bluuebunny/crossref_metadata_2025 huggingface dataset:
Teratoma with a malignant somatic component in pediatric patients: The Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP) experience
Authors: Terenziani Monica , D'Angelo Paolo , Bisogno Gianni , Boldrini Renata , Cecchetto Giovanni , Collini Paola , Conte Massimo , De Laurentis Tina , Ilari Ilaria , Indolfi Paolo , Inserra Alessandro , Piva Luigi , Siracusa Fortunato , Spreafico Filippo , Tamaro Paolo , Lo Curto Margherita
Published: January 2010

Background

Teratoma with a malignant somatic component (TMSC) is rare but described in adults, whereas information on pediatric presentation is sparse.

Procedure

The Associazione Italiana Ematologia Oncologia Pediatrica identified 14 cases of TMSC. Clinical files and pathology specimens were reviewed.

Results

The series (9 female, 5 male) showed the following disease: testis (2), sacrococcygeal (3), ovary (3), retroperitoneum (3), mediastinum (2), and foot soft tissue (1). Distribution of the somatic component was: carcinoma (4), pancreatic neuroendocrine tumor (1), neuroblastoma (3), rhabdomyosarcoma (3), rhabdomyosarcoma plus liposarcoma, chondrosarcoma, neurogenic sarcoma (1), chondrosarcoma plus neuroectodermal sarcoma (1), malignant peripheral nerve sheath tumor (1). Three patients were in stage I, four in stage II, three in stage III, and four in stage IV. All but one patient underwent surgery and only females showed carcinoma components. Nine patients relapsed or progressed and eight died. Six patients are alive and disease‐free. Two patients underwent complete resection and four were treated based on transformed histologies. Relapse‐free and overall survival rates were 35.7% and 42.8%, respectively (median follow‐up, 31 months).

Conclusions

Prognosis for germ cell tumors (GCTs) containing MSC is worse than that for GCTs. The pediatric disease appears to be more heterogeneous in tumor site distribution and MSC histology than in adults. Our series suggests no effects of age, histology, or gender on outcome. Surgery has an essential role in localized disease, with complete resection highly desirable. Chemotherapy optimized for histology should include reagents directed to the somatic malignancy, if chemosensitive. Malignant GCT warrants GCT‐directed chemotherapy. Pediatr Blood Cancer 2010;54:532–537. © 2009 Wiley‐Liss, Inc.
Diffuse central nervous system protoplasmic astrocytoma
Authors: Manley Sue , Crooks Daniel , Artingstall Libby , Buxton Neil , Appleton Richard , Riordan Andrew , Cleary Gavin , Pizer Barry
Published: January 2010

Protoplasmic astrocytoma is an extremely rare form of grade II low grade glioma which usually presents as a discrete mass lesion. We describe a 3‐year‐old female with diffuse protoplasmic astrocytoma with parenchymal involvement and leptomeningeal spread. This tumour proved extremely difficult to diagnose and followed a progressive course. Three superficial biopsies did not give the diagnosis and this was only confirmed 8 months from presentation from a larger fourth biopsy taken deeper from the cerebellum. To our knowledge this case represents the distinct presentation of protoplasmic astrocytoma presenting as extensive diffuse meningeal disease. Pediatr Blood Cancer 2010;54:768–769. © 2009 Wiley‐Liss, Inc.
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

Aim

Thoracic 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 Methods

Files 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.

Results

All 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).

Conclusions

Thoracic 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

Background

In 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.

Methods

Oral 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.

Results

On 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.

Conclusions

The 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

Purpose

To 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.

Methods

We 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.

Results

Among 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%.

