bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptide separation with immobilized pI strips is an attractive alternative to in‐gel protein digestion for proteome analysis
Authors: Hubner Nina C. , Ren Shubin , Mann Matthias 
Published: November 2008

AbstractComplex protein mixtures have traditionally been separated by 2‐DE. Görg introduced IPGs as the first dimension of protein separation. In recent years, MS‐based proteomics has increasingly become the method of choice for identifying and quantifying large number of proteins. In that technology, to decrease analyte complexity, proteins are often separated by 1‐D SDS‐gel electrophoresis before online MS analysis. Here, we investigate a recently introduced device for peptide separation with IPGs (Agilent OFFGEL). Loading capacity for optimal peptide focusing is below 100 μg and – similar to 2‐D gels – IEF is more efficient in the acidic than the basic pH region. The 24‐well fractionation format resulted in about 40% additional peptide identifications but less than 20% additional protein identifications than the 12‐well format. Compared to in‐gel digestion, peptide IEF consistently identified a third more proteins with equal number of fractions. Low protein starting amounts (10 μg) still resulted in deep proteome coverage. Advantages of the in‐gel format include better reliability and robustness. Considering its superior performance, diminished sample and work‐up requirements, peptide IEF will become a method of choice for sample preparation in proteomics.
Inclusion of human errors assessment in failure frequency analysis—A case study for the transportation of ammonia by rail in Malaysia
Authors: Hassan Che Rosmani Che , Balasubramaniam Puvaneswaran A/L , Raman Abdul Aziz Abdul , Mahmood Noor Zalina , Hung Foo Chee , Sulaiman Nik Meriam Nik 
Published: November 2008

AbstractRisk is defined as the probability of a specific adverse event occurring within a specific period, while Quantitative risk assessment (QRA) is the development of a quantitative estimate of risk based on engineering evaluation and mathematical techniques by combining estimate of incident consequences and frequencies. In view of the increase in the use of railways as the mode of transportation for hazardous materials throughout the world, the associated risk analysis should be taken into concern. In this study, the failure frequency of the transportation of ammonia from the Petronas fertilizers Kedah (PFK) plant in Gurun (Northern part of Peninsular Malaysia), to the Chemical Company Malaysia (CCM) fertilizer's facilities in Port Klang (South‐western part of Peninsular Malaysia) was evaluated by incorporating the human error assessment. The study highlighted the importance of human error contributions in the failure frequency analysis and its impact on the selected failure scenarios. Besides, it also shows that the application of the human error assessment and reduction technique (HEART), which is a useful human reliability analysis tool, should be used in parallel with the fuzzy arithmetic approach to reduce the uncertainties involved in the estimation of human error probabilities, and hence, to reduce the likelihood of incorrect risks estimates being assessed. The results suggested that the commonly applied approach in quantitative risk assessments, which only consider equipment failures in the failure frequency estimations, are clearly an underestimate of the potential causes of failures leading to hazardous material releases, and hence, the calculated risks based do not reflect the actual risks. © 2008 American Institute of Chemical Engineers Process Saf Prog, 2009
Thiol‐disulfide redox equilibria of glutathione metaboloma compounds investigated by tandem mass spectrometry
Authors: Rubino Federico M. , Pitton Marco , Caneva Enrico , Pappini Marco , Colombi Antonio 
Published: November 2008

