bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protecting TCP from a misbehaving receiver
Authors: Cheng Rung‐Shiang , Lin Hui‐Tang 
Published: June 2006

AbstractThis study presents the design and implementation of a robust TCP congestion control algorithm. TCP was originally designed for cooperative environments, and its evolution over the years has been built on the same basis. TCP expects the end hosts to cooperate with the TCP senders in implementing end‐to‐end congestion control. Therefore, misbehavior of a TCP receiver may result in an unfair division of the available bandwidth between the conforming flows and the irresponsible flows. Accordingly, this study examines the issues arising when conforming TCP connections are obliged to coexist with misbehaving connections. A modification to the TCP protocol is proposed to deal with various types of TCP misbehavior. Copyright © 2006 John Wiley & Sons, Ltd.
Effect of conjugated linoleic acid grafting on the hemocompatibility of polyacrylonitrile membrane
Authors: Kung Fu‐Chen , Yang Ming‐Chien 
Published: June 2006

AbstractPolyacrylonitrile (PAN) membrane was hydrolyzed with NaOH(aq) and grafted with conjugated linoleic acid (CLA) via esterification with 1,3‐propanediol. The resulting CLA grafted PAN membranes were characterized using Fourier transform infrared spectrometry (FT‐IR) and X‐ray photoelectronic spectroscopy (XPS). The effects of CLA grafting on the blood coagulation, platelet aggregation, and oxidative stress were evaluated using human blood. The complete blood count (CBC) and coagulation time (CT) was evaluated in vitro for hemocompatibility. After CLA grafting, the proliferation of human umbilical vein endothelial cells (HUVECs) on the membranes were improved. In addition, the production of reactive oxygen species (ROS) was measured by the chemiluminescence (CL) method to evaluate the oxidative stress. The results showed that the CLA‐grafted PAN membrane could keep the CBC values more stable than unmodified PAN membrane. The CLA‐grafted PAN membranes also showed longer CT. CLA‐grafted PAN membrane could keep the CL counts of hydrogen peroxide and superoxide values more stable than unmodified PAN membrane. These results suggest that a CLA‐grafted PAN membrane could offer protection for patients against oxidative stress and would be helpful for reducing the dosage of anticoagulant during hemodialysis. Copyright © 2006 John Wiley & Sons, Ltd.
Proteomic analysis of estrogen response of premalignant human breast cells using a 2‐D liquid separation/mass mapping technique
Authors: Zhao Jia , Zhu Kan , Lubman David M. , Miller Fred R. , Shekhar Malthy P. V. , Gerard Brigitte , Barder Timothy J. 
Published: June 2006

AbstractA 2‐D liquid‐phase separation method based on chromatofocusing and nonporous silica RP‐HPLC followed by ESI‐TOF‐MS was used to analyze proteins in whole cell lysates from estrogen‐treated and untreated premalignant, estrogen‐responsive cell line MCF10AT1 cells. 2‐D mass maps in the pH range 4.6–6.0 were generated with good correlation to theoretical Mr values for intact proteins. Proteins were identified based on intact Mr, pI and PMF, or MS/MS sequencing. About 300 unique proteins were identified and 120 proteins in mass range 5–75 kDa were quantified upon treatment of estrogen. Around 40 proteins were found to be more highly expressed (>four‐fold) and 17 were down‐regulated (>four‐fold) in treated cells. In our study, we found that many altered proteins have characteristics consistent with the development of a malignant phenotype. Some of them have a role in the ras pathway or play an important role in signal pathways. These changed proteins might be essential in the estrogen regulation mechanism. Our study highlights the use of the MCF10AT1 cell line to examine estrogen‐induced changes in premalignant breast cells and the ability of the 2‐D mass mapping technique to quantitatively study protein expression changes on a proteomic scale.
Proteomic analysis of autoantibodies in patients with hepatocellular carcinoma
Authors: Takashima Motonari , Kuramitsu Yasuhiro , Yokoyama Yuichiro , Iizuka Norio , Harada Toshio , Fujimoto Masanori , Sakaida Isao , Okita Kiwamu , Oka Masaaki , Nakamura Kazuyuki 
Published: June 2006

