bluuebunny/crossref_metadata_2025_split huggingface dataset:
Up‐regulation of p21CIP1 expression mediated by ERK‐dependent and ‐independent pathways contributes to hepatocyte growth factor‐induced inhibition of HepG2 hepatoma cell proliferation
Authors: Shirako Erika , Hirayama Naoki , Tsukada Yu‐ichi , Tanaka Toshiaki , Kitamura Naomi 
Published: November 2007

AbstractStrong activation of the ERK signal is required for hepatocyte growth factor (HGF) to inhibit proliferation of the human hepatocellular carcinoma cell line HepG2. However, it is still to be elucidated whether the activation alone is sufficient to induce the inhibitory effect. In this study, we constructed HepG2 cell clones expressing a high level of epidermal growth factor receptor (EGFR), and examined the effect of the strong activation of ERK on the proliferation of the cell clones. EGF treatment of the cell clones induced strong activation of ERK similar to HGF treatment, but did not inhibit cell proliferation. HGF treatment of the cell clones up‐regulated the expression of a Cdk inhibitor p16INK4a, which has previously been shown to be required to inhibit the proliferation of HepG2 cells, but EGF treatment did not. Furthermore, EGF treatment of the cell clones did not induce the up‐regulation of another Cdk inhibitor p21CIP1, whereas HGF treatment did. Knockdown of p21 by siRNA restored the proliferation of HepG2 cells inhibited by HGF, and restored Cdk2 activity suppressed in HGF‐treated HepG2 cells. These results suggest that strong activation of ERK alone is not sufficient, and some other pathway(s), which is activated through the HGF receptor but not through EGFR, is also required to induce the up‐regulation of p16 and p21 expression, and also suggest that in addition to the up‐regulated expression of p16, that of p21 contributes to the suppression of Cdk2 activity leading to the inhibition of proliferation of HGF‐treated HepG2 cells. J. Cell. Biochem. 104: 176–188, 2008. © 2007 Wiley‐Liss, Inc.
Fused‐core particle technology as an alternative to sub‐2‐μm particles to achieve high separation efficiency with low backpressure
Authors: Cunliffe Jennifer M. , Maloney Todd D. 
Published: November 2007

AbstractFused‐Core particles have recently been introduced as an alternative to using sub‐2‐μm particles in chromatographic separations. Fused‐Core particles are composed of a 1.7 μm solid core surrounded by a 0.5 μm porous silica layer (dp = 2.7 μm) to reduce mass transfer and increase peak efficiency. The performance of two commercially available Fused‐Core particles (Advanced Materials Technology Halo C18 and Supelco Ascentis Express C18) was compared with sub‐2‐μm particles from Waters, Agilent, and Thermo Scientific. Although the peak efficiencies were only ∼︁80% of those obtained by the Waters Acquity particles, the 50% lower backpressure allowed columns to be coupled in series to increase peak efficiency to 92 750 plates. The low backpressure and high efficiencies of the Fused‐Core particles offer a viable alternative to using sub‐2‐μm particles and very‐high‐pressure LC instrumentation.
Magnetic resonance microneurography of rabbit sciatic nerve on a 1.5‐T clinical MR system correlated with gross anatomy
Authors: Shen Jun , Wang Hua‐Qiao , Zhou Cui‐Ping , Liang Bi‐Ling 
Published: November 2007

AbstractThis study was performed to investigate the feasibility and accuracy of magnetic resonance (MR) microneurography of the rabbit sciatic nerve on a 1.5‐T clinical MR system by correlation with the gross anatomy. The 3D T2‐weighted imaging (3D‐T2WI), 3D T2‐weighted imaging plus spectral presaturation with inversion recovery (SPIR), and T1‐weighted imaging (T1WI) of the sciatic nerve in ten rabbits were performed on a 1.5‐T MR system. The radiological anatomy of the sciatic nerve was observed and correlated with the gross anatomy. The anterior–posterior diameter of the sciatic nerve trunk was measured on 3D T2WI and on gross anatomy. The T1 and T2 relaxation times were also measured with multiecho spin echo and mixed sequence, respectively. The tibial nerve and peroneal nerve in the sciatic nerve trunk in all ten rabbits could be clearly displayed on T2WI and T2WI. The fine branches of the gastrocnemius nerve, posterior femoral cutaneous nerve, and the posterior gluteal nerve could be clearly depicted on T2WI. The T1 and T2 relaxation times of the sciatic nerves were 915 and 40 ms, respectively. The anterior–posterior diameter of sciatic nerve trunk was measured grossly, and on T2WI was 3.17 ± 0.21 mm and 3.15 ± 0.19 mm, respectively. There was no statistically significant difference (t = 0.768, P = 0.462). With the 1.5‐T clinical MR system, the microneurography of the sciatic nerve could be revisualized, and the finer structure of the sciatic nerve trunk could be clearly and accurately delineated. © 2007 Wiley‐Liss, Inc. Microsurgery, 2008.
Effects of various protocols of ischemic preconditioning on rat tram flaps
Authors: Wang Honggang , Li Zhiyong , Liu Xiaolin 
Published: November 2007

