bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facts and artifacts in proteomics of body fluids. What proteomics of saliva is telling us?
Authors: Messana Irene , Inzitari Rosanna , Fanali Chiara , Cabras Tiziana , Castagnola Massimo 
Published: May 2008

AbstractThis review briefly depicts several salient points of the current status of knowledge on salivary peptidoma. It outlines the intrinsic difficulties in its characterization connected to different factors of variability, such as: i) the high genetic polymorphisms, complicated by individual insertions/deletions and alternative splicing; ii) complex post‐translational maturations comprehending different proteolytic cleavages, glycosylation, phosphorylation and sulfation processes; iii) physiological variations and different contributions to the whole. Moreover, several technological and analytical problems and pitfalls that had to be surmounted during our studies focussed on the extensive qualitative and quantitative characterization of salivary peptidoma and mainly based on LC‐MS analyses of intact naturally occurring peptides are here described. The hope is that the information provided might be helpful to other groups engaged on the analysis of saliva or other body fluids for clinical applications.
Fibre gratings and devices for sensors and lasers
Authors: Canning J. 
Published: May 2008

AbstractAlthough mainstream grating writing, more often than not using single photon excitation of germanosilicate based defects with CW 244 nm light, remains the key technology for complex devices it is now being complemented by a whole host of processes which can enhance and tailor the properties of both conventional and not‐so‐conventional fibre Bragg gratings. Further, processes for writing of gratings in non‐germanosilicate fibres have also continued to develop and include multi‐photon excitation directly into the band edge of the glass. It is now possible to custom tailor a gratings property based on the application and the nature of production as well as custom tailor the grating writing process to suit the type of fibre and application. Examples and suggestions where these can benefit sensors and lasers are outlined.
New Synthesis Method Using Magnesium Alkoxides as Carrier Materials for Ziegler‐Natta Catalysts with Spherical Morphology
Authors: Tanase Shohjiroh , Katayama Kiyokazu , Inasawa Susumu , Okada Fumio , Yamaguchi Yukio , Sadashima Takanori , Yabunouchi Nobuhiro , Konakazawa Takehito , Junke Tadanori , Ishihara Nobuhide 
Published: May 2008

AbstractIn this study, novel carrier materials were synthesized by addition of metal dihalide compounds in the synthesis reaction of magnesium diethoxide using metallic magnesium, ethanol and iodine. Poly(propylene) polymerizations were then investigated with the MgCl2‐supported TiCl4 catalysts using these carrier materials. As results, magnesium diethoxide with extremely large particle sizes and spherical shapes were obtained and the angles of repose of PP particles obtained by using their catalysts as a flowability index showed high values. Furthermore, in order to confirm key points for excellent catalyst performance from detailed characterizations, SEM images, compositions and WAXS were measured.magnified image
Unified finite element discretizations of coupled Darcy–Stokes flow
Authors: Karper Trygve , Mardal Kent‐Andre , Winther Ragnar 
Published: May 2008

AbstractIn this article, we discuss some new finite element methods for flows which are governed by the linear stationary Stokes system on one part of the domain and by a second order elliptic equation derived from Darcy's law in the rest of the domain, and where the solutions in the two domains are coupled by proper interface conditions. All the methods proposed here utilize the same finite element spaces on the entire domain. In particular, we show how the coupled problem can be solved by using standard Stokes elements like the MINI element or the Taylor–Hood element in the entire domain. Furthermore, for all the methods the handling of the interface conditions are straightforward. © 2008 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009
Measuring blood pressure knowledge and self‐care behaviors of African Americans
Authors: Peters Rosalind M. , Templin Thomas N. 
Published: May 2008

AbstractThe purpose of this study was to develop and conduct preliminary psychometric assessment of instruments measuring knowledge and self‐care practices regarding behaviors needed for blood pressure (BP) control among African Americans. Items were empirically derived and scored on a 7‐point, bipolar scale. The instruments were evaluated in a sample of 306 community‐dwelling African Americans. Results revealed acceptable reliability and validity of the BP Knowledge Scale. Results for the BP Self‐Care Scale were mixed. A structural equation model of these scales, recorded BP, and covariates fit well. There was an unexpected positive correlation between self‐care and BP suggesting a potential bi‐directional relationship. The scales demonstrated acceptable psychometric properties and, with minor revisions, may have clinical utility as measures of BP knowledge and self‐care. © 2008 Wiley Periodicals, Inc. Res Nurs Health 31:543–552, 2008
The treatment of leprosy in 19th‐century London: a case study from St Marylebone cemetery
Authors: Walker D. 
Published: May 2008

