bluuebunny/crossref_metadata_2025_split huggingface dataset:
A versatile peptide pI calculator for phosphorylated and N‐terminal acetylated peptides experimentally tested using peptide isoelectric focusing
Authors: Gauci Sharon , van Breukelen Bas , Lemeer Simone M. , Krijgsveld Jeroen , Heck Albert J. R. 
Published: November 2008

AbstractWe experimentally demonstrate the use of an in‐house developed pI calculator which takes into account peptide PTM such as phosphorylation and N‐terminal acetylation. The pI calculator was utilized for a large set of peptides derived from a complex zebrafish lysate fractionated using peptide IEF, whereby a good correlation between the calculated (theoretical) pI and the experimental pI could be established. This pI calculator permits the implementation of optimal pK values depending on the experimental conditions and a reliable calculation of peptide pI which can be utilized as a filtering technique in validating peptide identifications. Our data reveal that the shift due to a phosphorylation or N‐terminal acetylation is highly dependent on the presence of acidic or basic residues in the peptide. Furthermore, using this pI calculator, we revealed previously unknown position‐specific pKs of asparagine and carbamidomethylated cysteine depending on their location in the peptide. Collectively, this peptide pI calculator is a welcome addition to the versatility and robustness of IEF for the separation and confident identification of (post‐translationally modified) peptides.
Difference gel electrophoresis
Authors: Timms John F. , Cramer Rainer 
Published: November 2008

AbstractDIGE is a protein labelling and separation technique allowing quantitative proteomics of two or more samples by optical fluorescence detection of differentially labelled proteins that are electrophoretically separated on the same gel. DIGE is an alternative to quantitation by MS‐based methodologies and can circumvent their analytical limitations in areas such as intact protein analysis, (linear) detection over a wide range of protein abundances and, theoretically, applications where extreme sensitivity is needed. Thus, in quantitative proteomics DIGE is usually complementary to MS‐based quantitation and has some distinct advantages. This review describes the basics of DIGE and its unique properties and compares it to MS‐based methods in quantitative protein expression analysis.
Stable isotopic labeling in proteomics
Authors: Gevaert Kris , Impens Francis , Ghesquière Bart , Van Damme Petra , Lambrechts Anja , Vandekerckhove Joël 
Published: November 2008

AbstractLabeling of proteins and peptides with stable heavy isotopes (deuterium, carbon‐13, nitrogen‐15, and oxygen‐18) is widely used in quantitative proteomics. These are either incorporated metabolically in cells and small organisms, or postmetabolically in proteins and peptides by chemical or enzymatic reactions. Only upon measurement with mass spectrometers holding sufficient resolution, light, and heavy labeled peptide ions or reporter peptide fragment ions segregate and their intensity values are subsequently used for quantification. Targeted use of these labels or mass tags further leads to specific monitoring of diverse aspects of dynamic proteomes. In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications.
The pre‐omics era: The early days of two‐dimensional gels
Authors: O'Farrell Patrick H. 
Published: November 2008

AbstractI present a personal view of the beginning of two‐dimensional gels and unsanctioned proteomics. I was still a young graduate student in the early 1970s when I developed methods for two‐dimensional gel electrophoresis that became widely used. Though the method gave us the capacity to do things that had never been done, the value of global enumeration of proteins was not appreciated, and we were still two decades away from the invention of the term proteomics. I describe a period of exploration where, by exercising our new capability, we conducted the first proteomic type expression experiments, and made unforeseen contributions to advances in biology. Detection of single‐amino acid substitutions validated genetic selections in cultured cells, and revealed a regulatory system that maintains the accuracy of protein synthesis by assuring an unbiased supply of its substrates. We documented biologic control with a dynamic range >108 fold, and, in a surprising turn, we identified an approach that provided a major breakthrough in recombinant DNA technology, the ability to express cloned sequences in Escherichia coli. The challenge then and now is to use a capability for global analysis to produce new insights into fundamental aspects of biology and to drive substantive technical advances.
Exhaled nitric oxide and respiratory symptoms in a community sample of school aged children
Authors: Kovesi Tom , Dales Robert 
Published: November 2008