AbstractTo detect autoantibodies that could be diagnostic markers for hepatocellular carcinoma (HCC), we analyzed serum autoantibodies comprehensively that showed immunoreactivity to proteins in tumor tissue obtained from patients with HCC. Fifteen paired samples of HCC tissue and corresponding nontumorous liver tissue as well as five normal liver tissue samples were used in the study. A combination of proteomics and SEREX (serologic analysis of recombinant cDNA expression libraries) technique was used. Tissue proteins were separated by 2‐DE, transferred onto PVDF membranes, and immunoblotted with autologous sera. By comparing each immunoblot pattern, we identified four immunoreactive spots with stronger staining intensity in tumorous tissues than in corresponding nontumorous tissues and in normal liver tissues. Matched proteins on 2‐DE gels were identified by LC‐MS/MS. These immunoreactive proteins were heat shock 70 kDa protein 1 (HSP70), glyceraldehyde 3‐phosphate dehydrogenase, peroxiredoxin, and manganese superoxide dismutase (Mn‐SOD). In HCC sera, occurrences of autoantibodies against these proteins were 7/15 (46.7%), 5/15 (33.3%), 5/15 (33.3%), and 6/15 (40.0%), respectively, whereas 2/20 (10.0%), 7/20 (35.0%), 0/20 (0.0%), and 2/20 (10.0%) were in control sera. Immunoblot analysis using commercially available purified proteins was performed to confirm the specificity of autoantibodies. By statistical analysis, autoantibodies against HSP70, peroxiredoxin, and Mn‐SOD showed significantly high‐frequency immunoreaction in HCC sera. The three antibodies were considered patient‐specific antibodies in HCC and may be candidate diagnostic biomarkers for HCC.
Construction of quantitative proteome reference maps of mouse spleen and lymph node based on two‐dimensional gel electrophoresis
Authors: Kimura Yayoi , Yokoyama Ryo , Ishizu Yuri , Nishigaki Toshio , Murahashi Yasuaki , Hijikata Atsushi , Kitamura Hiroshi , Ohara Osamu 
Published: June 2006

AbstractQuantitative features of the proteome are extremely useful for studying cellular processes at a molecular level. In this study, we attempted to construct quantitative reference proteome maps of the mouse spleen and lymph node based on 2‐DE followed by protein identification using MS. We analyzed more than 1000 spots on the 2‐DE images and consequently were able to determine that 919 spots were derived from 328 different genes. To obtain statistically reliable information of the protein levels from these 2‐DE images, we measured the volumes of the respective spots on 2‐DE images obtained by four to six independent experimental runs. These measurements were used to calculate the variability of the volumes of the respective spots on 2‐DE following subcellular fractionation, which enabled us to discriminate differentially produced proteins from those within the range of intrinsic variability. More importantly, while the 2‐DE data have been traditionally collected in a gel image‐based manner, the resultant quantitative 2‐DE data could be analyzed using the same procedure as that for mRNA expression profiles. This greatly assists in bridging the gap between the analyses of transcriptomes and proteomes and enables the integration of this data on the same informational platform.
Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage
Authors: de Torre Carlos , Ying Sai‐Xia , Munson Peter J. , Meduri G. Umberto , Suffredini Anthony F. 
Published: June 2006

AbstractTo assess markers of lung inflammation, we used SELDI‐TOF and 2‐DE to study changes in bronchoalveolar lavage (BAL) protein in 33 subjects challenged with local bronchial lung endotoxin and saline and in 11 patients with acute respiratory distress syndrome (ARDS). Differences in the SELDI‐TOF spectra were assessed by t‐test after baseline subtraction, normalization to total ion current and alignment by m/z calibration. The temporal changes in acute inflammatory BAL (6, 24 and 48 h following endotoxin challenge) on hydrophobic binding chip surfaces revealed the differential presence of proteins of 9, 14, 18 and 28 kDa (all p <0.001) in the inflammatory BAL. This differential pattern was also found in the ARDS BAL. Principal component analysis of the entire SELDI‐TOF spectra separated normal BAL, experimental and clinical lung inflammation supporting the notion of a distinctive protein pattern associated with acute lung inflammation. An analysis of the hydrophobic fraction of the inflammatory BAL using 2‐DE, identified increased levels of apolipoprotein A1, and S100 calcium‐binding proteins A8 and A9 in the inflammatory BAL. This pattern was also found in ARDS BAL after immunoblot analysis. These approaches will be useful to improve current methods of monitoring lung inflammation and to identify new therapeutic targets.
Prostatic tissue protein alterations due to delayed time to freezing
Authors: Jackson David , Rowlinson Rachel A. , Eaton Cassie K. , Nickson Janice A. , Wilson Ian D. , Mills Jonathan D. , Wilkinson Robert W. , Tonge Robert P. 
Published: June 2006