AbstractA young adult male, context [825], exhibiting a suite of proliferative and erosive skeletal changes, was excavated from the old burial ground of St Marylebone, London, in 2005 by the Museum of London Archaeology Service (MoLAS). Although pathognomonic rhinomaxillary changes were absent, a number of lesions were of a type previously recorded in individuals suffering from lepromatous leprosy, including resorption of the alveolar process of the maxillae and the digits of the right hand, osteomyelitis in the left ulna and collapse of the left ankle. Whilst this infectious disease was widespread in medieval Britain, it had declined by the 19th century, and has been identified in only one other post‐medieval archaeological context. The right leg of [825] had been surgically amputated. This form of intervention was a recognised treatment for the complications of the disease, where neuropathic damage of limbs led to life‐threatening infection. The healing of the amputation demonstrates the success of the operation, and the skill of the surgeon. Although the identity of the affected individual is unknown, burial within St Marylebone cemetery implies a level of status not frequently associated with leprosy sufferers in the past. Copyright © 2008 John Wiley & Sons, Ltd.
Coalition lobbying in Tanzania: the experiences of local NGOs
Authors: Elliott‐Teague Ginger L. 
Published: May 2008

Abstract

Among the few papers that have been written on interest group behaviour in developing countries, none considers how groups cooperate to influence public policy. This paper is intended to help fill that gap in the literature. It does so by comparing the formation and development of four non‐governmental organization (NGO) campaigns in Tanzania between 1997 and 2004. Three of these NGO campaigns were able to establish coalitions while one was not. The NGOs involved were attempting to influence public policy on three pieces of legislation: the Land Acts of 1999, the NGO Act of 2002 and the Environmental Management Act of 2004. Two theories of coalition formation, one of population ecology and one of resource dependency are used in the paper to assess their relevance to the Tanzanian experience. The paper finds that these theories do not adequately explain coalition formation in Tanzania.

Of several factors predicted by these theories, only two are found to be related to coalition formation in the Tanzanian case. However, when coalitions do form they allow individual groups to pool scarce resources, share information and expertise and enhance the legitimacy of the policy argument.

Copyright © 2008 John Wiley & Sons, Ltd.
The Epstein–Barr virus oncoprotein, latent membrane protein‐1, reprograms germinal centre B cells towards a Hodgkin's Reed–Sternberg‐like phenotype
Authors: Vockerodt M , Morgan SL , Kuo M , Wei W , Chukwuma MB , Arrand JR , Kube D , Gordon J , Young LS , Woodman CB , Murray PG 
Published: May 2008

AbstractAlthough the latent membrane protein‐1 (LMP1) of the Epstein–Barr virus (EBV) is believed to be important for the transformation of germinal centre (GC) B cells, the precise contribution of this viral oncogene to lymphoma development is poorly understood. In this study, we used a non‐viral vector‐based method to express LMP1 in primary human GC B cells. Gene expression profiling revealed that LMP1 induced in GC B cells transcriptional changes characteristic of Hodgkin's lymphoma cell lines. Strikingly, LMP1 down‐regulated the expression of B‐cell‐specific genes including B‐cell receptor components such as CD79A, CD79B, CD19, CD20, CD22, and BLNK. LMP1 also induced the expression of ID2, a negative regulator of B‐cell differentiation. Our data suggest that in EBV‐positive cases, LMP1 is likely to be a major contributor to the altered transcriptional pattern characteristic of Hodgkin/Reed–Sternberg cells, including the loss of B‐cell identity. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Foetal death following lactic acidosis induced by ethanol, cocaine and metformin
Authors: Jones JB , McLellan D , McKenna K 
Published: May 2008

