bluuebunny/crossref_metadata_2025_split huggingface dataset:
X‐ray analysis of phosphoglycerate kinase 2, a sperm‐specific isoform from Mus musculus
Authors: Sawyer Gregory M. , Monzingo Arthur F. , Poteet Ethan C. , O'Brien Deborah A. , Robertus Jon D. 
Published: November 2007

AbstractPhosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X‐linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3‐phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 Å resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the “open” form; that is the N‐terminal domain that can bind 3PG and the C‐terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13° rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C‐terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Ranking predicted protein structures with support vector regression
Authors: Qiu Jian , Sheffler Will , Baker David , Noble William Stafford 
Published: November 2007

AbstractProtein structure prediction is an important problem of both intellectual and practical interest. Most protein structure prediction approaches generate multiple candidate models first, and then use a scoring function to select the best model among these candidates. In this work, we develop a scoring function using support vector regression (SVR). Both consensus‐based features and features from individual structures are extracted from a training data set containing native protein structures and predicted structural models submitted to CASP5 and CASP6. The SVR learns a scoring function that is a linear combination of these features. We test this scoring function on two data sets. First, when used to rank server models submitted to CASP7, the SVR score selects predictions that are comparable to the best performing server in CASP7, Zhang‐Server, and significantly better than all the other servers. Even if the SVR score is not allowed to select Zhang‐Server models, the SVR score still selects predictions that are significantly better than all the other servers. In addition, the SVR is able to select significantly better models and yield significantly better Pearson correlation coefficients than the two best Quality Assessment groups in CASP7, QA556 (LEE), and QA634 (Pcons). Second, this work aims to improve the ability of the Robetta server to select best models, and hence we evaluate the performance of the SVR score on ranking the Robetta server template‐based models for the CASP7 targets. The SVR selects significantly better models than the Robetta K*Sync consensus alignment score. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Photosensitized luminescent lanthanide (III) clusters encapsulated with polyphenylsilsesquioxane
Authors: Manseki Kazuhiro , Yanagida Shozo 
Published: November 2007

AbstractAn inorganic–organic lanthanide (III) cluster encapsulated with polyphenylsilsesquioxane (PPSQ), which would be a suitable luminescent material for violet LEDs excitation will be reported. The cluster with adjacent 9 terbium (III) ions in close proximity (3.6 ∼ 3.7 Å), in which lanthanide (III) ions are stabilized with organic photosensitizing compounds, 16 hexylsalicylates, has been successfully introduced. The terbium (III) cluster was highly soluble in PPSQ and had high thermostability. By the ligand excitation of the cluster‐doped PPSQ at around near‐UV light region (e.g., 360–380 nm), the terbium (III) cluster displayed strong green luminescence with a maximum intensity at 547 nm (intra‐4f transition of terbium (III) ion: 5D4 → 7F5). It was likely that energy transfer from excited hexylsalicylates to terbium (III) ions mediated sensitized emission of Tb (III) ions in PPSQ. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A comparative investigation of the damage build‐up in GaN and Si during rare earth ion implantation
Authors: Gloux Florence , Ruterana Pierre , Lorenz K. , Alves E. 
Published: November 2007

AbstractThe medium range implantation of rare earth ions at room temperature in GaN layers leads to the formation of point defect clusters, basal and prismatic stacking faults from the lowest fluence. When a threshold fluence of about 3 × 1015 at/cm2 is reached, a highly disordered ‘nanocrystalline layer’ (NL) is observed to form at the surface. This layer is made of a mixture of misoriented nanocrystallites and voids. Beyond this NL, I1, I2 and E basal stacking faults (BSFs) have been identified, as well as in GaN implanted at lower fluences than the threshold. Prismatic stacking faults (PSFs) with Drum atomic configuration connect the I1 BSFs. A similar investigation of the damage in Eu implanted Si shows a completely different behaviour; in this case, from the relatively low fluence 1 × 1014 at/cm2, amorphization starts in patches at the projected range and extends very rapidly towards the surface and the bulk, to form a uniform amorphous layer already at 2 × 1014 at/cm2. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gallium nitride and GaN:Eu nanocrystalline luminescent powders
Authors: Flores G. A. Hirata 
Published: November 2007

