bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance assessment of kernel density clustering for gene expression profile data
Authors: Shu Guoping , Zeng Beiyan , Chen Yiping P. , Smith Oscar H. 
Published: June 2003

AbstractKernel density smoothing techniques have been used in classification or supervised learning of gene expression profile (GEP) data, but their applications to clustering or unsupervised learning of those data have not been explored and assessed. Here we report a kernel density clustering method for analysing GEP data and compare its performance with the three most widely‐used clustering methods: hierarchical clustering, K‐means clustering, and multivariate mixture model‐based clustering. Using several methods to measure agreement, between‐cluster isolation, and within‐cluster coherence, such as the Adjusted Rand Index, the Pseudo F test, the r2 test, and the profile plot, we have assessed the effectiveness of kernel density clustering for recovering clusters, and its robustness against noise on clustering both simulated and real GEP data. Our results show that the kernel density clustering method has excellent performance in recovering clusters from simulated data and in grouping large real expression profile data sets into compact and well‐isolated clusters, and that it is the most robust clustering method for analysing noisy expression profile data compared to the other three methods assessed. Copyright © 2003 John Wiley & Sons, Ltd.
Reproducibility assessment of independent component analysis of expression ratios from DNA microarrays
Authors: Kreil David Philip , MacKay David J. C. 
Published: June 2003

AbstractDNA microarrays allow the measurement of transcript abundances for thousands of genes in parallel. Most commonly, a particular sample of interest is studied next to a neutral control, examining relative changes (ratios). Independent component analysis (ICA) is a promising modern method for the analysis of such experiments. The condition of ICA algorithms can, however, depend on the characteristics of the data examined, making algorithm properties such as robustness specific to the given application domain. To address the lack of studies examining the robustness of ICA applied to microarray measurements, we report on the stability of variational Bayesian ICA in this domain. Microarray data are usually preprocessed and transformed. Hence we first examined alternative transforms and data selections for the smallest modelling reconstruction errors. Log‐ratio data are reconstructed better than non‐transformed ratio data by our linear model with a Gaussian error term. To compare ICA results we must allow for ICA invariance under rescaling and permutation of the extracted signatures, which hold the loadings of the original variables (gene transcript ratios) on particular latent variables. We introduced a method to optimally match corresponding signatures between sets of results. The stability of signatures was then examined after (1) repetition of the same analysis run with different random number generator seeds, and (2) repetition of the analysis with partial data sets. The effects of both dropping a proportion of the gene transcript ratios and dropping measurements for several samples have been studied. In summary, signatures with a high relative data power were very likely to be retained, resulting in an overall stability of the analyses. Our analysis of 63 yeast wild‐type vs. wild‐type experiments, moreover, yielded 10 reliably identified signatures, demonstrating that the variance observed is not just noise. Copyright © 2003 John Wiley & Sons, Ltd.
Regio‐ and Stereoselective Reductive Coupling of Bicyclic Alkenes with Propiolates Catalyzed by Nickel Complexes: A Novel Route to Functionalized 1,2‐Dihydroarenes and γ‐Lactones
Authors: Rayabarapu Dinesh Kumar , Cheng Chien‐Hong 
Published: June 2003

Abstract7‐Oxabenzonorbornadienes derivatives 1 a–d underwent reductive coupling with alkyl propiolates CH3CCCO2CH3 (2 a), PhCCCO2Et (2 b), CH3(CH2)3CCCO2CH3 (2 c), CH3(CH2)4CCCO2CH3 (2 d), TMSCCCO2Et (2 e), (CH3)3CCCO2CH3 (2 f) and HCCCO2Et (2 g) in the presence of [NiBr2(dppe)] (dppe=Ph2PCH2CH2PPh2), H2O and zinc powder in acetonitrile at room temperature to afford the corresponding 2alkenyl‐1,2‐dihydronapthalen‐1‐ol derivatives 3 a–n with remarkable regio‐ and diastereoselectivity in good to excellent yields. Similarly, the reaction of 7azabenzonorbornadienes derivative 1 e with propiolates 2 a, b and d proceeded smoothly to afford reductive coupling products 2alkenyl‐1,2‐dihydronapthalene carbamates 3 o–p in good yields with high regio‐ and stereoselectivity. This nickel‐catalyzed reductive coupling can be further extended to the reaction of 7oxabenzonorbornene derivatives. Thus, 5,6‐di(methoxymethyl)‐7‐oxabicyclo[2.2.1]hept‐2‐ene (4) reacted with 2 a and 2 d to furnish cyclohexenol derivatives bearing four cis substituents 5 a and b in 81 and 84 % yield, respectively. In contrast to the results of 4 with 2, the reaction of dimethyl 7oxabicyclo[2.2.1]hept‐5‐ene‐2,3‐dicarboxylate (6) with propiolates 2 a–d afforded the corresponding reductive coupling/cyclization products, bicyclo[3.2.1]γ‐lactones 7 a–d in good yields. The reaction provides a convenient one‐pot synthesis of γ‐lactones with remarkably high regio‐ and stereoselectivity.
Phosphadicarbaborane Analogues of Ferrocene: New Isomers of [closo‐(η5‐C5H5)FePC2B8H10]
Authors: Štíbr Bohumil , Holub Josef , Bakardjiev Mario , Pavlík Ivan , Tok Oleg L. , Wrackmeyer Bernd 
Published: June 2003