AbstractClinical studies often produce fresh tissue samples, which ideally should be immediately snap frozen for storage and subsequent analysis. However, this is often not practically possible, and there is inevitably a time period during which the sample is stored on ice. The delay in freezing may allow endogenous degradation of proteins to occur, affecting 2‐D gel protein profiles. This study aims to investigate the type and extent of this degradation by examining how the time‐to‐freezing delay alters prostatic tissue protein profile. The prostate carcinoma‐3 cell line (PC‐3), prostate cancer xenografts and canine prostate were used with fluorescence 2‐D DIGE to assess protein degradation. It was found that 30‐min processing time had minimal effects on the protein profile. Longer delays had little visible effect, but subtle alterations in protein profile began to accumulate as time increased. These data support the practice of completing tissue processing as rapidly as possible, and indicate that short processing times do not notably perturb the 2‐D gel spot pattern from prostatic tissue.
Proteomic analysis of the acid‐soluble organic matrix of the chicken calcified eggshell layer
Authors: Mann Karlheinz , Maček Boris , Olsen Jesper V. 
Published: June 2006

AbstractThe major difference between inorganic minerals and biominerals is the presence of an organic matrix consisting of proteins, glycoproteins, proteoglycans, and polysaccharides, which is synthesized by specialized cells under genetic control before or during mineralization. The organic matrix is thought to play a major role in the assembly of the biomineral and determination of its mechanical properties. The recent elucidation of the chicken genome provided an opportunity to explore the matrix proteome of a biomineral using up‐to‐date MS‐based technology. We identified 520 proteins in this matrix including the ten matrix proteins already known before. The identified proteins were divided into three abundance groups using the exponentially modified protein abundance index described recently which was roughly calibrated with the few known data on protein yield derived from Edman sequence analysis. A small group of 32 highly abundant proteins contained the presently known eggshell‐specific proteins and all of the other known eggshell matrix constituents identified before with much less sensitive conventional methods. The present study, which is the first comprehensive proteomic study of a vertebrate biomineral, is intended as a starting point for the detailed molecular characterization of eggshell matrix proteins, their interactions in the matrix network and functional studies.
Synthesis and characterization of a novel electroluminescent polymer based on a phenoxazine derivative
Authors: Ito Yuichi , Shimada Takahiro , Ha Jaekook , Vacha Martin , Sato Hisaya 
Published: June 2006

AbstractWe report the preparation of a new electroluminescent polymer by the oxidative coupling copolymerization of N‐(4‐n‐butylphenyl)phenoxazine and 9,9‐di‐n‐butylfluorene with ferric(III) chloride. The reaction yields soluble polymers with a weight‐average molecular weight as high as 9000. The reactivity has been studied with respect to the reaction time, temperature, and feed ratio of the comonomers. Under optimum conditions, a copolymer with a 50% comonomer incorporation ratio can be obtained in a 75% yield. The polymers have been characterized with differential scanning calorimetry, cyclic voltammetry, and optical spectroscopy. A simple single‐layer light‐emitting‐diode device of an indium tin oxide/polymer/Mg–Ag structure shows a luminance of 200 cd/m2 at an 18‐V operating voltage. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4338–4345, 2006
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface
Authors: Fan Hao , Wang Xiaoqin , Zhu Jiang , Robillard George T. , Mark Alan E. 
Published: June 2006

AbstractHydrophobins are small (∼100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self‐assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily β‐strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in α‐helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self‐assembly on a hydrophobic solid/water interface. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Substitution of Nd at Ba site in Gd123
Authors: Mirzadeh M. , Akhavan M. 
Published: June 2006

