bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response ofNeobenedenia girellae(Monogenea) oncomiracidia to brightness and black-and-white contrast
Authors: ISHIDA M. , KAWANO F. , UMEDA N. , HIRAZAWA N. 
Published: June 2007

SUMMARYNeobenedenia girellae, a capsalid monogenean, is a significant pathogen due to both its ability to cause high mortality in fishes and its low host specificity. Established control methods have both advantages and disadvantages. Biological control measures with no unfavourable effects on the environment should be incorporated into the control strategy. The response ofN. girellaeoncomiracidia to brightness and black-and-white contrast was investigated to search for an alternative approach of disease prevention or control. Japanese flounder,Paralichthys olivaceus(Paralichthyidae), were exposed to oncomiracidia in an aquarium divided into areas of different brightness (∼1·3, 41·3 and 138·0 lux). The number of parasites on the fish group reared in 138·0 lux was significantly higher than on those reared in the lower brightness levels. Thus, the fish tended to be more vulnerable to infection byN. girellaeunder brighter conditions. Challenge trials using host fish mucus and whole live fish were established to detect the response by oncomiracidia to black-and-white contrast on a whiteversusa black background. Markedly moreN. girellaeoncomiracidia attached to black-painted areas and dark-coloured fish (normal spotted halibut,Verasper variegatus(Pleuronectidae) compared with white-painted areas and light-coloured fish (mal-colouredV. variegatus) on a white-coloured background. On a black-coloured background, moreN. girellaeoncomiracidia tended to attach to white-painted areas and light-coloured fish. Thus, black-and-white contrast is considered important for host finding byN. girellaeoncomiracidia. The simplicity of the positive phototactic behaviour and the response to black-and-white contrast may lead to the development of a simple, practical and inexpensive method to controlN. girellaeoutbreaks.
Knowledge of whelk dyes and pigments in Anglo-Saxon England
Authors: Biggam C. P. 
Published: June 2007

AbstractThis article aims to evaluate the likelihood that whelk dye was known in Anglo-Saxon England, either in the form of imported cloth and textile products, and/or as an activity carried out in England. The nature of whelk dye and the likely processing options available to early societies are considered in the light of extant records and modern experimentation in Israel and Britain. The currently available ‘hard’ evidence is then presented from archaeology, manuscript studies, and the chemical analysis of textiles. Finally, the semantic and literary evidence is considered, including three passages from texts by Bede and Aldhelm, and a new interpretation of OE cornwurma.
Æthelthryth of Ely in a lost calendar from Munich
Authors: Gretsch Mechthild 
Published: June 2007

AbstractA fragment of a calendar, written s. viii2/4, either in England or in an Anglo-Saxon centre on the Continent was preserved in Munich until 1939, but was subsequently lost. While still extant, the fragment had been printed, and from this edition it can be seen that, in addition to universally culted saints, the entries included the obits of five Anglo-Saxons, Æthelthryth among them. After a brief review of how the commemorations of the universal saints relate to the earliest manuscripts of the Martyrologium Hieronymianum and to Bede's Martyrology, the article focuses on the English obits, in particular on the question of what light may be shed on the origin and first ambience of the calendar by its commemoration of Æthelthryth and by the form in which her obit there appears.
A Welsh record of an Anglo-Saxon political mutilation
Authors: Boyle Elizabeth 
Published: June 2007

AbstractA previously unidentified annal-entry in the Welsh chronicles Brut y Tywysogion and Brenhinedd y Saesson records the blinding of the sons of Ealdorman Ælfhelm as part of the ‘palace revolution’ of 1006. This article discusses how the Old English names Wulfheah and Ufegeat were recorded by Welsh scribes in accordance with Welsh phonological and orthographical norms. Possible Anglo-Saxon sources for the annal-entry are briefly considered and the transmission of the annal-entry in the Welsh sources is analysed.
Glacio-lacustrine aragonite deposition, meltwater evolution and glacial history during isotope stage 3 at Radok Lake, Amery Oasis, northern Prince Charles Mountains, East Antarctica
Authors: Goodwin Ian D. , Hellstrom John 
Published: June 2007

