. The arsenic species focusing resulted in LOD improvement by a factor of 100–800. The combined use of C18 and anion exchange SPE and dynamic pH junction to CE analysis of chicken litter and soils helps to increase the detection sensitivity. Recoveries of spiked samples ranged between 70 and 72%.
Statistical mixture design optimization of extraction media and mobile phase compositions for the characterization of green tea
Authors: Alves de Almeida Aline , Spacino Scarminio Ieda 
Published: February 2007

AbstractThe influence of different solvents on the extraction medium and the RP‐HPLC mobile phase composition were investigated by statistical mixture designs to optimize solvent proportions to prepare the fingerprint of a medicinal herbal extract. For modeling, the number of peaks was used as a measure of fingerprint information. The optimum compositions of solvent to extract chemical substances from green tea and for mobile phase chromatographic analysis were ethyl acetate/ethanol/dichloromethane (20:5:75 v/v/v) and MeOH/ACN/water (7.5:57.5:35 v/v/v), respectively. This system results in 26 peaks in the chromatographic fingerprint. These results show that an incorrect choice of modifiers for mobile phase composition and solvent extraction hampers the detection of a maximum number of peaks and produces a poor chromatographic fingerprint.
Chiral separation of β‐blocker drug nadolol by HPLC – A kinetic and equilibrium study
Authors: Wang Xin , Ching Chi Bun 
Published: February 2007

AbstractA Chiralpak AD‐H column packed with amylose tris(3,5‐dimethylphenylcarbamate) coated on silica gel was used to study the enantioseparation of nadolol by HPLC. The bed voidage, axial dispersion coefficient, overall mass transfer coefficients as well as equilibrium constants for the chromatographic enantiomeric separation were evaluated by moment analysis on the basis of the solid film linear driving force model. The equilibrium constants were found to be 3.81, 5.24, 9.45 and 19.41 for the stereoisomers (SRS)‐, (SRR)‐, (RSS)‐ and (RSR)‐nadolol, respectively. Their overall mass transfer coefficients were found to be 1841.8, 1254.8, 799.4 and 401.7 min–1 respectively. Temperature effect on the enantiomeric separation and thermodynamic properties including enthalpy and entropy change of binding to the amylose tris(3,5‐dimethylphenylcarbamate) stationary phase were also investigated. The moment analysis and the parameters obtained were used to simulate nadolol elution profiles. The simulated results matched the experimental profiles well, which confirmed the validity of model parameters obtained in this study.
Determination of dopamine and serotonin in human urine samples utilizing microextraction online with liquid chromatography/electrospray tandem mass spectrometry
Authors: El‐Beqqali Aziza , Kussak Anders , Abdel‐Rehim Mohamed 
Published: February 2007

AbstractA specific LC‐MS‐MS method for the determination of dopamine and serotonin (5‐hydroxytryptamine; 5HT) in human urine is described. The analytes were extracted from urine and preconcentrated by microextraction in a packed syringe (MEPS). The new method is very promising, very easy to use, fully automated, of low cost, and rapid in comparison to previously used methods. The method was validated and the standard curves were evaluated by means of quadratic regression and weighted by inverse of the concentration: 1/x for the calibration range 50–4000 μg/L. The MEPS applied polymer (silica‐C8) could be used more than 300 times. The extraction recovery was about 50%. The results showed close correlation coefficients (r2 >0.999) for all analytes in the calibration range studied. The accuracy of MEPS‐LC‐MS‐MS was 100–101% for dopamine and 99–100% for 5HT. The interday precision (n = 3 days), expressed as the RSD%, was 6.0–7.7% for dopamine and 6.1–11% for 5HT. MEPS reduced the handling time by 12 times compared to a published method.
A GC method for simultaneous analysis of bornesitol, other polyalcohols and sugars in coffee and its substitutes
Authors: Ruiz‐Matute Ana Isabel , Montilla Antonia , del Castillo Maria Dolores , Martínez‐Castro Isabel , Luz Sanz Maria 
Published: February 2007