AbstractIn this study, we report on the fabrication and luminescent properties of pure and europium‐doped gallium nitride (GaN) powders obtained by means of two different chemical methods. Firstly, GaN and GaN:Eu microcrystalline powders were successfully prepared by using the combustion synthesis of metallic nitrates as the precursors (method A). By using a second processing route, GaN and (Ga1–x Eux )N powders are synthesized from metallic oxides (method B) yielding directly nanocrystalline‐phase gallium nitride and Eu‐doped gallium nitride luminescent materials. In the present work, we report two excellent methods to produce nanocrystalline or microcrystalline gallium nitride (GaN) and Eu‐doped GaN powders with different Eu concentrations. The GaN:Eu materials were characterized by photoluminescence and cathodoluminescence measurements showing strong luminescence due to f–f transition lines within Eu3+(4f6) electron emission configuration. Furthermore we present a crystallographic characterization conducted by X‐ray diffraction (XRD), luminescence properties including photoluminescence and local cathodoluminescence spectra and monochromatic imaging at low‐temperature to detect the areas from where the emission is originated within the GaN:Eu grains.Our results show that (Ga0.95Eu0.05)N powders are cathodoluminescent with the main emission occurring at λ = 611 nm which is originated from the 5D0 → 7F2 transitions within the Eu3+ electronic levels. Low‐temperature monochromatic cathodoluminescence images taken on microcrystalline powders (produced by method A), indicate that the main emission at λ = 611 nm is originated within nanocrystalline areas of the GaN:Eu3+ microcrystalline grains. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Well‐Defined Poly(N‐glycosyl 1,2,3‐triazole) Multivalent Ligands: Design, Synthesis and Lectin Binding Studies
Authors: Geng Jin , Lindqvist Josefina , Mantovani Giuseppe , Chen Gaojian , Sayers Claire T. , Clarkson Guy J. , Haddleton David M. 
Published: November 2007

AbstractGlycopolymers have been synthesised by post‐functionalisation of well‐defined alkyne‐functional polymers with sugar azides to yield N‐glycosyl 1,2,3‐triazole functional polymers. The Cu(I)‐catalysed Huisgen cycloaddition was used to attach α‐mannoside, β‐galactoside and β‐lactoside derivatives via an azide functionality bound directly to the sugar anomeric carbon. Three different catalytic systems were investigated for the click reactions; [(PPh3)3Cu(I)Br], TBTA/Cu(I)Br and bathophenanthrolinedisulphonic acid disodium salt/Cu(I)Br. The latter of these was found to be the most efficient for the attachment of the larger/more sterically hindered disaccharide lactose moiety. The interaction of the lactose‐ and galactose‐bearing glycopolymers with Ricinus Communis Agglutinin (RCA I) lectin was investigated by affinity HPLC analysis. The rate of the interaction between mannose polymer and concanavalin A (Con A) lectin was assessed by turbidimetry. The results from the lectin conjugation studies indicate that the glycopolymers prepared in this work are able to function as multivalent ligands, further suggesting that the attachment of the triazole directly to the sugar anomeric carbon has no significant effect on the interaction of these glycopolymers with Con A and RCA I.
Desorption electrospray ionization of aerosol particles
Authors: Dong Jianan , Rezenom Yohannes H. , Murray Kermit K. 
Published: November 2007