AbstractThe late Quaternary glacial history of the Amery Oasis, and Prince Charles Mountains is of significant interest because about 10% of the total modern Antarctic ice outflow is discharged via the adjacent Lambert Glacier system. A glacial thrust moraine sequence deposited along the northern shoreline of Radok Lake between 20–10 ka bp, overlies a layer of thin, aragonite crusts which provide important constraints on the glacial history of the Amery Oasis. The modern Radok Lake is fed by the terminal meltwaters of the alpine Battye Glacier. The aragonite crusts were deposited in shallow water of ancestral Radok Lake 53 ka bp, during the A3 warm event in Isotope Stage 3. Oxygen isotope (δ18O) analysis of the last glacial-age aragonite crusts indicates that they precipitated from freshwater with a δ18OSMOW composition of -36%, which is 8% more depleted than the present water (-28%) in Radok Lake. A regional oxygen isotope (δ18O) and elevation relationship for snow is used to determine the source of meltwater and glacial ice in Radok Lake during the A3 warm event. This relationship indicates that Radok Lake received meltwater from the confluence of both Battye Glacier ice and an expansion of grounded western Lambert Glacier ice in the Amery embayment.
Early Palaeozoic intracratonic shears and post-tectonic cooling in the Rauer Group, Prydz Bay, East Antarctica constrained by40Ar/39Ar thermochronology
Authors: Wilson Christopher J.L. , Quinn Cameron , Tong Laixi , Phillips David 
Published: June 2007

AbstractThe Rauer Group, in Prydz Bay, contains reworked Archaean-Proterozoic crust in high-strain zones that formed during a pervasive high-temperature ductile deformation event related to intracratonic mechanisms. The effects of this event extend southwards from Prydz Bay into the southern Prince Charles Mountains. The associated structural evolution involved development of ductile and brittle structures that formed during an approximately north–south directed transpressional deformation event that is confined to high-grade (>800°C) shear zones in the Rauer Group. Minerals from the Rauer Group, yield40Ar/39Ar cooling ages ranging from 560 to 460 Ma. Thermal histories derived from hornblende, biotite and feldspar suggest that the onset of rapid cooling began sometime prior to 510 Ma with cooling rates ofc. 42 to 33°C myr-1fromc. 510 Ma toc. 500 Ma. Whereas,40Ar/39Ar data obtained from plagioclase and K–feldspar suggest a slower cooling fromc. 500 Ma toc. 460 Ma with cooling rates from 5 to 2°C myr-1. These results demonstrate that the early Palaeozoic cooling history and comparable palaeostress regimes are regionally extensive, which has important implications for the tectonothermal and stress-field variability across Gondwana. The elevated thermal conditions would induce lithospheric weakening and promote the early Palaeozoic intraplate orogeny observed in eastern Antarctica with the development of a large intracratonic shear system.
Structure and ligand-binding site characteristics of the human P2Y11 nucleotide receptor deduced from computational modelling and mutational analysis
Authors: Zylberg Jacques , Ecke Denise , Fischer Bilha , Reiser Georg 
Published: June 2007

The P2Y11-R (P2Y11 receptor) is a less explored drug target. We computed an hP2Y11-R (human P2Y11) homology model with two templates, bovine-rhodopsin (2.6 Å resolution; 1 Å=0.1 nm) and a hP2Y1–ATP complex model. The hP2Y11-R model was refined using molecular dynamics calculations and validated by virtual screening methods, with an enrichment factor of 5. Furthermore, mutational analyses of Arg106, Glu186, Arg268, Arg307 and Ala313 confirmed the adequacy of our hP2Y11-R model and the computed ligand recognition mode. The E186A and R268A mutants reduced the potency of ATP by one and three orders of magnitude respectively. The R106A and R307A mutants were functionally inactive. We propose that residues Arg106, Arg268, Arg307 and Glu186 are involved in ionic interactions with the phosphate moiety of ATP. Arg307 is possibly also H-bonded to N6 of ATP via the backbone carbonyl. Activity of ATP at the F109I mutant revealed that the proposed π-stacking of Phe109 with the adenine ring is a minor interaction. The mutation A313N, which is part of a hydrophobic pocket in the vicinity of the ATP C-2 position, partially explains the high activity of 2-MeS-ATP at P2Y1-R as compared with the negligible activity at the P2Y11-R. Inactivity of ATP at the Y261A mutant implies that Tyr261 acts as a molecular switch, as in other G-protein-coupled receptors. Moreover, analysis of cAMP responses seen with the mutants showed that the efficacy of coupling of the P2Y11-R with Gs is more variable than coupling with Gq. Our model also indicates that Ser206 forms an H-bond with Pγ (the γ-phosphate of the triphosphate chain of ATP) and Met310 interacts with the adenine moiety.
A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane
Authors: Dufe Veronica T. , Ingner Daniel , Heby Olle , Khomutov Alex R. , Persson Lo , Al-Karadaghi Salam 
Published: June 2007

