bluuebunny/crossref_metadata_2025_split huggingface dataset:
The significance of volcanic eruption strength and frequency for climate
Authors: Miles G. M. , Grainger R. G. , Highwood E. J. 
Published: November 2004

AbstractA simple physical model of the atmospheric effects of large explosive volcanic eruptions is developed. Using only one input parameter—the initial amount of sulphur dioxide injected into the stratosphere—the global‐average stratospheric optical‐depth perturbation and surface temperature response are modelled. The simplicity of this model avoids issues of incomplete data (applicable to more comprehensive models), making it a powerful and useful tool for atmospheric diagnostics of this climate forcing mechanism. It may also provide a computationally inexpensive and accurate way of introducing volcanic activity into larger climate models. The modelled surface temperature response for an initial sulphur‐dioxide injection, coupled with emission‐history statistics, is used to demonstrate that the most climatically significant volcanic eruptions are those of sufficient explosivity to just reach into the stratosphere (and achieve longevity). This study also highlights the fact that this measure of significance is highly sensitive to the representation of the climatic response and the frequency data used, and that we are far from producing a definitive history of explosive volcanism for at least the past 1000 years. Given this high degree of uncertainty, these results suggest that eruptions that release around and above 0.1 Mt SO2 into the stratosphere have the maximum climatic impact. Copyright © 2004 Royal Meteorological Society
Influence of styrene on grafting efficiency of maleic anhydride onto natural rubber
Authors: Saelao J. , Phinyocheep P. 
Published: November 2004

AbstractGrafting of maleic anhydride (MA) onto natural rubber (NR) has been investigated by using a radical initiated grafting process. NR was masticated to lower molecular weight than the original NR before treatment with 0.5–1.5% by mole of benzoyl peroxide (BPO) and 5–25% by mole of MA in toluene solution. Fourier transform infrared spectroscopy (FTIR) and titration method were used to analyze the fixation of MA on the NR. The reaction temperature was varied from 60 to 80°C. The % grafting of MA was higher at higher temperatures. Compared to the reaction without styrene, the addition of 0.1% by mole of styrene in the grafting process increased % MA grafting up to two times. It is postulated that the styrene may act as a charge transfer complex for the reaction of NR with MA. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 28–38, 2005
Chemical degradation of epoxidized natural rubber using periodic acid: Preparation of epoxidized liquid natural rubber
Authors: Phinyocheep P. , Phetphaisit C. W. , Derouet D. , Campistron I. , Brosse J. C. 
Published: November 2004

AbstractOxidative degradation of epoxidized natural rubber (ENR) was effectively performed in latex phase by using periodic acid at 30°C. The ENR was prepared from the epoxidation of natural rubber in latex phase using performic acid generated in situ by the reaction of hydrogen peroxide and formic acid. The prepared ENR latex was subsequently treated with periodic acid. It was found that the higher the amount of the periodic acid employed the faster the molecular weight of the ENR decreased. Different epoxidation levels of the ENR had no significant effect on the degradation reaction. Based on 1H NMR analysis, the epoxide content in the epoxidized liquid natural rubber (ELNR) obtained was about the same as that observed in the ENR before degradation. FT‐IR analysis showed an increase in carbonyl signal after prolonged reaction time or when higher amounts of periodic acid were employed. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 6–15, 2005
Significant glomerular basement membrane thickening in hyperglycemic and normoglycemic diabetic‐prone BB Wistar rats
Authors: Carlson Edward C. , Vari Richard C. , Audette Janice L. , Finke Michelle A. , Ressler Michael J. 
Published: November 2004

