bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance evaluation for asynchronous MC‐CDMA systems with a symbol timing offset
Authors: Park Myonghee , Ko Kyunbyoung 
Published: December 2008

AbstractThis paper models a symbol timing offset (STO) with respect to the guard period and the maximum access delay time for asynchronous multicarrier‐code division multiple access systems over frequency‐selective multipath fading channels. Analytical derivation shows that STO causes desired signal power degradation and generates self‐interferences. This effect of the STO on the average bit error rate (BER) and the effective signal‐to‐noise ratio (SNR) is evaluated using the semi‐analytical method, and the approximated BER and the SNR loss caused by STO are then obtained as closed‐form expressions. The tightness between the semi‐analytical result and the approximated one is verified for the different STOs and SNRs. Furthermore, the derived analytical results are verified via Monte Carlo simulations. Copyright © 2008 John Wiley & Sons, Ltd.
A Versatile Bisporphyrinoid Motif for Supramolecular Chirogenesis
Authors: Borovkov Victor , Inoue Yoshihisa 
Published: December 2008

AbstractDuring the last decade there has been continuously growing interest in the phenomenon of supramolecular chirogenesis, which is a smart combination of chirality and supramolecular chemistry effectively used for investigations of various aspects of living organisms, modern physical and naturalsciences, and also for technological applications. Thanks to their spectral, chemical, and physicochemical properties, porphyrinoids have been found to be one of the best suited classes of compounds for study of this subject. Out of a vast number of the porphyrinoid‐based supramolecular systems employed for this purpose, a bisporphyrinoid motif has been shown to be the simplest, yet widely applicable, structural element that satisfies the requirements for the desired chirogenic properties and ease of synthetic methodology. The aim of this microreview is to highlight the advantages and versatility of this type of chromophoric arrangement for supramolecular chirogenesis.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Novel quasi‐interpenetrating network/functionalized multi‐walled carbon nanotubes double‐network composite matrices for DNA sequencing by CE
Authors: Zhou Dan , Yang Liping , Yang Runmiao , Song Weihua , Peng Shuhua , Wang Yanmei 
Published: December 2008

AbstractPoly(N, N‐dimethylacrylamide) (PDMA)‐functionalized multi‐walled carbon nanotubes (MWNT‐PDMA) were prepared via atom transfer radical polymerization and then added into quasi‐interpenetrating network (quasi‐IPN) composed of linear polyacrylamide (3.3 MDa) and PDMA to form polymer/nanotube double‐network composite sieving matrices for DNA sequencing by CE. The CE results show that, compared with quasi‐IPN, the novel composite matrices can improve ssDNA sequencing performances due to the formation of a double‐network consisting of a flexible quasi‐IPN polymer network and a rigid MWNT network based on a unique tubular structure, which makes the total sieving networks more restricted and stable and increases the apparent molecular weight of the matrices. The effects of MWNT‐PDMA concentration in matrices and molecular weight of PDMA side chains in MWNT‐PDMA on ssDNA sequencing performances were studied in detail. Furthermore, these double‐network composite matrices were also compared with other matrices and the results indicate that they are promising ones for DNA sequencing. The separation provided with high resolution, speediness, excellent reproducibility and easy loading owing to the addition of MWNT‐PDMA is likely to achieve full automation, especially for capillary array electrophoresis and microchip electrophoresis.
New applications and developments in the use of multiplex ligation‐dependent probe amplification
Authors: Kozlowski Piotr , Jasinska Anna J. , Kwiatkowski David J. 
Published: December 2008

AbstractMultiplex ligation‐dependent probe amplification (MLPA) is a commonly used technique for determining relative DNA sequence dosage (or copy number) in a complex DNA sample. Originally MLPA was designed as a copy number analysis tool for detecting disease‐causing genomic mutations and has been successfully applied in the testing and identification of hundreds of genomic mutations in numerous genes including DMD, BRCA1, NF1, and TSC2. More recently, several modifications of the original technique have been implemented. Arguably the most important enhancement of MLPA has been probe generation by chemical synthesis, enabling the facile creation of novel probe sets for any desired application. Other newer applications of MLPA include methylation status determination, copy number analysis in segmentally duplicated regions, expression profiling, and transgene genotyping. MLPA has a potential major role in the analysis of common copy number variation in genome‐wide association analyses, which may be enhanced by future improvements to increase throughput and lower costs, such as array‐MLPA.
Development of new substrates for high‐sensitive genotyping of minority mutated alleles
Authors: Galbiati Silvia , Damin Francesco , Di Carlo Gabriele , Ferrari Maurizio , Cremonesi Laura , Chiari Marcella 
Published: December 2008

