bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and identification of plasma proteins that bind GlialCAM using ProteinChip™ Arrays, SELDI‐TOF MS, and nano‐LC MS/MS
Authors: Favre‐Kontula Linda , Sattonnet‐Roche Pascale , Magnenat Edith , Proudfoot Amanda E. I. , Boschert Ursula , Xenarios Ioannis , Vilbois Francis , Antonsson Bruno 
Published: January 2008

AbstractIn order to fully understand biological processes it is essential to identify interactions in protein complexes. There are several techniques available to study this type of interactions, such as yeast two‐hybrid screens, affinity chromatography, and coimmunoprecipitation. We propose a novel strategy to identify protein–protein interactions, comprised of first detecting the interactions using ProteinChips and SELDI‐TOF MS, followed by the isolation of the interacting proteins through affinity beads and RP‐HPLC and finally identifying the proteins using nano‐LC MS/MS. The advantages of this new strategy are that the primary high‐throughput screening of samples can be performed with small amounts of sample, no specific antibody is needed and the proteins represented on the SELDI‐TOF MS spectra can be identified with high confidence. Furthermore, the method is faster and less labor‐intensive than other current approaches. Using this novel method, we isolated and identified the interactions of two mouse plasma proteins, mannose binding lectin C and properdin, with GlialCAM, a type 1 transmembrane glycoprotein that belongs to the Ig superfamily.
Tools for analyzing and predicting N‐terminal protein modifications
Authors: Meinnel Thierry , Giglione Carmela 
Published: January 2008

AbstractThe vast majority of the proteins encoded in any genome naturally undergo a large number of different N‐terminal modifications, hindering their characterization by routine proteomic approaches. These modifications are often irreversible, usually cotranslational and are crucial, as their occurrence may reflect or affect the status, fate and function of the protein. For example, large signal peptide cleavages and N‐blocking mechanisms reflect targeting to various cell compartments, whereas N‐ligation events tend to be related to protein half‐life. N‐terminal positional proteomic strategies hold promise as a new generation of approaches to the fine analysis of such modifications. However, further biological investigation is required to resolve problems associated with particular low‐abundance or challenging N‐terminal modifications. Recent progress in genomics and bioinformatics has provided us with a means of assessing the impact of these modifications in proteomes. This review focuses on methods for characterizing the occurrence and diversity of N‐terminal modifications and for assessing their contribution to function in complete proteomes. Progress is being made towards the annotation of databases containing information for complete proteomes, and should facilitate research into all areas of proteomics.
Phosphoproteomic analysis of Leishmania donovani pro‐ and amastigote stages
Authors: Morales Miguel A. , Watanabe Reiko , Laurent Christine , Lenormand Pascal , Rousselle Jean‐Claude , Namane Abdelkader , Späth Gerald F. 
Published: January 2008

AbstractFollowing transmission to the vertebrate host, the protozoan parasite Leishmania donovani differentiates into the pathogenic amastigote stage that is adapted for intracellular survival. This developmental transition is induced by environmental factors including elevated temperature and acidic pH and is likely transduced by signaling cascades involving protein kinases and their downstream phosphoprotein substrates. These signaling networks are highly adapted to the specific nutritional and physiological requirements of the organism and thus studying Leishmania phosphorylation may allow important insight into the parasite‐specific biology. We used a gel‐based approach to investigate qualitative and quantitative changes of the phosphoproteome of the major L. donovani life cycle stages. Phosphoproteins were purified by immobilized metal affinity chromatography (IMAC), separated by IEF and SDS‐PAGE using pH 4–7 IPG immobiline strips, revealed by fluorescent multiplex staining, and identified by MALDI‐MS and MS/MS. Our analysis allowed us to establish a first repertoire of the Leishmania phosphoproteome and to identify phosphoproteins implicated in stress‐ and heat shock response, RNA/protein turnover, metabolism, and signaling.
MPA: A multiple peak alignment algorithm to perform multiple comparisons of liquid‐phase proteomic profiles
Authors: Toppo Stefano , Roveri Antonella , Vitale Maria Pia , Zaccarin Mattia , Serain Elena , Apostolidis Emanuele , Gion Massimo , Maiorino Matilde , Ursini Fulvio 
Published: January 2008