AbstractThermal isomerisation of the ferraphosphadicarbaborane [1‐Cp‐closo‐1,2,4,5‐FePC2B8H10] (1a; Cp = η5‐C5H5−) at elevated temperatures (180−350 °C) leads to the formation of three new isomeric complexes. These were characterized by multinuclear (1H, 11B, 31P, and 13C) NMR spectroscopy and mass spectrometry as [1‐Cp‐closo‐1,2,3,8‐FePC2B8H10] (1b), [1‐Cp‐closo‐1,10,2,4‐FePC2B8H10] (1c), and closo‐[1,2,4,10‐FePC2B8H10] (1d). The formation of 1b is accompanied by an unusual agglomeration of the P and C heteroatoms. Complexes 1b and 1c have also been isolated as side products from the direct reaction between nido‐[7,8,9‐PC2B8H11] (2) and [CpFe(CO)2]2 in refluxing mesitylene, and 1a and 1b from the pyrolysis of [7‐Fp‐(η1‐nido‐7,9,10‐PC2B8H10)] [3; Fp = CpFe(CO)2] at 350 °C. NMR intercomparisons of all five [1‐Cp‐closo‐FePC2B8H10] isomers thus far isolated have been made. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Stereoisomer Discrimination Through π‐Stacking Interactions in Spirocyclic Phosphazenes Bearing 2,2′‐Dioxybiphenyl Units
Authors: Gabino A. Carriedo  , Garcia‐Alonso Francisco J. , García‐Alvarez Jose L. , Pappalardo Giuseppe C. , Punzo Francesco , Rossi Patrizia 
Published: June 2003

AbstractThe molecular structure of the 2,2′‐dioxybiphenyl spirocyclic tetrachlorocyclotriphosphazene [N3P3Cl4(O2C12H8)] (3) was determined by X‐ray crystallography. The structure and conformation of 3 in the crystal are compared and discussed with respect to those of its analogues trispiro and dispiro derivatives, [N3P3(O2C12H8)3] (1) and [N3P3Cl2(O2C12H8)2] (2), respectively. Both the (R) and (S) stereoisomers are present in the lattice of 3 as arranged in pairs (R)···(S) held together through sandwich‐type π‐stacking interactions of the (C7−C12)/(C7−C12)′ phenyl rings of the 2,2′‐dioxybiphenyl groups. The polymer‐like assembly of 2 was formed by interactions between the (R) and (S) portions of two meso molecules [in the sequence ···(R)···(S)···(R)···(S)···(R)···(S)···]. In this case, the pertinent phenyl rings involved in the noncovalent π‐interactions assume a parallel‐displaced configuration. To the best of our knowledge, no chiral discrimination in cyclic phosphazenes has been hitherto described, and the present findings provide the first evidence for the discrimination of stereoisomers in spirophosphazenes and the noncovalent forces that govern the chiral recognition in these systems. The energy of the π‐stacking interaction increases with increasing number of 2,2′‐dioxybiphenyl groups; i.e., on passing from 3 to 2. In the case of molecule 1, the discrimination of enantiomers does not take place at all because the π‐stacking interaction becomes impossible because of steric hindrance. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
The Reactivity of Allyl and Olefin‐Hydride Niobocene Derivatives Towards Isocyanides. X‐ray Crystal Structure of [Nb(η5‐C5H4SiMe3)2{η3‐CH(R)CHCH(R)}] (R = SiMe2tBu)
Authors: del Hierro Isabel  , Fernández‐Galán Rafael , Prashar Sanjiv , Antiñolo Antonio , Fajardo Mariano , Rodríguez Ana M. , Otero Antonio 
Published: June 2003