AbstractWe used rat transverse rectus abdominis musculocutaneous (TRAM) flaps to investigate whether the ischemic cycle duration and number of cycles influenced the effectiveness of ischemic preconditioning (IPC). First, the animals were divided into one control group and four treatment groups. Controls received no preconditioning; flaps with IPC were treated by two cycles of pedicel clamping and reperfusion for either 5 or 10 min. Then the best of IPC protocols in first part was selected, and flaps were subjected to one or three cycles of IPC before 4 h of normothermic ischemia. The preconditioned flap survival area had improved 2.5–3 times over that of the control area by postoperative day 7. Serum creatine phosphokinase (CPK), water content, and malondialdehyde (MDA) in muscle were significantly decreased in the preconditioned groups after 4 h of reperfusion. Especially, 2 and 3 cycles of the 10/5‐min combination were more effective than other protocols of IPC. © 2007 Wiley‐Liss, Inc. Microsurgery, 2008.
Microsurgical anatomy of dorsal root entry zone of brachial plexus
Authors: Xiang Jian‐Ping , Liu Xiao‐Ling , Xu Yang‐Bing , Wang Jian‐Yun , Hu Jun 
Published: November 2007

AbstractThe purpose of this study was to describe microsurgical anatomy of the dorsal root entry zone (DREZ) and provide an anatomic basis for the approach of DREZ lesion in treating radiculopathy of brachial plexus avulsion injuries. We studied 100 dorsal cervical roots and DREZ/posterior horn complexes in 20 adult cadavers. At each root level the following data were recorded: widths of laminectomy, numbers of posterior rootlets, angle of the inferior rootlets with the spinal cord, and distance from posterior median sulcus to posterolateral sulcus. On cross‐sectional plane, the length and width of dorsal horn and the angle between longitudinal axis of dorsal horn and sagittal plane of spinal cord were measured. The results showed that the spinal cord segment and the entry of dorsal roots from C5 to T1 were exposed clearly after laminectomy from C4 to C7. The average number of roolets of C5‐T1 roots was about 7.76 and C6 has the most. From up to down, the angle from the inferior rootlet to spinal cord of C5‐T1 diminished gradually. The average distance from posterior median sulcus to posterolateral sulcus was 2.95 mm. The average length, width, and angle of posterior horn were 3.47 mm, 1.346 mm, and 35.9°, respectively. Our study demonstrated that the spinous process and lamina of the C4 to C7 vertebrae should be resected to expose the C5‐T1 when DREZ lesions are employed to treat pain after brachial plexus avulsion. The lesion‐making apparatus should be inserted at an angle of 30°–40°, the width of lesion should be less than 1.2 mm and the lesion depth less than 3.1 mm. © 2007 Wiley‐Liss, Inc. Microsurgery, 2008.
Low levels of maternal serum PAPP‐A in the first trimester and the risk of pre‐eclampsia
Authors: Spencer Kevin , Cowans Nicholas J. , Nicolaides Kypros H. 
Published: November 2007

