bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capture and analysis of quantitative proteomic data
Authors: Lau King Wai , Jones Andrew R. , Swainston Neil , Siepen Jennifer A. , Hubbard Simon J. 
Published: July 2007

AbstractWhilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of the data obtained. These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding MS scans in the experiment, construction of representative ion chromatograms, location of the true peptide ion chromatogram start and end, elimination of background signal in the mass spectrum and chromatogram and calculation of both peptide and protein ratios/abundances. A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. Currently, although there is no single consensus on precisely how to calculate protein and peptide abundances, many common themes have emerged which identify and reduce many of the key sources of error. These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge.
Methods for the detection and analysis of protein–protein interactions
Authors: Berggård Tord , Linse Sara , James Peter 
Published: July 2007

AbstractA large number of methods have been developed over the years to study protein–protein interactions. Many of these techniques are now available to the nonspecialist researcher thanks to new affordable instruments and/or resource centres. A typical protein–protein interaction study usually starts with an initial screen for novel binding partners. We start this review by describing three techniques that can be used for this purpose: (i) affinity‐tagged proteins (ii) the two‐hybrid system and (iii) some quantitative proteomic techniques that can be used in combination with, e.g., affinity chromatography and coimmunoprecipitation for screening of protein–protein interactions. We then describe some public protein–protein interaction databases that can be searched to identify previously reported interactions for a given bait protein. Four strategies for validation of protein–protein interactions are presented: confocal microscopy for intracellular colocalization of proteins, coimmunoprecipitation, surface plasmon resonance (SPR) and spectroscopic studies. Throughout the review we focus particularly on the advantages and limitations of each method.
Affinity reagent resources for human proteome detection: Initiatives and perspectives
Authors: Stoevesandt Oda , Taussig Michael J. 
Published: July 2007

AbstractEssential to the ambition of characterising fully the human proteome are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. Although a large number of affinity reagents are available commercially, their quality is often questionable and only a fraction of the proteome is covered. In order for more targets to be examined, there is a need for broad availability of panels of affinity reagents, including binders against proteins of unknown functions. The most familiar affinity reagents are antibodies and their fragments, but engineered forms of protein scaffolds and nucleic acid aptamers with similar diversity and binding properties are becoming viable alternatives. Recent initiatives in Europe and the USA have been established to improve both the availability and quality of reagents for affinity proteomics, with the ultimate aim of creating standardised collections of well‐validated binding molecules for proteome analysis. As well as coordinating affinity reagent production through existing resources and technology providers, these projects aim to benchmark key molecular entities, tools, and applications, and establish the bioinformatics framework and databases needed. The benefits of such reagent resources will be seen in basic research, medicine and the biotechnology and pharmaceutical industries.
Crop proteomics: Aim at sustainable agriculture of tomorrow
Authors: Salekdeh Ghasem Hosseini , Komatsu Setsuko 
Published: July 2007

AbstractThe advent of proteomics has made it possible to identify a broad spectrum of proteins in living systems. This capability is especially useful for crops as it may give clues not only about nutritional value, but also about yield and how these factors are affected by adverse conditions. In this review, we describe the recent progress in crop proteomics and highlight the achievements made in understanding the proteomes of major crops. The major emphasis will be on crop responses to abiotic stresses. Rigorous genetic testing of the role of possibly important proteins can be conducted. The increasing ease with the DNA, mRNA and protein levels can be conducted and connected suggests that proteomics data will not be difficult to apply to practical crop breeding.
Input‐to‐state stabilizing sub‐optimal NMPC with an application to DC–DC converters
Authors: Lazar M. , Heemels W. P. M. H. , Roset B. J. P. , Nijmeijer H. , van den Bosch P. P. J. 
Published: July 2007