AbstractThe new allylniobocene complexes [NbCp′2(η3‐CHRCHCHR′)] [Cp′ = η5‐C5H4SiMe3; R = R′ = SiMe2tBu (1); R = H, R′ = SiPh3 (2)] have been prepared and characterised. The molecular structure of 1 has been determined by X‐ray diffraction studies, which confirm that the allyl ligand is η3‐bonded to the metal centre. The reactivity of the niobocene complexes 1, 2, [NbCp′2H(η2‐CH2=CH2)] (3), and [NbCp′2(η3‐CH2CHCH2)] (4) towards aliphatic, tBuNC, nBuNC, and aromatic, CNC6H3Me2‐2,6, isocyanide compounds has been studied. From these reactions the new alkylniobocene [NbCp′2(CH2CH3)(CNR)] [R = tBu (5), C6H3Me2‐2,6 (6), nBu (7)], η1‐allylniobocene derivatives [NbCp′2(η1‐CH2CHCHSiPh3)(CNC6H3Me2‐2,6)] (8), and a family of the first neutral η1‐iminoacylniobocene complexes [NbCp′2{η1‐C(=NR)R′}(CNR)] (R = C6H3Me2‐2,6, R′ = Et (9); R = nBu, R′ = Et (10); R = C6H3Me2‐2,6, R′ = CH2CH=CHSiPh3 (11); R = C6H3Me2‐2,6, R′ = CH2CH=CH2 (12)] were prepared. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
The volatile composition of samples from the blend of monovarietal olive oils and from the processing of mixtures of olive fruits
Authors: Angerosa Franca , Basti Carla 
Published: June 2003

AbstractThe volatile fraction deriving from the lipoxygenase pathway of samples obtained by processing olive fruits of 2 cultivars in known proportions was compared with that of samples deriving from the blending of oils extracted from the same cultivars and in the same proportions. The varieties considered for the mixtures were Coratina and Koroneiki, Coratina and Frantoio, and Dritta and Bosana, respectively.The results confirmed that the accumulation of each volatile compound from the lipoxygenase pathway in the monovarietal oils was different and closely dependent on the genetic store of each variety. The concentrations of the mentioned compounds appeared to change in a way proportional to the percent of each monovarietal oil in the samples obtained by blending 2 monovarietal oils. Instead, the oils obtained by processing mixtures of fruits from the 2 corresponding cultivars showed a striking accumulation of volatile compounds, especially of C6‐compounds, which reached higher concentration at different percentages depending on the cultivars processed.
Effects of microwave treatment on the oxidative stability of peanut (Arachis hypogaea) oils and the molecular species of their triacylglycerols
Authors: Yoshida Hiromi , Hirakawa Yuki , Tomiyamaa Yuka , Mizushina Yoshiyuki 
Published: June 2003

AbstractPeanut seeds (Arachis hypogaea) were roasted for 6, 12, 20, or 30 min at a frequency of 2450 MHz using a microwave oven. The quality characteristics and the compositions of the oils, i.e. their tocopherol distributions and the molecular species of the triacylglycerols (TAGs) were investigated. These results were compared with those of an unroasted oil sample. Only minor increases (p <0.05) in chemical and physical properties of the oils, such as the carbonyl value, the p‐anisidine value and the color development occurred after a prolonged roasting period. Compared to the original level, more than 92 wt‐% tocopherols remained after 30 min of roasting. A modified thin‐layer chromatography argentation procedure provided 12 different groups of TAGs, based on both the degrees of unsaturation and the total fatty acid chain‐length. Although significant increases (p <0.05) generated in these chemical and physical changes of the oils after 20 min of roasting, no significant loss (p >0.05) was observed in the molecular species of the TAGs during microwave roasting. These results indicate that phospholipids may be attributed to the quality characteristics of peanut oils during microwave roasting.
Toolbox for modification of the lecithin headgroup
Authors: Doig Steven D. , Diks Rob M. M. 
Published: June 2003