AbstractBackgroundLow levels of pregnancy associated plasma protein‐A (PAPP‐A) have been previously shown to be associated with pregnancies that subsequently develop pre‐eclampsia. The objective of this study was to establish the relative risk for pre‐eclampsia at various PAPP‐A levels as an aid to counselling and follow up of pregnancies.MethodsMaternal serum PAPP‐A and free ß‐human chorionic gonadotropin (ß‐hCG) levels at 11 to 13 weeks of gestation from 224 singleton pregnancies that subsequently developed pre‐eclampsia were compared to those from 47 770 normal singleton pregnancies resulting in live births after 37 weeks with birth weight greater than or equal to the 10th centile of normal for gestation. In all cases, the measured PAPP‐A and free ß‐hCG levels were expressed as multiple of the median (MoM). The association between metabolite levels and the incidence of pre‐eclampsia was assessed by comparing the relative incidence at a number of MoM cut‐offs and at various centiles. At various marker levels, the likelihood ratio for pre‐eclampsia was also calculated.ResultsIn the pre‐eclampsia group the median PAPP‐A MoM was significantly reduced (0.772 MoM, p < 0.0001) whilst the median free β‐hCG MoM was not different from controls (0.981 MoM, p = 0.26). With decreasing levels of PAPP‐A, the likelihood ratio for pre‐eclampsia increased. At the 5th centile of normal (PAPP‐A MoM 0.415) the odds ratio was increased 4‐fold and at this cut‐off 15% of cases of pre‐eclampsia would be identified.ConclusionsThe graphical presentation of a likelihood ratio curve for pre‐eclampsia at any PAPP‐A MoM level is likely to be useful in counselling women with low levels of PAPP‐A and a normal karyotype. Use of low levels of PAPP‐A for selecting women for further follow‐up with uterine artery Doppler may further improve the clinical discrimination. Copyright © 2007 John Wiley & Sons, Ltd.
Crystal structure and functional analysis identify the P‐loop containing protein YFH7 of Saccharomyces cerevisiae as an ATP‐dependent kinase
Authors: Gueguen‐Chaignon Virginie , Chaptal Vincent , Larivière Laurent , Costa Narciso , Lopes Philippe , Morera Solange , Nessler Sylvie 
Published: November 2007

AbstractGenome sequencing projects have revealed that P‐loop proteins are highly represented in all organisms and that many of them have no attributed function. They are characterized by a conserved nucleotide‐binding domain and carry different activities implicated in many cellular processes. Saccharomyces cerevisiae YFH7 is one of these P‐loop proteins of unknown function. In this work we tried to integrate bioinformatics, structure, and enzymology to discover the function of YFH7. Sequence analysis revealed that yeast YFH7 is a yeast‐specific protein showing weak similarity with the phosphoribulokinase/uridine kinase/bacterial pantothenate kinase (PRK/URK/PANK) subfamily of P‐loop containing kinases. A large insertion of about 100 residues distinguishes YFH7 from other members of the family. The 1.95 Å resolution crystal structure of YFH7 solved using the SAD method confirmed that YFH7 has a fold similar to the PRK/URK/PANK family, with the characteristic core, lid, and NMPbind domains. An additional α/β domain of novel topology corresponds to the large sequence insertion. Structural and ligand binding analysis combined with enzymatic assays suggest that YFH7 is an ATP‐dependent small molecule kinase with new substrate specificity. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Context‐specific amino acid substitution matrices and their use in the detection of protein homologs
Authors: Goonesekere Nalin C. W. , Lee Byungkook 
Published: November 2007

AbstractThe sequence homology detection relies on score matrices, which reflect the frequency of amino acid substitutions observed in a dataset of homologous sequences. The substitution matrices in popular use today are usually constructed without consideration of the structural context in which the substitution takes place. Here, we present amino acid substitution matrices specific for particular polar–nonpolar environment of the amino acid. As expected, these matrices [context‐specific substitution matrices (CSSMs)] show striking differences from the popular BLOSUM62 matrix, which does not include structural information. When incorporated into BLAST and PSI‐BLAST, CSSM outperformed BLOSUM matrices as assessed by ROC curve analyses of the number of true and false hits and by the accuracy of the sequence alignments to the hit sequences. These findings are also of relevance to profile–profile‐based methods of homology detection, since CSSMs may help build a better profile. Profiles generated for protein sequences in PDB using CSSM‐PSI‐BLAST will be made available for searching via RPSBLAST through our web site http://lmbbi.nci.nih.gov/. Proteins 2008; 71:910–919. Published 2007 Wiley‐Liss, Inc.
Crystal structure of an archaeal specific DNA‐binding protein (Ape10b2) from Aeropyrum pernix K1
Authors: Kumarevel Thirumananseri , Sakamoto Keiko , Gopinath Subash C. B. , Shinkai Akeo , Kumar Penmetcha K. R. , Yokoyama Shigeyuki 
Published: November 2007