The critical role of polyamines in key processes such as cell growth, differentiation and macromolecular synthesis makes the enzymes involved in their synthesis potential targets in the treatment of certain types of cancer and parasitic diseases. Here we present a study on the inhibition of human and Leishmania donovani ODC (ornithine decarboxylase), the first committed enzyme in the polyamine biosynthesis pathway, by APA (1-amino-oxy-3-aminopropane). The present study shows APA to be a potent inhibitor of both human and L. donovani ODC with a Ki value of around 1.0 nM. We also show that L. donovani ODC binds the substrate, the co-enzyme pyridoxal 5′-phosphate and the irreversible inhibitor α-difluoromethylornithine (a curative agent of West African sleeping sickness) with less affinity than human ODC. We have also determined the three-dimensional structure of human ODC in complex with APA, which revealed the mode of the inhibitor binding to the enzyme. In contrast with earlier reports, the structure showed no indication of oxime formation between APA and PLP (pyridoxal 5′-phosphate). Homology modelling suggests a similar mode of binding of APA to L. donovani ODC. A comparison of the ODC–APA–PLP structure with earlier ODC structures also shows that the protease-sensitive loop (residues 158–168) undergoes a large conformational change and covers the active site of the protein. The understanding of the structural mode of APA binding may constitute the basis for the development of more specific inhibitors of L. donovani ODC.
Transcriptional regulation of the distal promoter of the rat pyruvate carboxylase gene by hepatocyte nuclear factor 3β/Foxa2 and upstream stimulatory factors in insulinoma cells
Authors: Boonsaen Thirajit , Rojvirat Pinnara , Surinya Kathy H. , Wallace John C. , Jitrapakdee Sarawut 
Published: June 2007

PC (pyruvate carboxylase) plays a crucial role in intermediary metabolism including glucose-induced insulin secretion in pancreatic islets. In the present study, we identified two regions of the 1.2 kb distal promoter, the −803/−795 site and the −408/−403 E-box upstream of the transcription start site, as the important cis-acting elements for transcriptional activation of the luciferase reporter gene. Site-directed mutagenesis of either one of these sites in the context of this 1.2 kb promoter fragment, followed by transient transfections in the insulinoma cell line, INS-1, abolished reporter activity by approx. 50%. However, disruption of either the −803/−795 or the −408/−403 site did not affect reporter gene activity in NIH 3T3 cells, suggesting that this promoter fragment is subjected to cell-specific regulation. The nuclear proteins that bound to these −803/−795 and −408/−403 sites were identified by gel retardation assays as HNF3β (hepatocyte nuclear factor 3β)/Foxa2 (forkhead/winged helix transcription factor box2) and USFs (upstream stimulatory factors), USF1 and USF2, respectively. Chromatin immunoprecipitation assays using antisera against HNF3β/Foxa2, USF1 and USF2 demonstrated that endogenous HNF3β/Foxa2 binds to the −803/−795 Foxa2 site, and USF1 and USF2 bind to the −408/−403 E-box respectively in vivo, consistent with the gel retardation assay results. Although there are weak binding sites located at regions −904 and −572 for PDX1 (pancreatic duodenal homeobox-1), a transcription factor that controls expression of β-cell-specific genes, it did not appear to regulate PC expression in INS-1 cells in the context of the 1.2 kb promoter fragment. The results presented here show that Foxa2 and USFs regulate the distal promoter of the rat PC gene in a cell-specific manner.
Prediction of Ras-effector interactions using position energy matrices
Authors: Kiel Christina , Serrano Luis 
Published: June 2007

AbstractMotivation: One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein–protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences.Results: Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types.Availability: All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/).Contact: christina.kiel@crg.esSupplementary information: Supplementary data are available at Bioinformatics online.
Improving gene quantification by adjustable spot-image restoration
Authors: Daskalakis Antonis , Cavouras Dionisis , Bougioukos Panagiotis , Kostopoulos Spiros , Glotsos Dimitris , Kalatzis Ioannis , Kagadis George C. , Argyropoulos Christos , Nikiforidis George 
Published: June 2007

