bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute life threatening event (ALTE) in an infant with human coronavirus HCoV‐229E infection
Authors: Simon Arne , Völz Sebastian , Höfling Katja , Kehl Alexandra , Tillman Ramona , Müller Andreas , Kupfer Bernd , Eis‐Hübinger Anna‐Maria , Lentze Michael J. , Bode Udo , Schildgen Oliver 
Published: March 2007

AbstractIn this short report we discuss the temporal association between an acute life threatening event (ALTE) and a RT‐PCR confirmed coronavirus HCoV‐229E infection in a 4 months old otherwise healthy infant. More detailed microbiological investigations of affected children even without apparent signs of a respiratory tract infection may help to clarify the etiology in some patients and extend our understanding of the pathogenesis. PCR‐based techniques should be utilized to increase the sensitivity of detection for old and new respiratory viral pathogens in comparable cases. Pediatr Pulmonol. 2007; 42:393–396. © 2007 Wiley‐Liss, Inc.
The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis
Authors: Cho Eun‐Hee , Kim Mi‐Ryung , Kim Hyun‐Jung , Lee Do‐Yeon , Kim Pan‐Kyeom , Choi Kyung Mook , Ryu Ohk‐Hyun , Kim Chan‐Wha 
Published: March 2007

AbstractDiabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end‐stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2‐DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100–300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI‐Q‐TOF (ESI‐quadrupole‐TOF) MS. Among the identified proteins, vitamin D‐binding protein (DBP) and pigment epithelium‐derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.
Anticancer effects of aloe‐emodin on HepG2 cells: Cellular and proteomic studies
Authors: Lu Guo Dong , Shen Han‐Ming , Ong Choon Nam , Chung Maxey C. M. 
Published: March 2007

AbstractAloe‐emodin (AE) is one of the main bioactive anthraquinones of Rheum palmatum, a widely used herbal medicine. Several recent studies suggested that AE possesses potent anticancer properties, although the mechanisms are yet to be fully elucidated. The present study aimed to identify the molecular targets of AE in a human hepatocellular carcinoma cell line, HepG2. We first found that AE was more cytotoxic and effective in inducing apoptosis and cell cycle arrest than its analog emodin (EM). Proteomic study using 2‐D DIGE revealed that AE affected multiple proteins associated with oxidative stress, cell cycle arrest, antimetastasis, and hepatitis C virus replication. For example, peroxiredoxins (PRDX) and DJ‐1, both of which are redox‐sensitive proteins, were among those markedly up‐regulated, suggesting the presence of oxidative stress in AE‐treated cells. Further biochemical studies demonstrated that AE enhanced the intracellular level of reactive oxygen species and oxidation of PRDX‐2, ‐4, and DJ‐1. In addition, AE inhibited DNA synthesis via up‐regulation of the CDK4 inhibitor p16 and inhibition of Rb phosphorylation. Furthermore, AE was able to decrease cell migration via up‐regulation of the metastasis inhibitor, nm23. Taken together, AE induced anticancer effects in HepG2 cells via multiple pathways by affecting different protein targets.
Highlights of the first BSPR London Regional Meeting and Fifth Imperial Proteomics Day
Authors: Nagy Judit M. 
Published: March 2007

AbstractNow that the genomics revolution is tailing off proteomics promises an even more radical transformation of biological and medical research. Ultimately, the clues to the mysteries of biological processes will lye within the proteins present at a given time. Proteomics, the characterization of complex protein mixtures, builds on a wide range of expertise from protein chemistry to mass spectrometry and bioinformatics. Each step from sample preparation, high resolution protein separation to protein identification is underpinned by the latest technological developments in protein separation and mass spectrometry and supported by powerful computational image and data analysis algorithms which requires large scale data management and storage facilities. The success of proteomics depends on further developments in technology which need a wide range of scientific expertise. This meeting, the first BSPR London Regional Meeting, brought together scientists from a broad background who share a common interest in novel solutions for the characterization of complex protein mixtures.
Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain
Authors: Speranskiy Kirill , Cascio Michael , Kurnikova Maria 
Published: March 2007