AbstractDNA binding proteins are essential in all organisms, and they play important roles in both compacting and regulating the genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of Alba or Sso10b, which is a small, abundant, basic protein that binds DNA. Here, we present the crystal structure of Ape10b2 from Aeropyrum pernix K1 at 1.70 Å. Although the overall structure resembles the known Alba protein fold, a significant conformational change was observed in the loop regions. Specifically, the L5 loop is slightly longer, as compared to those of other known proteins, and the flexibility of this loop may facilitate the interaction with double stranded DNA. In addition, we showed that Ape10b2 binds to 16 and 39 bp duplex DNAs with high affinity. On the basis of our analyses, we have created a putative protein‐DNA complex model. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Full‐color nanostructured thin‐film electroluminescent device utilizing ZnS nanocrystals doped with activator‐ions
Authors: Toyama T. , Adachi D. , Okamoto H. 
Published: November 2007

AbstractWe have studied nanostructured (NS‐) thin‐film electroluminescent (TFEL) devices utilizing the ZnS nanocrystals (NCs) with the mean crystal sizes of ca. 2–4 nm doped with activator‐ions. As compared to the conventional TFEL device, we have achieved a remarkable reduction in the operation voltages by >100 V0–p. Moreover, toward full‐color emissions, EL emissions of three primary colors, i.e., red, green, and blue have been derived from Mn2+, Tb3+, and Tm3+ ions, respectively. In this article, we review the studies on the fundamental properties of ZnS NCs as well as the device performance of the NS‐TFEL devices. We also discuss the excitation mechanisms of the activator‐ions in the ZnS NCs. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Energy transfer from Si nanocrystals to Er ions near a metal layer
Authors: Fujii M. , Nakamura T. , Miura S. , Inui M. , Hayashi S. 
Published: November 2007

AbstractEr ions can be excited efficiently by energy transfer from Si nanocrystals. There are several different kinds of energy transfer processes depending on the distance between Si nanocrystals and Er ions. Among them, Förster‐type dipole–dipole interaction is considered to have the longest interaction distance. In this work, we study how the long‐distance interaction is modified when Er–Si‐nanocrystals coupled system is placed near a metal layer. We show that the energy transfer rate is strongly modified by the metal layer and the rate oscillates depending on the distance between the metal and the coupled system. From the quantitative analysis of the oscillation behavior, the energy transfer efficiency as well as the rate is estimated as a function of the energy transfer wavelength, and the evidence of resonant energy transfer is demonstrated. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Near‐field light emission from dark‐states in semiconductor quantum dots
Authors: Pistone G. , Savasta S. , Di Stefano O. , Martino G. , Girlanda R. , Portolan S. 
Published: November 2007

AbstractWe theoretically study the carrier capture and distribution among the available energy levels of a symmetric semiconductor quantum dot under continuous‐wave excitation resonant with the barrier energy levels. We find that at low temperature all the dot level‐occupations but one, the second (dark) energy level,decrease monotonically with energy. The second energy level, displays a steady‐state carrier density exceeding that of the lowest level more than a factor two (see the figure). This nonequilibrium effect does not origin from radiative recombination before relaxation to lower energy levels, but at the opposite, it is consequence of carrier trapping due to the symmetry‐induced suppression of radiative recombination of the second (dark) energy level. While the observation of such effect by means of far‐field spectroscopy is prevented, scanning near‐field optical microscopy, able to detect the evanescent waves generated by dark‐states occupations, can be adopted to inspect such nonequilibrium effects at the nanoscale. Exciton‐level occupations of the dot (normalized at the maximum) calculated for two different temperatures. See Sect. 3 for a detailed description of the results here displayed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microstructure, dielectric, and piezoelectric properties of 0.38Bi(Gax Sc1–x)O3–0.62PbTiO3 high temperature piezoelectric ceramics
Authors: Jiang Yihang , Qin Baoquan , Zhao Yi , Jiang Yuzhi , Xiao Dingquan , Zhu Jianguo 
Published: November 2007

Abstract0.38Bi(Gax Sc1–x )O3–0.62PbTiO3 (BGSPTx) ceramics have been prepared by using the conventional mixed oxide method. X‐ray diffraction analysis revealed that BGSPTx has a pure perovskite structure, and the crystal symmetry of BGSPTx changed from rhombohedral to tetragonal with increasing Ga content (x). The Curie temperature (TC) of BGSPTx ceramics is in the range of 448–467 °C for different x. The ferroelectric phase transition of BGSPTx was found to be of the first order type according to the Curie–Weiss law. For x = 0.125, BGSPTx ceramics show enhanced piezoelectric properties: piezoelectric constant d33 = 420 pC/N and d31 = –142 pC/N, planar and thickness electromechanical coupling factors kp = 56.27% and kt = 56.00%, respectively. The high‐TC of BGSPTx coupled with its excellent piezoelectric properties suggests those future high‐temperature applications. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Probing Glycans With the Copper(I)‐Catalyzed [3+2] Azide–Alkyne Cycloaddition
Authors: Hanson Sarah R. , Greenberg William A. , Wong Chi‐Huey 
Published: November 2007