Conclusions

The 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

A 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

In 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

In 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

Infection 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

Progression 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

Thymol 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

The 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

MS, 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

A 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

The 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

Numerical 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.
A dynamic soil chamber system coupled with a tunable diode laser for online measurements of δ13C, δ18O, and efflux rate of soil‐respired CO2
Authors: Powers Heath H. , Hunt John E. , Hanson David T. , McDowell Nate G.
Published: January 2010

High frequency observations of the stable isotopic composition of CO2 effluxes from soil have been sparse due in part to measurement challenges. We have developed an open‐system method that utilizes a flow‐through chamber coupled to a tunable diode laser (TDL) to quantify the rate of soil CO2 efflux and its δ13C and δ18O values (δ13CR and δ18OR, respectively). We tested the method first in the laboratory using an artificial soil test column and then in a semi‐arid woodland. We found that the CO2 efflux rates of 1.2 to 7.3 µmol m−2 s−1 measured by the chamber‐TDL system were similar to measurements made using the chamber and an infrared gas analyzer (IRGA) (R2 = 0.99) and compared well with efflux rates generated from the soil test column (R2 = 0.94). Measured δ13C and δ18O values of CO2 efflux using the chamber‐TDL system at 2 min intervals were not significantly different from source air values across all efflux rates after accounting for diffusive enrichment. Field measurements during drought demonstrated a strong dependency of CO2 efflux and isotopic composition on soil water content. Addition of water to the soil beneath the chamber resulted in average changes of +6.9 µmol m−2 s−1, −5.0‰, and −55.0‰ for soil CO2 efflux, δ13CR and δ18OR, respectively. All three variables initiated responses within 2 min of water addition, with peak responses observed within 10 min for isotopes and 20 min for efflux. The observed δ18OR was more enriched than predicted from temperature‐dependent H2O‐CO2 equilibration theory, similar to other recent observations of δ18OR from dry soils (Wingate L, Seibt U, Maseyk K, Ogee J, Almeida P, Yakir D, Pereira JS, Mencuccini M. Global Change Biol. 2008; 14: 2178). The soil chamber coupled with the TDL was found to be an effective method for capturing soil CO2 efflux and its stable isotope composition at high temporal frequency. Published in 2010 by John Wiley & Sons, Ltd.
A new class of anthocyanin‐procyanidin condensation products detected in red wine by electrospray ionization multi‐stage mass spectrometry analysis
Authors: Sun Baoshan , Fernandes Tiago A. , Spranger M. Isabel
Published: January 2010

In our previous work, we have identified, in a model wine solution containing malvidin 3‐glucoside, epicatechin and acetaldehyde, a new condensation product – hydroxylethyl‐malvidin‐3‐glucoside‐ethyl‐epicatechin. The objective of this work was to verify the presence of such new condensation products in red wine. For this purpose, red wine was fractionated into various fractions by column chromatography on LiChroprep RP 18 and on Toyopearl 40 (F). The phenolic composition of each fraction was verified by HPLC‐DAD and direct‐infusion ESI‐MSn analysis. In addition to the well‐known anthocyanins and their acetyl and coumaroyl derivatives, and several direct and indirect anthocyanin‐(epi)catechin condensation products, a new class of pigmented products, namely hydroxyethyl‐anthocyanin‐ethyl‐flavanol compounds, have been detected in red wine. The new class of pigmented products would be expected to be the major pigments responsible for the color of aged red wine. Copyright © 2010 John Wiley & Sons, Ltd.
The effects of differentiated water supply after anthesis and nitrogen fertilization on δ15N of wheat grain
Authors: Raimanová Ivana , Haberle Jan
Published: January 2010

