bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quadriceps muscle strength and voluntary activation after polio
Authors: Beelen Anita , Nollet Frans , de Visser Marianne , de Jong Bareld A. , Lankhorst Gustaaf J. , Sargeant Anthony J. 
Published: July 2003

AbstractQuadriceps strength, maximal anatomical cross‐sectional area (CSA), maximal voluntary activation (MVA), and maximal relaxation rate (MRR) were studied in 48 subjects with a past history of polio, 26 with and 22 without postpoliomyelitis syndrome (PPS), and in 13 control subjects. It was also investigated whether, apart from CSA, MVA and MRR were determinants of muscle strength. Polio subjects had significantly less strength, CSA, and MRR in the more‐affected quadriceps than control subjects. MVA was reduced in 18 polio subjects and normal in all controls. PPS subjects differed from non‐PPS subjects only in that the MVA of the more‐affected quadriceps was significantly lower. Both CSA and MVA were found to be associated with muscle strength. Quadriceps strength in polio subjects was dependent not only on muscle mass, but also on the ability to activate the muscles. Since impaired activation was more pronounced in PPS subjects, the new muscle weakness and functional decline in PPS may be due not only to a gradual loss of muscle fibers, but also to an increasing inability to activate the muscles. Muscle Nerve 28: 218–226, 2003
An asymptotically optimal greedy heuristic for the multiperiod single‐sourcing problem: The cyclic case
Authors: Romeijn H. Edwin , Romero Morales Dolores 
Published: July 2003

AbstractThe dynamics of the environment in which supply chains evolve requires that companies frequently redesign their logistics distribution networks. In this paper we address a multiperiod single‐sourcing problem that can be used as a strategic tool for evaluating the costs of logistics network designs in a dynamic environment. The distribution networks that we consider consist of a set of production and storage facilities, and a set of customers who do not hold inventories. The facilities face production capacities, and each customer's demand needs to be delivered by a single facility in each period. We deal with the assignment of customers to facilities, as well as the location, timing, and size of inventories. In addition, to mitigate start and end‐of‐study effects, we view the planning period as a typical future one, which will repeat itself. This leads to a cyclic model, in which starting and ending inventories are equal. Based on an assignment formulation of the problem, we propose a greedy heuristic, and prove that this greedy heuristic is asymptotically feasible and optimal in a probabilistic sense. We illustrate the behavior of the greedy heuristic, as well as some improvements where the greedy heuristic is used as the starting point of a local interchange procedure, on a set of randomly generated test problems. © 2003 Wiley Periodicals, Inc. Naval Research Logistics 50: 412–437, 2003
Fully‐automated hex‐dominant mesh generation with directionality control via packing rectangular solid cells
Authors: Yamakawa Soji , Shimada Kenji 
Published: July 2003

AbstractA new fully automatic hex‐dominant mesh generation technique of an arbitrary 3D geometric domain is presented herein. The proposed method generates a high‐quality hex‐dominant mesh by: (1) controlling the directionality of the output hex‐dominant mesh; and (2) avoiding ill‐shaped elements induced by nodes located too closely to each other. The proposed method takes a 3D geometric domain as input and creates a hex‐dominant mesh consisting mostly of hexahedral elements, with additional prism and tetrahedral elements. Rectangular solid cells are packed on the boundary of and inside the input domain to obtain ideal node locations for a hex‐dominant mesh. Each cell has a potential energy field that mimics a body‐centred cubic (BCC) structure (seen in natural substances such as NaCl) and the cells are moved to stable positions by a physically based simulation. The simulation mimics the formation of a crystal pattern so that the centres of the cells provide ideal node locations for a hex‐dominant mesh. Via the advancing front method, the centres of the packed cells are then connected to form a tetrahedral mesh, and this is converted to a hex‐dominant mesh by merging some of the tetrahedrons. Copyright © 2003 John Wiley & Sons, Ltd.
Preparative isolation of swainsonine from locoweed: extraction and puriﬁcation procedures
Authors: Gardner Dale R. , Lee Stephen T. , Molyneux Russell J. , Edgar John A. 
Published: July 2003