AbstractA 33‐year‐old, 34‐week gestation patient with metformin treated gestational diabetes presented with lactic acidosis. Subsequent examination and ultrasound confirmed foetal death. Examination of the blood and urine provided evidence of ethanol and cocaine use on the day prior to admission.Lactic acidosis has been reported after the use of metformin, but it is exceptionally rare. Precipitants such as ethanol and cocaine create a biochemically favourable environment in which lactic acidosis can occur. Therefore, in patients receiving metformin who have ingested such agents, lactic acidosis should be considered. Copyright © 2008 John Wiley & Sons.
Brainstorming in diabetes
Authors: Amiel SA 
Published: May 2008

AbstractThis lecture was given in memory of Dr Arnold Bloom to the 2008 Annual Professional Section Conference of Diabetes UK. In it, the author reviews insights gained by clinical research into the problems of hypoglycaemia unawareness in type 1 diabetes. Novel neuroimaging data suggest that a change in cortical responses to hypoglycaemia may be important to the syndrome of unawareness. Taking the neuroimaging methods into the study of people with insulin resistance suggests that an insulin responsive element of brain glucose metabolism is less insulin sensitive in people with peripheral insulin resistance, and that this ‘ central insulin resistance’ may be particularly evident in brain regions involved in appetite control and reward responses. The lecture concluded with an update of the UK islet transplant programme, now active for people with type 1 diabetes and intractable hypoglycaemia and also those with unstable glucose control after successful renal transplantation. Copyright © 2008 John Wiley & Sons.
Immunoproteomic identification of the hypothetical protein NMB1468 as a novel lipoprotein ubiquitous in Neisseria meningitidis with vaccine potential
Authors: Hsu Chi‐An , Lin Wei‐Ru , Li Jung‐Chen , Liu Yi‐Lung , Tseng Yen‐Tzu , Chang Chun‐Mien , Lee Yeong‐Sheng , Yang Chiou‐Ying 
Published: May 2008

AbstractMany potential vaccine candidates for serogroup B Neisseria meningitidis (NMB) have been identified by reverse vaccinology, a genome‐based approach. However, some candidates may be unseen owing to uncertain annotation or their peculiar properties. In this study, we describe the preparation and identification of a novel lipoprotein expressed in all meningococcal strains tested. mAb were first prepared from mice immunized with a meningococcal B strain isolated in Taiwan. Total proteins from the immunizing strain were separated by 2‐DE in duplicate. Clone 4‐7‐3, which crossreacted to 174 tested meningococcal isolates, was used as the primary antibody for Western blotting. The immunoreactive spot was identified by LC‐mass spectrometric analysis of the corresponding spot from the silver‐stained gel and confirmed by molecular biology approach to be a novel lipoprotein encoded by the hypothetical NMB1468 gene. The potential use of this protein, designated Ag473/NMB1468, as a vaccine component was evaluated using the recombinant protein produced in Escherichia coli. Immunized mice were found to be protected from developing meningococcal disease after intraperitoneal inoculation with a lethal dose of meningococcal strain Nm22209, suggesting that Ag473/NMB1468 may be a promising vaccine candidate. This study also demonstrates the usefulness of the immunoproteomic approach in identification of novel vaccine candidates.
MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post‐translational modifications
Authors: Ahmad Ishtiaq , Qazi Wajahat M. , Khurshid Ahmed , Ahmad Munir , Hoessli Daniel C. , Khawaja Iffat , Choudhary M. Iqbal , Shakoori Abdul R. , Nasir‐ud‐Din  
Published: May 2008

AbstractPost‐translational modification (PTM) of a protein is an important event in regulating cellular functions. An algorithm, MAPRes, has been developed for mining associations among PTM sites and the preferred amino acids in their vicinity. The algorithm has been implemented to O‐glycosylation and O‐phosphorylation data (phosphorylated/glycosylated Ser/Thr/Tyr). The association patterns mined by MAPRes demonstrate significant correlations and the results are in conformity with the existing methods. These association rules/patterns will be helpful in predicting the sequences/motifs involved for specific PTMs in proteins.
Proteomic map of peripheral blood mononuclear cells
Authors: Vergara Daniele , Chiriacò Fernanda , Acierno Raffaele , Maffia Michele 
Published: May 2008