The δ15N signature of plants integrates various processes in soil and plant. In this study, the effect of different water regimes applied during the period of grain growth of winter wheat on grain δ15N was examined in a 4‐year field experiment. The treatments comprised water shortage (S), an ample water supply (W), and rain‐fed crop (R). Zero fertilization (N0) and 200 kg N.ha−1 in mineral fertilizer (N1) treatments were studied. The grain 15N was determined during grain growth and at maturity. The water regime, nitrogen application and year had a significant effect on mature grain δ15N (p < 0.001). Water and nitrogen explained 54.6% of the variability of δ15N in the experiment, the year accounted for 10.7% and the interactions for another 19.6% of the total variability. The analysis of non‐mature grain δ15N showed significant effects of N and year but not of water. Nitrogen fertilization reduced the δ15N of mature grain in years by 0.7–6.3‰ in comparison with N0 plants; the reduction was more pronounced under stress (average reduction by 4.1‰) than under rain‐fed (2.4‰) and ample water supply (2.2‰). Water stress decreased the grain δ15N in fertilized wheat, by 0.1–2.1‰ and 0.6–3.6‰ in experimental years, on average by 1.30‰ and 1.79‰ in comparison with the R and W water supply, respectively. The effect of water supply was not significant in non‐fertilized wheat. A significant negative linear relationship between grain N concentration and δ15N in maturity or during the grain growth (R2 = 0.83, R2 = 0.76, respectively) was found. The observed sources of grain δ15N variability should be taken into consideration when analyzing and interpreting the data on the δ15N signature of plant material from field conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Desulfurization of cysteine‐containing peptides resulting from sample preparation for protein characterization by mass spectrometry
Authors: Wang Zhouxi , Rejtar Tomas , Zhou Zhaohui Sunny , Karger Barry L.
Published: January 2010

In this study, we have examined two cysteine modifications resulting from sample preparation for protein characterization by mass spectrometry (MS): (1) a previously observed conversion of cysteine into dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine into alanine. Using model peptides, the conversion of cysteine into dehydroalanine via β‐elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37°C, pH 7.0–9.0) without disulfide reduction and alkylation. Furthermore, the surprising conversion of cysteine into alanine was shown to occur by heating cysteine‐containing peptides in the presence of a phosphine (tris(2‐carboxyethyl)phosphine hydrochloride (TCEP)). The formation of alanine from cysteine, investigated by performing experiments in H2O or D2O, suggested a radical‐based desulfurization mechanism unrelated to β‐elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis. Copyright © 2010 John Wiley & Sons, Ltd.
Evaluation and performance of desorption electrospray ionization using a triple quadrupole mass spectrometer for quantitation of pharmaceuticals in plasma
Authors: Kennedy Joseph H. , Wiseman Justin M.
Published: January 2010

The present work describes the methodology and investigates the performance of desorption electrospray ionization (DESI) combined with a triple quadrupole mass spectrometer for the quantitation of small drug molecules in human plasma. Amoxepine, atenolol, carbamazepine, clozapine, prazosin, propranolol and verapamil were selected as target analytes while terfenadine was selected as the internal standard common to each of the analytes. Protein precipitation of human plasma using acetonitrile was utilized for all samples. Limits of detection were determined for all analytes in plasma and shown to be in the range 0.2–40 ng/mL. Quantitative analysis of amoxepine, prazosin and verapamil was performed over the range 20–7400 ng/mL and shown to be linear in all cases with R2 >0.99. In most cases, the precision (relative standard deviation) and accuracy (relative error) of each method were less than or equal to 20%, respectively. The performance of the combined techniques made it possible to analyze each sample in 15 s illustrating DESI tandem mass spectrometry (MS/MS) as powerful tool for the quantitation of analytes in deproteinized human plasma. Copyright © 2010 John Wiley & Sons, Ltd.
Real‐time measurement of peroxyacetyl nitrate using selected ion flow tube mass spectrometry
Authors: Hastie Donald R. , Gray John , Langford Vaughan S. , Maclagan Robert G. A. R. , Milligan Daniel B. , McEwan Murray J.
Published: January 2010