AbstractWe have applied desorption electrospray ionization to aerosol particles. Ions were formed from aerosols by merging suspended dry particles with an electrospray of solvent in a modified ion trap mass spectrometer. Dry aerosol particles were generated using a fluidized bed powder disperser and directed toward the inlet of the mass spectrometer. A nanospray source was used to create a spray of solvent droplets directed at the inlet and at a right angle with respect to the aerosol. Ions generated by the interaction of the particles and electrospray were transferred into the ion trap mass spectrometer. Using this method, pure samples of caffeine and erythromycin A were analyzed. In addition, commonly available food and drug powders including instant cocoa powder, artificial sweetener and ibuprofen were analyzed. Copyright © 2007 John Wiley & Sons, Ltd.
An environment for dataflow program development of parallel processing system‐harray
Authors: Yatnana Hayato , Kohdate Jun , Members Toshiaki Yasue, Associate , Muraoka Yoichi 
Published: November 2007

AbstractThis paper considers the dataflow program development environment for the system programmer who develops the compiler and proposes a method to improve the debugging efficiency. The conventional debugging methods are either: (1) to monitor the packet in the dataflow ring, or (2) to specify the function containing a bug. The former contains unsolved problems such as the determination of start timing for the data monitoring and the presentation of a large amount of information to the user. The latter contains a problem in that the debugging is impossible at the dataflow level.This paper aims at the solution of those problems, and the detailed debugging is executed on the software, not on the real machine. The information presentation on a dataflow graph is considered for systematic presentation of the debugging information. As the development environment, the parallel processing system Harray proposed by the authors is considered. In the proposed system, a two‐stage process is employed in which the first step is to specify the macro‐block (which is a task unit in Harray) containing the bug, and the second step is the detailed debugging of the specified macro‐block. The debugging within the macroblock is executed on the software, and the debugging efficiency is improved by: (1) diagram representation for easier visual recognition, and (2) backward tracing function.
Edge surface detection with subvoxel accuracy from 3‐d images
Authors: Kimura Shigeru , Ozawa Shinji 
Published: November 2007

AbstractA method is described for edge surface detection with subvoxel accuracy for three‐dimensional (3‐D) images. Direct extension of the subpixel edge detection method for 2‐D images into 3‐D applications has to deal with an explosion of operational combinations that make the method impractical. To overcome such a shortcoming, this paper proposes a practical approach consisting of two major steps: (1) extraction of local edge information; and (2) estimation of global edge surface from local edge information.To extract the candidate edge points as local edge information, we make use of the connected three voxels located on the straight lines referred to as the edge estimation axes. The coordinates of candidate edge points are derived from intensity gradients of three neighboring voxels along the edge estimation axis. Then, a planar fitting is performed on a set of candidate edge points to estimate a global edge surface in 3‐D.The key points of the method directly affecting the accuracy are the selection of the edge estimation axis and the weighting of the candidate edge points. The implementation reflecting these points is described.
Word spotting system based on stochastic models of phonemic segments
Authors: Okada Michio , Kohda Masaki 
Published: November 2007

AbstractThis paper presents a new architecture for word spotting, one of the most important technologies in continuous speech recognition. If the word spotting algorithm can automatically create standard word and phrase models from phonemic segment models smaller than single words, it is able to facilitate large vocabulary spotting. It is also flexible in accommodating acoustic variation in phonetic units within continuously spoken speech.The word spotting algorithm proposed here has the following features: (1) Local spectrum sequence in speech are referred to as “acoustic events,” and each phonetic segment is represented as a sequence of these events. Local spectrum variations are accommodated in terms of probabilistic models, and variations in the temporal structure of phonemic segments are handled by using dynamic time warping matching method for event sequences. (2) In continuous speech used for learning, the event sequence that make up the phonemic segment are automatically learned through an iterative process of altering the boundaries of phonemic segments. (3) Phonetic strings in phonetic orthography may be joined into phonemic segments appropriate to the phonemic environment, automatically creating any desired standard patterns for words or phrases. The performance of this algorithm is demonstrated in phoneme recognition, word spotting and phrase spotting.
Improved reslicing by voxel‐project‐method
Authors: Nakanishi Mamoru 
Published: November 2007

