bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of β‐hairpin structure
Authors: Skwierawska Agnieszka , Makowska Joanna , Ołdziej Stanisław , Liwo Adam , Scheraga Harold A. 
Published: October 2008

AbstractWe previously studied a 16‐amino acid‐residue fragment of the C‐terminal β‐hairpin of the B3 domain (residues 46–61), [IG(46–61)] of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG (46–61) by systematically shortening the peptide by one residue at a time from both the C‐ and the N‐terminus. To determine the structure and stability of two resulting 12‐ and 14‐amino acid‐residue peptides, IG(48–59) and IG(47–60), respectively, we carried out circular dichroism, NMR, and calorimetric studies of these peptides in pure water. Our results show that IG(48–59) possesses organized three‐dimensional structure stabilized by hydrophobic interactions (Tyr50–Phe57 and Trp48–Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (Tm = 310 K) measured by differential scanning calorimetry (DSC). The melting temperature of IG(47–60) determined by DSC is Tm = 330 K and its structure is similar to that of the native β‐hairpin at all (lower) temperatures examined (283–313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a β‐hairpin structural element. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Authors: Lu Yan , Derreumaux Philippe , Guo Zhi , Mousseau Normand , Wei Guanghong 
Published: October 2008

AbstractAggregation of the full‐length amyloid‐β (Aβ) and β2‐microglobulin (β2m) proteins is associated with Alzheimer's disease and dialysis‐related amyloidosis, respectively. This assembly process is not restricted to full‐length proteins, however, many short peptides also assemble into amyloid fibrils in vitro. Remarkably, the kinetics of amyloid‐fibril formation of all these molecules is generally described by a nucleation‐polymerization process characterized by a lag phase associated with the formation of a nucleus, after which fibril elongation occurs rapidly. In this study, we report using long molecular dynamics simulations with the OPEP coarse‐grained force field, the thermodynamics and dynamics of the octamerization for two amyloid 7‐residue peptides: the β2m83‐89 NHVTLSQ and Aβ16‐22 KLVFFAE fragments. Based on multiple trajectories run at 310 K, totaling 2.2 μs (β2m83‐89) and 4.8 μs (Aβ16‐22) and starting from random configurations and orientations of the chains, we find that the two peptides not only share common but also very different aggregation properties. Notably, an increase in the hydrophobic character of the peptide, as observed in Aβ16‐22 with respect to β2m83‐89 impacts the thermodynamics by reducing the population of bilayer β‐sheet assemblies. Higher hydrophobicity is also found to slow down the dynamics of β‐sheet formation by enhancing the averaged lifetime of all configuration types (CT) and by reducing the complexity of the CT transition probability matrix. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Spontaneous β‐helical fold in prion protein: The case of PrP(82‐146)
Authors: Saracino Gloria A.A. , Villa Alessandra , Moro Giorgio , Cosentino Ugo , Salmona Mario 
Published: October 2008

AbstractThe presence of amyloid is a hallmark of Gerstmann‐Sträussler‐Scheinker (GSS) disease, which is a prion disease caused by germ line mutations in the PRNP gene. The major component of amyloid is a fragment spanning residues from 81‐82 to 144‐153, part of the minimal sequence thought to play a crucial role in the conversion reaction and to sustain prion replication. We present here a molecular dynamics study on the 82‐146 peptide from the human prion protein. The aim is to identify its aggregation‐prone folds. The 82‐146 prion sequence corresponds to a naturally occurring prion peptide able to form fibrils rich in parallel β‐sheets. A spontaneous right‐handed β‐helical arrangement with 13 residues per turn can be observed in the 103‐135 segment of the 82‐146 peptide. The observed fold is in accordance with the evidence of a parallel β‐sheet organization in amyloid and with experiments on 82‐146 discussed in the literature. To elucidate the conformational properties that trigger this peptide's aggregation propensity, the conformational behavior of peptides of different length (106‐126 and 113‐120 prion segments) was also investigated. Simulation analysis has led to some interesting considerations on sequence specific flexibility and the effects of growth. Comparing peptides of different length allows the localization of the origin of the β‐helix conformational propensity in the 106‐126 segment, though longer sequences appear necessary for a clear β‐helical arrangement. Structural features of the observed 82‐146 β‐helical fold are compatible with the “dock and lock” mechanism proposed to interpret peptide aggregation kinetics. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Quality assurance in safe automation
Authors: Summers Angela E. , Hearn William H. 
Published: October 2008