AbstractA GC method has been developed for the determination of polyalcohols and sugars in aqueous extracts from green coffee beans, ground roasted coffee beans submitted to either conventional or torrefacto processes, coffee blends and soluble instant coffees. Bornesitol was detected in aqueous coffee extracts for the first time. Mannitol, myo‐inositol, mannose, fructose, galactose, glucose and sucrose have also been determined. Results seem to indicate that coffee manufacturing processes, such as roasting or decaffeination, do not affect the polyalcohol content. Coffee substitutes based on cereals, carob or chicory, have also been studied. The possibility to characterize their presence in coffee extracts was evaluated.
Temperature effects on separation on zirconia columns: Applications to one‐ and two‐dimensional LC separations of phenolic antioxidants
Authors: Cacciola Francesco , Jandera Pavel , Mondello Luigi 
Published: February 2007

AbstractThe effects of temperature and mobile phase on LC chromatographic separation of phenolic antioxidants on zirconia‐based columns were investigated. Unlike silica‐based materials, zirconia columns show excellent thermal stability over a wide range of temperatures and enable high‐temperature separations. Enthalpic and entropic contributions to the retention of phenolic compounds on ZR‐Carbon and ZR‐Carbon C18 columns were determined from retention versus temperature plots in order to elucidate the retention mechanism of sample compounds over the temperature range up to 140°C. High‐temperature liquid chromatography on ZR‐Carbon columns was used for comprehensive LC×LC two‐dimensional separation systems based on the different selectivity of a Zorbax SB micro‐column used in the first dimension and a ZR‐Carbon column used in the second dimension. Two‐dimensional LC×LC systems employing a setup with two alternately operated parallel ZR‐Carbon columns in the second dimension were used for the analysis of phenolic antioxidants in beer and wine samples.
Analysis of aromatic and terpenic constituents of pepper extracts by capillary electrochromatography
Authors: Musenga Alessandro , Mandrioli Roberto , Ferranti Anna , D'Orazio Giovanni , Fanali Salvatore , Raggi Maria Augusta 
Published: February 2007

AbstractAn original method based on CEC has been developed for the determination of aromatic and terpenic compounds in extracts of spices obtained from Piper nigrum. The method is based on the use of a fused silica capillary (effective length: 23.5 cm, internal diameter: 100 μm) packed with a C18 sorbent (packing length: 23 cm, particle size: 5 μm). The mobile phase is a 50 mM, pH 6.0 ammonium acetate/ACN (10:90 v/v) mixture. Applying a 30 kV voltage, the following 11 compounds were separated and analysed: terpinen‐4‐ol, caryophyllene oxide, limonene, α‐pinene, 3‐carene, β‐pinene, α‐humulene, β‐caryophyllene, α‐phellandrene, eugenol and piperine. Compound determination is carried out using a diode‐array detector set at 265 and 338 nm for α‐phellandrene and piperine, respectively, and at 210 nm (reference subtraction at 282 nm) for all the other analytes. The optimised method has been validated with good results in terms of linearity, limits of quantitation, detection and precision. The CEC method was successfully applied to the analysis of essential oils and methanolic extracts of ‘black’, ‘white’ and ‘green’ pepper.
Magneto‐motive detection of tissue‐based macrophages by differential phase optical coherence tomography
Authors: Oh Junghwan , Feldman Marc D. , Kim Jihoon , Kang Hyun Wook , Sanghi Pramod , Milner Thomas E. 
Published: February 2007

AbstractBackground and ObjectivesA novel method to detect tissue‐based macrophages using a combination of superparamagnetic iron oxide (SPIO) nanoparticles and differential phase optical coherence tomography (DP‐OCT) with an external oscillating magnetic field is reported.Study Design/Material and MethodsMagnetic force acting on iron‐laden tissue‐based macrophages was varied by applying a sinusoidal current to a solenoid containing a conical iron core that substantially focused and increased magnetic flux density.ResultsNanoparticle motion was detected with DP‐OCT, which can detect tissue movement with nanometer resolution. Frequency response of iron‐laden tissue movement was twice the modulation frequency since the magnetic force is proportional to the product of magnetic flux density and gradient.ConclusionsResults of our experiments indicate that DP‐OCT can be used to identify tissue‐based macrophage when excited by an external focused oscillating magnetic field. Lasers Surg. Med. 39:266–272, 2007. © 2007 Wiley‐Liss, Inc.