AbstractWe present a homology based model of the ligand binding domain (LBD) of the homopentameric alpha1 glycine receptor (GlyR). The model is based on multiple sequence alignment with other members of the nicotinicoid ligand gated ion channel superfamily and two homologous acetylcholine binding proteins (AChBP) from the freshwater (Lymnaea stagnalis) and saltwater (Aplysia californica) snails with known high resolution structure. Using two template proteins with known structure to model three dimensional structure of a target protein is especially advantageous for sequences with low homology as in the case presented in this paper. The final model was cross‐validated by critical evaluation of experimental and published mutagenesis, functional and other biochemical studies. In addition, a complex structure with strychnine antagonist in the putative binding site is proposed based on docking simulation using Autodock program. Molecular dynamics (MD) simulations with simulated annealing protocol are reported on the proposed LBD of GlyR, which is stable in 5 ns simulation in water, as well as for a deformed LBD structure modeled on the corresponding domain determined in low‐resolution cryomicroscopy structure of the alpha subunit of the full‐length acetylcholine receptor (AChR). Our simulations demonstrate that the beta‐sandwich central core of the protein monomer is fairly rigid in the simulations and resistant to deformations in water. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain 7
Authors: Miyazono Ken‐ichi , Tsujimura Masanari , Kawarabayasi Yutaka , Tanokura Masaru 
Published: March 2007

AbstractMarR family proteins, MarR, MexR, and EmrR, are known as bacterial regulators for a phenotype resistant to multiple antibiotic drugs. Genomic data have indicated the presence of bacterial‐type transcriptional regulators, including MarR family proteins in archaea, though the archaeal transcription system is close to that of eukaryote. To elucidate the structural basis of the transcriptional regulation mechanism of archaeal MarR family proteins, the crystal structure of the ST1710 protein, which was identified as an archaeal EmrR homologue, StEmrR, from hyperthermophilic archaeon Sulfolobus tokodaii strain 7 was determined at 1.45‐Åresolution. The protein was composed of two N‐ and C‐terminal dimerization domains, and the DNA‐binding domain consisted of a winged helix motif, as in the case of bacterial MarR family proteins. Despite the relatively low overall structural similarity between StEmrR and bacterial MarR family proteins, the structure of the DNA‐binding domain displayed high structural similarity. A comparison with the crystal structures of bacterial MarR family proteins revealed that structural variation was mainly due to the different orientation of the two helices at the N‐ and C‐termini. Our results indicated that the distance between the two DNA‐binding domains of MarR family proteins would be changed by the rotation of the two terminal helices to interact with the target DNA. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Predicting protein domain interactions from coevolution of conserved regions
Authors: Kann Maricel G. , Jothi Raja , Cherukuri Praveen F. , Przytycka Teresa M. 
Published: March 2007

AbstractThe knowledge of protein and domain interactions provide crucial insights into their function within a cell. Several computational methods have been proposed to detect interactions between proteins and their constitutive domains. In this work, we focus on approaches based on correlated evolution (coevolution) of sequences of interacting proteins. In this type of approach, often referred to as the mirrortree method, a high correlation of evolutionary histories of two proteins is used as an indicator to predict protein interactions. Recently, it has been observed that subtracting the underlying speciation process by separating coevolution due to common speciation divergence from that due to common function of interacting pairs greatly improves the predictive power of the mirrortree approach. In this article, we investigate possible improvements and limitations of this method. In particular, we demonstrate that the performance of the mirrortree method that can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions). We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Comprehensive statistical analysis of residues interaction specificity at protein–protein interfaces
Authors: Anashkina Anastasya , Kuznetsov Eugene , Esipova Natalia , Tumanyan Vladimir 
Published: March 2007