AbstractThe thiol group of cysteine plays a pivotal role in structural and functional biology. We use mass spectrometry to study glutathione‐related homo‐ and heterodimeric disulfides, aiming at understanding the factors affecting the redox potentials of different disulfide/thiol pairs. Several electrospray ionization (ESI)‐protonated disulfides of cysteamine, cysteine, penicillamine, N‐acetylcysteine, N‐acetylpenicillamine, γGluCySH, HSCyGly, and glutathione were analyzed on a triple quadrupole instrument to measure their energy‐resolved tandem mass spectra. Fission of the disulfide bond yields RSH*H+ and RS+ ions. The logarithm of the intensity ratio of the RS+/RSH*H+ fragments in homodimeric disulfides is proportional to the normal reduction potential of their RSSR/RSH pairs determined by nuclear magnetic resonance (NMR) in solution, the more reducing ones yielding the higher ratios. Also in some R1S‐SR2 disulfides, the ratio of the intensities of the RSH + H+ and RS+ ions of each participating thiol shows a linear relationship with the Nernst equation potential difference of the corresponding redox pairs. This behavior allows us to measure the redox potentials of some disulfide/thiol pairs by using different thiol‐reducing probes of known oxidoreductive potential as reference. To assist understanding of the fission mechanism of the disulfide bond, the fragments tentatively identified as ‘sulfenium’ were themselves fragmented; accurate mass measurement of the resulting second‐generation fragments demonstrated a loss of thioformaldehyde, thus supporting the assigned structure of this elusive intermediate of the oxidative stress pathway. Understanding this fragmentation process allows us to employ this technique with larger molecules to measure by mass spectrometry the micro‐redox properties of different disulfide bonds in peptides with catalytic and signaling biological activity. Copyright © 2008 John Wiley & Sons, Ltd.
The growth of thin NiO films on Ag(001) studied by scanning tunneling microscopy and spectroscopy
Authors: Großer Stephan , Hagendorf Christian , Neddermeyer Henning , Widdra Wolf 
Published: November 2008

AbstractWe have used scanning tunneling microscopy and spectroscopy to study the growth of NiO films on Ag(001) at a coverage of 1.5 monolayers. The films have been obtained by reactive deposition of Ni in O2 atmosphere. Particular attention has been paid to the development of the growth morphology of the deposit as a function of substrate and annealing temperature. For room temperature deposition, the Ag(001) surface is completely covered with the (2 × 1) NiO precursor structure with a thickness of one monolayer and small double‐layer NiO islands. The Ag(001) substrate surface is nearly unaffected. Subsequent annealing leads to drastic changes of the morphology of the film. The (2 × 1) precursor structure gradually disappears with annealing time and transforms to double‐layer NiO islands. One part of these NiO islands is embedded in the initially flat Ag substrate, and additional Ag islands appear on the surface. Local I/U characteristics (I: tunneling current, U: tunneling bias) have been measured on each kind of island and we found characteristic differences for the various parts of the surface, e.g. for Ag, the (2 × 1) precursor, double‐layer and trilayer NiO. These differences can be used to directly map the individual species on the surface. Copyright © 2008 John Wiley & Sons, Ltd.
Inclusion, subsumption, JJ‐paths, and structured path testing: a Redress
Authors: Yates D. F. , Malevris N. 
Published: November 2008

AbstractIntroduced in 1976 by Hennell, Woodward, and Hedley, the Linear Code Sequence and Jump (LCSAJ) has since been named the jump‐to‐jump path (JJ‐path). If all JJ‐paths in a piece of code have been tested, then it is guaranteed, for example, that all of the code's branches and all of its statements will likewise have been tested. JJ‐path testing is thus said to include both branch and statement testing. Over the years, much work has been carried out on the inclusion relation, and this is also true of a closely‐linked relation that is known as subsumption. Not surprisingly, some of the work in the literature has focussed on the criteria of executing all JJ‐paths and sequences of such, and how these criteria relate to other path coverage and test data criteria. Unfortunately, certain results involving JJ‐paths in the context of inclusion, as portrayed in a widely referenced and influential paper, are in error. Consequently, the main purpose of this paper is to rectify this situation. Copyright © 2008 John Wiley & Sons, Ltd.
Effects of Survivin on cell proliferation and apoptosis in MG‐63 cells in vitro
Authors: Liang Xinjun , Da Mingxu , Zhuang Zhiqiang , Wu Weiguang , Wu Zhuang , Wu Yanfeng , Shen Huiyong 
Published: November 2008

