bluuebunny/crossref_metadata_2025_split huggingface dataset:
RPA repair recognition of DNA containing pyrimidines bearing bulky adducts
Authors: Petruseva Irina O. , Tikhanovich Irina S. , Chelobanov Boris P. , Lavrik Olga I. 
Published: April 2008

AbstractRecognition of new DNA nucleotide excision repair (NER) substrate analogs, 48‐mer ddsDNA (damaged double‐stranded DNA), by human replication protein A (hRPA) has been analyzed using fluorescence spectroscopy and photoaffinity modification. The aim of the present work was to find quantitative characteristics of RPA–ddsDNA interaction and RPA subunits role in this process. The designed DNA structures bear bulky substituted pyrimidine nitrogen bases at the inner positions of duplex forming DNA chains. The photoreactive 4‐azido‐2,5‐difluoro‐3‐ pyridin‐6‐yl (FAP) and fluorescent antracenyl, pyrenyl (Antr, Pyr) groups were introduced via different linker fragments into exo‐4N of deoxycytidine or 5C of deoxyuridine. J‐dU‐containing DNA was used as a photoactive model of undamaged DNA strands. The reporter group was a fluorescein residue, introduced into the 5′‐phosphate end of one duplex‐forming DNA strand. RPA–dsDNA association constants and the molar RPA/dsDNA ratio have been calculated based on fluorescence anisotropy measurements under conditions of a 1:1 RPA/dsDNA molar ratio in complexes. The evident preference for RPA binding to ddsDNA over undamaged dsDNA distinctly depends on the adduct type and varies in the following way: undamaged dsDNA < Antr‐dC‐ddsDNA < mmdsDNA < FAPdU‐, Pyr‐dU‐ddsDNA < FAP‐dC‐ddsDNA (KD = 68 ± 1; 25 ± 6; 13 ± 1; 8 ± 2, and 3.5 ± 0.5 nM correspondingly) but weakly depends on the chain integrity. Interestingly the bulkier lesions not in all cases have a greater effect on RPA affinity to ddsDNA. The experiments on photoaffinity modification demonstrated only p70 of compactly arranged RPA directly interacting with dsDNA. The formation of RPA–ddsDNA covalent adducts was drastically reduced when both strands of DNA duplex contained virtually opposite located FAP‐dC and Antr‐dC. Thus RPA requires undamaged DNA strand presence for the effective interaction with dsDNA bearing bulky damages and demonstrates the early NER factors characteristic features underlying strand discrimination capacity and poor activity of the NER system toward double damaged DNA. Copyright © 2008 John Wiley & Sons, Ltd.
Characterization of 111In and 177Lu‐labeled antibodies binding to CD44v6 using a novel automated radioimmunoassay
Authors: Nestor Marika , Andersson Karl , Lundqvist Hans 
Published: April 2008

AbstractTargeted cancer therapies rely on bifunctional molecules, typically a protein that specifically recognizes tumor cells and a toxic component which is linked to the protein. Therefore, development of such therapies includes detailed characterizations of protein‐cell interactions in order to find a good targeting agent. Knowledge of factors such as antibody‐antigen specificity, as well as cellular uptake, retention and affinity of the antibody are necessary in order to be successful.In this paper, we have used a novel instrument, LigandTracer® Yellow, to characterize the interactions of 111In and 177Lu‐labeled monoclonal antibodies (MAbs) with CD44v6. Uptake studies with varying specific radioactivity of the chimeric MAb U36 and with an irrelevant antibody for the CD44v6 receptor verified the reliability of the method, as well as the specificity of the antibody‐receptor binding. Uptake, retention, and affinity were very similar for the 111In and 177Lu‐labeled conjugate, and were in line with earlier studies using manual methods. The fact that no adverse effects from labeling were seen, together with the high retention, could make these conjugates promising candidates for imaging and therapy of certain cancer types in the future. The novel LigandTracer technology reduced the workload and reagent spending while providing data with superior time resolution. The obtained results were in agreement with previously reported findings. In addition the real‐time detection and higher time resolution made more detailed studies of the interactions possible. Copyright © 2008 John Wiley & Sons, Ltd.
Utility of formaldehyde cross‐linking and mass spectrometry in the study of protein–protein interactions
Authors: Sutherland Brent W. , Toews Judy , Kast Juergen 
Published: April 2008

AbstractFor decades, formaldehyde has been routinely used to cross‐link proteins in cells, tissue, and in some instances, even entire organisms. Due to its small size, formaldehyde can readily permeate cell walls and membranes, resulting in efficient cross‐linking, i.e. the formation of covalent bonds between proteins, DNA, and other reactive molecules. Indeed, formaldehyde cross‐linking is an instrumental component of many mainstream analytical/cell biology techniques including chromatin immunoprecipitation (ChIP) of protein‐DNA complexes found in nuclei; immunohistological analysis of protein expression and localization within cells, tissues, and organs; and mass spectrometry (MS)‐compatible silver‐staining methodologies used to visualize low abundance proteins in polyacrylamide gels. However, despite its exquisite suitability for use in the analysis of protein environments within cells, formaldehyde has yet to be commonly employed in the directed analysis of protein–protein interactions and cellular networks. The general purpose of this article is to discuss recent advancements in the use of formaldehyde cross‐linking in combination with MS‐based methodologies. Key advantages and limitations to the use of formaldehyde over other cross‐linkers and technologies currently used to study protein–protein interactions are highlighted, and formaldehyde‐based experimental approaches that are proving very promising in their ability to accurately and efficiently identify novel protein–protein and multiprotein interaction complexes are presented. Copyright © 2008 John Wiley & Sons, Ltd.
In vivoevaluation andin vitrometabolism of leuprolide in mice—mass spectrometry‐based biomarker measurement for efficacy and toxicity
Authors: Sofianos Zacharias D. , Katsila Theodora , Kostomitsopoulos Nikolaos , Balafas Vaggelis , Matsoukas John , Tselios Theodoros , Tamvakopoulos Constantin 
Published: April 2008