AbstractThis article focuses on the synthesis of computationally friendly sub‐optimal nonlinear model predictive control (NMPC) algorithms with guaranteed robust stability. To analyse the robustness of the MPC closed‐loop system, we employ the input‐to‐state stability (ISS) framework. To design ISS sub‐optimal NMPC schemes, a new Lyapunov‐based method is proposed. ISS is ensured via a set of constraints, which can be specified as a finite number of linear inequalities for input affine nonlinear systems. Furthermore, the method allows for online optimization over the ISS gain of the resulting closed‐loop system. The potential of the developed theory for the control of fast nonlinear systems, with sampling periods below 1 ms, is illustrated by applying it to control a Buck‐Boost DC–DC converter. Copyright © 2007 John Wiley & Sons, Ltd.
Computational aerodynamic analysis of a blunt trailing‐edge airfoil modification to the NREL Phase VI rotor
Authors: Chao D. D. , van Dam C. P. 
Published: July 2007

AbstractThe effects of modifying the inboard portion of the experimental NREL Phase VI rotor using a thickened, blunt trailing‐edge (or flatback) version of the S809 design airfoil are studied using a compressible, three‐dimensional, Reynolds‐averaged Navier–Stokes method. A motivation for using such a thicker airfoil design coupled with a blunt trailing edge is to alleviate structural constraints while reducing blade weight and maintaining the power performance of the rotor. The numerical results for the baseline Phase VI rotor are benchmarked against wind tunnel measurements obtained at freestream velocities of 5, 7 and 10ms−1. The calculated results for the modified rotor are compared against those of the baseline rotor. The results of this study demonstrate that a thick, blunt trailing‐edge blade profile is viable as a bridge to connect structural requirements with aerodynamic performance in designing future wind turbine rotors. Copyright © 2007 John Wiley & Sons, Ltd.
Diet quality of young people in southern Spain evaluated by a Mediterranean adaptation of the Diet Quality Index-International (DQI-I)
Authors: Mariscal-Arcas M. , Romaguera D. , Rivas A. , Feriche B. , Pons A. , Tur J. A. , Olea-Serrano F. 
Published: July 2007

The aim of this study was to assess whether the recently developed Diet Quality Index-International (DQI-I) was useful to evaluate the diet quality of a young Mediterranean population. A cross-sectional nutritional survey was carried out in southern Spain (Granada-Andalucia) from 2002 to 2005. Dietary information (24 h recall and FFQ) and socio-demographic and lifestyle data were collected from a representative sample of the population (n288, 44·1 % females and 55·9 % males) aged 6–18 years (mean 12·88 (sd2·78) years). DQI-I was designed according to the method of Kimet al.modified by Turet al.for Mediterranean populations. It focused on four main characteristics of a high-quality diet (variety, adequacy, moderation and overall balance). This young population from southern Spain obtained 56·31 % of the total DQI-I score, indicating a poor-quality diet. A higher score was associated with a longer breakfast and greater physical activity. The DQI-I may require further modification for application in Mediterranean populations, differentiating between olive oil and saturated fats, among other changes. Further research is needed to develop a new diet quality index adapted to the Mediterranean diet.
β-Carotene and canthaxanthin alter the pro-oxidation and antioxidation balance in rats fed a high-cholesterol and high-fat diet
Authors: Shih Chun-Kuang , Chang Jui-Hung , Yang Shwu-Huey , Chou Tsui-Wei , Cheng Hsing-Hsien 
Published: July 2007