AbstractOsteosarcoma is the most frequent primary malignant tumor of the skeleton and occurs mainly in children and adolescent. The prognosis of osteosarcoma is very poor due to its aggressive and no effective treatment. This study is the first to investigate the anti‐cancer effects of antisense pEGFP‐C1‐Survivin on human osteosarcoma cells. It was shown in our results that Survivin blockaded could significantly induce apoptosis and inhibit the invasive of osteosarcoma cells line MG‐63. The effects were probably produced by the decreased expression of Survivin induced by antisense pEGFP‐C1‐Survivin which was examined by RT‐PCR and western blotting. All these suggested that Survivin should be very important in the development of osteosarcoma and Survivin blockaded by using antisense pEGFP‐C1‐Survivin could markedly inhibit the proliferation and invasion of osteosarcoma cells line MG‐63, partially reversed their malignant phenotype. Targeting Survivin might be a promising option in the treatment of osteosarcoma.
Chromosomal Imbalances are Associated with Increased Proliferation and Might Contribute to Bone Destruction in Cholesteatoma
Authors: Ecsedi Szilvia , Rákosy Zsuzsa , Vízkeleti Laura , Juhász Attila , Sziklai István , Ádány Róza , Balázs Margit 
Published: November 2008

ObjectivesOur aim was to evaluate the copy number alterations of chromosomes 3, 7, 8, and 17 in middle ear cholesteatomas and define the association between the rate of cell proliferation and chromosome number changes.MethodsTissues were obtained from 16 patients. Fluorescence in situ hybridization was performed on tumor imprint preparations. Cell proliferation was characterized with Ki‐67 monoclonal antibody on cholesteatoma samples and on postauricular skins as control.ResultsDifferent degrees of aneusomy were found for all chromosomes except for chromosome 3. Chromosome copy number alterations were associated with elevated proliferative rate and related also with the aggressiveness of the lesions.ConclusionsBased on our results, we assume that aneusomy of chromosomes 7, 8, and 17 might play an important role during invasion of the adjacent bony structures of cholesteatoma, as well as associate with increased cell proliferation activity, which might lead to the aggressive behavior of the tissue.
Optimal financial education
Authors: Subrahmanyam Avanidhar 
Published: November 2008

AbstractWhen agents first invest in financial markets, they are relatively inexperienced. The agents best positioned to educate the inexperienced stand to earn trading profits at the expense of inexperienced agents. Owing to this phenomenon, we show that the equilibrium amount of financial education does not fully correct the biases of the inexperienced agents. In a dynamic setting, large levels of uninformed trading volume may be generated by the inexperienced agents. This is because, in equilibrium, the experienced intermediaries may delay educating the inexperienced in order to earn commissions in earlier rounds of trade.
Spatial and temporal structure of the trematode component community inValvata macrostoma(Gastropoda, Prosobranchia)
Authors: FALTÝNKOVÁ A. , VALTONEN E. T. , KARVONEN A. 
Published: November 2008

SUMMARYWe conducted the first comprehensive study on the spatiotemporal structure of trematode communities in the large-mouthed valve snail,Valvata macrostoma. A total of 1103 snails were examined monthly between May and October 2007 from Lake Konnevesi, Central Finland, from a shallow (1–2 m deep) and an offshore site (5–6 m deep), located ca. 50–70 m apart. Snails were infected by 10 trematode species. The species composition and prevalence were strikingly different between the sites with high species diversity in the shallow site (all 10 species; total prevalence of sporocysts/rediae 12·1%, metacercariae 55·4%) compared to the deeper site (3 species; prevalence 15·0% and 1·9%, respectively). This difference persisted throughout our study and is probably related to the spatial distribution of bird definitive hosts, whereas the seasonal parasite dynamics are likely to be affected by changes in the age-structure of the snail population. The probability of sporocyst infections increased with snail size, but no such trend was observed in redial or metacercarial infections which decreased with host size. Our results show that generally well-described spatiotemporal differences in trematode infection of molluscs can emerge in very narrow spatial and temporal scales, which emphasizes the importance of these factors in community studies.
‘… into another kind of life in which anything might happen …’ Popular music and late modernity, 1910–1930
Authors: Baxendale John 
Published: November 2008

One evening in Leeds, in about 1913, the young J.B. Priestley had a brush with modernity:… hot and astonished in the Empire, we discovered ragtime … It was as if we had been still living in the nineteenth century and then suddenly found the twentieth glaring and screaming at us. We were yanked into our own age, fascinating, jungle-haunted, monstrous … Out of these twenty noisy minutes in a music hall, so long ago, came fragmentary but prophetic outlines of the situation in which we find ourselves now, the menace to old Europe, the domination of America, the emergence of Africa, the end of confidence and any feeling of security, the nervous excitement, the frenzy, the underlying despair of our century … here was something new, strange, curiously disturbing … (Priestley 1962, pp. 66–7)
Of Two Lives One? Jean-Charles-Marguerite-Guillaume Grimaud and the Question of Holism in Vitalist Medicine
Authors: Williams Elizabeth A. 
Published: November 2008