AbstractThe trihydroxy indolizidine alkaloid swainsonine, a plant toxin with potent α‐mannosidase‐inhibitory activity and chemotherapeutic potential, was isolated in gram quantities from locoweed (Astragalus lentiginosus). The key isolation and puriﬁcation step was a continuous liquid/liquid extraction procedure using dichloromethane to extract a basiﬁed aqueous methanol solution obtained after isolation of the polar base fraction by ion‐exchange. The concentration of swainsonine was increased from ca. 7% in the polar base material to 68% using the liquid/liquid extraction procedure. Pure swainsonine was then obtained by recrystallisation from ammonia‐saturated chloroform or by sublimation. Small samples of swainsonine were also puriﬁed by formation of the chloroform‐soluble methylboronate derivative, from which the alkaloid could be regenerated easily by hydrolysis. Copyright © 2003 John Wiley & Sons, Ltd.
Three different origins for apparent triploid/diploid mosaics
Authors: Daniel Art , Wu Zhanhe , Darmanian Artur , Collins Felicity , Jackson Julianne 
Published: July 2003

AbstractFour apparent triploid/diploid mosaic cases were studied. Three of the cases were detected at prenatal diagnosis and the other was of an intellectually handicapped, dysmorphic boy. Karyotypes were performed in multiple tissues if possible, and the inheritance of microsatellites was studied with DNA from fetal tissues and parental blood. Non‐mosaic triploids have a different origin from these mosaics with simple digyny or diandry documented in many cases. Three different mechanisms of origin for these apparent mosaics were detected: (1) chimaerism with karyotypes from two separate zygotes developing into a single individual, (2) delayed digyny, by incorporation of a pronucleus from a second polar body into one embryonic blastomere, and (3) delayed dispermy, similarly, by incorporation of a second sperm pronucleus into one embryonic blastomere. In three of the four cases, there was segregation within the embryos of triploid and diploid cell lines into different tissues from which DNA could be isolated. In case 2 originating by digyny, the same sperm allele at each locus could be detected in both triploid and diploid tissues, which is supportive evidence for the involvement of a single sperm and for true mosaicism rather than chimaerism. Similarly, in case 4 originating by dispermy, the same single ovum allele at each locus could be detected in diploid and triploid tissues, confirming mosaicism. In the chimaeric case (case 3), the diploid line had the karyotype 47,XY,+16 while the triploid line was 69,XXY. This suggests a chimaera, since, in a true mosaic, the triploid line should also contain the additional chromosome 16. Supporting the interpretation of a chimaeric origin for this case, the DNA data showed that the triploidy was consistent with MII non‐disjunction (i.e. involving a diploid ovum). In the mosaic cases (1, 2, 4), there was no evidence of the involvement of a diploid sperm or a diploid ova, and in triploid/diploid mosaicism, an origin from a diploid gamete is excluded, since all such conceptuses would be simple triploids. In one of these triploid/diploid mosaics detected at prenatal diagnosis by CVS, the triploid line seemed to be sequestered into the extra‐fetal tissues (confined placental mosaicism). This fetus developed normally and a normal infant was born with no evidence of triploidy in newborn blood or cord blood at three months of age. Copyright © 2003 John Wiley & Sons, Ltd.
Imaging technologies for the detection of multiple stains in proteomics
Authors: Miura Kenji 
Published: July 2003

AbstractLaser‐based scanners and charge‐coupled device (CCD) camera systems are evolving to have greater functional capabilities for capturing images from a range of staining technologies used in gel electrophoresis and electroblotting. Digitizing Coomassie Brilliant Blue (CBB) stained gels and silver stained gels has now become possible using a laser‐based gel scanner, the FLA‐5000 fluorescent image analyzer system. Also, a simultaneous dual fluorescent imaging function has been incorporated into the FLA‐5000 system, utilizing dichroic mirrors with both the optical system and the emission filter. In the workflow of routine proteomics research, the relationship between SYPRO dye staining and fluorescent detection using the FLA‐5000 system have become symbiotic. Additionally in many cases, subsequent staining of the gel with CBB is useful for future research, and thus imaging instruments should be able to handle both staining formats. Digitizing the CBB stained gel can now be easily performed by the FLA‐5000 fluorescent image analyzer system using a fluorescent board as an epi‐illumination background. A cooled CCD camera system has the potential of imaging not only chemiluminescent membranes but also digitizing molecular weight markers and fluorescent detection of SYPRO dye‐stained gels. With Multi Gauge software version 2.0 it is now a simple task to combine two images into one, as commonly required in dual detection experiments. The LAS‐3000 system was designed to capture chemiluminescent images and to digitize the images automatically. Thus, new capabilities added to gel imaging systems make them capable of detecting and displaying multiple signals more conveniently.
High‐content proteomics: Fluorescence multiplexing using an integrated, high‐sensitivity, multiwavelength charge‐coupled device imaging system
Authors: Lopez Mary F. , Mikulskis Alvydas , Golenko Eva , Herick Klaus , Spibey Carole A. , Taylor Ian , Bobrow Mark , Jackson Peter 
Published: July 2003