AbstractAn unsurpassed level of sensitivity was reached in the detection of minority mutated alleles. A low‐density microarray was printed on a substrate specifically designed to provide an interference effect which amplifies the collection of the light emitted on the support and reinforces the intensity of excitation light. Optimal performance of the array was obtained by maximizing the probe density and the binding efficiency to the target through a polymeric coating made by the adsorption of a copolymer of N,N‐dimethylacrylamide (97% of moles), N,N‐acryloyloxysuccinimide (2%) and 3‐(trimethoxysilyl)propyl methacrylate (1%) synthesized by free radical copolymerization. The new substrate was used in the identification of fetal mutations in the maternal plasma DNA. Amino‐modified amplicons from genomic DNA corresponding to the locus of eight β‐thalassemia mutations were immobilized and interrogated with dual‐color oligonucleotide targets. Compared with the conventional glass substrates, the new substrate showed a great enhancement of fluorescence signals thanks to the combination of the optics with the highly efficient polymeric coating, allowing specific detection of all mutations. The high sensitivity and selectivity obtained made it possible to develop assays for the identification of paternally inherited mutations on fetal DNA in the maternal plasma in couples at risk for β‐thalassemia.
High‐throughput analysis of DNA fragments using a miniaturized CE system combined with a slotted‐vial array sample introduction system
Authors: Fan Xiao‐Feng , Li Qi , Wang Shi‐Li , Xu Zhang‐Run , Du Wen‐Bin , Fang Qun , Fang Zhao‐Lun 
Published: December 2008

AbstractAn automated nanoliter sample introduction system was combined to a liquid‐core waveguide (LCW)‐based microfluidic CE system for high‐throughput analysis of DNA fragments. The main component of the sample introduction system was a motor‐driven plate, on which a circular array of bottom‐slotted vials containing sample/buffer solutions was placed. A 7 cm‐long LCW capillary served as both the sample probe and separation channel. The inlet terminal of the capillary could pass through the slots of the vials for electrokinetic sample introduction, and the capillary outlet was immersed in the solution of a reservoir, behind which a PMT facing directly to the outlet was positioned. A diode laser was used as excitation source for LCW LIF detection. Performance of the system was demonstrated through the separation of DNA fragments. Baseline separation was achieved for all 11 fragments of ΦX174‐HaeIII digest DNA with a throughput of 33/h. Theoretical plate number for 603 bp fragment was 7.3×106/m, corresponding to a plate height 0.14 μm. The detection limitation for 603 bp fragment was 0.4 ng/μL with a precision of 2.2% RSD for the peak height. Automated sample changing and introduction were achieved with only 0.3 nL gross sample consumption for each cycle.
Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: A comparison with commercially available materials
Authors: Fredlake Christopher P. , Hert Daniel G. , Root Brian E. , Barron Annelise E. 
Published: December 2008

AbstractElectrophoresis‐based DNA sequencing is the only proven technology for the de novo sequencing of large and complex genomes. Miniaturization of capillary array electrophoresis (CAE) instruments can increase sequencing throughput and decrease cost while maintaining the high quality and long read lengths that has made CAE so successful for de novo sequencing. The limited availability of high‐performance polymer matrices and wall coatings designed specifically for microchip‐sequencing platforms continues to be a major barrier to the successful development of a commercial microchip‐sequencing instrument. It has been generally assumed that the matrices and wall coatings that have been developed for use in commercial CAE instruments will be able to be implemented directly into microchip devices with little to no change in sequencing performance. Here, we show that sequencing matrices developed specifically for microchip electrophoresis systems can deliver read lengths that are 150–300 bases longer on chip than some of the most widely used polymer‐sequencing matrices available commercially. Additionally, we show that the coating ability of commercial matrices is much less effective in the borosilicate chips used in this study. These results lead to the conclusion that new materials must be developed to make high‐performance microfabricated DNA‐sequencing instruments a reality.
Advantages and limitations of next‐generation sequencing technologies: A comparison of electrophoresis and non‐electrophoresis methods
Authors: Hert Daniel G. , Fredlake Christopher P. , Barron Annelise E. 
Published: December 2008