AbstractThe diabetic‐prone BioBreeding Wistar rat (BB/DP) is an autoimmune model of insulin‐dependent diabetes mellitus. Approximately 80–90% of the animals are hyperglycemic (BB/DPh) by 90–120 days of age while those that do not become diabetic in adolescence (BB/DPn) remain normoglycemic for life. Likewise, rats in the diabetes‐resistant (BB/DR) strain are normoglycemic. Although renal morphological studies have been carried out in this model, ultrastructural observations of age‐ and diabetes‐related extracellular matrix (ECM) changes, including glomerular basement membrane (GBM) morphometry, are not available. Moreover, possible renal changes in the relatively uncommon BB/DPn control animals have not been reported. The current electron microscopic study was carried out to investigate temporal changes in detergent‐treated acellular ECM in BB/DPh rats at 2 weeks, 3 months, 6 months, and 1 year postonset of moderate hyperglycemia. Age‐matched BB/DR and BB/DPn control animals were also examined. Our data demonstrate age‐ and diabetes‐related alterations in mesangial matrix distributions and GBM widths and show for the first time significant increases in GBM thickening in both hyperglycemic (BB/DPh) and normoglycemic (BB/DPn) rats when compared to age‐matched BB/DR controls. Surprisingly, the rate of increase is greatest in BB/DPn animals. Although the pathogenesis of diabetic basement membrane disease is not completely understood, GBM thickening is widely regarded as a morphological consequence of hyperglycemia. However, data in the current investigation show that ECM alterations, including significantly increased GBM thickness, may occur in genetically diabetic animals in the absence of hyperglycemia. © 2004 Wiley‐Liss, Inc.
Peptide‐chelating agent conjugate for selective targeting of somatostatin receptor type 1: Synthesis and characterization
Authors: Mansi Rosalba , Tesauro Diego , De Capua Antonia , Fattorusso Roberto , Caracò Corradina , Aloj Luigi , Benedetti Ettore , Morelli Giancarlo 
Published: November 2004

AbstractPreviously reported results suggest that the analogue of the somatostatin des‐AA1,2,5[D‐Trp8,IAmp9]‐somatostatin (CH‐275) peptide bearing chelating agents able to coordinate radioactive metals could be used for scintigraphic imaging of tumor lesions overexpressing sstr1. An efficient synthetic procedure for the preparation of the somatostatin analogue CH‐275 and its conjugate DTPAGlu–Gly–CH‐275, bearing the chelating agent DTPAGlu (DTPAGlu = N,N‐bis[2‐[bis(carboxy‐ethyl)amino]ethyl]‐L‐glutamic acid) on the N‐terminus, by solid‐phase peptide synthesis and 9‐flourenymethyoxycarbonyl (Fmoc) chemistry, is here reported. Rapid and efficient labeling of DTPAGlu–Gly–CH‐275 was achieved by addition of 111In(III) to the compound. Typical yields were greater than 97% as determined by reversed phase high performance liquid chromatography (HPLC) at specific activities in the range 4–9 GBq/μmol (100–250 Ci/mmol). A preliminary biological assay of the binding ability of 111In–DTPAGlu–Gly–CH‐275 indicates, however, that the labeled compound does not display any specific interaction with somatostatin sstr1 receptors in the tested cell lines. To confirm this unexpected negative result, competition binding experiments were carried out, in which fixed tracer amounts of the 125I‐labeled somatostatin‐14 were incubated with the receptor‐expressing cells in the presence of DTPAGlu–Gly–CH‐275 or CH‐275 at concentrations ranging from 10−10 to 10−3 M. While CH‐275 shows a IC50 of 80 nM similar to that already found in displacement experiments on CHO–K1 sstr1‐transfected cells, DTPAGlu–Gly–CH‐275 displays instead very low or negligible affinity towards this receptor. The NMR solution characterization indicates that the presence of DTPAGlu does not influence the conformational and chemical features of the peptide moiety, thus suggesting that the loss in binding activity should be due to steric hindrance of either the chelating agent DTPAGlu or its indium complex. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Influence of cytoplasmic deletions on the filopodia‐inducing effect of syndecan‐3
Authors: Berndt Christine , Montañez Eloi , Villena Joan , Fabre Myriam , Vilaró Senén , Reina Manuel 
Published: November 2004

AbstractSyndecans, transmembrane heparan sulfate proteoglycans (HSPG), mediate cell—cell and cell—matrix adhesion thereby controlling cell movement and shape. Syndecan cytoplasmic domains are very short (ca. 30 amino acids) and divided into two constant regions (C1 and C2) separated by one variable (V) region. Here we attempted to map the cytoplasmic region responsible for the filopodia‐inducing effect of syndecan‐3. We found that only the C1‐region was necessary for this effect. In addition, the deletion of the C2‐region led to extensive membrane blebbing. Nevertheless, the elimination of the entire cytoplasmic region did not affect delivery of syndecan‐3 to the plasma membrane. These results indicate that the different regions of syndecan‐3 cytoplasmic domain have different functions probably by binding to distinct proteins.
Neuropsychological assessment of chronic non‐malignant pain patients treated in a multidisciplinary pain centre
Authors: Sjøgren Per , Christrup Lona L. , Petersen Morten Aa. , Højsted Jette 
Published: November 2004