AbstractWe calculated interchain contacts on the atomic level for nonredundant set of 4602 protein‐protein interfaces using an unbiased Voronoi‐Delaune tessellation method, and made 20×20 residue contact matrixes both for homodimers and heterocomplexes. The area of contacts and the distance distribution for these contacts were calculated on both the residue and the atomic levels. We analyzed residue area distribution and showed the existence of two types of interresidue contacts: stochastic and specific. We also derived formulas describing the distribution of contact area for stochastic and specific interactions in parametric form. Maximum pairing preference index was found for Cys‐Cys contacts and for oppositely charged interactions. A significant difference in residue contacts was observed between homodimers and heterocomplexes. Interfaces in homodimers were enriched with contacts between residues of the same type due to the effects of structure symmetry. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures
Authors: Ausili Alessio , Cobucci‐Ponzano Beatrice , Di Lauro Barbara , D'Avino Rossana , Perugino Giuseppe , Bertoli Enrico , Scirè Andrea , Rossi Mosè , Tanfani Fabio , Moracci Marco 
Published: March 2007

AbstractThe identification of the determinants of protein thermal stabilization is often pursued by comparing enzymes from hyperthermophiles with their mesophilic counterparts while direct structural comparisons among proteins and enzymes from hyperthermophiles are rather uncommon. Here, oligomeric β‐glycosidases from the hyperthermophilic archaea Sulfolobus solfataricus (Ssβ‐gly), Thermosphaera aggregans (Taβ‐gly), and Pyrococcus furiosus (Pfβ‐gly), have been compared. Studies of FTIR spectroscopy and kinetics of thermal inactivation showed that the three enzymes had similar secondary structure composition, but Ssβ‐gly and Taβ‐gly (temperatures of melting 98.1 and 98.4°C, respectively) were less stable than Pfβ‐gly, which maintained its secondary structure even at 99.5°C. The thermal denaturation of Pfβ‐gly, followed in the presence of SDS, suggested that this enzyme is stabilized by hydrophobic interactions. A detailed inspection of the 3D‐structures of these enzymes supported the experimental results: Ssβ‐gly and Taβ‐gly are stabilized by a combination of ion‐pairs networks and intrasubunit S‐S bridges while the increased stability of Pfβ‐gly resides in a more compact protein core. The different strategies of protein stabilization give experimental support to recent theories on thermophilic adaptation and suggest that different stabilization strategies could have been adopted among archaea. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Human DEAD‐box ATPase DDX3 shows a relaxed nucleoside substrate specificity
Authors: Franca Raffaella , Belfiore Amalia , Spadari Silvio , Maga Giovanni 
Published: March 2007

AbstractHuman DDX3 (hDDX3) is a DEAD‐box protein shown to possess RNA‐unwinding and adenosine triphosphatase (ATPase) activities. The hDDX3 protein has been implicated in nuclear mRNA export, cell growth control, and cancer progression. In addition, a role of this protein in the replication of human immunodeficiency virus Type 1 and in the pathogenesis of hepatitis C virus has been recently proposed. Its enzymological properties, however, are largely unknown. In this work, we characterized its ATPase activity. We show that hDDX3 ATPase activity is stimulated by various ribo‐ and deoxynucleic acids. Comparative analysis with different nucleoside triphosphate analogs showed that the hDDX3 ATPase couples high catalytic efficiency to a rather relaxed substrate specificity, both in terms of base selection and sugar selection. In addition, its ability to recognize the L‐stereoisomers of both 3′ deoxy‐ and 2′,3′ dideoxy‐ribose, points to a relaxed stereoselectivity. On the basis of these results, we hypothesize the presence of structural determinants on both the base and the sugar moieties, critical for nucleoside binding to the enzyme. Our results expand the knowledge about the DEAD‐box RNA helicases in general and can be used for rational design of selective inhibitors of hDDX3, to be tested as potential antitumor and antiviral agents. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Performance comparison of thermal insulated packaging boxes, bags and refrigerants for single‐parcel shipments
Authors: Singh S. P. , Burgess Gary , Singh Jay 
Published: March 2007

