bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thoracic neuroblastic tumors in childhood
Authors: Demir Hacı Ahmet , Yalçın Bilgehan , Büyükpamukçu Nebil , Kale Gülsev , Varan Ali , Akyüz Canan , Kutluk Tezer , Büyükpamukçu Münevver 
Published: January 2010

AbstractAimThoracic neuroblastic tumors (NBTs) are reported to have better prognosis. We aimed to review clinical characteristics, treatment results, and outcome of our patients with thoracic NBT.Patients and MethodsFiles of 87 children treated at our hospital between 1973 and 2007 with the diagnoses of thoracic NBT were reviewed for clinical and pathological characteristics. Treatment results and outcomes of these cases were examined.ResultsAll but one tumors were located in posterior mediastinum, one in the posterior chest wall. Median age of all was 2.1 years (range, 0.03–14; F/M: 1.42). Fifteen cases had ganglioneuromas (GN), 26 ganglioneuroblastomas (GNBL), and 46 neuroblastomas (NBLs). Stages were: I, 20.5%; II, 22.1%; III, 38.2%; IV, 14.7%; IVS, 4.5%. Stages III and IV were more common in cases over 1 year of age. In 20 patients diagnoses were incidental. Twenty‐two of 87 (25.3%) had symptomatic spinal cord compression and 15 (17.3%) had Horner syndrome. Ten‐year overall and event‐free survival rates were 71.2% and 67.4%, respectively. Survival rates did not differ depending on the age being younger or older than 1 year. Ten‐year survival rates were 88.8% in stages I, II, IVS; 65.3% in stage III and 27.8% in stage IV (P = 0.0002).ConclusionsThoracic NBLs had a favorable prognosis. This might be a result of earlier diagnosis and some distinct biological characteristics. Favorable prognosis would suggest less aggressive treatment for such patients. Further studies on the biological characteristics of NBLs in the thoracic site and their association with outcome should be done. Pediatr Blood Cancer 2009;54:885–889 © 2009 Wiley‐Liss, Inc.
Phase I trial of two schedules of vincristine, oral irinotecan, and temozolomide (VOIT) for children with relapsed or refractory solid tumors: A Children's Oncology Group phase I consortium study
Authors: Wagner Lars M. , Perentesis John P. , Reid Joel M. , Ames Matthew M. , Safgren Stephanie L. , Nelson Marvin D. , Ingle Ashish M. , Blaney Susan M. , Adamson Peter C. 
Published: January 2010

AbstractBackgroundIn preclinical models, temozolomide, and vincristine are additive or synergistic with irinotecan. We examined this three‐drug combination in children with relapsed solid tumors. Patients received orally administered irinotecan together with temozolomide and vincristine on two different schedules, using cefixime to reduce irinotecan‐associated diarrhea.MethodsOral irinotecan was given daily on days 1–5 and 8–12 (Schedule A), or on days 1–5 (Schedule B). Temozolomide was given on days 1–5, with vincristine 1.5 mg/m2administered on days 1 and 8 (Schedule A) or day 1 (Schedule B) in 21‐day courses.ResultsOn Schedule A, the maximum tolerated dose of oral irinotecan was 35 mg/m2/day combined with temozolomide 100 mg/m2/day and vincristine on days 1 and 8. Dose‐limiting toxicities in 4 of 12 patients included hepatotoxicity, abdominal pain, anorexia, hypokalemia, and thrombocytopenia at 50 mg/m2/day. Using Schedule B, 0 of 6 patients experienced dose‐limiting toxicity (DLT) at the highest doses studied of oral irinotecan 90 mg/m2/day, temozolomide 150 mg/m2/day × 5, and vincristine on day 1. First‐course and cumulative toxicity was greater with Schedule A.UGT1A1*28genotype did not correlate with DLT. At the irinotecan dose of 90 mg/m2/day, the mean SN‐38 AUCinfwas 63 ng/ml hr. Activity was seen in sarcoma patients, and overall eight patients received ≥6 courses.ConclusionsThe 5‐day schedule of VOIT was well tolerated and provided SN‐38 exposures similar to those achieved with intravenous IRN. Activity on this and prior studies suggests a potential role for VOIT in a spectrum of childhood solid tumors. Pediatr Blood Cancer 2010;54:538–545. © 2009 Wiley‐Liss, Inc.
Signal detection of rosuvastatin compared to other statins: data‐mining study using national health insurance claims database
Authors: Choi Nam‐Kyong , Chang Yoosoo , Choi Yu Kyong , Hahn Seokyung , Park Byung‐Joo 
Published: January 2010