The on‐line detection of gaseous peroxyacetyl nitrate (PAN) using selected ion flow tube mass spectrometry (SIFT‐MS) has been investigated using a synthetic sample of PAN in air at a humidity of ∼30%. Using the H3O+ reagent ion, signals due to PAN at m/z 122, 77 and 95 have been identified. These correspond to protonated PAN, protonated peractetic acid and its water cluster, respectively. These products and their energetics have been probed through quantum mechanical calculations. The rate coefficient of H3O+ has been estimated to be 4.5 × 10−9 cm3 s−1, leading to a PAN sensitivity of 138 cps/ppbv. This gives a limit of detection of 20 pptv in 10 s using the [M+H]+ ion of PAN at m/z 122. Copyright © 2010 John Wiley & Sons, Ltd.
A quick and easy method to identify bacteria by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry
Authors: Pennanec Xaviera , Dufour Alain , Haras Dominique , Réhel Karine
Published: January 2010

Concerns with water quality have increased in recent years, in part due to the more frequent contamination of water by pathogens like E. coli and L. pneumophila. Current methods for the typing of bacteria in water samples are based on culture of samples on specific media. These techniques are time‐consuming, subject to the impact of interferents and do not totally meet all the requirements of prevention. There is a need for accurate and rapid identification of these microorganisms. This report deals with the detection of bacteria, more precisely of Legionella spp., and the development of an analytical strategy for a rapid and unambiguous identification of these pathogens in water from diverse origins. Therefore, a protein mass mapping using matrix‐assisted laser desorption/ionisation mass spectrometry (MALDI MS) of whole bacteria combined with a home‐made database of bacteria spectra is applied. A large variety of different bacteria and microorganisms is used to approach the actual composition of samples with numerous interferents. The objective is to propose a universal method for sampling preparation before MALDI MS analysis and optimised spectrometric conditions for reproducible intense peaks. Several experimental factors known to influence signal quality such as time and media of culture have been studied. The proposed method gives promising results for a sure differentiation of Legionella species and subspecies and a rapid identification of bacteria which are the most dangerous or difficult to eradicate. This method is easy to perform with an excellent reproducibility. The analytical protocol and the corresponding database were validated on samples from different origins (cooling tower, plumbing hot water). Copyright © 2010 John Wiley & Sons, Ltd.
Anti‐retroviral activity of TRIM5α
Authors: Nakayama Emi E. , Shioda Tatsuo
Published: January 2010

Human immunodeficiency virus type 1 (HIV‐1) shows a very narrow host range limited to humans and chimpanzees. Experimentally, HIV‐1 does not infect Old World monkeys, such as rhesus (Rh) and cynomolgus (CM) monkeys, and fails to replicate in activated CD4 positive T lymphocytes obtained from these monkeys. In contrast, simian immunodeficiency virus isolated from a macaque monkey (SIVmac) can replicate well in both Rh and CM. In 2004, tripartite motif 5α (TRIM5α) was identified as a host factor which plays an important role in the restricted host range of HIV‐1. Rh and CM TRIM5α restrict HIV‐1 infection but not SIVmac, while in comparison, anti‐viral activity of human TRIM5α against those viruses is very weak. TRIM5α consists of the RING, B‐box 2, coiled‐coil and SPRY (B30.2) domains. The RING domain is frequently found in E3 ubiquitin ligase and TRIM5α is degraded via the ubiquitin‐proteasome pathway during HIV‐1 restriction. TRIM5α recognises the multimerised capsid (viral core) of an incoming virus by its α‐isoform specific SPRY domain and is believed to be involved in innate immunity to control retroviral infection. Differences in amino acid sequences in the SPRY domain of TRIM5α of different monkey species were found to affect species‐specific restriction of retrovirus infection, while differences in amino acid sequences in the viral capsid protein determine viral sensitivity to restriction. Accurate structural analysis of the binding surface between the viral capsid protein and TRIM5α SPRY is thus required for the development of new antiretroviral drugs that enhance anti‐HIV‐1 activity of human TRIM5α. Copyright © 2009 John Wiley & Sons, Ltd.
Kinematic reconfigurability control for an environmental mobile robot operating in the Amazon rain forest
Authors: Freitas Gustavo , Gleizer Gabriel , Lizarralde Fernando , Hsu Liu , dos Reis Ney Robinson Salvi
Published: January 2010