AbstractA perfect process would have no hazards, but perfection is impossible in the real world. Nearly all process units have inherent risk associated with their design and operation. Safe operation is maintained with a risk reduction strategy relying on a wide variety of safety systems. This article focuses on the most common safety systems for managing process deviations during planned operating modes—instrumented safety systems (ISSs), such as safety alarms, safety controls, and safety instrumented systems. Rigorous quality assurance is necessary to achieve real‐world risk reduction, so this article follows the Plan, Do, Check, and Act process to discuss quality assurance and its application to ISS. © 2008 American Institute of Chemical Engineers Process Saf Prog 2008
Preface: phys. stat. sol. (c) 5/12
Authors: Nassiopoulou Androula G. , Argitis Panagiotis , Papanikolaou Nikos 
Published: October 2008

AbstractDear reader of this issue,We introduce to you a collection of Original Papers, Invited and Contributed Articles presented at the Micro&Nano 2007 Conference (3rd International Conference on Micro‐Nanoelectronics, Nanotechnology and MEMs), held in Athens, Greece on 18–21 November 2007.Micro&Nano 2007 was the third of a series of conferences held at NCSR Demokritos every three years which aim at gathering together all scientists and engineers working in the challenging field of micro‐nanoelectronics, nanotechnology and MEMs in an interactive forum and stimulating discussions on the latest achievements and new developments in this rapidly evolving field.The main topics of Micro&Nano 2007 were:– Micro and nano‐fabrication and processing,– Materials,– Devices,– Quantum devices and molecular electronics,– Integration, circuits and systems,– Industry and technology transferA total of 250 scientists representing 23 countries attended. There were a total of 205 presentations, 71 of which were oral (including 10 invited talks) and 134 were posters presented in two different sessions.The conference opening ceremony was honored by the presence of the General Secretary of Research and Technology Prof. I. Tsoukalas. During the ceremony, an honorary plaque was awarded to Prof. G. Kamarinos from the Polytechnical University of Grenoble, France, acknowledging his contributions to the early stages of microelectronics research in Greece. In addition, Dr. A. G. Nassiopoulou, Conference Chairperson and Director of the Institute of Microelectronics (IMEL) of NCSR Demokritos, gave an overview on the development of microelectronics research in Greece from the mid 1980s to the present day. She also presented the National Scientific Society “Micro&Nano” founded in 2004 (www.micro‐nano.gr).The next conference Micro&Nano will be held at the same place in the year 2010. We look forward to seeing you at that conference.We would like to thank all delegates, our session chairs, delegates who helped with refereeing and all committee members for their contribution to the success of the conference.Our acknowledgements also go to our sponsors for their financial support, NCSR Demokritos for hosting and supporting the conference and the General Secretariat of Research and Technology Greece, under whose auspices the conference was held. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Scutellarin‐induced endothelium‐independent relaxation in rat aorta
Authors: Pan Zhenwei , Feng Tieming , Shan Luchen , Cai Benzhi , Chu Wenfeng , Niu Huili , Lu Yanjie , Yang Baofeng 
Published: October 2008