AbstractThe detection of proteins in 2‐D gels and their subsequent identification by MS is still the “gold standard” in proteomics. Fluorescent detection has increasingly replaced colorimetric and radiometric detection on gels and blots. The reasons for this are multiple and varied and include higher sensitivity, better quantitation, increased dynamic range, speed, safety and ease of use. Unlike other methods, fluorescent protein detection is also typically very consistent in response from protein to protein and in many cases is compatible with MS methods for protein identification. The superior sensitivity and benefits achieved by fluorescent techniques have spurred the development of instrumentation capable of delivering precise, sensitive, high‐resolution image acquisition over a wide variety of excitation and emission wavelengths. This report focuses on applications using the highly sensitive, charge‐coupled device based ProXPRESS™ multilabel imager, readily configurable for image acquisition over a wide variety of wavelengths (380–700 nm and ultraviolet (UV)) using xenon lamp or UV excitation. The ability to simultaneously detect enzyme activities or protein modifications with different color fluorescent probes in addition to total protein amounts (multiplexing) allows the further mining of proteomic data content from a single set of protein samples. To this end, the development of instrumentation that enables a multiplexing strategy will become central to in‐depth proteomic studies. The ProXPRESS maximizes the efficiency of experimental strategies that require flexibility and multicolor fluorescence detection.
Comparison of the Escherichia coli proteomes for recombinant human growth hormone producing and nonproducing fermentations
Authors: Champion Kathleen M. , Nishihara Julie C. , Aldor Ilana S. , Moreno G. Tony , Andersen Dana , Stults Kathy L. , Vanderlaan Martin 
Published: July 2003

AbstractTwo‐dimensional electrophoretic analyses of Escherichia coli cells producing recombinant human growth hormone (Nutropin™) in fermentations were conducted. The resulting two‐dimensional protein profiles were compared with those of nonproducing (blank) cells. A qualitative comparison was performed to address regulatory issues in the biopharmaceutical industry, and a semiquantitative comparison was performed to reveal information about the physiological state of the cells. The protein spots unique to production fermentation profiles were all related to recombinant human growth hormone (hGH); these included intact hGH, charge variants of hGH, and a proteolytically cleaved form of hGH, as expected. There were no E. coli host cell proteins unique to either the production or blank fermentation profiles. Rather, all detectable differences in E. coli proteins were quantitative in nature. Specifically, the levels of IbpA (inclusion body binding protein A), Ivy (inhibitor of vertebrate lysozyme), and a cleaved form of GroEL (Hsp60 homolog) were higher in hGH production profiles, whereas the levels of GlmU protein and PspA (phage shock protein A) were higher in blank profiles. In general, the high degree of similarity between proteomes for hGH‐producing and nonproducing cells suggests that E. coli proteins from a nonproducing (blank) fermentation are appropriate for eliciting antibodies that are then used in immunoassays to measure host cell proteins in samples from production fermentations.
Inhibitor affinity chromatography: Profiling the specific reactivity of the proteome with immobilized molecules
Authors: Lolli Graziano , Thaler Florian , Valsasina Barbara , Roletto Fulvia , Knapp Stefan , Uggeri Mauro , Bachi Angela , Matafora Vittoria , Storici Paola , Stewart Albert , Kalisz Henryk M. , Isacchi Antonella 
Published: July 2003