This study investigated the effects of β-carotene and canthaxanthin on lipid peroxidation and antioxidative enzyme activities in rats fed a high-cholesterol, high-fat diet. Wistar rats were divided into six groups. Negative control group (group NC) received a high-fat (150 g/kg) diet; cholesterol control group (group CC) received a high-cholesterol (10 g/kg), high-fat diet. The other four groups were fed a high-cholesterol, high-fat diet supplemented with crystal β-carotene (group BC), β-carotene beadlet (group BB), canthaxanthin beadlet (group CX) or α-tocopherol (group AT). Blood and livers were collected for analysis after 6 weeks of feeding. Group BB had significantly lower hepatic thiobarbituric acid reactive substance (TBARS) and conjugated diene concentrations, whereas group CX had a significantly lower plasma TBARS concentration than did group CC. In erythrocytes, glutathione peroxidase activities were significantly greater in groups BC, BB and CX than in group CC. Moreover, compared with group CC, catalase activities were significantly greater in groups BB and CX, and superoxide dismutase (SOD) activity was significantly greater in group BB. In livers, SOD activities were significantly greater in groups BC, BB and CX, and glutathione reductase activities were significantly greater in groups BB and CX than in group CC. Compared with group CC, hepatic retinol and α-tocopherol concentrations were significantly greater in groups BC, BB and CX, whereas plasma and hepatic cholesterol concentrations were significantly lower in group BC. These findings suggest that β-carotene and canthaxanthin altered the pro-oxidation and antioxidation balance and suppressed cholesterol-induced oxidative stressviamodulation of antioxidant system and cholesterol metabolism.
Influence of body composition, muscle strength, diet and physical activity on total body and forearm bone mass in Chinese adolescent girls
Authors: Huat Foo Leng , Zhang Qian , Zhu Kun , Ma Guansheng , Greenfield Heather , Fraser David R. 
Published: July 2007

The aim of the present study was to determine association between body composition, muscle strength, diet and physical exercise with bone mineral content (BMC) and bone area (BA) in 283 Chinese adolescent girls aged 15 years in Beijing, China. Body composition, pubertal stage, physical activity and dietary intakes were assessed using standard validated protocols. Total body and forearm bone, lean body mass (LBM) and fat body mass (FBM) were determined by dual X-ray absorptiometry. Multivariate linear regression analyses were carried out to examine the predictors of BMC and BA, after controlling for potential confounders. The subjects had a mean age of 15·0 (sd 0·9) years and 99·6 % of them had reached menarche. Multivariate analyses showed that LBM, FBM, handgrip muscle strength and milk intake were significant independent determinants of BMC and BA of the total body and/or forearm sites. LBM was found to be a stronger independent determinant than FBM of BMC and BA, whereas handgrip muscle strength was only found as significant determinant of BMC and BA at the forearm sites than in total body BMC and BA. Further, total physical activity level had a significant positive association with handgrip and LBM. This suggested that greater muscle strength and higher LBM may reflect higher levels of physical activity. Therefore, continuous healthy lifestyle practices such as adequate intake of milk and continuous participation in physical activity should be encouraged throughout adolescence to optimise bone growth during this period.
Influence of lycopene and vitamin C from tomato juice on biomarkers of oxidative stress and inflammation
Authors: Jacob Karin , Periago María J. , Böhm Volker , Berruezo Gaspar Ros 
Published: July 2007

A human study was carried out to investigate whether tomato juice, rich in natural lycopene and fortified with vitamin C, is able to reduce several biomarkers of oxidative stress and inflammation and whether the effect can be attributed to lycopene, vitamin C or any other micronutrient. Following a 2-week depletion phase, volunteers were assigned randomly to ingest either tomato juice with (LC) or without (L) vitamin C fortification for 2 weeks (daily dose 20·6 mg lycopene and 45·5/435 mg vitamin C). Plasma and urine were analysed for carotenoids and vitamin C, lipid status, antioxidant capacity, thiobarbituric acid reactive substances (TBARS) and 8-epi-PGF2α, protein carbonyls, cytokines IL-1β and TNFα and C-reactive protein (CRP). The consumption of tomato juice led to a reduction in total cholesterol levels (L: 157·6v. 153·2 mg/dl,P = 0·008; LC: 153·4v. 147·4 mg/dl,P = 0·002) and that of CRP (L: 315·6v. 262·3 μg/l,P = 0·017; LC: 319·2v. 247·1 μg/l,P = 0·001) in both groups. The vitamin C-fortified juice slightly raised the antioxidant capacity in urine and decreased TBARS in plasma and urine. All other markers were affected to a lesser extent or remained unchanged. Cholesterol reduction was correlated with lycopene uptake (P = 0·003), whereas the other effects could not be related with particular micronutrients. Any beneficial effects of tomato consumption for human health cannot be attributed only to lycopene and, as the additional supplementation with ascorbic acid indicates, a variety of antioxidants might be needed to optimize protection against chronic diseases.
Echinococcus granulosus from Mexican pigs is the same strain as that in Polish pigs
Authors: Cruz-Reyes A. , Constantine C.C. , Boxell A.C. , Hobbs R.P. , Thompson R.C.A. 
Published: July 2007