AbstractThe projection processing has frequently been applied in recent years, where the three‐dimensional image composed of a large number slices, such as X‐ray CT and MRI, is used as the input. In such processings, the cross section is produced with arbitrary position and inclination, or the three‐dimensional image is reprojected on an arbitrary plane. In the generation of the cross section especially, the highspeed processing is required as a pre‐processing for the image understanding. The voxel‐search method and the voxel‐projection method have been employed as the methods for projection. The voxel‐search method has been used widely because of the better image quality, but has a problem in that the speed improvement by parallel structure is difficult. The voxel‐projection method, on the other hand, can easily be implemented on a parallel system, but the deterioration of the image quality has been a problem.This paper aims at the method to generate cross section which can realize the same image quality as in the conventional voxel‐search method while maintaining the parallelism of the voxel‐projection method. The image deterioration, such as the missing of the image data and the striped pattern of intensities on the image, are remedied. The scanning place determination is proposed for the former problem, which can determine the object of projection according to the inclination of the cross section. The average distribution technique is proposed for the latter problem, and it is shown that the cross section with a satisfactory image quality can be generated. Thus, it is shown that the voxel‐projection method can be applied to the cross section generation, paving the way to the realization of the cross section generation system with the speed improved by the parallel processing.
Bidirectional learning for neural network having butterfly structure
Authors: Morita Tatsuya , Nakajima Kazuyoshi 
Published: November 2007

AbstractThe number of interconnections between cells in a neural network, which is proportional to square of the number, causes a problem in the structure of the network when the number is large. The fast Fourier transform is a method to speed up matrix operation by using a butterfly operation.This paper proposes a method of reducing the number of connections between cells in a neural network by using a multilayer structure which is based on a butterfly operation. Since the neural network inevitably a multilayer structure, it is necessary to employ a new learning method which replaces the conventional backpropagation method.To satisfy this condition, this paper proposes an inverse function method which generates an intermediate target of learning in an inverse direction from a teacher signal at the last stage, and a bidirectional learning method which is an improvement of the inverse function method. The bidirectional learning method improves the learning effect, since the learning process is more stable than the inverse function method, and intermediate targets are generated taking into account the state of the output of each step. This is demonstrated by using a two‐dimensional pattern transform problem.
A unified theory of the family of projection filters for signal and image estimation
Authors: Koide Yuji , Yamashita Yukihiko , Ogawa Hidemitsu 
Published: November 2007

AbstractIn an image restoration problem, there are many problems involved in accurate estimation of the original form from the restricted form. The family of projection filters, comprising the projection filter, the partial projection filter, and the averaged projection filter, has a good performance in such estimation problems. To construct these filters, we have to solve a system of operator equations. These operator equations have been solved in several ways and there were subtle differences between each expression of the form of solution. Besides, there were some properties already known for one filter, while not known for another filter. If we can discuss these three filters together, we can clarify unknown properties at the same time and give the unified form for each filter. One of authors has in fact had some success in this regard. However, the filter forms obtained there were more complicated than the original forms obtained respectively. To solve this problem, we propose another system of operator equations which can give almost the same form as the original and discuss the unified theory of the family of projection filter.
Accumulation of glial fibrillary acidic protein and histone H4 in brain storage bodies of Tibetan terriers with hereditary neuronal ceroid lipofuscinosis
Authors: Katz M. L. , Sanders D. N. , Mooney B. P. , Johnson Gary S. 
Published: November 2007