AbstractA range of packaging solutions exists for products that must be kept within a specific temperature range throughout the supply‐and‐distribution chain. This report summarizes the results of studies conducted over a span of 2 years by the Consortium for Distribution Packaging at Michigan State University. Thermal insulation packaging materials such as expanded polystyrene, polyurethane, corrugated fibreboard, ThermalCor® and other composite packaging such as thermal insulating bags were studied. Phase change materials such as gel packs were also evaluated. Properties such as R‐value, melting point and heat absorption were examined and are reported. Copyright © 2007 John Wiley & Sons, Ltd.
Nondestructive Mechanical Release of Ordered Polymer Microfiber Arrays from Porous Templates
Authors: Grimm Silko , Schwirn Kathrin , Göring Petra , Knoll Heiko , Miclea Paul T. , Greiner Andreas , Wendorff Joachim H. , Wehrspohn Ralf B. , Gösele Ulrich , Steinhart Martin 
Published: March 2007

AbstractThe fabrication of one‐dimensional (1D) nanostructures and microstructures inside the pores of porous templates is intensively investigated. The release of these structures is commonly accomplished by etching and destroying the templates. The 1D nanostructures and microstructures tend to condense because of the occurrence of capillary forces during drying of the specimens. It is shown that highly ordered arrays of polymer microfibers can be easily detached from silanized porous templates by mechanical lift‐off. This procedure leaves the templates intact, thus allowing their recycling, and does not involve the use of solutions or solvents, thus circumventing condensation. Therefore, mechanical lift‐off may enable the up‐scaling of template‐based approaches to the fabrication of highly ordered assemblies of 1D nanostructures and microstructures.
Performance of wavelet based Multi‐Chip Rate DS‐CDMA signals over multi‐path Nakagami‐mfading channels
Authors: Öztürk Ertan 
Published: March 2007

AbstractMulti‐Chip Rate/Direct Sequence‐Code Division Multiple Access (MCR/DS‐CDMA) technique using scaled chip waveforms has been designed as an alternative to multi‐data rate DS‐CDMA techniques having constant chip rates. In this work, the probability of error (Pe) expression for MCR/DS‐CDMA signals is derived over multi‐path Nakagami‐mfading channels to investigate the effects of chip waveforms on it. This paper also proposes the use of orthogonal wavelets as chip waveforms of MCR/DS‐CDMA signals over the considered channel. For numerical calculations, Daubechies‐22 (D22) wavelet is used because its side lobes are 40 dB below its main lobe in frequency domain. D22is compared with a Square Root Raised Cosine (SRRC) chip waveform. In the numerical calculations, only first four scales of the chip waveforms relating to four different chip/data rates are considered. The results for thePeperformance and the capacity (the number of user per Hertz for a samePelevel) show that D22significantly outperforms the SRRC chip waveform at all data rates, due to low cross correlations among different scales of orthogonal wavelets. Besides, by increasing the number of scales, the advantage of the use of orthogonal wavelets will increase furthermore. Copyright © 2007 John Wiley & Sons, Ltd.
Engineering Oilseed Plants for a Sustainable, Land‐Based Source of Long Chain Polyunsaturated Fatty Acids
Authors: Damude Howard G. , Kinney Anthony J. 
Published: March 2007

AbstractNumerous clinical studies have demonstrated the cardiovascular and mental health benefits of including very long chain omega‐3 polyunsaturated fatty acids, namely eicospentaenoic acid (EPA) and docosohexaenoic acid (DHA) in the human diet. Certain fish oils can be a rich source of omega‐3 long chain polyunsaturated fatty acids although processed marine oils are generally undesirable as food ingredients because of the associated objectionable flavors and contaminants that are difficult and cost‐prohibitive to remove. Oilseed plants rich in omega‐3 fatty acids, such as flax and walnut oils, contain only the 18‐carbon omega‐3 polyunsaturated fatty acid alpha‐linolenic acid, which is poorly converted by the human body to EPA and DHA. It is now possible to engineer common omega‐6 rich oilseeds such as soybean and canola to produce EPA and DHA and this has been the focus of a number of academic and industrial research groups. Recent advances and future prospects in the production of EPA and DHA in oilseed crops are discussed here.
Effects of maternal hyperhomocysteinemia induced by high methionine diet on the learning and memory performance in offspring
Authors: Baydas Giyasettin , Koz Sema T. , Tuzcu Mehmet , Nedzvetsky Victor S. , Etem Ebru 
Published: March 2007