This paper addresses the active control problem of reconfigurable mobile robots on irregular terrain. Different kinematic control strategies to improve robot mobility are proposed based on (a) ground clearance and orientation, (b) ground clearance and stability margin, and (c) wheel traction efficiency. Owing to conflicting objectives associated with these strategies, a multi‐objective optimization approach is formulated to determine a set of optimal solutions and establish a trade‐off optimal solution. The proposed control is validated through numerical simulations and experimental tests using an amphibious wheel‐legged robot, named Environmental Hybrid Robot, designed for environmental monitoring in the Amazon rain forest. © 2010 Wiley Periodicals, Inc.
Analysis of textile fibers by in‐air PIXE
Authors: Jezeršek D. , Jakomin S. , Šmit Ž.
Published: January 2010

Trace elements in textile fibers were analyzed by the in‐air particle induced X‐ray emission (PIXE) method. Individual fibers were used as a target, representing minute material available in forensic or archeological applications. For quantification of the concentrations, the X‐ray production was assumed to occur in a thin cylindrical target that intersects the central part of the beam. The irradiated volume and the distribution of escape lengths were calculated in the model. The impact beam intensity was axially symmetric Gaussian, as shown by calculation and cross‐scan measurements. The normalization procedure relied on the argon signal from the air, which was checked by the chopper method. For a set of fibers, elements characteristic of the fibers and their dressings were determined. Copyright © 2010 John Wiley & Sons, Ltd.
A Bayesian approach to joint modeling of protein–DNA binding, gene expression and sequence data
Authors: Xie Yang , Pan Wei , Jeong Kyeong S. , Xiao Guanghua , Khodursky Arkady B.
Published: January 2010

The genome‐wide DNA‐protein‐binding data, DNA sequence data and gene expression data represent complementary means to deciphering global and local transcriptional regulatory circuits. Combining these different types of data can not only improve the statistical power, but also provide a more comprehensive picture of gene regulation. In this paper, we propose a novel statistical model to augment protein–DNA‐binding data with gene expression and DNA sequence data when available. We specify a hierarchical Bayes model and use Markov chain Monte Carlo simulations to draw inferences. Both simulation studies and an analysis of an experimental data set show that the proposed joint modeling method can significantly improve the specificity and sensitivity of identifying target genes as compared with conventional approaches relying on a single data source. Copyright © 2010 John Wiley & Sons, Ltd.
Robust non‐linear mixed modelling of longitudinal PSA levels after prostate cancer treatment
Authors: Subtil F. , Rabilloud M.
Published: January 2010

The objective of this study was to develop a robust non‐linear mixed model for prostate‐specific antigen (PSA) measurements after a high‐intensity focused ultrasound (HIFU) treatment for prostate cancer. The characteristics of these data are the presence of outlying values and non‐normal random effects. A numerical study proved that parameter estimates can be biased if these characteristics are not taken into account. The intra‐patient variability was described by a Student‐t distribution and Dirichlet process priors were assumed for non‐normal random effects; a process that limited the bias and provided more efficient parameter estimates than a classical mixed model with normal residuals and random effects. It was applied to the determination of the best dynamic PSA criterion for the diagnosis of prostate cancer recurrence, but could be used in studies that rely on PSA data to improve prognosis or compare treatment efficiencies and also with other longitudinal biomarkers that, such as PSA, present outlying values and non‐normal random effects. Copyright © 2010 John Wiley & Sons, Ltd.
Hybrid pooled–unpooled design for cost‐efficient measurement of biomarkers
Authors: Schisterman Enrique F. , Vexler Albert , Mumford Sunni L. , Perkins Neil J.
Published: January 2010