AbstractStructural and superconducting behaviors of Gd(Ba2−x Ndx)Cu3O7+δ with 0.0 ≤ x ≤ 0.8 have been studied by X‐ray diffraction and electrical and magnetic measurements. The XRD patterns show the samples with x ≤ 0.5 are isostructure 123 phase, and an orthorhombic–tetragonal phase transition occurs at x = 0.2. The transition temperature decreases linearly with increasing Nd content. This behavior is also observed in the curves of the room‐temperature resistivity versus Nd doping. The metal–insulator and superconductor–insulator transitions occur at x cMIT = 0.3 and x cSIT = 0.35, respectively. The conduction mechanisms of the normal‐state resistivity are the Coulomb gap (CG) for x < x cMIT, two‐dimensional variable‐range hopping (2D‐VRH) at x cMIT ≤ x ≤ x cSIT, and 3D‐VRH for x > x cSIT. The pinning energy derived from the thermally activated flux creep model, and coupling energy derived from the Ambegaokar–Halperin theory decrease with increasing applied magnetic field as a power‐law relation, and decrease as Nd content increases. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ultrasonic study of Jahn–Teller effect in charge‐ordered Nd1−xCax MnO3 (x = 0.4–0.8) manganites
Authors: Liu Yi , Kong Hui , Su Jinrui , Zhu Changfei 
Published: June 2006

AbstractThe ultrasonic, magnetic and transport properties of charge‐ordered manganites Nd1−x Cax MnO3 (x = 0.4, 0.5, 0.6, 0.7 and 0.8) were studied between 15 and 300 K. Resistivity and magnetization measurements show that all the samples undergo a charge‐ordering transition at low temperature. Upon cooling from 300 K, an obvious softening of sound velocity above the charge‐ordering transition temperature (T CO) and dramatic stiffening below T CO were observed for all samples. This feature gives clear evidence for strong electron–phonon coupling in these compounds. The Jahn–Teller coupling energy E JT increases with increasing Ca concentration x, and reaches the maximum at around x = 0.6, which is similar in characteristics to the T CO. The results imply that the charge‐ordering in Nd1−x Cax MnO3 is dominated by the Jahn–Teller effect. Our analyses suggested that the type of cooperative Jahn–Teller distortion be Q 2‐mode for x ≤ 0.6, and change to Q 3 mode at around x = 0.6 in the CO state. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modelling non‐exponential polarization relaxations in interacting dipole systems
Authors: Kühn M. , Kliem H. 
Published: June 2006

AbstractRelaxational polarization processes of many polar dielectrics can be described in the time domain by stretched exponential functions which is referred to as Kohlrausch behaviour. For an interacting system of statistically distributed permanent dipoles arranged between two coplanar electrodes numerical calculations of the transient polarization curves are performed showing these long lasting relaxations. The electrostatic dipole–dipole interaction is considered and the electrodes are taken into account using the method of image dipoles. The dipoles are fluctuating thermally activated in double well potentials according to the Boltzmann statistics. The computation is based on deterministic local field calculations and on weighted probabilistic dynamic Monte Carlo steps. In this paper we focus on the small signal response after applying a step function of the electric field. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In‐plane anisotropy in uniaxially‐strained GaN films detected by optical diffraction technique
Authors: Adachi Satoru , Toda Yasunori , Ishiguro Tetsuro , Hoshino Katsuyuki , Arakawa Yasuhiko 
Published: June 2006

AbstractThe cover picture of this issue of physica status solidi (c) has been taken from the article [1].
Traditional healthy mediterranean diet: estrogenic activity of plants used as food and flavoring agents
Authors: Agradi Elisabetta , Vegeto Elisabetta , Sozzi Andrea , Fico Gelsomina , Regondi Simona , Tomè Franca 
Published: June 2006