AbstractIn the field of proteomics extensive efforts have been focused on the knowledge of proteins expressed by different cell types. In particular, enormous progress has been done in the characterization of blood cellular components. In this work, we have established a public 2‐DE database for human peripheral blood mononuclear cells (PBMCs) proteins. Two hundred and forty‐six spots corresponding to 174 different proteins have been identified on 2‐DE gels from PBMCs isolated from six healthy individuals. All the identified proteins have been classified in thirteen categories on the basis of their differential functions or cellular localization and annotated at the http://physiology.unile.it/proteomics. The role of several proteins has been discussed in relation to their biological function. We intend to show the potentiality of PBMCs to investigate the proteomics changes possibly associated with a large number of pathologies such as autoimmune, neurodegenerative and cancer diseases.
Aorta protein networks in marginal and acute zinc deficiency
Authors: Beattie John H. , Gordon Margaret‐Jane , Rucklidge Garry J. , Reid Martin D. , Duncan Gary J. , Horgan Graham W. , Cho Young‐Eun , Kwun In‐Sook 
Published: May 2008

AbstractHuman zinc deficiency is a global problem and may influence the development of cardiovascular disease. Our objective was to determine Zn deficiency affected pathways and protein interactions in rat aorta and their likely influence on stress‐induced atherogenesis. In two separate studies, rats were given diets acutely (<1 mg Zn/kg) or marginally (6 mg Zn/kg) deficient in Zn. Both studies included Zn adequate controls (35 mg Zn/kg) and the acute deficiency study included a pair‐fed group. After 6 wk, proteins from thoracic aorta were separated by 2‐DE. Proteins affected by zinc deficiency were identified by principal component analysis. Multiple correlations of identified proteins indicated protein networks of related function. Proteins clusters decreased in zinc deficiency were related to fatty acid and carbohydrate metabolism. Structurally related proteins, including zyxin and over nine transgelin 1 proteins, were either increased or decreased by acute and marginal deficiencies. PKCα was significantly decreased in Zn deficiency suggesting that Zn may regulate the phosphorylation of target proteins. Zn deficiency‐related changes in structural, carbohydrate and fatty acid‐related proteins may be disadvantageous for maintaining vascular health and are consistent with a protective role for zinc in the development of atherosclerosis.
Proteomic analysis of cellular protein alterations using a hepatitis B virus‐producing cellular model
Authors: Tong Aiping , Wu Lihong , Lin Qingsong , Lau Quek Choon , Zhao Xia , Li Jiong , Chen Ping , Chen Lijuan , Tang Hong , Huang Canhua , Wei Yu‐quan 
Published: May 2008

AbstractHepatitis B virus (HBV) is one of the major etiological factors responsible for acute and chronic liver disease and for the development of hepatocellular carcinoma (HCC). To determine the effects of HBV replication on host cell‐protein expression, we utilized 2‐DE and MS/MS analysis to compare and identify differentially expressed proteins between an HBV‐producing cell line HepG2.2.15 and its parental cell line HepG2. Of the 66 spots identified as differentially expressed (± over twofold, p <0.05) between the two cell lines, 62 spots (corresponding to 61 unique proteins) were positively identified by MS/MS analysis. These proteins could be clearly divided into three major groups by cluster and metabolic/signaling pathway analysis: proteins involved in retinol metabolism pathway, calcium ion‐binding proteins, and proteins associated with protein degradation pathways. Other proteins identified include those that function in diverse biological processes such as signal transduction, immune regulation, molecular chaperone, electron transport/redox regulation, cell proliferation/differentiation, and mRNA splicing. In summary, we profiled proteome alterations between HepG2.2.15 and HepG2 cells. The proteins identified in this study would be useful in revealing the mechanisms underlying HBV‐host cell interactions and the development of HCC. This study can also provide some useful clues for antiviral research.
Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy
Authors: Sui Shaohui , Wang Jinglan , Yang Bing , Song Lina , Zhang Jiyang , Chen Ming , Liu Jinfeng , Lu Zhuang , Cai Yun , Chen Shuo , Bi Wei , Zhu Yunping , He Fuchu , Qian Xiaohong 
Published: May 2008