AbstractSamples of Echinococcus granulosus from seven pigs from Mexico were compared with isolates of the parasite from pigs in Poland and representative strains and species of Echinococcus. Isolates from pigs in Mexico were found to be genetically identical to E. granulosus from Polish pigs and distinct from other major genotypes by sequencing part of the mitochondrial cytochrome c oxidase I (COI) mtDNA locus, restriction fragment length polymorphism (RFLP) of the polymerase chain reaction (PCR) amplified rDNA internal transcribed spacer (ITS) 1 using five different enzymes, and random amplified polymorphic DNA (RAPD) analysis. These results were complemented by data on hook morphology and together strengthen the view that Echinococcus maintained in a cycle involving pigs and dogs is a distinct strain that is conserved genetically in different geographical areas. The present study supports the close relationship of the cervid, camel and pig strains and raises the question of their taxonomic status.
Extracranial glomus faciale tumour
Authors: Connor S E J , Gleeson M J , Odell E 
Published: July 2007

AbstractObjectives:To describe a unique presentation of a predominantly extracranial glomus faciale tumour. To discuss the role of imaging in the differential diagnosis and evaluation of a hypervascular parotid mass. To review the previous literature concerning the glomus faciale tumour.Case report:A 54-year-old woman presented with a six-month history of facial weakness, pain and a parotid mass. Ultrasound revealed a hypervascular parotid mass and pre-operative core biopsy suggested a paraganglioma. Computed tomography defined its deep extent and demonstrated involvement of the petrous temporal bone along the descending portion of the facial nerve canal with a pattern of permeative lucency. A tumour was surgically removed which arose from the facial nerve from the second genu to the proximal divisions within the parotid gland and histology confirmed a paraganglioma.Conclusions:A facial nerve glomus faciale tumour should be considered in the differential diagnosis of a hypervascular parotid mass and may present in a predominantly extracranial location. Computed tomography will prove helpful in such a case in order to limit the differential diagnosis and to define the extent of skull base involvement.
The Changing Ecology of Foreign Policy-Making in China: The Ascension and Demise of the Theory of “Peaceful Rise”
Authors: Glaser Bonnie S , Medeiros Evan S 
Published: July 2007

AbstractChina's rapidly proliferating global interests and evolving political environment have begun to change the international and domestic context for its foreign policy-making. This article explores the changing inputs into and processes associated with foreign policy-making in China today. It does this by analysing the shifting fortunes of “peaceful rise,” one of the first new foreign policy concepts to be introduced under the Hu Jintao administration. The authors draw several implications from this narrow debate for understanding contemporary foreign policy-making in China. It provides an example of how new foreign policy ideas and strategies can come from outside the formal, central government bureaucracy, and underscores the growing relevance of think-tank analysts and university-based scholars. Finally, the authors argue that the Chinese leadership's decision to eschew “peaceful rise” in favour of “peaceful development” was fundamentally a question of terminology and thus preserved China's strategy of reassuring other nations.
Building China's Telecommunications Network: Industrial Policy and the Role of Chinese State-Owned, Foreign and Private Domestic Enterprises
Authors: Harwit Eric 
Published: July 2007