AbstractScutellarin is a flavonoid extracted from the traditional Chinese herb,Erigeron breviscapusHand Mazz. In the present study, the vasorelaxant effects of scutellarin and the underlying mechanism were investigated in isolated rat aorta. Scutellarin (3, 10, 30, 100 µm) caused a dose‐dependent relaxation in both endothelium‐intact and endothelium‐denuded rat aortic rings precontracted with noradrenaline bitartrate (IC50= 7.7 ± 0.6 µm), but not with potassium chloride. Tetraethylammonium, glibenclamide, atropine, propranolol, indomethacin and N(G)‐nitro‐l‐arginine methyl ester had no influence on the vasorelaxant effect of scutellarin, which further excluded the involvement of potassium channels, muscarinic receptor, nitric oxide pathway and prostaglandin in this effect. Pretreatment with scutellarin decreased the tonic phase, but not the phasic phase of the noradrenaline bitartrate induced tension increment. Scutellarin also alleviated Ca2+‐induced vasoconstriction in Ca2+‐depleted/noradrenaline bitartrate pretreated rings in the presence of voltage‐dependent calcium channel blocker verapamil. The noradrenaline bitartrate evoked intracellular calcium increase was inhibited by scutellarin. Scutellarin had no effect on phorbol‐12,13‐diacetate induced contraction in a calcium‐free bath solution. These results showed that scutellarin could relax thoracic artery rings in an endothelium‐independent manner. The mechanism seems to be the inhibition of extracellular calcium influx independent of the voltage‐dependent calcium channel. Copyright © 2008 John Wiley & Sons, Ltd.
The inhibitory effect of bamboo extract on the development of 7,12‐dimethylbenz[a]anthracene (DMBA)‐induced breast cancer
Authors: Lin Yanling , Collier Abby C. , Liu Wanyu , Berry Marla J. , Panee Jun 
Published: October 2008

AbstractThe incidence of breast cancer among women is high and increasing. This study investigated the inhibitory effect of an extract from bambooPhyllostachys edulison the development of 7,12‐dimethylbenz[a]anthracene (DMBA)‐induced breast cancer in female Sprague‐Dawley rats. The rats were fed with bamboo extract (BEX) supplemented diet or control diet, and treated with DMBA after 3 weeks of the dietary regime. The incidence of mammary tumors was monitored by palpation for the next 11 weeks. At the end of the experiment, blood samples were collected for total antioxidant capacities (TAC) assay and liver samples for phase II enzyme activity assays. The TAC values, total contents of phenolics and flavonoids of BEX were also measured. The results showed that BEX delayed the onset of mammary tumor by 1 week, decreased the tumor incidence by 44% and tumor multiplicity by 67%, and increased the total sulfotransferases (SULT) activity by 63%. BEX showed high levels of TAC, total phenolic and total flavonoids. However, the serum TAC values were not affected by BEX supplementation. In summary, the results indicate that BEX possesses a potent anti‐breast cancer effect, and the upregulation of SULT activity, therefore estrogen metabolism may be the underlying mechanism. Copyright © 2008 John Wiley & Sons, Ltd.
Simultaneous determination and confirmation of melamine and cyanuric acid in animal feed by zwitterionic hydrophilic interaction chromatography and tandem mass spectrometry
Authors: Heller David N. , Nochetto Cristina B. 
Published: October 2008

AbstractWe developed a new method to analyze animal feed and feed ingredients for melamine and cyanuric acid. The method is capable of extracting and detecting both melamine and cyanuric acid in a single procedure, whether present as free compounds or bound together as the melamine:cyanurate complex. A novel chromatographic system based on zwitterionic hydrophilic interaction chromatography (ZIC‐HILIC) columns enables separation and detection of both compounds in one run. Samples are extracted with a strong aqueous acid which is then diluted to bring the concentration within the working range of the method. The method is applicable over the range of 0.5 to 50 micrograms/gram (µg/g). Samples at higher concentrations may be diluted into this range, which is equivalent to 3.6–360 ng/mL in the injection solvent. Analytes are detected using liquid chromatography/tandem mass spectrometry. The data confirm the presence of both compounds according to criteria recommended by the US FDA Center for Veterinary Medicine. The LC/MS/MS method provides an alternative to derivatization and gas chromatography‐mass spectrometry for regulatory analysis of feed samples. Published in 2008 by John Wiley & Sons, Ltd.
‘Health management’ in the private sector in the context of HIV/AIDS: progress and challenges faced by company programmes in South Africa
Authors: George Gavin , Quinlan Tim 
Published: October 2008