AbstractPurposeTo detect adverse drug reaction (ADR) signals of rosuvastatin compared to other statins with a novel data‐mining approach based on relative risk (RR) using the national health insurance claims database, and to evaluate the usefulness of this method as a tool for signal detection.MethodsWe used the Health Insurance Review & Assessment Service (HIRA) claims database (Seoul, Korea). Serious adverse events (SAE) were defined as any diagnostic code at the time of hospitalization within 12 weeks from a statin prescription date, regardless of causality. Among statin users, RRs were calculated to compare the proportion of rosuvastatin‐specific SAE pairs for rosuvastatin users with the corresponding proportion of drug‐SAE pairs for users of other statins. Any SAE for which the lower limit of the RR's 95% confidence interval was greater than 1 was defined as a signal. All detected signals were reviewed to determine whether the signals corresponded with published adverse events (AEs) exclusive to rosuvastatin.ResultsAmong 96 236 elderly outpatients who received rosuvastatin, or other statins, from January 2005 to September 2005, 40 304 drug‐SAE pairs and 376 SAEs were observed. Twenty‐five (6.6%) SAEs were detected as signals by the RR‐based data‐mining approach. Among the 13 references AEs published to be exclusive to rosuvastatin, 8 (61.5%) were found to correspond with the detected signals with a positive predictive value (PPV) of 32%.ConclusionsThe RR‐based data‐mining approach successfully detected signals for rosuvastatin using a national health insurance claims database. This approach could be useful for safety surveillance of marketed products. Copyright © 2010 John Wiley & Sons, Ltd.
Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina
Authors: Gallo Giuseppe , Renzone Giovanni , Alduina Rosa , Stegmann Efthimia , Weber Tilmann , Lantz Anna Eliasson , Thykaer Jette , Sangiorgi Fabio , Scaloni Andrea , Puglia Anna Maria 
Published: January 2010

AbstractA differential proteomic analysis, based on 2‐DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin‐like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated with 203 ORFs in the A. balhimycina genome. These data, providing insights on the major metabolic pathways/molecular processes operating in this organism, were used to compile 2‐DE reference maps covering 3–10, 4–7 and 4.5–5.5 pH gradients available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal‐proteome‐maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis, energetic and redox balance, sugar/amino sugar metabolism, balhimycin biosynthesis and transcriptional regulation or with hypothetical and/or unknown function. Interestingly, proteins involved in the biosynthesis of balhimycin precursors, such as amino acids, amino sugars and central carbon metabolism intermediates, were upregulated during antibiotic production. qRT‐PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub‐set of differentially expressed proteins, showed that most proteins required for the biosynthesis of balhimycin precursors are downregulated in both mutants. These findings suggest that primary metabolic pathways support anabolic routes leading to balhimycin biosynthesis and the differentially expressed genes are interesting targets for the construction of high‐yielding producer strains by rational genetic engineering.
Screening of Ole e 1 polymorphism among olive cultivars by peptide mapping and N‐glycopeptide analysis
Authors: Castro Antonio Jesús , Bednarczyk Audrey , Schaeffer‐Reiss Christine , Rodríguez‐García María Isabel , Van Dorsselaer Alain , de Dios Alché Juan 
Published: January 2010