AbstractThe liver is the largest organ in the body, with many complex, essential functions, such as metabolism, deintoxication, and secretion, often regulated via post‐translational modifications, especially phosphorylation. Thus, the detection of phosphoproteins and phosphorylation sites is important to comprehensively explore human liver biological function. The human Chang liver cell line is among the first derived from non‐malignant tissue, and its phosphoproteome profile has never been globally analyzed. To develop the complete phosphoproteome and probe the roles of protein phosphorylation in normal human liver, we adopted a shotgun strategy based on strong cation exchange chromatograph, titanium dioxide and LC‐MS/MS to isolate and identify phosphorylated proteins. Two types of MS approach, Q‐TOF and IT, were used and compared to identify phosphosites from complex protein mixtures of these cells. A total of 1035 phosphorylation sites and 686 phosphorylated peptides were identified from 607 phosphoproteins. A search using the public database of PhosphoSite showed that approximately 344 phosphoproteins and 760 phosphorylation sites appeared to be novel. In addition, N‐terminal phosphorylated peptides were a greater fraction of all identified phosphopeptides. With GOfact analysis, we found that most of the identified phosphoproteins are involved in regulating metabolism, consistent with the liver's role as a key metabolic organ.
Identification of estrogen‐responsive proteins in MCF‐7 human breast cancer cells using label‐free quantitative proteomics
Authors: Zhu Zheying , Boobis Alan R. , Edwards Robert J. 
Published: May 2008

Abstract17β‐Estradiol (E2) is a key regulatory steroid hormone that is involved in the control of a number of developmental and other functions. The aim of the present work was to identify estrogen‐dependent proteomic changes by determining the levels of expressed proteins in MCF‐7 human breast cancer cells following treatment with E2. A number of methods exist for differential analysis of complex proteomic mixtures. Here, a label‐free mass spectrometric approach comparing the ion intensities of tryptic peptides was adopted, which was combined with prefractionation of whole cell lysate proteins by 1‐D SDS‐PAGE. Using this approach, 60 proteins were found to be affected by E2. These comprised 55 up‐regulated and five down‐regulated proteins. These proteins varied widely in their physiochemical properties with pIs of 4–12 and molecular weights of 9–500 kDa. Pathway analysis revealed that the majority of changes were related and together describe an up‐regulated pathway consistent with the events of cell proliferation. The quantitative approach used here is relatively straightforward, avoids the use of costly labelling reagents, was reproducible within acceptable limits and has a linear response over a useful concentration range.
Comparison of two anoxia models in rainbow trout cells by a 2‐DE and MS/MS‐based proteome approach
Authors: Wulff Tune , Hoffmann Else K. , Roepstorff Peter , Jessen Flemming 
Published: May 2008

AbstractIn the literature, a variety of ways have been used to obtain anoxia, and most often results are compared between studies without taking into consideration how anoxia has been obtained. Here, we provide a comprehensive study of two types of anoxia, using a proteomics approach to compare changes in protein expression. The two investigated situations were 30 min of chemical anoxia (10 mM NaN3) followed by reoxygenation overnight (CR) and 2 h of N2‐induced anoxia (achieved by flushing with N2) followed by reoxygenation overnight (NR), after which samples were resolved by 2‐DE. Forty‐five protein spots changed their abundance in response to CR and 35 protein spots changed their abundance in response to NR, but only six proteins changed their abundance in response to both stimuli. By the means of MS/MS, 40 protein spots were identified including proteins involved in processes like cell protection and protein synthesis. It was also revealed that the level of a number of keratins was down‐regulated. This study therefore provides a valuable comparison of two different anoxia models and shows that great care should be taken when comparing the effects of anoxia in studies that have used different types and durations of anoxia.
Incorporating high‐throughput proteomics experiments into structural biology pipelines: Identification of the low‐hanging fruits
Authors: Pache Roland A. , Aloy Patrick 
Published: May 2008

AbstractThe last years have seen the emergence of many large‐scale proteomics initiatives that have identified thousands of new protein interactions and macromolecular assemblies. However, unfortunately, only a few among the discovered complexes meet the high‐quality standards required to be promptly used in structural studies. This has thus created an increasing gap between the number of known protein interactions and complexes and those for which a high‐resolution 3‐D structure is available. Here, we present and validate a computational strategy to distinguish those complexes found in high‐throughput affinity purification experiments that will stand the best chances to successfully express, purify and crystallize with little further intervention. Our method suggests that there are some 50 complexes recently discovered in yeast that could readily enter the structural biology pipelines.