SummaryThe neuronal ceroid lipofuscinoses (NCLs) are inherited neurodegenerative diseases characterized by massive accumulation of autofluorescent storage bodies in neurons and other cells. A late‐onset form of NCL occurs in Tibetan terrier dogs. Gel electrophoretic analyses of isolated storage body proteins from brains of affected dogs indicated that a protein of approximately 50 kDa was consistently prominent and a 16 kDa component was present in some brain storage body preparations. Mass spectral analysis identified the 50 kDa protein as glial fibrillary acidic protein (GFAP), isoform 2. GFAP identification was supported by immunoblot and immunohistochemical analyses. Histone H4 was the major protein in the 16 kDa component. Specific accumulation of GFAP and histone H4 in storage bodies has not been previously reported for any of the NCLs. Tibetan terrier NCL may be the canine correlate of one of the human adult‐onset NCLs for which the genetic bases and storage body compositions have not yet been determined.
Temporal variation in CO2 efflux from soil and snow surfaces in a Japanese cedar (Cryptomeria japonica) plantation, central Japan
Authors: Lee Mi‐Sun , Lee Jae‐Seok , Koizumi Hiroshi 
Published: November 2007

AbstractCO2 efflux from soil and snow surfaces was measured continuously in a Japanese cedar (Cryptomeria japonica D. Don) forest in central Japan using an open dynamic chamber system. The chamber opens and closes automatically and records measurements based on an open‐flow dynamic method. Between May and December, mean soil CO2 efflux ranged from 1,529 mg CO2 m−2 h−1 in September to 255 mg CO2 m−2 h−1 in December. The seasonal change in CO2 efflux from the soil paralleled the seasonal pattern of soil temperature. No marked diurnal trends in soil CO2 efflux were observed on days without rainfall, whereas significant pulses in soil CO2 efflux were observed on days with rainfall. In this plantation, soil CO2 efflux frequently responded to rainfall. Measurements of changes from litter‐covered soil to snow‐covered surfaces revealed that CO2 efflux decreased from values of ca. 250 mg CO2 m−2 h−1 above soil to less than 33 mg CO2 m−2 h−1 above snow. Soil temperature alone explained 66% of the overall variation in soil CO2 efflux, but explained approximately 85% of the variation when data from two anomalous periods were excluded. Moreover, we found a significant correlation between soil CO2 efflux and soil moisture (which explained 44% of the overall variation) using a second‐order polynomial function. Our results suggest that the seasonality of CO2 efflux is affected not only by soil temperature and moisture, but also by drying and rewetting cycles and by litterfall pulses.
Brachial Artery Intima‐Media Thickness and Echogenicity in Relation to Lipids and Markers of Oxidative Stress in Elderly Subjects:‐The Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) Study
Authors: Lind Lars , Andersson Jessika , Rönn Monika , Gustavsson Thomas , Holdfelt Peter , Hulthe Johannes , Elmgren Anders , Zilmer Kersti , Zilmer Mihkel 
Published: November 2007

AbstractThe aim of the present study was to relate brachial artery intima‐media thickness (IMT) and the grey scale median of the intima‐media complex (IM‐GSM) to traditional cardiovascular risk factors and markers of inflammation and oxidative stress. In the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study, a population‐based study of 1016 subjects aged 70, brachial artery IMT and IM‐GSM, who were evaluated by ultrasound. Lipids, thirteen markers of inflammation and nine markers of oxidative stress were measured. The Framingham risk score was related to IMT (p < 0.0001), but not to the IM‐GSM. In univariate analysis, HDL‐cholesterol, serum triglycerides, fasting glucose, smoking, HOMA insulin resistance index and oxidized LDL levels were related to IMT. HDL and LDL‐cholesterol, triglycerides, VCAM‐1, e‐selectin, leukocyte count, conjugated diens, baseline conjugated diens (BCD)‐LDL, antibodies to oxLDL, the GSSG/GSH glutathione ratio and homocysteine were related to IM‐GSM. In multiple regression models, HDL‐cholesterol, fasting glucose and oxLDL levels were the independently related to IMT (p = 0.01–0.04), while serum triglycerides, BCD‐LDL and the GSSG/GSH ratio were independently related to IM‐GSM (p = 0.0001–0.004). In conclusion, in addition to traditional lipid variables, markers of oxidative stress were associated with both thickness and echogenicity of the brachial artery intima‐media complex. Thus, both thickness and echogenicity of the brachial artery intima‐media complex might be useful biomarkers in the future.