ArgumentMontpellier vitalists upheld a medical perspective akin to modern “holism” in positing the functional unity of creatures imbued with life. While early vitalists focused on the human organism, Jean-Charles-Marguerite-Guillaume Grimaud investigated digestion, growth, and other physiological processes that human beings shared with simpler organisms. Eschewing modern investigative methods, Grimaud promoted a medically-grounded “metaphysics.” His influential doctrine of the “two lives” broke with Montpellier holism, classifying some vital phenomena as “higher” and others as “lower” and attributing the “nobility” of the human species to the predominance of the former. In place of Montpellier teaching that attributed health to the holistic equilibration of vital activities, Grimaud embraced spiritualist dualisms of soul and body, Creator and created. Celebrating the divinely-ordained “wisdom” evident in involuntary physiological processes, he argued that such life functions were incomprehensible to human investigators. While Grimaud's work encouraged inquiry into the division between the central and “vegetative” nervous systems that became paradigmatic in nineteenth-century neuroscience, it also opened Montpellier vitalism to charges of conservatism and obscurantism that are still lodged against it to the present day.
Origins of intrusions in children’s dietary recalls: data from a validation study concerning retention interval and information from school food-service production records
Authors: Baxter Suzanne Domel , Royer Julie A , Guinn Caroline H , Hardin James W , Smith Albert F 
Published: November 2008

AbstractObjectiveTo use data from a published validation study concerning retention interval and school food-service production records to examine intrusions (uneaten items reported eaten) in the school-meal parts of 24 h recalls.DesignFor that study, children were observed eating two school meals (breakfast, lunch) and interviewed under one of six conditions from two target periods (previous day (PDTP), prior 24 h (24TP)) crossed with three interview times (morning, afternoon (AIT), evening). For the present article, a catalogue was constructed of foods available for that study’s school meals. The study’s intrusions were classified as stretches (on children’s meal trays but uneaten), internal confabulations (in children’s school food-service environments for that meal but not on children’s trays) or external confabulations (not in children’s school food-service environments for that meal). Occurrence, types and amounts of intrusions were investigated.Setting/subjectsSix schools; sixty fourth-grade children (ten per condition).ResultsFor breakfast, for the 24TPv. PDTP, reported items were less likely to be intrusions, internal confabulations and external confabulations; and intrusions were more likely to be stretches. For lunch, for the 24TP-AIT conditionv. the other five conditions, reported items were less likely to be intrusions and external confabulations. Mean amounts reported eaten were smaller for stretches than for internal confabulations or external confabulations at breakfast, and for stretches than for internal confabulations at lunch.ConclusionsAccuracy was better for the 24TP (with fewer intrusions of which proportionally more were stretches which had smaller amounts reported eaten) than for the PDTP. Studies with 24 h recalls should minimize retention interval to improve accuracy.
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
Authors: Zhang Hao , Lundegaard Claus , Nielsen Morten 
Published: November 2008