Abstract‘Health management’ of employees is becoming a common imperative for companies that do business in regions where there is an HIV epidemic. Private sector initiatives in South Africa have evolved considerably. However, core components of HIV/AIDS‐oriented workplace programmes, voluntary counselling and testing and anti‐retroviral treatment, are not as effective as expected, despite considerable investment in them. There is some evidence to suggest gradual improvement in employee participation, yet this is coupled with employees defaulting from treatment programmes. This article explores reasons for these developments, the focus being on the economic and financial challenges facing private sector workplace health programmes. Copyright © 2008 John Wiley & Sons, Ltd and ERP Environment.
Integration of Thin‐Film‐Fracture‐Based Nanowires into Microchip Fabrication
Authors: Jebril Seid , Elbahri Mady , Titazu Getachew , Subannajui Kittitat , Essa Samia , Niebelschütz Florentina , Röhlig Claus‐Christian , Cimalla Volker , Ambacher Oliver , Schmidt Bernd , Kabiraj Debdulal , Avasti Devesh , Adelung Rainer 
Published: October 2008

AbstractOne‐step device fabrication through the integration of nanowires (NWs) into silicon microchips is still under intensive scientific study as it has proved difficult to obtain a reliable and controllable fabrication technique. So far, the techniques are either costly or suffer from small throughput. Recently, a cost‐effective method based on thin‐film fracture that can be used as a template for NW fabrication was suggested. Here, a way to integrate NWs between microcontacts is demonstrated. Different geometries of microstructured photoresist formed by using standard photolithography are analyzed. Surprisingly, a very simple “stripe” geometry is found to yield highly reproducible fracture patterns, which are convenient templates for fault‐tolerant NW fabrication. Microchips containing integrated Au, Pd, Ni, and Ti NWs and their suitability for studies of conductivity and oxidation behavior are reported, and their suitability as a hydrogen sensor is investigated. Details of the fabrication process are also discussed.
Channel assignment for multicast in multi‐channel multi‐radio wireless mesh networks
Authors: Hoang Lan Nguyen , Uyen Trang Nguyen 
Published: October 2008

AbstractOne of the most effective approaches to enhance the throughput capacity of wireless mesh networks (WMN) is to use systems with multiple channels and multiple radios per node. Multi‐channel multi‐radio (MCMR) networks require efficientchannel assignment(CA) algorithms to determine which channel a link should use for data transmission in order to maximize network throughput. The problem of CA has been studied extensively for unicast communications, but addressed only recently for multicast. We propose a CA algorithm named Minimum interference Multi‐channel Multi‐radio Multicast (M4) that minimizes interference among nodes in a multicast routing tree and uses both orthogonal and overlapping channels such as those in IEEE 802.11b/g systems. Simulation results show that M4 outperforms the Multi Channel Multicast algorithm proposed. in various scenarios with respect to average packet delivery ratio, throughput and end‐to‐end delay. Copyright © 2008 John Wiley & Sons, Ltd.
Predicting Different Patterns of Sexual Identity Development Over Time Among Lesbian, Gay, and Bisexual Youths: A Cluster Analytic Approach
Authors: Rosario Margaret , Schrimshaw Eric W. , Hunter Joyce 
Published: October 2008

AbstractRecent research has suggested that the sexual identity development of lesbian, gay, and bisexual (LGB) youths may not follow a single pattern, but may follow a variety of pathways. Although some research documenting variability in identity development exists, unclear are the potential individual and social contexts that predict these different patterns, as well as the contexts that predict changes in identity integration over time. This report longitudinally examined these issues in an ethnically diverse sample of 156 LGB youths (ages 14–21) in New York City. Cluster analytic techniques identified two patterns of sexual identity formation (i.e., early and more recent), and three patterns of sexual identity integration (i.e., high, middling, and low). Gender and sexual abuse were found to predict identity formation; and, gay‐related stress, social support, negative social relationships, sexual orientation, sexual identity, and gender were found to predict patterns of sexual identity integration and changes in integration over 1 year. These findings document different patterns of sexual identity development and identify potential contextual barriers and facilitating factors that may be used to develop interventions to promote healthy LGB identity development.
Photolithographic Approaches for Fabricating Highly Ordered Nanopatterned Arrays
Authors: Li Xiaoru , Song Guojun , Peng Zhi , She Xilin , Li Jianjiang , Sun Jin , Zhou Di , Li Peidong , Shao Zengjun 
Published: October 2008