AbstractPresent proteomic studies increasingly address experimental strategies focused on multiple comparisons of proteomic profiles. To accomplish semiautomatic protein separations based on 2‐D LC, the Beckman Coulter PF2D has been developed. Here, we present a novel general purpose tool called MPA (multiple peak alignment) able to perform multiple comparisons of proteomic profiles both in a pairwise guided fashion and in a fully automatic mode using a strategy based on dynamic programing and progressive alignment of time series. The tool is available at http://grup.cribi.unipd.it/people/stefano/mpa/.
Identification of collapsin response mediator protein‐2 as a potential marker of colorectal carcinoma by comparative analysis of cancer cell secretomes
Authors: Wu Chih‐Ching , Chen Hua‐Chien , Chen Su‐Jen , Liu Hao‐Ping , Hsieh Yi‐Yueh , Yu Chia‐Jung , Tang Reiping , Hsieh Ling‐Ling , Yu Jau‐Song , Chang Yu‐Sun 
Published: January 2008

AbstractThe cancer cell secretome may contain many potentially useful biomarkers. We therefore sought to identify proteins in the conditioned media of colorectal carcinoma (CRC) cell lines but not in those from other cancer cell lines. The secretomes of 21 cancer cell lines derived from 12 cancer types were analyzed by SDS‐PAGE combined with MALDI‐TOF MS. Among the 325 proteins identified, collapsin response mediator protein‐2 (CRMP‐2) was chosen for evaluation as a potential CRC biomarker, since it was selectively detected in the CRC cell line secretome and has never been reported as a cancer biomarker. Immunohistochemical analysis of 169 CRC specimens showed that CRMP‐2 was positively detected in 58.6% of the tumors, but weakly or not detected in >90% of the adjacent nontumor epithelial cells. Moreover, the CRMP‐2‐positive rate was significantly increased in earlier stage tumors and lymph node metastasis. Plasma CRMP‐2 levels were significantly higher in CRC patients (N = 201) versus healthy controls (N = 201) (61.3 ± 34.6 vs. 40.2 ± 24.3 ng/mL, p = 0.001). Our results indicate that comparative analysis of cancer cell secretome is a feasible strategy for identifying potential cancer biomarkers, and that CRMP‐2 may be a novel CRC biomarker.
Glutathione‐S‐transferase pi as a model protein for the characterisation of chemically reactive metabolites
Authors: Jenkins Rosalind E. , Kitteringham Neil R. , Goldring Christopher E. P. , Dowdall Samantha M. J. , Hamlett Jane , Lane Catherine S. , Boerma Jan‐Simon , Vermeulen Nico P. E. , Park B. Kevin 
Published: January 2008

AbstractChemically reactive metabolites (CRMs) are thought to be responsible for a number of adverse drug reactions through modification of critical proteins. Methods that defined the chemistry of protein modification at an early stage would provide invaluable tools for drug safety assessment. Here, human GST pi (GSTP) was exploited as a model target protein to determine the chemical, biochemical and functional consequences of exposure to the hepatotoxic CRM of paracetamol (APAP), N‐acetyl‐p‐benzoquinoneimine (NAPQI). Site‐specific, dose‐dependent modification of Cys47 in native and His‐tagged GSTP was revealed by MS, and correlated with inhibition of glutathione (GSH) conjugating activity. In addition, the adaptation of iTRAQ labelling technology to define precisely the quantitative relationship between covalent modification and protein function is described. Multiple reaction monitoring (MRM)‐MS of GSTP allowed high sensitivity detection of modified peptides at physiological levels of exposure. Finally, a bioengineered mutant cytochrome P450 with a broad spectrum of substrate specificities was used in an in vitro reaction system to bioactivate APAP: in this model, GSTP trapped the CRM and exhibited both reduced enzyme activity and site‐specific modification of the protein. These studies provide the foundation for the development of novel test systems to predict the toxicological potential of CRMs produced by new therapeutic agents.
The 1st European Summer School on ‘Proteomic Basics’ – The Students View 12–18 August, 2007 Kloster Neustift, Brixen/Bressanone, South Tyrol, Italy
Authors: Collins Emily S. , Little Samantha J. 
Published: January 2008