AbstractMotivation: One of the major factors that complicate the task of microarray image analysis is that microarray images are distorted by various types of noise. In this study a robust framework is proposed, designed to take into account the effect of noise in microarray images in order to assist the demanding task of microarray image analysis. The proposed framework, incorporates in the microarray image processing pipeline a novel combination of spot adjustable image analysis and processing techniques and consists of the following stages: (1) gridding for facilitating spot identification, (2) clustering (unsupervised discrimination between spot and background pixels) applied to spot image for automatic local noise assessment, (3) modeling of local image restoration process for spot image conditioning (adjustable wiener restoration using an empirically determined degradation function), (4) automatic spot segmentation employing seeded-region-growing, (5) intensity extraction and (6) assessment of the reproducibility (real data) and the validity (simulated data) of the extracted gene expression levels.Results: Both simulated and real microarray images were employed in order to assess the performance of the proposed framework against well-established methods implemented in publicly available software packages (Scanalyze and SPOT). Regarding simulated images, the novel combination of techniques, introduced in the proposed framework, rendered the detection of spot areas and the extraction of spot intensities more accurate. Furthermore, on real images the proposed framework proved of better stability across replicates. Results indicate that the proposed framework improves spots’ segmentation and, consequently, quantification of gene expression levels.Availability: All algorithms were implemented in Matlab™ (The Mathworks, Inc., Natick, MA, USA) environment. The codes that implement microarray gridding, adaptive spot restoration and segmentation/intensity extraction are available upon request. Supplementary results and the simulated microarray images used in this study are available for download from: ftp://users:bioinformatics@mipa.med.upatras.grContact: daskalakis@med.upatras.grSupplementary information: Supplementary data are available at Bioinformatics online.
Genomic mutation consequence calculator
Authors: Major John E. 
Published: June 2007

AbstractSummary: The genomic mutation consequence calculator (GMCC) is a tool that will reliably and quickly calculate the consequence of arbitrary genomic mutations. GMCC also reports supporting annotations for the specified genomic region. The particular strength of the GMCC is it works in genomic space, not simply in spliced transcript space as some similar tools do. Within gene features, GMCC can report on the effects on splice site, UTR and coding regions in all isoforms affected by the mutation. A considerable number of genomic annotations are also reported, including: genomic conservation score, known SNPs, COSMIC mutations, disease associations and others. The manual interface also offers link outs to various external databases and resources. In batch mode, GMCC returns a csv file which can easily be parsed by the end user.Audience: GMCC is intended to support the many tumor resequencing efforts, but can be useful to any study investigating genomic mutations.Availability: GMCC is freely available via a web portal with a manual mode and a batch query mode. It may be found at this URL: http://cbio.mskcc.org/gmccContact: majorj@mskcc.orgSupplementary information: A FAQ and examples can be found at the URL above.
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
Authors: Buness Andreas , Kuner Ruprecht , Ruschhaupt Markus , Poustka Annemarie , Sültmann Holger , Tresch Achim 
Published: June 2007

AbstractMotivation: In cancer, chromosomal imbalances like amplifications and deletions, or changes in epigenetic mechanisms like DNA methylation influence the transcriptional activity. These alterations are often not limited to a single gene but affect several genes of the genomic region and may be relevant for the disease status. For example, the ERBB2 amplicon (17q21) in breast cancer is associated with poor patient prognosis. We present a general, unsupervised method for genome-wide gene expression data to systematically detect tumor patients with chromosomal regions of distinct transcriptional activity. The method aims to find expression patterns of adjacent genes with a consistently decreased or increased level of gene expression in tumor samples. Such patterns have been found to be associated with chromosomal aberrations and clinical parameters like tumor grading and thus can be useful for risk stratification or therapy.Results: Our approach was applied to 12 independent human breast cancer microarray studies comprising 1422 tumor samples. We prioritized chromosomal regions and genes predominantly found across all studies. The result highlighted not only regions which are well known to be amplified like 17q21 and 11q13, but also others like 8q24 (distal to MYC) and 17q24-q25 which may harbor novel putative oncogenes. Since our approach can be applied to any microarray study it may become a valuable tool for the exploration of transcriptional changes in diverse disease types.Availability: The R source codes which implement the method and an exemplary analysis are available at http://www.dkfz.de/mga2/people/buness/CTP/.Contact: a.buness@gmx.deSupplementary information: Supplementary data are available at Bioinformatics online.
ChemDB update—full-text search and virtual chemical space
Authors: Chen Jonathan H. , Linstead Erik , Swamidass S. Joshua , Wang Dennis , Baldi Pierre 
Published: June 2007

AbstractChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB.Availability: ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu.Contact: pfbaldi@ics.uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments
Authors: Kim Namshin , Lee Christopher 
Published: June 2007

AbstractSummary: We have developed a quick web-based application for designing conserved genomic PCR and RT-PCR primers from multigenome alignments targeting specific exons or introns. We used Pygr (The Python Graph Database Framework for Bioinformatics) to query intervals from multigenome alignments, which gives us less than a millisecond access to any intervals of any genome within multigenome alignments. PRIMER3 was used to extract optimal primers from a gene of interest. QPRIMER creates an electronic genomic PCR image from a set of conserved primers as well as summary pages for primer alignments and products. QPRIMER supports human, mouse, rat, chicken, dog, zebrafish and fruit fly.Availability: http://www.bioinformatics.ucla.edu/QPRIMER/Contact: leec@mbi.ucla.edu