AbstractAn inhibitor affinity chromatography (IAC) method has been developed for the analysis of inhibitor‐protein interactions as a complementary approach to two‐dimensional electrophoresis for functional proteomics studies. The procedure was developed utilizing a cyclin‐dependent kinase 2 (Cdk2) inhibitor coupled to a polymeric resin and validated using a number of proteins interacting with the inhibitor with different specificities. Cdk2 and the other kinases bound and eluted from the resin in accordance with the relative in vitro potency of the inhibitor for each enzyme. Molecular interactions with the Cdk2 inhibitor were compared for HCT116 cancer cells versus rat pancreatic acinar cells. Proteins interacting with the ligand on the IAC matrix were identified by mass spectrometry. Isothermal calorimetry was used to confirm and quantitatively evaluate the binding affinity of some of the interacting proteins. Heat‐shock protein (Hsp) 70 and Hsp27 were the strongest interactors with the inhibitor, displaying binding affinities comparable to those of Cdk2. These results support the use of IAC as a general method for the rapid identification and qualitative evaluation of the in vivo targets and potential side effects of a given drug.
Proteomic analysis of rat heart in ischemia and ischemia‐reperfusion using fluorescence two‐dimensional difference gel electrophoresis
Authors: Sakai Jun , Ishikawa Hironori , Kojima Shinichi , Satoh Hideshi , Yamamoto Setsuko , Kanaoka Masaharu 
Published: July 2003

AbstractIschemia‐reperfusion injury is a major complication occurring in acute myocardial infarction, cardiopulmonary bypass surgery, and heart transplantation. The aim of this study was to identify proteins that were involved in ischemia‐reperfusion injury using fluorescence two‐dimensional difference gel electrophoresis. We compared the 100 000×g precipitate fractions of normal, ischemic and ischemia‐reperfused rat hearts and detected six spots which changed more than two‐fold in expression level and two additional spots related to these spots. Using peptide mass fingerprinting by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry, we identified five of these spots as protein disulfide isomerase A3 (PDA3), one as 60 kDa heat shock protein (HSP60) and two as elongation factor Tu (EF‐Tu). HSP60 was increased during ischemia and decreased to normal expression level after reperfusion. EF‐Tu was increased in ischemia but not decreased by reperfusion. We also found that several protein spots of PDA3 shifted towards a higher isoelectric point in ischemia and ischemia‐reperfusion. Our data strongly suggested that PDA3 underwent dephosphorylation during ischemia and reperfusion and serine 343 of PDA3 was one of the phosphorylation sites.
Using standard positions and image fusion to create proteome maps from collections of two‐dimensional gel electrophoresis images
Authors: Luhn Sven , Berth Matthias , Hecker Michael , Bernhardt Jörg 
Published: July 2003

AbstractDatabases for two‐dimensional protein gels pose new challenges in extracting meaningful information from large numbers of experiments. In order to create expression profiles, positions of corresponding protein spots across all gel images have to be established. In larger gel sets errors may accumulate rapidly during this spot matching process, effectively limiting the number of samples available for data mining. Here we present a novel approach for organizing spot data based on the concept of a standard position for a protein species. Standard positions are meaningful average positions that are determined using all occurrences of a protein species. They can be extended to spots that are not annotated via interpolation. The standard position of a spot can serve as a unifying index across all gels in a database, thus allowing creation and analysis of expression profiles that span the whole collection. The standard position gives a much more accurate estimation of a spot's position on a gel than can be obtained using theoretical isoelectric point and molecular weight. Positional indexing is a complement to a priori identifications (e.g. by mass spectrometry or Edman degradation). Moreover it can be used in advance to select spots that are worth identifying because they show relevant expression profiles. Furthermore, we show how to combine all spots that occur on any of the gels into one synthetic but nevertheless realistic‐looking image. This composite image is produced such that all spots have their standard positions. It can serve as a proteome reference map for an organism. As an application, we have computed a reference map from 23 gel images of Bacillus subtilis, using an enhanced prerelease version of the gel analysis software Delta2D (DECODON, Greifswald, Germany).
Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology
Authors: Steinberg Thomas H. , Agnew Brian J. , Gee Kyle R. , Leung Wai‐Yee , Goodman Terrie , Schulenberg Birte , Hendrickson Jill , Beechem Joseph M. , Haugland Richard P. , Patton Wayne F. 
Published: July 2003