AbstractFifty postgraduate and postdoctoral delegates from all over Europe attended the week‐long ‘1st European Summer School on Proteomic Basics’ in Kloster Neustift in the Italian South Tyrol in August 2007. Invited proteomics experts gave tutorial lectures on Proteomics techniques with an emphasis on sample preparation, protein separation and purification in the first of an annual series of Proteomics Summer Schools funded by the EU and the Volkswagen Stiftung.
Growth hormone action in the developing neural retina: A proteomic analysis
Authors: Baudet Marie‐Laure , Hassanali Zahra , Sawicki Grzegorz , List Edward O. , Kopchick John J. , Harvey Steve 
Published: January 2008

AbstractThe possible presence and action of growth hormone (GH) in the neural retina was investigated in newborn mice. The neural retina was found to be a site of GH gene expression, as GH mRNA was abundant in cells of the retinal ganglion cell layer, in which GH was also detected. It was also a site of GH action, since GH receptor (GHR) immunoreactivity mirrored that of GH. Actions of GH within the eye were indicated by a reduction in its axial length and retinal width (its neuroblastic, inner plexiform, and optic fiber layers) in GHR gene disrupted mice (GHR−/−), in comparison with wild type (GHR+/+) littermates. In the absence of GH signaling, four proteins in the retinal proteome of the GHR−/− mice (identified by 2‐D gels and MS) differed in abundance with those in the wild type mice. Brain abundant membrane attached signal protein‐1 (BASP‐1) was down‐regulated, whereas protein kinase C inhibitor 1, cyclophilin A, KH domain‐containing, RNA‐binding, signal transduction‐associated protein 3 were up‐regulated in GHR−/− mice. These proteins are involved in retinal vascularization, neural proliferation and neurite outgrowth. GH might thus have hitherto unsuspected roles in these processes during retinal development.
Nucleophilicity of metal carbonyl anions in vinylic substitution reactions
Authors: Sazonov Petr K. , Artamkina Galina A. , Beletskaya Irina P. 
Published: January 2008

AbstractSecond order rate constants are reported for the reactions of metal carbonyl anions ([M(CO)nL]−) with several vinyl halides: PhCClC(CN)2, Z‐ and E‐Ph(CN)CCHHal (Hal = Cl, Br) which follow the addition–elimination (AdNE) substitution mechanism. The obtained data show that the nucleophilic reactivity of [M(CO)nL]− anions towards vinyl halides increases in the same order as in aliphatic SN2 reactions, but much more steeply, by 14 orders of magnitude in the row log{$k_{[{\bf M}({\bf CO})_n {\bf L}]{\bf M'}} {\rm /}k_{[{\bf CpMo}({\bf CO})_3 ]{\bf K}}$}: [CpFe(CO)2]− (∼14), [Re(CO)5]− (7.8), [Mn(CO)5]− 2.1, [CpW(CO)3]− (0.7) > [CpMo(CO)3]− (0). A good correlation exists between nucleophilicities of [M(CO)nL]− anions towards vinyl (sp2‐carbon) and alkyl halides (sp3‐carbon) with slope 2.7. The reactivity of [M(CO)nL]− in a halogen–metal exchange process (with Z‐PhC(CN)CHI) follows a similar ‘large’ scale as in the AdNE process. The nucleophilicity of [M(CO)nL]− anions correlates better with their one‐electron oxidation potentials (Eox) than with their basicity (pKa of [M(CO)nL]H). Copyright © 2008 John Wiley & Sons, Ltd.
Ethnicity and participation in cancer self‐help groups
Authors: Avis Mark , Elkan Ruth , Patel Seeta , Walker Barbara‐Anne , Ankti Neruma , Bell Caroline 
Published: January 2008