Abstract
Motivation: MHC:peptide binding plays a central role in activating the immune surveillance. Computational approaches to determine T-cell epitopes restricted to any given major histocompatibility complex (MHC) molecule are of special practical value in the development of for instance vaccines with broad population coverage against emerging pathogens. Methods have recently been published that are able to predict peptide binding to any human MHC class I molecule. In contrast to conventional allele-specific methods, these methods do allow for extrapolation to uncharacterized MHC molecules. These pan-specific human lymphocyte antigen (HLA) predictors have not previously been compared using independent evaluation sets.
Result: A diverse set of quantitative peptide binding affinity measurements was collected from Immune Epitope database (IEDB), together with a large set of HLA class I ligands from the SYFPEITHI database. Based on these datasets, three different pan-specific HLA web-accessible predictors NetMHCpan, adaptive double threading (ADT) and kernel-based inter-allele peptide binding prediction system (KISS) were evaluated. The performance of the pan-specific predictors was also compared with a well performing allele-specific MHC class I predictor, NetMHC, as well as a consensus approach integrating the predictions from the NetMHC and NetMHCpan methods.
Conclusions: The benchmark demonstrated that pan-specific methods do provide accurate predictions also for previously uncharacterized MHC molecules. The NetMHCpan method trained to predict actual binding affinities was consistently top ranking both on quantitative (affinity) and binary (ligand) data. However, the KISS method trained to predict binary data was one of the best performing methods when benchmarked on binary data. Finally, a consensus method integrating predictions from the two best performing methods was shown to improve the prediction accuracy.
Contact: mniel@cbs.dtu.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
Tomato Ribonuclease LX with the Functional Endoplasmic Reticulum Retention Motif HDEF Is Expressed during Programmed Cell Death Processes, Including Xylem Differentiation, Germination, and Senescence
Authors: Lehmann Karin , Hause Bettina , Altmann Dorit , Köck Margret 
Published: November 2008

Abstract
We have studied the subcellular localization of the acid S-like ribonuclease (RNase) LX in tomato (Lycopersicon esculentum Mill.) cells using a combination of biochemical and immunological methods. It was found that the enzyme, unexpectedly excluded from highly purified vacuoles, accumulates in the endoplasmic reticulum. The evidence that RNase LX is a resident of the endoplasmic reticulum (ER) is supported by an independent approach showing that the C-terminal peptide HDEF of RNase LX acts as an alternative ER retention signal in plants. For functional testing, the cellular distribution of chimeric protein constructs based on a marker protein, Brazil nut (Bertholletia excelsa) 2S albumin, was analyzed immunochemically in transgenic tobacco (Nicotiana tabacum) plants. Here, we report that the peptide motif is necessary and sufficient to accumulate 2S albumin constructs of both vacuolar and extracellular final destinations in the ER. We have shown immunochemically that RNase LX is specifically expressed during endosperm mobilization and leaf and flower senescence. Using immunofluorescence, RNase LX protein was detected in immature tracheary elements, suggesting a function in xylem differentiation. These results support a physiological function of RNase LX in selective cell death processes that are also thought to involve programmed cell death. It is assumed that RNase LX accumulates in an ER-derived compartment and is released by membrane disruption into the cytoplasma of those cells that are intended to undergo autolysis. These processes are accompanied by degradation of cellular components supporting a metabolic recycling function of the intracellular RNase LX.
Cytosolic Glutamine Synthetase in Soybean Is Encoded by a Multigene Family, and the Members Are Regulated in an Organ-Specific and Developmental Manner
Authors: Morey Kevin J. , Ortega Jose Luis , Sengupta-Gopalan Champa 
Published: November 2008

Abstract
Gln synthetase (GS) is the key enzyme in N metabolism and it catalyzes the synthesis of Gln from glutamic acid, ATP, and NH4 +. There are two major isoforms of GS in plants, a cytosolic form (GS1) and a chloroplastic form (GS2). In leaves, GS2 functions to assimilate ammonia produced by nitrate reduction and photorespiration, and GS1 is the major isoform assimilating NH3produced by all other metabolic processes, including symbiotic N2 fixation in the nodules. GS1 is encoded by a small multigene family in soybean (Glycine max), and cDNA clones for the different members have been isolated. Based on sequence divergence in the 3′-untranslated region, three distinct classes of GS1 genes have been identified (α, β, and γ). Genomic Southern analysis and analysis of hybrid-select translation products suggest that each class has two distinct members. The α forms are the major isoforms in the cotyledons and young roots. The β forms, although constitutive in their expression pattern, are ammonia inducible and show high expression in N2-fixing nodules. The γ1 gene appears to be more nodule specific, whereas the γ2 gene member, although nodule enhanced, is also expressed in the cotyledons and flowers. The two members of the α and β class of GS1 genes show subtle differences in the expression pattern. Analysis of the promoter regions of the γ1 and γ2 genes show sequence conservation around the TATA box but complete divergence in the rest of the promoter region. We postulate that each member of the three GS1 gene classes may be derived from the two ancestral genomes from which the allotetraploid soybean was derived.