Abstract
In this work, we report that large area metal nanowire and polymer nanotube arrays were successfully patterned by photolithographic approach using anodic aluminum oxide (AAO) templates. Nanowires were produced by electrochemical deposition, and nanotubes by solution-wetting. The highly ordered patterns of nanowire and nanotube arrays were observed using scanning electron microscopy (SEM) and found to stand free on the substrate. The method is expected to play an important role in the application of microdevices in the future.
Effectiveness and safety of loop electrosurgical excision procedure for cervical neoplasia in rural India
Authors: Sankaranarayanan Rengaswamy , Keshkar Vijay , Kothari Ashok , Kane Shubhada , Fayette Jean‐Marie , Shastri Surendra 
Published: October 2008

AbstractObjectiveTo evaluate the effectiveness and safety of loop electrosurgical excision procedure (LEEP) to treat cervical intraepithelial neoplasia (CIN) in rural India.MethodWomen with CIN colposcopic features unsuitable for cryotherapy were treated with LEEP using a “see‐and‐treat” approach. Women with unsatisfactory colposcopy had diagnostic LEEP. Cure was defined as no clinical or histologic evidence of CIN at 1‐year follow‐up. Factors influencing cure rates were evaluated by χ2 tests.ResultsOf the 1141 women who underwent LEEP (569 see‐and‐treat; 572 unsatisfactory colposcopy), 634 had histologically proven CIN. Of those, 489 reported for follow‐up and 459 (93.9%) had no evidence of disease. Cure rates were 98.1% for women with CIN 1, 93.6% for CIN 2, and 85.0% for CIN 3. Patients with CIN 2–3 had significantly lower cure rates.ConclusionCure rates for LEEP provided by newly trained doctors in rural India were similar to those reported in the gynecological literature.
Gene Expression Data Classification Using Consensus Independent Component Analysis
Authors: Zheng Chun-Hou , Huang De-Shuang , Kong Xiang-Zhen , Zhao Xing-Ming 
Published: October 2008

Abstract
We propose a new method for tumor classification from gene expression data, which mainly contains three steps. Firstly, the original DNA microarray gene expression data are modeled by independent component analysis (ICA). Secondly, the most discriminant eigenassays extracted by ICA are selected by the sequential floating forward selection technique. Finally, support vector machine is used to classify the modeling data. To show the validity of the proposed method, we applied it to classify three DNA microarray datasets involving various human normal and tumor tissue samples. The experimental results show that the method is efficient and feasible.
A DSRPCL-SVM Approach to Informative Gene Analysis
Authors: Xiong Wei , Cai Zhibin , Ma Jinwen 
Published: October 2008

Abstract
Microarray data based tumor diagnosis is a very interesting topic in bioinformatics. One of the key problems is the discovery and analysis of informative genes of a tumor. Although there are many elaborate approaches to this problem, it is still difficult to select a reasonable set of informative genes for tumor diagnosis only with microarray data. In this paper, we classify the genes expressed through microarray data into a number of clusters via the distance sensitive rival penalized competitive learning (DSRPCL) algorithm and then detect the informative gene cluster or set with the help of support vector machine (SVM). Moreover, the critical or powerful informative genes can be found through further classifications and detections on the obtained informative gene clusters. It is well demonstrated by experiments on the colon, leukemia, and breast cancer datasets that our proposed DSRPCL-SVM approach leads to a reasonable selection of informative genes for tumor diagnosis.
Applying Intelligent Computing Techniques to Modeling Biological Networks from Expression Data
Authors: Lee Wei-Po , Yang Kung-Cheng 
Published: October 2008

AbstractConstructing biological networks is one of the most important issues in systems biology. However, constructing a network from data manually takes a considerable large amount of time, therefore an automated procedure is advocated. To automate the procedure of network construction, in this work we use two intelligent computing techniques, genetic programming and neural computation, to infer two kinds of network models that use continuous variables. To verify the presented approaches, experiments have been conducted and the preliminary results show that both approaches can be used to infer networks successfully.