AbstractThe imposing structural complexity and heterogeneity of glycans has made the study of their precise biological roles challenging. However, recently developed synthetic and screening techniques have enabled the study of many aspects of glycan activity that were previously inaccessible. Among these new methods, the Copper(I)‐catalyzed Azide–Alkyne [3+2] Cycloaddition (CuAAC) has provided a means to mimic multivalent glycan display, manipulate cellular glycans in vivo for visualization and isolation, and generate useful inhibitors of glycoprotein processing.
Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide
Authors: Hatfield Marcus P. D. , Palermo Nicholas Y. , Csontos József , Murphy Richard F. , Lovas Sándor 
Published: November 2007

AbstractThe accuracy of the determination of the energy of interaction between Phe20 and the Pro5‐Thr6‐Tyr7‐Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc‐pVTZ level of theory. The most accurate determination resulted from acetylation of the α‐amino group combined with methyl amidation of the α‐carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the α‐amino group with the replacement of the α‐carbonyl group with a hydrogen and the hydrogenation of the α‐amino group with methylation of the α‐carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Results of total hip replacement using the Robodoc surgical assistant system: clinical outcome and evaluation of complications for 97 procedures
Authors: Schulz Arndt P. , Seide Klaus , Queitsch Christian , von Haugwitz Andrea , Meiners Jan , Kienast Benjamin , Tarabolsi Mohamad , Kammal Michael , Jürgens Christian 
Published: November 2007

AbstractBackgroundA computerized robotic surgical system was developed from 1986 by the Thomas J. Watson Research Center. In 1992 the system unit Orthodoc® and the milling robot Robodoc® were first used on humans. We present the results achieved with Robodoc‐assisted total hip arthroplasty in 97 hips.MethodsBetween 1997 and 2002, 143 total hip replacements (128 patients) were performed using the Robodoc system. This is a consecutive series. Complete follow‐up was possible in 97 hips at a mean follow‐up period of 3.8 years.ResultsTechnical complications directly related to the robotic device occurred in nine cases (9.3%). The pre‐operative Merle d'Aubigne score was determined at 8.1 points compared to a post‐operative mean score of 16.2. There was no sign of femoral stem loosening on radiographs.ConclusionsRobotic‐assisted total hip arthroplasty with the Orthodoc/ Robodoc system achieves equal results as compared to a manual technique. However, there was a high number of technical complications directly or indirectly related to the robot. Copyright © 2007 John Wiley & Sons, Ltd.
Probabilistic automata push‐down
Authors: Chen Zhi‐Zhong , Kasai Takumi 
Published: November 2007

AbstractThis paper discusses the basic properties of the probabilistic push‐down automaton (PPDA). Intuitively speaking, PPDA is obtained by adding a probabilistic property to the nondeterministic transition of the nondeterministic push‐down automaton (NPDA). According to the property of the error in the accepting condition, PPDA is classified into a two‐sided error PPDA, a one‐sided error PPDA, and bounded error PPDA. Moreover, the acception error is considered not only for 1/2, but also for an arbitrary cut‐point, to discuss the relations among classes of languages. Major results are as follows.The class of languages accepted by bounded error PPDA is not the same as that accepted by NPDA. In the case of two‐sided error PPDA and the bounded error PPDA, the class of acceptable languages does not depend on the cut‐point. In the case of a one‐sided PPDA, the class of acceptable languages depends to some extent on the cut‐point. In other words, there exists an infinite hierarchy. Kolmogorov complexity is used in the proof of the major theorem.
Analysis of catastrophic phenomena in a multiprogramming system
Authors: Yokohira Tokumi , Miyahara Hideo 
Published: November 2007

AbstractThis paper presents a state analysis of multiprogramming, using the concept of cusp catastrophe in the theory of catastrophe. Based on the result, the catastrophic phenomena in the multiprogramming system are analyzed. It is shown first that the multiprogramming system exhibits two stable states, i.e., monostable and bistable states, for the change of job generation rate and the change of the maximum multiprogramming level. Then it is shown that a rapid change (catastrophe) of the performance of the multiprogramming system, such as the mean number of jobs in the system, throughput and response time, may occur with the change of the stable state of the system. Furthermore, it is shown that for any given job generation rate, there exists a maximum multiprogramming level which maximizes the throughput and minimizes the response time.