AbstractObjectiveTo test the association between reported allergy and allergic diseases, respiratory symptoms, and the fractional concentration of exhaled nitric oxide (FeNO), in a community sample of school aged children.MethodologyWe administered a respiratory questionnaire and measured FeNO in a cross‐sectional study of 1,135 children.ResultsFeNO was significantly greater in children with reported asthma (20.3 (standard deviation (SD) 21.3) parts per billion (ppb)) or allergies (18.1 (SD 18.0) ppb) than in healthy children (14.0 (SD 13.4) ppb). It was greater in children with asthma and reported allergies (22.8 (SD 23.6) ppb), than in children with asthma but no allergies (15.8 (SD 15.6) ppb) (overall P‐value between disease groups = 0.002). FeNO was not related to respiratory symptoms in healthy children. Eczema was associated with an elevated FeNO concentration, even in the absence of respiratory symptoms. Some children with reported allergies but not asthma who had respiratory symptoms suggestive of asthma had elevated FeNO concentrations, and the proportion of healthy children with reported bronchitis or pneumonia in the past year who had an abnormally high FeNO concentration was significantly elevated.ConclusionsIn a community sample of children, FeNO concentrations appear to reflect allergic conditions, including allergic asthma, reported allergies, and eczema, rather than just asthma, particularly since asthma in children may be non‐allergic. FeNO is similarly elevated in school aged children with reported asthma or reported allergies. FeNO is higher in children with asthma and allergies than in children with asthma alone. However, an elevated FeNO may help alert the clinician to the possibility of undiagnosed asthma. Pediatr. Pulmonol. 2008; 43:1198–1205. © 2008 Wiley‐Liss, Inc.
A random mapping with preferential attachment
Authors: Hansen Jennie C. , Jaworski Jerzy 
Published: November 2008

AbstractIn this article we investigate the asymptotic structure of a random mapping model with preferential attachment, T, which maps the set {1,2,…,n} into itself. The model T was introduced in a companion article [Hansen and Jaworski, Random Struct Algorithms 33 (2008), 105–126] and the asymptotic structure of the associated directed graph G which represents the action of T on the set {1,2,…,n} was investigated in [Hansen and Jaworski, Random Struct Algorithms 33 (2008), 105–126] and [Hansen and Jaworski, Adv Appl Probab 40 (2008), 183–205] in the case when the attraction parameter ρ > 0 is fixed as n →∞. In this article we consider the asymptotic structure of G when the attraction parameter ρ  ρ(n) is a function of n as n →∞. We show that there are three distinct regimes during the evolution of G: (i) ρn →∞ as n →∞, (ii) ρn → β > 0 as n →∞, and (iii) ρn → 0 as n →∞. It turns out that the asymptotic structure of G is, in some cases, quite different from the asymptotic structure of well‐known models such as the uniform random mapping model and models with an attracting center. In particular, in regime (ii) we obtain some interesting new limiting distributions which are related to the incomplete gamma function. © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2009
Avoiding small subgraphs in Achlioptas processes
Authors: Krivelevich Michael , Loh Po‐Shen , Sudakov Benny 
Published: November 2008

AbstractFor a fixed integer r, consider the following random process. At each round, one is presented with r random edges from the edge set of the complete graph on n vertices, and is asked to choose one of them. The selected edges are collected into a graph, which thus grows at the rate of one edge per round. This is a natural generalization of what is known in the literature as an Achlioptas process (the original version has r = 2), which has been studied by many researchers, mainly in the context of delaying or accelerating the appearance of the giant component.In this article, we investigate the small subgraph problem for Achlioptas processes. That is, given a fixed graph H, we study whether there is an online algorithm that substantially delays or accelerates a typical appearance of H, compared to its threshold of appearance in the random graph G(n, M). It is easy to see that one cannot accelerate the appearance of any fixed graph by more than the constant factor r, so we concentrate on the task of avoiding H. We determine thresholds for the avoidance of all cycles Ct, cliques Kt, and complete bipartite graphs Kt,t, in every Achlioptas process with parameter r ge 2. © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2009
Virtual teams: understanding the impact of fear
Authors: Casey Valentine , Richardson Ita 
Published: November 2008