AbstractSystematic parallel analysis of the phosphorylation status of networks of interacting proteins involved in the regulatory circuitry of cells and tissues is certain to drive research in the post‐genomics era for many years to come. Reversible protein phosphorylation plays a critical regulatory role in a multitude of cellular processes, including alterations in signal transduction pathways related to oncogene and tumor suppressor gene products in cancer. While fluorescence detection methods are likely to offer the best solution to global protein quantitation in proteomics, to date, there has been no satisfactory method for the specific and reversible fluorescent detection of gel‐separated phosphoproteins from complex samples. The newly developed Pro‐Q Diamond phosphoprotein dye technology is suitable for the fluorescent detection of phosphoserine‐, phosphothreonine‐, and phosphotyrosine‐containing proteins directly in sodium dodecyl sulfate (SDS)‐polyacrylamide gels and two‐dimensional (2‐D) gels. Additionally, the technology is appropriate for the determination of protein kinase and phosphatase substrate preference. Other macromolecules, such as DNA, RNA, and sulfated glycans, fail to be detected with Pro‐Q Diamond dye. The staining procedure is rapid, simple to perform, readily reversible and fully compatible with modern microchemical analysis procedures, such as matrix‐assisted laser desorption/ionization‐time of flight (MALDI‐TOF) mass spectrometry. Pro‐Q Diamond dye technology can detect as little as 1–2 ng of β‐casein, a pentaphosphorylated protein, and 8 ng of pepsin, a monophosphorylated protein. Fluorescence signal intensity correlates with the number of phosphorylated residues on the protein. Through combination of Pro‐Q Diamond phosphoprotein stain with SYPRO® Ruby protein gel stain, Multiplexed Proteomics technology permits quantitative, dichromatic fluorescence detection of proteins in 2‐D gels. This evolving discovery platform allows the parallel determination of protein expression level changes and altered post‐translational modification patterns within a single 2‐D gel experiment. The linear responses of the fluorescence dyes utilized, allow rigorous quantitation of changes over an unprecedented 500–1000‐fold concentration range.
Redox proteomics: Identification of oxidatively modified proteins
Authors: Ghezzi Pietro , Bonetto Valentina 
Published: July 2003

AbstractReactive oxygen and nitrogen species may cause various types of chemical modifications on specific proteins, Such modifications if irreversible are often associated with permanent loss of function and may lead to the elimination or to the accumulation of the damaged proteins. Reversible modifications, particularly at the cysteine residues, may have a dual role of protection from cysteine irreversible oxidation and modulation of protein function (redox regulation). Here we will review the techniques available for identifying proteins based on their redox state. In particular, we will focus on protein carbonylation, tyrosine nitration and thiol‐disulfide chemistry of cysteines, with special emphasis on glutathionylation, because these are the fields where the tools of proteome analysis have been applied.
Identification of proteins undergoing glutathionylation in oxidatively stressed hepatocytes and hepatoma cells
Authors: Fratelli Maddalena , Demol Hans , Puype Magda , Casagrande Simona , Villa Pia , Eberini Ivano , Vandekerckhove Joel , Gianazza Elisabetta , Ghezzi Pietro 
Published: July 2003

AbstractProtein glutathionylation is a post‐translational modification consisting of the formation of a mixed disulfide between protein cysteines and glutathione (GSH). To identify proteins undergoing glutathionylation in primary rat hepatocytes and in human HepG2 hepatoma cells, we radiolabeled the intracellular GSH pool with L‐[35S] cysteine. Cells were then exposed to oxidative stress. Proteins were separated by two‐dimensional gel electrophoresis under nonreducing conditions, and glutathionylated proteins were located by autoradiography and identified by mass spectrometry after tryptic digestion. Several proteins previously not known to undergo glutathionylation were thus recognized. Among the identified proteins some are the same or belong to the same functional class as those we have already identified in a previous paper on T cell blasts (actin, nucleophosmin, phosphogluconolactonase, myosin, profilin, cyclophilin A, stress 70 protein, ubiquitin in HepG2 cells and actin, peroxiredoxin 5, cytochrome C oxidase, heat shock cognate 70 in hepatocytes) while others are newly recognized (Ran specific GTPase activating protein, histidine triad nucleotide binding protein 2 in HepG2 cells and enoyl CoA hydratase in hepatocytes). The technique described proved equally applicable to a variety of cell types.