AbstractIn the present paper, we have used 2‐DE coupled to MS analysis to examine the molecular variability of the Ole e 1 allergen in three olive cultivars (cvs). Our results confirmed that the predicted polymorphism of Ole e 1 at cDNA level is extended to the expressed protein. The profiles of both the Ole e 1 peptides and the N‐glycan variants significantly changed among cvs. We observed that Picual and Arbequina cvs presented the highest and lowest degree of Ole e 1 polymorphism, respectively. Some of these peptides and N‐glycans were distributed in a cv‐specific manner. The putative implications of this molecular polymorphism in the development of the allergy symptoms are discussed.
Distinct proteomic features of two fibrogenic liver cell populations: Hepatic stellate cells and portal myofibroblasts
Authors: Bosselut Nelly , Housset Chantal , Marcelo Paulo , Rey Colette , Burmester Thorsten , Vinh Jöelle , Vaubourdolle Michel , Cadoret Axelle , Baudin Bruno 
Published: January 2010

AbstractIn chronic liver diseases, the accumulation of extracellular matrix leading to fibrosis is caused by myofibroblasts, the origins of which are debatable. We performed a comparative proteomic study to identify markers and gain insight into distinct functions of myofibroblasts derived either from hepatic stellate cells (HSCs) or from portal mesenchymal cells. After isolation from normal liver and culture in similar conditions, myofibroblastic HSCs (MF‐HSCs) presented enlarged cytoplasms whereas portal myofibroblasts (PMFs) were more proliferative, and formed more stress fibers. The two cell types were subjected to comparative analyses by 2‐D MS/MS. Six proteins were overexpressed in PMFs, with myofibroblast‐related typical functions. Among them, cofilin‐1 showed the greatest difference in expression and a lower pI than expected. Immunoblot demonstrated higher levels of phosphorylation, a modification of the protein implicated in stress fiber formation. Eleven proteins, mostly involved in stress response, were overexpressed in MF‐HSCs. Cytoglobin had the highest level of overexpression, as confirmed by reverse transcription quantitative real‐time PCR, immunoblot and immunocytochemical analyses. These results identify cytoglobin as the best marker for distinguishing MF‐HSCs from PMFs and suggest different functions for the two cell populations in the liver wound healing response, with a prominent role for PMFs in scar formation.
The secreted and surface proteomes of the adult stage of the carcinogenic human liver fluke Opisthorchis viverrini
Authors: Mulvenna Jason , Sripa Banchob , Brindley Paul J. , Gorman Jeffrey , Jones Malcolm K. , Colgrave Michelle L. , Jones Alun , Nawaratna Sujeevi , Laha Thewarach , Suttiprapa Sutas , Smout Michael J. , Loukas Alex 
Published: January 2010

AbstractInfection with the human liver fluke, Opisthorchis viverrini, is a serious public health problem in Thailand, Laos and nearby locations in Southeast Asia. Both experimental and epidemiological evidence strongly implicate liver fluke infection in the etiology of one of the liver cancer subtypes, cholangiocarcinoma (CCA). To identify parasite proteins critical for liver fluke survival and the etiology of CCA, OFFGEL electrophoresis and multiple reaction monitoring were employed to characterize 300 parasite proteins from the O. viverrini excretory/secretory products and, utilizing selective labeling and sequential solubilization, from the host‐exposed tegument. The excretory/secretory included a complex mixture of proteins that have been associated with cancers, including proteases of different mechanistic classes and orthologues of mammalian growth factors and anti‐apoptotic proteins. Also identified was a cysteine protease inhibitor which, in other helminth pathogens, induces nitric oxide production by macrophages, and, hence may contribute to malignant transformation of inflamed cells. More than 160 tegumental proteins were identified using sequential solubilization of isolated teguments, and a subset of these was localized to the surface membrane of the tegument by labeling living flukes with biotin and confirming surface localization with fluorescence microscopy. These included annexins, which are potential immuno‐modulators, and orthologues of the schistosomiasis vaccine antigens Sm29 and tetraspanin‐2. Novel roles in pathogenesis were suggested for the tegument–host interface since more than ten surface proteins had no homologues in the public databases. The O. viverrini proteins identified here provide an extensive catalogue of novel leads for research on the pathogenesis of opisthorchiasis and the development of novel interventions for this disease and CCA, as well as providing a scaffold for sequencing the genome of this fluke.
Differential protein expression on the cell surface of colorectal cancer cells associated to tumor metastasis
Authors: Luque‐García Jose Luis , Martínez‐Torrecuadrada Jorge Luis , Epifano Carolina , Cañamero Marta , Babel Ingrid , Casal J. Ignacio 
Published: January 2010