AbstractDistributed software development has become the norm for the software industry today. As a result many organizations are leveraging the expertise of their existing staff by establishing virtual teams. Here we outline the results from three independent case studies undertaken over a period of 8 years. The first study considered the operation of virtual teams whose members were situated in two locations in the same country. The second investigated why U.S. and Irish team members who worked very successfully while collocated, experienced serious problems when operating in virtual teams. The third focused on virtual testing teams with members based in Ireland and Malaysia. The Irish staffs had extensive experience of having projects offshored to them and were now responsible for offshoring part of their work. The results from each case study highlighted the importance and impact fear played and the consequences this had for the success of the respective strategies. Copyright © 2008 John Wiley & Sons, Ltd.
Structure Identification of Triacylglycerols in the Seed Oil of Momordica Charantia L. Var. Abbreviata Ser.
Authors: Fu Wei‐chang , Gu Xiao‐hong , Tao Guan‐jun , Tang Jian , Jiang Zai‐liang 
Published: November 2008

AbstractTriacylglycerols (TGs) in the seed oil of Momordica charantia L. var. abbreviata Ser. (MCV) were separated by non‐aqueous reversed‐phase (NARP)‐HPLC. Many of the TGs contain two different fatty acyl chains, such as palmitic (P), stearic (S), oleic (O), linoleic (L), and conjugated linolenic acid (CLn). Seven pairs of AAB/ABA‐type TGs might present in the seed oil of MCV, namely CLnCLnP/CLnPCLn, CLnCLnS/CLnSCLn, CLnCLnO/CLnOCLn, CLnCLnL/CLnLCLn, SSCLn/SCLnS, OOCLn/OCLnO and LLCLn/LCLnL. The positional isomers of a AAB/ABA‐type TGs pair yielded mass spectra showing a significant difference in relative abundance ratios of the fragment ions [AA]+ to [AB]+, which were produced by preferred losses of the fatty acid from the 1/3‐position compared to the 2‐position of the glycerol backbone. The precise stereospecific structures of the predominant regioisomers of TGs in AAB/ABA pairs were identified by atmospheric pressure chemical ionization mass spectrometry (APCI‐MS) according to the special relative abundance ratios of the fragment ions [AA]+ to [AB]+. TGs with CLn occupying the sn‐2 position in seven pairs of AAB/ABA might be major constituents of the oil, such as CLnCLnS, LCLnL, CLnCLnP, and so on. Some of the TGs which were isolated and collected as fractions from the seed oil of MCV by NARP‐HPLC were further analyzed by 13C‐NMR. 13C‐NMR data of type‐AAA TGs containing α‐eleostearic acyl have been complemented.
Expression of Bcl‐2 in Olfactory Neuroblastoma and its Association with Chemotherapy and Survival
Authors: Kim Jeong‐Whun , Kong Gyu , Lee Chul Hee , Kim Dong Young , Rhee Chae‐Seo , Min Yang‐Gi , Kim Chul Woo , Chung Jin‐Haeng 
Published: November 2008

ObjectiveThis study aimed to identify the prognostic value of tumor markers in olfactory neuroblastoma (ONB).Study Design and SettingSeventeen patients with ONB (23 tumor specimens) were included. Each specimen was studied for bcl‐2, p53, MIC‐2 by immunohistochemistry and for N‐myc by chromogenic in situ hybridization.ResultsTwelve (70%) of 17 patients and 15 (65%) of 23 specimens showed positive reactivity for bcl‐2. Of seven patients who were treated with neoadjuvant chemotherapy, one patient with diffuse bcl‐2 expression achieved complete remission. Another patient without bcl‐2 expression had no response to chemotherapy. Five patients who showed partial positivity achieved partial remission. Survival and bcl‐2 expression tended to correlate, but it was not statistically significant (P = 0.06). All of the ONB specimens were negative for N‐myc. Positive immunoreactivity for MIC‐2 or p53 was found only in one specimen.ConclusionBcl‐2 expression was commonly found in ONB and the immunoreactivity for bcl‐2 might predict response to neoadjuvant chemotherapy. In addition, Bcl‐2 expression tended to be associated with worse survival.
Montelukast as an Adjunct to Oral and Inhaled Steroid Therapy in Chronic Nasal Polyposis
Authors: Stewart Rosemary A. , Ram Bhaskar , Hamilton Garun , Weiner John , Kane Kevin J. 
Published: November 2008