AbstractThe reference human genome provides an adequate basis for biological researchers to study the relationship between genotype and the associated phenotypes, but a large push is underway to sequence many more genomes to determine the role of various specificities among different individuals that control these relationships and to enable the use of human genome data for personalized and preventative healthcare. The current electrophoretic methodology for sequencing an entire mammalian genome, which includes standard molecular biology techniques for genomic sample preparation and the separation of DNA fragments using capillary array electrophoresis, remains far too expensive ($5 million) to make genome sequencing ubiquitous. The National Human Genome Research Institute has put forth goals to reduce the cost of human genome sequencing to $100 000 in the short term and $1000 in the long term to spur the innovative development of technologies that will permit the routine sequencing of human genomes for use as a diagnostic tool for disease. Since the announcement of these goals, several companies have developed and released new, non‐electrophoresis‐based sequencing instruments that enable massive throughput in the gathering of genomic information. In this review, we discuss the advantages and limitations of these new, massively parallel sequencers and compare them with the currently developing next generation of electrophoresis‐based genetic analysis platforms, specifically microchip electrophoresis devices, in the context of three distinct types of genetic analysis.
Determining arresters best positions in power system for lightning shielding failure protection using simulation optimization approach
Authors: Vahidi B. , Tavakoli M. R. Bank , Hosseinian S. H. 
Published: December 2008

AbstractThe lightning stroke to power system structures especially overhead lines makes severe damages and results in less reliable power supply. The invention of surge arresters was a revolution in these systems for protecting the precise equipments from lightning stroke overvoltages. Nowadays, with ever decreasing prices, using arrester not only for protecting certain instruments but also for decreasing total risk of flashover in overall network, is investigated by academic and industrial pioneers in this area. In this paper, our goal is to introduce a heuristic method for determining optimum positions for placing transmission lines surge arresters (TLSAs) with acceptable approximation, to get lowest possible value of shielding failure risk of flashover in a selected set of overhead lines. Simulation optimization based on neural net (i.e. Meta Model) and genetic algorithm (optimization algorithm) is invoked to suggest best positions for placing TLSAs. A case study on Kerman 230 kV network shows good achievement of simulation optimization for finding optimum positions of TLSAs. Comparison is also made with the results of transient simulation to reveal the effectiveness of the method. Copyright © 2008 John Wiley & Sons, Ltd.
Volatility forecasting with double Markov switching GARCH models
Authors: Chen Cathy W. S. , So Mike K. P. , Lin Edward M. H. 
Published: December 2008

AbstractThis paper investigates inference and volatility forecasting using a Markov switching heteroscedastic model with a fat‐tailed error distribution to analyze asymmetric effects on both the conditional mean and conditional volatility of financial time series. The motivation for extending the Markov switching GARCH model, previously developed to capture mean asymmetry, is that the switching variable, assumed to be a first‐order Markov process, is unobserved. The proposed model extends this work to incorporate Markov switching in the mean and variance simultaneously. Parameter estimation and inference are performed in a Bayesian framework via a Markov chain Monte Carlo scheme. We compare competing models using Bayesian forecasting in a comparative value‐at‐risk study. The proposed methods are illustrated using both simulations and eight international stock market return series. The results generally favor the proposed double Markov switching GARCH model with an exogenous variable. Copyright © 2008 John Wiley & Sons, Ltd.
Shikonin exerts antitumor activity via proteasome inhibition and cell death induction in vitro and in vivo
Authors: Yang Huanjie , Zhou Ping , Huang Hongbiao , Chen Di , Ma Ningfang , Cui Qiuzhi Cindy , Shen Shouxing , Dong Weihua , Zhang Xiaoyan , Lian Wen , Wang Xuejun , Dou Q. Ping , Liu Jinbao 
Published: December 2008