AbstractObjectives: Investigations of the benefits of membership of a cancer self‐help group have suggested that it leads to improved sense of support, increased ability to deal with life‐events, and decreased anxiety, confusion, depression and helplessness. However, some evidence suggests that people from black and ethnic groups are less likely to join a cancer self‐help group. The main aims of the reported study were: to explore possible reasons why people from some ethnic groups have not participated in self‐help to the same extent as the rest of the community; and to identify ways in which participation of people from ethnic groups can be increased.Methods: A qualitative interview‐based study of 68 people active in self‐help was carried out as a partnership between an academic institution and a community organisation.Results: A thematic analysis of the interview transcripts identified three main aspects of the value of being a member of a self‐help group, regardless of interviewees' self‐identified ethnicity: forming a sense of togetherness, learning from one other, and developing mutuality. We identify a number of reasons that discourage or encourage people from black and ethnic groups to join cancer self‐help groups.Conclusion: We discuss some limits, identified by interviewees, that affect development of feelings of togetherness and mutuality and we conclude with some brief recommendations about widening participation in cancer self‐help. Copyright © 2008 John Wiley & Sons, Ltd.
Beliefs about cancer causation and prevention as a function of personal and family history of cancer: a national, population‐based study
Authors: Lykins Emily L. B. , Graue Lili O. , Brechting Emily H. , Roach Abbey R. , Gochett Celestine G. , Andrykowski Michael A. 
Published: January 2008

AbstractObjective: Research suggests individuals possess multifaceted cognitive representations of various diseases. These illness representations consist of various beliefs, including causal attributions for the disease, and are believed to motivate, guide, and shape health‐related behavior. As little research has examined factors associated with beliefs about cancer causation, this study examined the relationship between personal and family history of cancer and beliefs about the causes and prevention of malignant disease.Methods: Data were obtained from 6369 adult respondents to the 2003 Health Information National Trends Survey, a national population‐based survey. Information about personal and family history of cancer and beliefs regarding cancer causation and prevention was obtained.Results: Results showed both a personal and family history of cancer were associated with differences in beliefs about the causes of cancer. In general, a personal history of cancer was not significantly linked to causal attributions for cancer relative to those without a personal history. In contrast, a family history of cancer tended to increase the likelihood a respondent viewed a particular cause as increasing cancer risk. Thus, personal and vicarious experience with cancer had dramatically diverging influences on attributions of cancer causation, which may be due to differing self‐protection motives.Conclusion: Results support the belief that illness representations, in this case the causal belief component, are influenced by both personal and vicarious experience with a disease and also suggest illness representations may influence receptivity to messages and interventions designed to increase appropriate cancer risk reduction behavior. Copyright © 2007 John Wiley & Sons, Ltd.
The EORTC QLQ‐CX24 cervical cancer‐specific quality of life questionnaire: psychometric properties in a South Asian sample of cervical cancer patients
Authors: Jayasekara Harindra , Rajapaksa Lalini C. , Greimel Elfriede R. 
Published: January 2008

AbstractObjective: The cervical cancer‐specific Quality of Life module of the European Organization for Research and Treatment of Cancer, EORTC QLQ‐CX24, was recently validated in an international field study that did not include cervical cancer patients from South Asia. The aim of our study was to assess the psychometric properties of the instrument in a sample of cervical cancer patients from Sri Lanka to assess its suitability for use in the South Asian region.Methods: One hundred and twelve newly diagnosed patients with cervical cancer completed the translated version of the QLQ‐CX24 in a cross‐sectional validation study. Psychometric evaluation assessed the instrument for scale structure, scale reliability, validity and acceptability.Results: The QLQ‐CX24 was found to be patient‐friendly with high compliance and low missing data. Only a few patients needed assistance for completion. Overall results for multitrait scaling analysis confirmed the scale structure although some items of the symptom experience scale exhibited problems regarding item‐scale correlations with its own scale. Cronbach's alpha coefficients for internal consistency ranging from 0.63 to 0.79 confirmed scale reliability. Construct validity was confirmed in two ways: the inter‐scale correlations were statistically significant (p<0.01) and their magnitude moderate (r = 0.52–0.58) while the scales and single‐item measures were able to discriminate between subgroups of patients differing with regard to treatment status.Conclusion: The translated version of the QLQ‐CX24 is a reliable and valid instrument to measure cervical cancer‐specific Quality of Life in Sri Lanka. The overall results are in line with the findings of the international field study. Copyright © 2007 John Wiley & Sons, Ltd.
Socio‐demographic, psychosocial and attitudinal predictors of help seeking after cancer diagnosis
Authors: Steginga Suzanne K. , Campbell Alistair , Ferguson Megan , Beeden Alison , Walls Melissa , Cairns Will , Dunn Jeff 
Published: January 2008