ObjectiveTo examine the potential of montelukast, a leukotriene receptor antagonist, as an adjunct to oral and inhaled steroid in subjects with chronic nasal polyps.Study DesignProspective, randomized controlled trial.Subjects and MethodsThirty‐eight consecutive adult patients with bilateral nasal polyps were randomized into two groups. Eighteen subjects were treated with oral prednisolone for 14 days and budenoside nasal spray for 8 weeks. Twenty subjects received similar treatment with additional oral montelukast for 8 weeks. Subjects completed a modified nasal ICSD symptom score at 8 and 12 weeks after beginning treatment and the SF‐36 quality of life questionnaire at 12 weeks.ResultsSymptom scores improved in both groups after treatment. Subjects treated with montelukast reported significantly less headache (P = 0.013), facial pain (P = 0.048) and sneezing (P = 0.03) than controls. Four weeks after completing treatment, no significant differences were recorded.ConclusionMontelukast therapy may have clinical benefit as an adjunct to oral and inhaled steroid in chronic nasal polyposis, but effects are not maintained after cessation of treatment.
Control of Chronic Otitis Media and Sensorineural Hearing Loss in C3H/HeJ Mice: Glucocorticoids Vs Mineralocorticoids
Authors: MacArthur Carol J. , Kempton J. Beth , DeGagne Jacqueline , Trune Dennis R. 
Published: November 2008

ObjectiveThe impact of glucocorticoids and mineralocorticoids on chronic otitis media (COM) in toll‐like receptor 4‐deficient C3H/HeJ mice was investigated.Study DesignTo evaluate control of COM by steroids with differences in their anti‐inflammatory (prednisolone, dexamethasone), and fluid absorption functions (fludrocortisone, aldosterone). A minimum sample size of five animals for each group was required based on power analysis calculations. Sample sizes ranged from 7 to 17 mice per treatment group.Subjects and MethodsAuditory brain stem response (ABR) thresholds were performed at baseline, 2 weeks and 4 weeks. Histopathologic test results were evaluated on all mice ears at the end of the study.ResultsAnalysis of variance (ANOVA) of ABR threshold change showed significant treatment effects (P < 0.05) by both steroid types at all time intervals and ABR frequencies except 4 weeks/8 kHz. Histologic assessment showed prednisolone‐treated mice (62%) had a higher rate of clearance of middle and inner ear inflammation than control mice (4%).ConclusionIt was concluded that steroid treatments can improve the physiology of chronic middle and inner ear disease seen with COM.
Plasmacytoid Dendritic Cells and Interferon Levels are Increased in Lymphatic Malformations
Authors: Fleming Jo Nadine , Hostikka Sirkka Liisa , Chen Eunice Y. , Schwartz Stephen M. , Perkins Jonathan A. 
Published: November 2008

ObjectiveDescribe the presence of plasmacytoid dendritic cells and type 1 interferon and the activation of interferon signaling pathway in lymphatic malformations.DesignRetrospective case series.MaterialsNineteen lymphatic malformations with matching clinical data were compared to control tissue (normal skin and lymph node).MethodsParaffin‐embedded tissue was evaluated for plasmacytoid dendritic cells, type 1 interferon, and type 1 interferon signaling with immunohistochemistry and RNA in situ hybridization. Staining results were compared with controls and correlated with clinical data with descriptive statistics and Mann‐Whitney tests.ResultsLymphatic malformations had increased staining for plasmacytoid dendritic cells, interferons alpha and beta, and phosphorylated signal transducer and activator of transcription 1 compared with controls (P < 0.05). Significantly increased interferon beta staining was present in recurrent lymphatic malformation tissue compared with nonrecurrent lymphatic malformations.ConclusionLymphatic malformations have unusual ongoing local immune activation, possibly affecting recurrence.
Some critical tracks
Authors: Chambers Iain 
Published: November 2008