AbstractIn an effort to produce structurally divergent lecithins for testing of their functional properties and use in food products, several tools have been developed to carry out modifications in the polar head group distribution of the native phospholipids in soybean lecithin. These tools include physical, chemical and enzymatic techniques. Using a combination of acetone de‐oiling, ethanol fractionation, N‐acetylation and enzymatic hydrolysis and transphosphatidylation with a phospholipase D from Streptomyces sp., a set of lecithins with modified head group distributions were produced. The kinetics of the enzymatic head group hydrolysis and transphosphatidylation was studied in detail. Reaction rates and selectivity (transphosphatidylation / hydrolysis) were affected by both lecithin concentration and donor alcohol concentration. Hydrolysis, forming phosphatidic acid, was strongly dependent on both concentrations, whilst transphosphatidylation, forming phosphatidyl glycerol (or phosphatidyl ethanolamine or phosphatidyl serine), was only influenced by the donor alcohol. This resulted in a reduction in selectivity at high initial lecithin concentrations and suggested the use of a reactant feeding strategy. Enrichment of the phosphatidyl choline content of native soybean lecithin was achieved by ethanol fractionation and phosphatidyl inositol enrichment was by N‐acetylation with acetic anhydride followed by de‐oiling. The application of these tools, together with others designed to modify the fatty acid composition of phospholipids, was used to produce 10‐100 g quantities of divergent lecithins and can be routinely used at lab‐scale.
Measurement of dissociation constants of inhibitors binding to Src SH2 domain protein by non‐covalent electrospray ionization mass spectrometry
Authors: Bligh S. W. Annie , Haley Terry , Lowe Peter N. 
Published: June 2003

AbstractA mass spectrometric protocol for identifying ligands with a wide range of affinities (3–101 µM) and quantitative spectral analysis for non‐covalent interactions have been developed using Src SH2 as a target. Dissociation constants of five compounds, three with a phospho moiety, one with a sulphonic acid group and one with carboxylic acid groups only, were determined using one‐ligand one‐binding‐site, two‐ligands one‐binding site and one‐ligand two‐binding‐sites models. The Kd values determined by ESI‐MS of the three compounds containing the phospho moiety (3.2–7.9 µM) were comparable to those obtained from a solution equilibrium fluorescence polarization assay. The compound with a sulphonate group is a much weaker binding ligand (Kd = 101 µM by ESI, ≫300 µM by FP) towards the Src SH2 protein. Two complexes with different stoichiometric ratios 1:1 and 2:1 (ligand–protein) were observed by ESI‐MS for the ligand GIXXX630X. Analysis of binding isotherms indicated the presence of two binding sites for the ligand with Kd values of 9.3 and 193 µM. These data confirmed that, for these polar compounds, non‐covalent ESI‐MS can measure affinity which very closely reflects the affinity measured under true solution equilibrium conditions. ESI‐MS has several key advantages over many solution methods: it can identify the existence of and measure the affinity of complexes other than simple 1:1 ligand–enzyme complexes. Moreover, ESI‐MS competition experiments can be readily performed to yield data on whether two ligands bind simultaneously or competitively at the same time as measuring the affinity of the ligand. Copyright © 2003 John Wiley & Sons, Ltd.
Change of soil hydrological properties of fens as a result of soil development
Authors: Schindler Uwe , Behrendt Axel , Müller Lothar 
Published: June 2003

AbstractThis study deals with the change and evaluation of hydrological properties of peat soils (Histosols) in the course of soil development. Ash content, volumetric water content, and dry bulk density, unsaturated hydraulic conductivity, water retention function, and wetting properties were measured for 84 fen sites in 19 fen regions of North‐Eastern Germany. Soil development resulted in porosity decrease. On the contrary, the macropore space and the capillary rise increased. With the start of consolidation processes and the development of segregation structure, a'noticeable reduction of the macropores and unsaturated hydraulic conductivity were observed. In course of soil development and decreasing of aggregate size, these processes reversed. Both parameters increased from segregation structure horizon to earthyfied fen and weak moorshyfied fen horizon, until they partly exceeded the starting values of pedogenetic almost unchanged fen in strongly moorshyfied stadium. Differences in wetting properties of peat could not be explained by the changes of peat properties in the course of soil development.
Laser‐Doppler flowmetry is reliable for early diagnosis of small‐bowel acute rejection in the mouse
Authors: Dindelegan George , Liden Hans , Kurlberg Göran , Oltean Mihai , Nilsson Ola , Åneman Anders , Lycke Nils , Olausson Michael 
Published: June 2003

AbstractThe purpose of the study was to investigate intestinal mucosal perfusion in mouse small‐bowel transplantation (SBT), using laser‐Doppler flowmetry. Heterotopic SBT was performed in syngeneic and allogeneic combinations. Mucosal perfusion was measured both in the native and in the grafted intestine at time of surgery and at 1, 3, 6, and 8 days postoperatively. Histology specimens were obtained at the same time and graded for rejection. No rejection was seen in the syngeneic group at any of the time points studied. The allografts displayed significant decreased mucosal perfusion on postoperative days 3, 6, and 8. Rejection was histologically evident on postoperative days 6 and 8. Laser‐Doppler perfusion in the rejecting intestinal allograft was decreased before onset of histological features of rejection. Mucosal blood flow measured by laser‐Doppler could be used as an early indicator of acute rejection in SBT. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:233–238 2003
A novel defected ground structure to improve the output power of a VCO
Authors: Liu H. W. , Sun X. W. , Cheng Z. Q. , Li Z. F. 
Published: June 2003