AbstractThis article uses theories of industrial policy to analyse the growth of China's telecommunications equipment industry over the past 20 years. It highlights the role of the Chinese government in shaping the sector, by first utilizing imported equipment, then promoting Sino-foreign joint ventures and finally fostering domestic companies. Significantly, the government encouraged market competition, and avoided the pitfall of monopoly state control. Today, key telecommunications players include joint ventures, state-owned companies and even a major Chinese private corporation. The article concludes that the government's fiscal and regulatory industrial polices were successful, in that they rapidly built a modern communications network while promoting a vibrant free-market competitive environment.
China's “New Remembering” of the Anti-Japanese War of Resistance, 1937–1945
Authors: Coble Parks M. 
Published: July 2007

AbstractIn today's China, memory of the Sino-Japanese War of 1937–45 is often a front page issue, a source of diplomatic friction between Beijing and Tokyo. Yet in Mao's era, public memory of this conflict virtually disappeared. Only the role of communist forces under Chairman Mao was commemorated; other memories were consigned to historical oblivion. This article examines the process by which memory of the war re-appeared in the reform era. Because the government has emphasized nationalism, the new memory of the war has stressed a patriotic nationalist narrative of heroic resistance. At the same time, a second major theme has been the emphasis on Japanese atrocities, virtually a “numbers game” in historical writing. Thus despite the voluminous publications which have appeared since the 1980s, the new writing on the war has stressed certain themes while neglecting others.
Embodied Masculinity: Sex and Sport in a (Post) Colonial Chinese City
Authors: Zheng Tiantian 
Published: July 2007

AbstractThis article examines the historical formation of local masculine identity in the city of Dalian in north-east China. I argue that the experiences of Dalian-Chinese men under Japanese colonialism (1905–45) established a model of masculine identity based on bodily resistance. The article explores Dalian men's encounter with colonialism by comparing two different forms of bodily experience: military calisthenics in Japanese-run schools for Chinese boys and street soccer. On the one hand, military calisthenics impressed Chinese schoolboys with a sense of subjugation focused on the body. Bodily movements were performed under the strict scrutiny of Japanese drill masters and formed an integral part of everyday rituals of obedience. On the other hand, street soccer emerged as a popular and potentially creative activity among Chinese schoolboys. In contrast with the controlled motions of military calisthenics, soccer offered a sense of freedom in its unrestricted and improvised movements. Matches against Japanese teams even more explicitly infused soccer with a spirit of nationalistic resistance. In conclusion, I argue that these bodily experiences are crucial to understanding the historical reformations of Dalian male gender identity.
Ancient imperial heritage and Islamic universal historiography: al-Dīnawarī’s secular perspective
Authors: Yücesoy Hayrettin 
Published: July 2007

AbstractThis article examines the historical work of the ninth-century Muslim scholar Abūanīfa al-Dīnawarī. Adopting the format of universal history, al-Dīnawarī constructed a historical narrative beginning with the first human Adam, continuing through the rise of Islam and culminating in the Caliphate. This paper argues that al-Dīnawarī’s work, appropriately entitled Longer narratives, represented an attempt to configure Islamic polity into world history through a reorientation of Sasanian imperial ideology and geographical consciousness in order to fit Islamic sensibilities. As an early example of belles-lettres (adab) oriented (belletrist, adabī) universal historiography, al-Dīnawarī’s work comes across as a perceptive outlook on history, which proved relevant to dynasties of diverse origins struggling to carve a space for themselves in the Persianate political landscape of the late and post-‘Abbāsid world.
Literacy and the ‘great divide’ in the Islamic world, 1300–1800
Authors: Hanna Nelly 
Published: July 2007

AbstractThe study proposes an approach to the history of literacy in the Islamic world that uses a flexible and gradated definition of literacy. It goes on to propose some factors that lay behind the acquisition of certain forms of literacy and of the way that they were put into practical use. Among these factors were the religious factor, which had consequences on a broad region; commercial conditions, which were an impetus to make use of the written word; and the development of a legal culture.