AbstractObjective: The objective is to describe cancer patients' patterns of use of psychosocial support services and identify socio‐demographic, psychosocial, and attitudinal predictors of service utilization.Methods: A cross‐sectional survey of 439 cancer patients (61.2% response) at a regional tertiary cancer center assessed patterns of support service utilization, cancer‐specific distress, social support and constraints, and attitudes to help seeking.Results: Patients less frequently received advice about psychosocial support in comparison with treatment‐related information. More than half the respondents were aware of social work support, support groups, and chaplain support; however, most did not utilize these services. For unaware patients, up to 47% would have utilized support services if they had known of their existence. The use of services was significantly related to being female, younger, and having greater cancer‐specific distress, more positive and less negative attitudes to help seeking. Future intention to contact a health professional for psychological support was predicted by more positive subjective norms and outcome expectations, higher cancer‐specific distress, and less negative attitudes to help seeking.Conclusion: Initiatives that encourage distressed patients to use psychosocial care services should highlight positive outcomes. Educational programs for health professionals to support psychosocial care in oncology are needed. Copyright © 2008 John Wiley & Sons, Ltd.
Generating unlabeled connected cubic planar graphs uniformly at random
Authors: Bodirsky Manuel , Gröpl Clemens , Kang Mihyun 
Published: January 2008

AbstractWe present an expected polynomial time algorithm to generate an unlabeled connected cubic planar graph uniformly at random. We first consider rooted connected cubic planar graphs, i.e., we count connected cubic planar graphs up to isomorphisms that fix a certain directed edge. Based on decompositions along the connectivity structure, we derive recurrence formulas for the exact number of rooted cubic planar graphs. This leads to rooted 3‐connected cubic planar graphs, which have a unique embedding on the sphere. Special care has to be taken for rooted graphs that have a sense‐reversing automorphism. Therefore we introduce the concept of colored networks, which stand in bijective correspondence to rooted 3‐connected cubic planar graphs with given symmetries. Colored networks can again be decomposed along the connectivity structure. For rooted 3‐connected cubic planar graphs embedded in the plane, we switch to the dual and count rooted triangulations. Since all these numbers can be evaluated in polynomial time using dynamic programming, rooted connected cubic planar graphs can be generated uniformly at random in polynomial time by inverting the decomposition along the connectivity structure. To generate connected cubic planar graphs without a root uniformly at random, we apply rejection sampling and obtain an expected polynomial time algorithm. © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2008
Harmonium Models for Video Classification
Authors: Yang Jun , Yan Rong , Liu Yan , Xing Eric P. 
Published: January 2008

AbstractAccurate and efficient video classification demands the fusion of multimodal information and the use of intermediate representations. Combining the two ideas into one framework, we propose a series of probabilistic models for video representation and classification using intermediate semantic representations derived from multimodal features of video. On the basis of a class of bipartite undirected graphical models named harmonium, we propose dual‐wing harmonium (DWH) model that represents video shots as latent semantic topics derived by jointly modeling the transcript keywords and color‐histogram features of the data. Our family‐of‐harmonium (FoH) and hierarchical harmonium (HH) model extends DWH by introducing variables representing category labels of data, which allows data representation and classification to be performed in the same model. Our models are among the few attempts of using undirected graphical models for representing and classifying video data. Experiments on a benchmark video collection show different semantic interpretations of video data under our models, as well as superior classification performance in comparison with several directed models. Copyright © 2008 Wiley Periodicals, Inc., A Wiley Company Statistical Analy Data Mining 1: 000‐000, 2008
Energy loss spectra of iron
Authors: Novák M. , Bereczky R. J. , Zhang Z. M. , Ding Z. J. , Tóth J. , Varga D. , Tökési K. 
Published: January 2008

AbstractWe present experimental and theoretical studies of the spectra of electrons backscattered from iron. The single surface and bulk excitation ratio in the energy range between 500 and 4000 eV are calculated. The contribution of single inelastically scattered electrons is derived from a dielectric response theory and from the experimental reflected electron energy spectra using different algorithms. We present surface excitation parameters in comparison with previous results as a function of the primary energy. Moreover, we show that our Monte Carlo simulations, using the corrected surface excitation parameters obtained experimentally, describe the reflected electron energy loss spectra in the investigated energy range reasonably well. Copyright © 2008 John Wiley & Sons, Ltd.