AbstractProgression to metastasis is the critical point in colorectal cancer (CRC) survival. However, the proteome associated to CRC metastasis is very poorly understood at the moment. In this study, we used stable isotope labeling by amino acids in cell culture to compare two CRC cell lines: KM12C and KM12SM, representing poorly versus highly metastatic potential, to find and quantify the differences in protein expression, mostly at the cell surface level. After biotinylation followed by affinity purification, membrane proteins were separated by SDS‐PAGE and analyzed using nanoflow LC‐ESI‐LTQ. A total of 291 membrane and membrane‐associated proteins were identified with a p value<0.01, from which 60 proteins were found to be differentially expressed by more than 1.5‐fold. We identified a number of cell signaling, CDs, integrins and other cell adhesion molecules (cadherin 17, junction plakoglobin (JUP)) among the most deregulated proteins. They were validated by Western blot, confocal microscopy and flow cytometry analysis. Immunohistochemical analysis of paired tumoral samples confirmed that these differentially expressed proteins were also altered in human tumoral tissues. A good correlation with a major abundance in late tumor stages was observed for JUP and 17‐β‐hydroxysteroid dehydrogenase type 8 (HSD17B8). Moreover, the combined increase in JUP, occludin and F11 receptor expression together with cadherin 17 expression could suggest a reversion to a more epithelial phenotype in highly metastatic cells. Relevant changes were observed also at the metabolic level in the pentose phosphate pathway and several amino acid transporters. In summary, the identified proteins provide us with a better understanding of the events involved in liver colonization and CRC metastasis.
Changes in the proteome of Salmonella enterica serovar Thompson as stress adaptation to sublethal concentrations of thymol
Authors: Di Pasqua Rosangela , Mamone Gianfranco , Ferranti Pasquale , Ercolini Danilo , Mauriello Gianluigi 
Published: January 2010

AbstractThymol is a natural biocide and component of some essential oils from herbs. Its inhibitory effect on the growth of different microorganisms is well documented. The precise targets of the antibacterial action of thymol is not yet been fully established, the action seems to take place in different ways. The strain Salmonella enterica serovar Thompson MCV1 was grown in the presence of a sublethal concentration (0.01%) of thymol. The proteins extracted from treated and untreated cells were subjected to 2‐D PAGE, followed by in‐gel spot digestion and subsequent MALDI‐TOF analysis. The analysis of gels showed many proteins that were either upregulated or downregulated by the presence of thymol, with significant changes in proteins belonging to different functional classes. In particular, the thioredoxin‐1 was not expressed in the treated cells, indicating that its absence could be a consequence of the stress caused by the presence of thymol. On the other hand, different chaperon proteins were upregulated or de novo synthesis such as GroEL and DnaK, key proteins in the protection mechanism toward thermal stress. Outer membrane proteins were upregulated in treated cells; indeed the bacterial envelope stress response is trigged by the accumulation of misfolded outer membrane proteins. Moreover, the thymol seems to impair the citrate metabolic pathway, as well as many enzymes involved in the synthesis of ATP. Definitely, thymol plays a role in altering very different pathways of cell metabolism.
Thioredoxin targets of the plant chloroplast lumen and their implications for plastid function
Authors: Hall Michael , Mata‐Cabana Alejandro , Åkerlund Hans‐Erik , Florencio Francisco J. , Schröder Wolfgang P. , Lindahl Marika , Kieselbach Thomas 
Published: January 2010