AbstractIn this paper, a novel defected ground structure (DGS), connected in parallel to two periodic structures with different center frequencies of the stopband, is proposed for increasing the output power of a voltage‐controlled oscillator (VCO) in microstrip circuits. To evaluate the effects of DGS on the output power, two GaAs field‐effect transistor (FET) VCOs have been designed and fabricated. One of them has a 50Ω microstrip line with DGS at the output section, while the other has only a 50Ω straight line. Measured results show that DGS rejects the second harmonic at the output and yields improved output power by 1–5%. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 279–281, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11038
Reflection and anomalous behavior of refractive index in defect photonic band gap structure
Authors: Srivastava Sanjeev K. , Ojha S. P. 
Published: June 2003

AbstractThis paper describes the reflectivity properties of layer‐by‐layer‐based photonic band gap (PBG) structures with a defect in their normal structures. The defect is created by the removal of a single material slab. To calculate reflectivity, we use a 2 × 2 matrix formulation. The defective PBG structure gives nearly 100% reflections in the near‐infrared region in addition to some parts of the visible region of the wavelengths for all possible angles, and thus acts as broadband reflector. Also, we study the anomalous behavior of the refractive index in these structures and find that the effective refractive index neff ≪ 1 nears the band edges. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 293–297, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11041
Use of B‐spline curves and genetic algorithms to reduce the sidelobe level in array‐patterns
Authors: Lue Wen‐Chia , Hsu Fang 
Published: June 2003

AbstractA method of minimizing the sidelobe level for linear array patterns by amplitude‐only adjustment in element excitations, which involves combining B‐spline techniques and genetic algorithms, is considered. We demonstrate this technique using a 30‐element linear array. It is also capable of limiting the coupling effects between adjacent elements. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 308–311, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11045
Bistatic phase function and fast solution of scattering by 2D random distributed scatterers
Authors: Guo Jianjun , Tsang Leung , Chang A. T. C. , Li Q. , Huang C.‐C. , Ding K.‐H. 
Published: June 2003

AbstractWe present large‐scale Monte Carlo simulation results of the phase functions in multiple scattering by dense media of small 2D particles. Solution of the Foldy–Lax equations with large number of unknowns is done efficiently using the sparse‐matrix canonical‐grid (SMCG) method. The SMCG method facilitates the use of FFT and results in an N log N‐type efficiency for CPU and O(N) for memory. This dependence is demonstrated by the simulation of CPU time using up to 50000 particles that are randomly distributed through random walk in a large area of 400 square wavelengths. The bistatic phase functions for a random medium are computed. The phase function converges with the number of particles and the number of realizations. The simulation results indicate that the nonsticky particles, sticky particles, and independent scattering have similar angular distribution patterns of the phase functions. However, the dense sticky particles show stronger scattering than the independent scattering, while the dense nonsticky particles have smaller scattering than that of the independent scattering. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 313–317, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11047
Structural proteome of human colostral fat globule membrane proteins
Authors: Fortunato Donatella , Giuffrida Maria Gabriella , Cavaletto Maria , Garoffo Lorenza Perono , Dellavalle Giuseppina , Napolitano Lorenzo , Giunta Carlo , Fabris Claudio , Bertino Enrico , Coscia Alessandra , Conti Amedeo 
Published: June 2003

AbstractMilk fat globule membrane (MFGM) contains proteins derived from the apical membrane of secreting epithelial cells of the mammary gland. Between 2–4% of total human milk protein content is associated with the fat globule fraction, as MFGM proteins. While MFGM proteins have very low classical nutritional value, they play important roles in various cell processes and defence mechanisms for the newborn. To date, fewer than 30 human MFGM proteins have been identified and characterized, either by immunological methods or by Edman sequencing and mass spectrometry. This study aimed to update the structural proteome of human colostral MFGM proteins and to create an annotated two‐dimensional electrophoresis (2‐DE) MFGM protein database available on‐line. More than one hundred 2‐DE spots derived from human colostral MFGM proteins were investigated by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry and proteins were identified by three different software packages available on the web (PeptIdent, MS‐Fit and ProFound); uncertain identifications were solved by nanoelectrospray ionization‐ion trap mass spectrometry using SEQUEST software.