AbstractIn this study, we suggest that chronic maternal hyperhomocysteinemia results in learning deficits in the offspring due to delayed brain maturation and altered expression pattern of neural cell adhesion molecule. Although the deleterious effects of hyperhomocysteinemia were extensively investigated in the adults, there is no clear evidence suggesting its action on the developing fetal rat brain and cognitive functions of the offspring. Therefore, in the present work we aimed to investigate effects of maternal hyperhomocysteinemia on the fetal brain development and on the behavior of the offspring. A group of pregnant rats received daily methionine (1 g/kg body weight) dissolved in drinking water to induce maternal hyperhomocysteinemia, starting in the beginning of gestational day 0. The levels of glial fibrillary acidic protein, S100B protein, and neural cell adhesion molecule were determined in the tissue samples from the pups. Learning and memory performances of the young‐adult offsprings were tested using Morris water maze test. There were significant reductions in the expressions of glial fibrillary acidic protein and S100B protein in the brains of maternally hyperhomocysteinemic pups on postnatal day 1, suggesting that hyperhomocysteinemia delays brain maturation. In conclusion, maternal hyperhomocysteinemia changes the expression pattern of neural cell adhesion molecule and therefore leads to an impairment in the learning performance of the offspring.
Monitoring process quality in off‐shore outsourcing: A model and findings from multi‐country survey
Authors: Aron Ravi , Bandyopadhyay Subhajyoti , Jayanty Siddharth , Pathak Praveen 
Published: March 2007

AbstractWe investigate how recent advances in information technology and telecommunications have led to real‐time monitoring of processes at the site of the provider by a buyer located across the globe. We construct a game‐theoretic model of the dynamics of the buyer–supplier interaction in the presence of moral hazard and incomplete contracting. We derive the Minimum Quality Threshold (MQT) below which the provider's output will certainly be inspected. Our findings show that the buyer can pick a level of monitoring and thereby force the provider to exceed the quality level of the MQT in output quality and avoid costly and wasteful inspection. Finally, our model explains why the production of processes that are complex and more prone to errors are actually monitored less by the buyers. We furnish the results of a comprehensive, multi‐year, multi‐country survey of the efficacy of monitoring in off‐shore outsourcing projects and demonstrate strong empirical support for the findings of the model.
Effect ofPlasmodium yoelii nigeriensisinfection on hepatic and splenic glutathione-S-transferase(s) in Swiss albino and db/+ mice: efficacy of mefloquine and menadione in antimalarial chemotherapy
Authors: AHMAD R. , SRIVASTAVA A. K. 
Published: March 2007

SUMMARYThe present report deals with the status of hepatic and splenic glutathione-S-transferase (GST) activities in mice during experimental infection withPlasmodium yoelii nigeriensisand subsequent treatment of infected mice with mefloquine (Mf) and menadione (Md). The infection caused significant decline in the hepatic and splenic glutathione-S-transferase (GST) activities of albino and db/+ mice. The decline was observed in the levels of both cytosolic and microsomal GST(s) of liver and spleen in both types of mice. Intraperitoneal administration of mefloquine at a dose of 5 mg/kg and menadione at a dose of 100 mg/kg, twice daily from day 1 p.i. (day 0) until day 10, caused restoration in the levels of hepatic as well as splenic GST(s), albeit to varying degrees. Mf was able to suppress parasitaemia by day 5 in the case of albino mice and by day 3 in the case of db/+ mice but was unable to cure both types of mice completely. On the other hand, Md caused a delay in maturation of infection in both cases, but could not cure the mice.