AbstractThe light‐dependent regulation of stromal enzymes by thioredoxin (Trx)‐catalysed disulphide/dithiol exchange is known as a classical mechanism for control of chloroplast metabolism. Recent proteome studies show that Trx targets are present not only in the stroma but in all chloroplast compartments, from the envelope to the thylakoid lumen. Trx‐mediated redox control appears to be a common feature of important pathways, such as the Calvin cycle, starch synthesis and tetrapyrrole biosynthesis. However, the extent of thiol‐dependent redox regulation in the thylakoid lumen has not been previously systematically explored. In this study, we addressed Trx‐linked redox control in the chloroplast lumen of Arabidopsis thaliana. Using complementary proteomics approaches, we identified 19 Trx target proteins, thus covering more than 40% of the currently known lumenal chloroplast proteome. We show that the redox state of thiols is decisive for degradation of the extrinsic PsbO1 and PsbO2 subunits of photosystem II. Moreover, disulphide reduction inhibits activity of the xanthophyll cycle enzyme violaxanthin de‐epoxidase, which participates in thermal dissipation of excess absorbed light. Our results indicate that redox‐controlled reactions in the chloroplast lumen play essential roles in the function of photosystem II and the regulation of adaptation to light intensity.
Sorting protein lists with nwCompare: A simple and fast algorithm for n‐way comparison of proteomic data files
Authors: Pont Frédéric , Fournié Jean Jacques 
Published: January 2010

AbstractMS, the reference technology for proteomics, routinely produces large numbers of protein lists whose fast comparison would prove very useful. Unfortunately, most softwares only allow comparisons of two to three lists at once. We introduce here nwCompare, a simple tool for n‐way comparison of several protein lists without any query language, and exemplify its use with differential and shared cancer cell proteomes. As the software compares character strings, it can be applied to any type of data mining, such as genomic or metabolomic datalists.
FragmentationAnalyzer: An open‐source tool to analyze MS/MS fragmentation data
Authors: Barsnes Harald , Eidhammer Ingvar , Martens Lennart 
Published: January 2010

AbstractA thorough understanding of the fragmentation processes in MS/MS can be a powerful tool in assessing the resulting peptide and protein identifications. We here present the freely available, open‐source FragmentationAnalyzer tool (http://fragmentation‐analyzer.googlecode.com) that makes it straightforward to analyze large MS/MS data sets for specific types of identified peptides, using a common set of peptide properties. This enables the detection of fragmentation pattern nuances related to specific instruments or due to the presence of post‐translational modifications.
Palaeoclimatic information from stable water isotopes of Holocene ice wedges on the Dmitrii Laptev Strait, northeast Siberia, Russia
Authors: Opel Thomas , Dereviagin Alexander Yu. , Meyer Hanno , Schirrmeister Lutz , Wetterich Sebastian 
Published: January 2010

AbstractThe stable isotopic composition (δ18O, δD, d) of three Holocene‐age ice wedges at the Dmitrii Laptev Strait, Russia (Oyogos Yar coast, 72.7°N, 143.5°E) was studied at high resolution (100 to 200 samples each) in order to develop palaeoclimatic records. AMS 14C ages of organic matter in the ice prove the Late Holocene age of the studied horizontal ice‐wedge profiles and indicate syngenetic growth associated with sediment accumulation. Co‐isotopic relationships of wedge ice close to the Global Meteoric Water Line point to a good suitability for palaeoclimate studies and all three profiles show similar isotopic features. A general Late Holocene winter warming trend is inferred from δ18O data changing from about −26‰ to values of −23‰ to −21‰, with periods of marked variability superimposed on the trend. This trend is accompanied by a shift in the d excess from 8‰–11‰ to 5‰–8‰, probably caused by varying proportions of differing moisture sources for precipitation. The highest winter temperatures and an increased influence of regional moisture in recent decades may reflect ongoing Arctic climate change. Copyright © 2010 John Wiley & Sons, Ltd.
Numerical simulations of bulk crystal growth on different scales: silicon and GeSi
Authors: Miller Wolfram 
Published: January 2010

AbstractNumerical modelling has become an important tool for improving or introducing new processes in bulk crystal growth. For a complete description, scales ranging from atomistic ones up to those of industrial furnaces have to be considered. This article presents methods used on different scales for the Czochralski growth of silicon as well as of Ge1–xSix alloys and for ingot casting of silicon. It shows the recent developments for the different scales and the attempts at coupling the approaches.