AbstractThe aim of the study was to investigate the influence of pain, sedation, pain medications and socio‐demographics on cognitive functioning in chronic non‐malignant pain patients. Chronic non‐malignant pain patients (N= 91) treated in a multidisciplinary pain centre were compared with age and sex matched healthy volunteers (N= 64). Furthermore four subgroups of patients were examined: Group 1 (N= 21) received no pain medications, group 2 (N= 19) were in long‐term oral opioid treatment, group 3 (N= 18) were treated with antidepressants and/or anticonvulsants and group 4 (N= 33) were treated with a combination of long‐term oral opioids and antidepressants and/or anticonvulsants. Assessments comprised pain (PVAS) and sedation (SVAS), Continuous Reaction Time (CRT) testing for sustained attention, Finger Tapping Test (FTT) testing for psychomotor speed, Paced Auditory Serial Addition Task (PASAT) testing for information processing and working memory and Mini Mental State Examination (MMSE). CRT and FTT were impaired in the total patient sample. Treatment with opioids was associated with poorer performance of PASAT. High scores of PVAS and SVAS were associated with poor performance of PASAT and CRT, respectively. MMSE seems to be too insensitive for detecting the milder forms of cognitive impairment found in chronic non‐malignant patients.
Feeding preferences of herring (Clupea harengus) and sprat (Sprattus sprattus) in the southern Baltic Sea
Authors: Casini Michele , Cardinale Massimiliano , Arrhenius Fredrik 
Published: November 2004

Abstract
No field studies have been performed on the selectivity of herring and sprat in the southern Baltic Sea in relation to their entire range of prey. Accordingly, we tested in the field the following hypotheses: (i) sprat and herring are selective feeders and (ii) sprat and herring selectivity is size- and season-dependent. The results show that (i) smaller herring and all size classes of sprat are strictly zooplanktivorous, selecting principally Temora longicornis and Bosmina maritima during the autumn and Pseudocalanus elongatus in winter; (ii) larger herring are essentially nektobenthos feeders, predating on Mysis mixta during the autumn and amphipods and polychaetes during the winter; and (iii) herring and sprat seem to avoid Acartia spp. in both autumn and winter. During the autumn, herring are zooplanktivorous up to 18–20 cm, whereas in winter herring feed on nektobenthos starting from 14–15 cm. Selectivity was not an absolute process but it was related to prey relative abundance in the sea and, possibly, to prey profitability (e.g. size, conspicuousness, and reaction time).
An alternative model of amino acid replacement
Authors: Crooks Gavin E. , Brenner Steven E. 
Published: November 2004

AbstractMotivation: The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment.Results: We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence–sequence, sequence–profile and profile–profile alignment.Contact: gec@compbio.berkeley.edu
GoArrays: highly dynamic and efficient microarray probe design
Authors: Rimour Sébastien , Hill David , Militon Cécile , Peyret Pierre 
Published: November 2004

AbstractMotivation: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex physicochemical constraints. Whereas there are more and more publicly available programs for microarray oligonucleotide design, most of them use the same algorithm or criteria to design oligos, with only little variation.Results: We show that classical approaches used in oligo design software may be inefficient under certain experimental conditions, especially when dealing with complex target mixtures. Indeed, our biological model is a human obligate parasite, the microsporidia Encephalitozoon cuniculi. Targets that are extracted from biological samples are composed of a mixture of pathogen transcripts and host cell transcripts. We propose a new approach to design oligonucleotides which combines good specificity with a potentially high sensitivity. This approach is original in the biological point of view as well as in the algorithmic point of view. We also present an experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos. A specific E.cuniculi microarray will overcome the difficulty to discriminate the parasite mRNAs from the host cell mRNAs demonstrating the power of the microarray approach to elucidate the lifestyle of an intracellular pathogen using mix mRNAs.Availability: Our method is implemented in the GoArrays software, available at http://www.isima.fr/bioinfo/goarrays/Contact: rimour@isima.fr for computing part, and pierre.peyret@univ-bpclermont.fr for collaborative projects.
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach
Authors: Sandelin Erik 
Published: November 2004

AbstractMotivation: Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting residue equivalences not all of which can be realized in the final MSTA. Hence to build a consistent MSTA, these methods have to select a conflict-free subset of equivalences.Results: Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.'s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997, Proc. 1st Ann. Int. Conf. Comput. Mol. Biol. (RECOMB-97), ACM Press, New York). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods. Given its speed and predictable complexity, our results show that T-Coffee is an attractive alternative for producing high-quality MSTAs.Availability: The software for Resolver, our implementation of Reinert et al.'s ILP formulation, and the dataset used in this study are available at http://www.sbc.su.se/~erik/resolverContact: erik@sbc.su.se
Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling
Authors: Liu Gang , Swihart Mark T. , Neelamegham Sriram 
Published: November 2004