Evaluating biomarkers in epidemiological studies can be expensive and time consuming. Many investigators use techniques such as random sampling or pooling biospecimens in order to cut costs and save time on experiments. Commonly, analyses based on pooled data are strongly restricted by distributional assumptions that are challenging to validate because of the pooled biospecimens. Random sampling provides data that can be easily analyzed. However, random sampling methods are not optimal cost‐efficient designs for estimating means. We propose and examine a cost‐efficient hybrid design that involves taking a sample of both pooled and unpooled data in an optimal proportion in order to efficiently estimate the unknown parameters of the biomarker distribution. In addition, we find that this design can be used to estimate and account for different types of measurement and pooling error, without the need to collect validation data or repeated measurements. We show an example where application of the hybrid design leads to minimization of a given loss function based on variances of the estimators of the unknown parameters. Monte Carlo simulation and biomarker data from a study on coronary heart disease are used to demonstrate the proposed methodology. Published in 2010 by John Wiley & Sons, Ltd.
Hierarchical multicast in wireless sensor networks with mobile sinks
Authors: Hwang Shiow‐Fen , Lu Kun‐Hsien , Su Yi‐Yu , Hsien Chi‐Sen , Dow Chyi‐Ren
Published: January 2010

In most studies of wireless sensor networks (WSNs), sensor nodes and sinks are typically stationary. However, mobile sinks are required in various applications of real‐life environments, and delivering sensed data to mobile sinks using ordinary routing protocols is very inefficient. Multicasting is an important process in the minimization of the number of transmissions in WSNs. Since sensor nodes have limited resources, many studies have focused on how to send data to specific receivers efficiently. This work presents a grid‐based hierarchical multicast (HM) routing protocol for WSNs with mobile sinks. Location servers (LSs) are adopted to manage the information about the locations of receivers and then a multicast tree is constructed distributively to reduce the update cost and energy consumed by sink mobility. The multicast tree can be shared by multiple sources, reducing the path construction overhead. Furthermore, effective maintenance mechanisms that make the multicast tree more stable and robust are presented. Finally, the performance of the proposed HM is investigated by simulation. Simulation results demonstrate that the proposed protocol has a lower energy consumption and higher multicast efficiency than distributed multicast routing protocol (DMRP) and hierarchical geographic multicast routing (HGMR), especially when many sources and receivers are involved. Copyright © 2010 John Wiley & Sons, Ltd.
Standard Outpatient Re‐Evaluation for Patients Not Admitted to the Hospital After Emergency Department Evaluation for Acute Abdominal Pain
Authors: Toorenvliet Boudewijn R. , Bakker Rutger F. R. , Flu Hans C. , Merkus Jos W. S. , Hamming Jaap F. , Breslau Paul J.
Published: January 2010

Background

The aim of the present study was to investigate the efficacy and safety of standard outpatient re‐evaluation for patients who are not admitted to the hospital after emergency department surgical consultation for acute abdominal pain.

Methods

All patients seen at the emergency department between June 2005 and July 2006 for acute abdominal pain were included in a prospective study using a structured diagnosis and management flowchart. Patients not admitted to the hospital were given appointments for re‐evaluation at the outpatient clinic within 24 h. All clinical parameters, radiological results, diagnostic considerations, and management proposals were scored prospectively.

Results

Five‐hundred patients were included in this analysis. For 148 patients (30%), the final diagnosis was different from the diagnosis after initial evaluation. Eighty‐five patients (17%) had a change in management after re‐evaluation, and 20 of them (4%) were admitted to the hospital for an operation. Only 6 patients (1.2%) had a delay in diagnosis and treatment, which did not cause extra morbidity.

Conclusions

Standard outpatient re‐evaluation is a safe and effective means of improving diagnostic accuracy and helps to adapt management for patients that are not admitted to the hospital after surgical consultation for acute abdominal pain at the emergency department.