AbstractDysregulation of the ubiquitin‐proteasome pathway plays an essential role in tumor growth and development. Shikonin, a natural naphthoquinone isolated from the traditional Chinese medicine Zi Cao (gromwell), has been reported to possess tumor cell‐killing activity, and results from a clinical study using a shikonin‐containing mixture demonstrated its safety and efficacy for the treatment of late‐stage lung cancer. In this study, we reported that shikonin is an inhibitor of tumor proteasome activity in vitro and in vivo. Our computational modeling predicts that the carbonyl carbons C1 and C4 of shikonin potentially interact with the catalytic site of β5 chymotryptic subunit of the proteasome. Indeed, shikonin potently inhibits the chymotrypsin‐like activity of purified 20S proteasome (IC50 12.5 μmol/L) and tumor cellular 26S proteasome (IC50 between 2–16 μmol/L). Inhibition of the proteasome by shikonin in murine hepatoma H22, leukemia P388 and human prostate cancer PC‐3 cultures resulted in accumulation of ubiquitinated proteins and several proteasome target proapoptotic proteins (IκB‐α, Bax and p27), followed by induction of cell death. Shikonin treatment resulted in tumor growth inhibition in both H22 allografts and PC‐3 xenografts, associated with suppression of the proteasomal activity and induction of cell death in vivo. Finally, shikonin treatment significantly prolonged the survival period of mice bearing P388 leukemia. Our results indicate that the tumor proteasome is one of the cellular targets of shikonin and inhibition of the proteasome activity by shikonin contributes to its antitumor property. © 2008 Wiley‐Liss, Inc.
Factors associated with incident and fatal pancreatic cancer in a cohort of middle‐aged women
Authors: Stevens Richard J. , Roddam Andrew W. , Spencer Elizabeth A. , Pirie Kirstin L. , Reeves Gillian K. , Green Jane , Beral Valerie ,   on behalf of the Million Women Study Collaborators
Published: December 2008

AbstractRisk factors for pancreatic cancer, other than smoking and diabetes, are not well‐established, especially for women. In a cohort of 1.3 million middle‐aged women, followed for 9.2 million person‐years for cancer incidence and 11.5 million person‐years for mortality, there were 1,338 incident pancreatic cancer cases and 1,710 deaths from the disease. Using proportional hazards models, we calculated adjusted relative risks (RRs) and 95% confidence intervals (CIs) by smoking, height, body mass index (BMI), alcohol consumption, physical activity and history of diabetes. Pancreatic cancer incidence was greater in current than never smokers (RR 2.39, CI 2.10–2.73), the risk increasing with the number of cigarettes smoked. The incidence of pancreatic cancer also increased with increasing BMI (RR 1.34, CI 1.13–1.57 for BMI ≥ 30 vs. 22.5–25 kg/m2), and with a history of diabetes (RR 1.58, CI 1.22–2.03, with vs. without such a history). These factors were also associated with increased mortality from pancreatic cancer. Height, alcohol consumption and physical activity showed little or no association with pancreatic cancer risk. © 2008 Wiley‐Liss, Inc.
The Bcl‐xL inhibitor of apoptosis is preferentially expressed in cutaneous squamous cell carcinoma compared with that in keratoacanthoma
Authors: Vasiljević Natasa , Andersson Kristin , Bjelkenkrantz Kaj , Kjellström Christer , Månsson Henrik , Nilsson Elise , Landberg Goran , Dillner Joakim , Forslund Ola 
Published: December 2008

AbstractKeratoacanthoma (KA) is difficult to histologically distinguish from squamous cell carcinoma (SCC). Therefore, although KA is a benign self‐resolving skin lesion, KA is commonly treated as SCC. Biomarkers to distinguish KA and SCC would thus be desirable. In search for specific markers, paraffin‐embedded tissue samples from 25 SCC and 64 KA were arranged in a tissue microarray (TMA) and stained for immunologic cell‐markers CD3, CD20 and CD68 as well as for proteins considered of relevance in tumorgenesis, namely NFκB/p65, IκB‐α, STAT3, p53, TRAP‐1, pRB, phosphorylated pRb, Cyld, p21, p16INK4, Survivin, Bcl‐xL, Caspase 3, Bak, FLK‐1/VEGF‐r2 and Ki‐67. In addition, the tumors were tested for presence of human papillomavirus by PCR. We detected that the two lesions differed significantly in expression of Bcl‐xL which was present in 84% of the SCC compared with only 15% in the KA (p < 0.001). The lower expression of the antiapoptotic protein Bcl‐xL in KA is consistent with a possible role of apoptosis in the regression of KA. © 2008 Wiley‐Liss, Inc.
Polymorphic loci of E2F2, CCND1 and CCND3 are associated with HER2 status of breast tumors
Authors: Justenhoven Christina , Pierl Christiane B. , Haas Susanne , Fischer Hans‐Peter , Hamann Ute , Baisch Christian , Harth Volker , Spickenheuer Anne , Rabstein Sylvia , Vollmert Caren , Illig Thomas , Pesch Beate , Brüning Thomas , Dippon Jürgen , Ko Yon‐Dschun , Brauch Hiltrud 
Published: December 2008