AbstractThe Italian‐style Mediterranean diet has been defined as healthy by epidemiologists and nutritionists. Besides being low fat, the Mediterranean diet is rich in biologically active minor compounds. Among these, phytoestrogens seem to have an impact on the prevention of chronic degenerative disease. It is important to understand how this occurs. The in vitro estrogenic activity of crude extracts from typical Mediterranean foods was tested using a yeast estrogen screen (YES), containing human estrogen receptor. Species belonging to Leguminosae, Apiaceae, Graminaceae, Iridaceae, Chenopodiaceae, Cruciferae and Solanaceae showed the greatest number of positive responses. These species include some foods which are traditionally widely consumed, such as beans and other legumes, tomatoes, cabbage, carrots and some cereals. The highest activity was found in the more polar extracts (aqueous, methanol and chloroform: methanol) indicating that polar compounds are mainly responsible for the estrogenic activity. This is also supported by the traditional cooking practices. According to data from in vitro tests, the estrogenic activity is present in numerous plants which are commonly used as food in the Mediterranean diet. Vegetable foods rich in phytoestrogens, as in the Mediterranean tradition, may contribute to the maintenance of health status. Copyright © 2006 John Wiley & Sons, Ltd.
Modelling a modified atmosphere packaging system for fresh scallops (Argopecten purpuratus)
Authors: Simpson R. , Carevic E. , Rojas S. 
Published: June 2006

AbstractSeafood is a highly perishable food, which has a relative short shelf‐life. Modified atmosphere packaging (MAP) is a system that offers a way of extending the shelf‐life of seafood products, maintaining quality and inhibiting bacterial growth. The objective of this research was to study and determine the optimal conditions for packaging scallops in a modified atmosphere system, which includes CO2/O2/N2 mixture, headspace:food ratio and storage temperature, utilizing an integrated mathematical model for MAP systems with its respective experimental validation. For validation purposes, two experiments were conducted, using gas mixtures of: (a) 45% CO2/10% O2/45% N2; and (b) 60% CO2/10% O2/30% N2. In addition, two experiments, at 6°C and 20°C, were conducted to obtain the shelf‐life model, utilizing the following gas mixtures: 30% CO2/10% O2/60% N2; 45% CO2/10% O2/45% N2; 60% CO2/10% O2/30% N2; and 75% CO2/10% O2/15% N2. Gas mixtures with CO2 concentrations between 30% and 70% and different headspace:food ratios were tested during simulations. The optimal conditions for scallop storage were a 60% CO2/10% O2/30% N2 gas mixture and a headspace:food ratio of 2:1. With these conditions, a simulated shelf‐life of 21 days was obtained. Optimal conditions consider maximum shelf‐life, an adequate film collapse criterion, and time to reach the pseudo‐equilibrium condition. The predictive mathematical model, coupled with experimental studies for specific products, can be efficiently utilized to evaluate packaging alternatives (size, material and selected thickness) for different temperatures and initial gas concentration scenarios of MAP products. Copyright © 2006 John Wiley & Sons, Ltd.
Software developer motivation in a high maturity company: a case study
Authors: Baddoo Nathan , Hall Tracy , Jagielska Dorota 
Published: June 2006

AbstractIn this article, we discuss the impact of software developer motivation on projects. Motivation has been reported to be an important determinant of productivity and quality of work in many industries. In this article, we explore specifically how motivation impacts on development work in software engineering. We describe work previously done to suggest that software developers may have a different profile of motivators to other professionals. We present data collected from nine developers working in a software organisation that has been assessed at CMM level 5. We find that the developers working in this high maturity development environment are highly motivated. We also report relationships between motivation and progress in development work and describe the impact of motivating factors on specific aspects of software development. Our main conclusion is that good software developers are proactive, flexible and adaptable, prepared to share knowledge with team and follow good practice, for example, documenting work. Also, and in particular reference to this high maturity company, good software developers are able to resolve complex problems, innovative and eager to try new technology. The biggest motivators to such performance in a high maturity organisation are pay and benefits, recognition and opportunities for achievement. These are closely followed by technically challenging work, job security and senior management support. Cost, time, product quality — in terms of reliability — and user satisfaction are all moderately good indicators of project success. User satisfaction, however, is the best indicator of all four as its importance assumes a temporal significance as a project progresses. Finally, we found that technical competency, interpersonal skills and adherence to good practices impact favourably on software project success. Copyright © 2006 John Wiley & Sons, Ltd.