… it is not a question of introducing out of nowhere a science of everyone's individual life, but of innovating and rendering critical an already existing practice. (Antonio Gramsci)Some years ago the concept of ambiguity was proposed as a central category in the analysis of everyday life. Henri Lefebvre, unorthodox French marxist and sociologist, suggested that precisely there, in the ‘explosive chronicle’ of daily life, it was both possible and necessary to find common ground between what was socially and culturally familiar and its eventual critique (Lefebvre 1958). The study of pop music, although rarely given attention in this context, brings us up immediately against the oscillating tensions of that cultural ambiguity which Lefebvre considered the heart of everyday life.
Introduction: aspects of the South Asia/West crossover
Authors: Oliver Paul 
Published: November 2008

‘Budding ethno-musicologists, step this way. If you ever wanted a bit of everything on a record, this is it,’ wrote a reviewer in the Melody Maker for 18 April 1981. The record that covered ‘a baffling amount of ground’ was Revenge of the Mozabites by the Suns of Arqa on Rocksteady Records MICKLO1. Other reviewers were as puzzled, and in some cases, stimulated by the issue. To Johnny Black writing in London Trax theysound as if they lost their front door key back in 1969 and have been trapped in the living room of 8 Higher Road, Urmston ever since, with only albums by the Incredible String Band, the Bauls of Bengal and Hapshash for company. From time to time they hear the John Peel prog, and have thus gleaned a passable understanding of dub. Towards the end of 1980 they were set free, had a shave and a haircut and trundled their acoustic guitars, castanets, tablas, fiddles and harmoniums to a portable recording studio in the back of a Morris 1000 Traveller where they recorded this album.
James Brown's ‘Superbad’ and the double-voiced utterance
Authors: Brackett David 
Published: November 2008

JB was proof that black people were different. Rhythmically and tonally blacks had to be from somewhere else. Proof that Africa was really over there for those of us who had never seen it – it was in that voice. (Thulani Davis, quoted Guralnick 1986, pp. 242–3)If there is any black man who symbolizes the vast differences between black and white cultural and aesthetic values, Soul Brother No. 1 (along with Ray Charles) is that man. (David Levering Lewis, quoted Guralnick 1986, p. 240)Brown has never been a critics' favorite principally because of the apparent monotony of so many of his post-1965 recordings. But attacking him for being repetitive is like attacking Africans for being overly fond of drumming. Where the European listener may hear monotonous beating, the African distinguishes subtle polyrhythmic interplay, tonal distinctions among the various drums, the virtuosity of the master drummer, and so on. Similarly, Brown sounds to some European ears like so much harsh shrieking. (Robert Palmer 1980, p. 141)During the 1960s James Brown single handedly demonstrated the possibilities for artistic and economic freedom that black music could provide if one constantly struggled against its limitations … He was driven by an enormous ambition and unrelenting ego, making him a living symbol of black self-determination … Motown may have been the sound of young America, but Brown was clearly the king of black America. (Nelson George 1988, pp. 98–9)
Questions of style: notes on Italian hip hop
Authors: Mitchell Tony 
Published: November 2008

In his article ‘Rock music and politics in Italy’, Umberto Fiori deploys the example of an open-air concert by Genesis in Tirrenia in the province of Pisa, promoted in the summer of 1982 by the Italian Communist Party (PCI) as part of its annual Feste dell'Unita, as a summary example of de-politicisation of the consumption and production of rock music in Italy, and the institutionalisation of the oppositional, dissenting aspects of rock music that had previously been so potent there throughout the 1970s. To Fiori, the Genesis concert representedan unmistakeable step forward in the slow process of the ‘normalisation’ of the relationship between rock and politics in Italy. Explosive material until a few years before, rock music in the 1980s seems to have returned to being a commodity like any other, even in Italy. The songs are once again simply songs, the public is the public. The musicians are only interested in their work, and the organisers make their expected profits. If they happen to be a political party, so much the better: they can also profit in terms of public image and perhaps even votes. … Italy now learnt how to institutionalise deviation and transgression. An ‘acceptable’ gap was re-established between fiction and reality, desire and action, and music and political practice. (Fiori 1984, pp. 261–2)