AbstractOverexpression of the human epidermal growth factor receptor 2 (HER2) in breast tumors is associated with bad prognosis. Therefore, it is highly relevant to further improve understanding of the regulatory mechanisms of HER2 expression. In addition to gene amplification, transcriptional regulation plays a crucial role in HER2 overexpression. In this study, we analyzed 3 polymorphisms E2F2_‐5368_A>G, CCND1_870_A>G and CCND3_‐677_C>T located in genes involved in cell cycle regulation in the GENICA population‐based and age‐matched breast cancer case‐control study from Germany. We genotyped 1,021 cases and 1,015 controls by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Statistical analyses were performed by conditional logistic regression. We observed no differences in genotype frequencies between breast cancer cases and controls. Subgroup analysis showed associations between carriers of the E2F2_‐5368_G allele (OR: 0.60, 95% CI: 0.42–0.85), carriers of the CCND1_870_G allele (OR: 0.66, 95% CI: 0.45–0.96) and carriers of the CCND3_‐677_T allele (OR: 1.72, 95% CI: 1.20–2.49) and HER2 expression in breast tumors. This finding points to an association of an increased expression of these cell cycle regulators with lower expression of HER2. An explanation for this observation might be that low expression of E2F2, CCND1 and CCND3 decrease levels of factors down‐regulating HER2. We conclude that the analyzed polymorphisms located in E2F2, CCND1 and CCND3 are potential markers for HER2 status of breast tumors. © 2008 Wiley‐Liss, Inc.
Growth, poverty and inequality in Ethiopia: Which way for pro‐poor growth?
Authors: Geda Alemayehu , Shimeles Abebe , Weeks John 
Published: December 2008

AbstractThe paper examines the pattern of poverty, growth and inequality in Ethiopia in the recent decade. The result shows that growth, to a large extent depends on structural factors such as initial conditions, vagaries of nature, external shocks and peace and stability both in Ethiopia and in the region. Using a rich household panel data, the paper also shows that there is a strong correlation between growth and inequality. In such set up, the effect of implementing a pro‐poor growth strategy, compared to allowing the status quo to prevail, can be quite dramatic. On the basis of realistic assumptions, the paper shows that from a baseline in 2000 of a 30 per cent poverty share, over 10 years at growth of 4 per cent per capita, poverty would decline from 44 to 26 per cent for distribution neutral growth (DNG) (i.e. no change in the aggregate income distribution). In contrast, were the growth increment distributed equally across percentiles (equally distributed gains of growth, EDG), the poverty would decline by over half, to 15 per cent, a difference of almost eleven percentage points. Thus, ‘distribution matters’, even, or especially in a poor country like Ethiopia. On the basis of these results the paper outlines policies that could help to design a sustainable pro‐poor growth strategy. Copyright © 2008 John Wiley & Sons, Ltd.
Dissociation kinetics determination of yttrium(III)‐polyaminocarboxylates using free‐ion selective radiotracer extraction (FISRE)
Authors: Jurkin Denis , Gildehaus Franz Josef , Wierczinski Birgit 
Published: December 2008

AbstractFree‐ion selective radiotracer extraction (FISRE) is a technique combining ion exchange and the use of radiotracers in order to determine labilities of metal complexes. The aminocarboxylate chelates 90Y‐EDTA, 90Y‐DTPA as well as 90Y‐DOTATOC, a radiopharmaceutical for neuroendocrine tumor treatment have been studied by FISRE using Chelex cation exchanger within the pH range 5.0–7.4. Time‐dependent speciation and dissociation rate constants have been determined in a time frame of 0.6 s–648 h. As indicated by thermodynamic constants, the lability decreases significantly with higher ligand denticity, cyclic coordination and upon peptide coupling resulting in the lability order Y‐EDTA>Y‐DTPA>Y‐DOTA>Y‐DOTATOC. Besides, studies of the effects of the metal/ligand ratio on FISRE suggest that – in contrast to EDTA and DTPA – cyclic ligands DOTA and DOTATOC tend to shield the ion exchanger from free yttrium ions after complex dissociation even at slight excess of metal ions. Copyright © 2008 John Wiley & Sons, Ltd.