Abstract
Motivation: Novel high-throughput genomic and proteomic tools are allowing the integration of information from a range of biological assays into a single conceptual framework. This framework is often described as a network of biochemical reactions. We present strategies for the analysis of such networks.
Results: The direct differential method is described for the systematic evaluation of scaled sensitivity coefficients in reaction networks. Principal component analysis, based on an eigenvalue–eigenvector analysis of the scaled sensitivity coefficient matrix, is applied to rank individual reactions in the network based on their effect on system output. When combined with flux analysis, sensitivity analysis allows model reduction or simplification. Using epidermal growth factor (EGF) mediated signaling and trafficking as an example of signal transduction, we demonstrate that sensitivity analysis quantitatively reveals the dependence of dual-phosphorylated extracellular signal-regulated kinase (ERK) concentration on individual reaction rate constants. It predicts that EGF mediated reactions proceed primarily via an Shc-dependent pathway. Further, it suggests that receptor internalization and endosomal signaling are important features regulating signal output only at low EGF dosages and at later times.
Contact: neel@eng.buffalo.edu
Supplemental data: http://www.eng.buffalo.edu/~neel/bio_reaction_network.html
OMGProm: a database of orthologous mammalian gene promoters
Authors: Palaniswamy Saranyan K. , Jin Victor X. , Sun Hao , Davuluri Ramana V. 
Published: November 2004

AbstractSummary: Sequence comparisons between human and rodents are increasingly being used for the identification of gene regulatory regions. The effectiveness of such an approach largely depends on the quality and availability of promoter sequences. We developed OMGProm by integrating three data sources: (1) experimentally supported full-length cDNA, promoter and first exon sequences; (2) homology information from HomoloGene and (3) the human and mouse genomic sequences. The current version of OMGProm contains 8550 promoter pairs of 6373 orthologous human and mouse genes, where supporting experimental evidence for transcription start site annotation exists in at least one species.Availability: OMGProm can be accessed from http://bioinformatics.med.ohio-state.edu/OMGPromContact: davuluri-1@medctr.osu.eduSupplementary information: Additional information on methods and implementation is available at http://bioinformatics.med.ohio-state.edu/OMGProm/si.jsp.
A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns
Authors: Gerth Victor E. , Vize Peter D. 
Published: November 2004

Abstract
Summary: The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.
Availability: Software is available on request from the authors and is free to academics.
Contact: pvize@ucalgary.ca
Supplementary information: Revisions and additional documentation to the Gene Expression Viewer are maintained at http://www.cbrbio.ucalgary.ca/3DModels and http://www.xenbase.org/3DModels. The idx3dIII Advanced Programming Interface is freely available for non-commercial use at http://www.idx3d.ch/
Protein homology detection by HMM–HMM comparison
Authors: Söding Johannes 
Published: November 2004

AbstractMotivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution.Results: We have generalized the alignment of protein sequences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach. The method (HHsearch) is benchmarked together with BLAST, PSI-BLAST, HMMER and the profile–profile comparison tools PROF_SIM and COMPASS, in an all-against-all comparison of a database of 3691 protein domains from SCOP 1.63 with pairwise sequence identities below 20%.Sensitivity: When the predicted secondary structure is included in the HMMs, HHsearch is able to detect between 2.7 and 4.2 times more homologs than PSI-BLAST or HMMER and between 1.44 and 1.9 times more than COMPASS or PROF_SIM for a rate of false positives of 10%. Approximately half of the improvement over the profile–profile comparison methods is attributable to the use of profile HMMs in place of simple profiles.Alignment quality: Higher sensitivity is mirrored by an increased alignment quality. HHsearch produced 1.2, 1.7 and 3.3 times more good alignments (‘balanced’ score &gt;0.3) than the next best method (COMPASS), and 1.6, 2.9 and 9.4 times more than PSI-BLAST, at the family, superfamily and fold level, respectively.Speed: HHsearch scans a query of 200 residues against 3691 domains in 33 s on an AMD64 2GHz PC. This is 10 times faster than PROF_SIM and 17 times faster than COMPASS.Availability: HHsearch can be downloaded from http://www.protevo.eb.tuebingen.mpg.de/download/ together with up-to-date versions of SCOP and PFAM. A web server is available at http://www.protevo.eb.tuebingen.mpg.de/toolkit/index.php?view=hhpredContact: johannes.soeding@tuebingen.mpg.de