AbstractThe study of pharmacologically active peptides is central for the understanding of cancer and the development of novel therapeutic approaches. In this context, both qualitative and quantitative determination of bioactive peptides in biological fluids/tissues and their effect on endogenous factors (e.g. hormones) are of great importance. A mass spectrometry‐based approach was developed and applied towards the measurement of leuprolide, a peptide drug for the treatment of prostate cancer, in mouse plasma. High‐pressure liquid chromatography coupled to a hybrid quadrupole linear ion trap (QqLIT) mass spectrometer, a platform that combines the benefits of triple QqLIT instruments, was employed for the study. Using the described methodology, we established that picomolar concentrations of leuprolide could be measured in mouse plasma (limit of quantification of 0.1 ng/ml). In order to optimize pharmacokinetic properties of analogs of leuprolide, a facilein vivomouse model was developed and leuprolide concentrations were determined in mouse plasma following intraperitoneal administration. In the same animal model, we demonstrated the versatility of the described MS‐based approach by the determination of plasma concentrations of testosterone, an established biomarker for the treatment of prostate cancer. Following dosing with leuprolide, circulating testosterone was increased significantly in comparison to vehicle‐treated mice. Finally,in vitrometabolism of leuprolide was evaluated by incubation of leuprolide with mouse kidney membranes, followed by identification of major metabolites by MS. Such studies provide the framework for future evaluation of novel leuprolide analogs with potential therapeutic advantages. Copyright © 2008 John Wiley & Sons, Ltd.
Unravelling contamination signals in biogenic silica oxygen isotope composition: the role of major and trace element geochemistry
Authors: Brewer Tim S. , Leng Melanie J. , Mackay Anson W. , Lamb Angela L. , Tyler Jonathan J. , Marsh Nicholas G. 
Published: April 2008

AbstractThe oxygen isotope composition of diatom silica (δ
18Odiatom) provides valuable information for palaeoclimate studies where carbonate proxies are either rare or absent in many lakes and ocean sediments. Unfortunately, mineral and rock fragments found alongside diatoms in most sediments can be problematic as the method used will liberate oxygen from all components within the sediment, producing both high‐frequency noise and low‐frequency excursions that can resemble climate signals. Removal of mineral contamination to date has largely relied upon the combination of chemical leaching and physical separation techniques (e.g. sieving, density). This combination can be inefficient and often significant proportions of contaminants are present in the ‘purified’ diatom sample. Using electron optical imaging and whole‐rock geochemistry on previously ‘purified’ diatom samples, a mass balance approach has been developed whereby the types and proportions of residual contaminants are identified. By integrating this information with measured oxygen isotope ratios of the contaminants, it is then possible to remove contamination effects from the δ18Odiatom record. Contamination effects relating to carbonates, tephra and silt are modelled for cores from Lake Tilo (Ethiopia) and Lake Baikal (Siberia). In both lakes the new modelled δ18Odiatom curves show less high‐frequency noise, thus enabling better resolution of low‐frequency climate signals. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons Ltd.
Oxygen isotope ratios of sedimentary biogenic silica reflect the European transcontinental climate gradient
Authors: Tyler J. J. , Leng M. J. , Sloane H. J. , Sachse D. , Gleixner G. 
Published: April 2008

AbstractOxygen isotope ratios of biogenic silica offer considerable potential in tracing past climate change using both marine and lacustrine sediment records. Despite recent improvements and standardisation in preparatory and analytical methods, evidence for a systematic relationship between climate parameters and the oxygen isotope composition of sedimentary diatom silica (δ18Osilica) is contradictory. In particular, observed differences between the δ18Osilica of living and sedimentary diatom silica in both lake and marine environments question the validity of applying isotope fractionation models derived from living diatoms to reconstructing climate from sediment records. In order to address this issue, oxygen isotope ratios of biogenic silica (δ18Osilica) are examined from a suite of lake surface sediment samples which span a large climatic gradient across western Europe. δ18Osilica values are strongly correlated with air temperature and the isotope composition of precipitation (δ18OP). When evaporation of lake waters is accounted for, the time‐averaged surface sediment data suggest a fractionation of ∼35‰ between water and biogenic silica. However, the effect of temperature appears less marked than that observed between contemporary diatoms and lake water over short timescales, suggesting that diagenetic processes may lead to a reduction in the temperature sensitivity of sediment δ18Osilica records. Comparison of δ18Osilica data with δD analysed from n‐alkanes of aquatic origin (n‐C17, n‐C21 and n‐C23) demonstrates that the slope of the regional δ18O:δD water line is preserved within the sediment record, offering exciting potential for palaeoclimate research. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons, Ltd.
The palaeohydrological evolution of Lago Chungará (Andean Altiplano, northern Chile) during the Lateglacial and early Holocene using oxygen isotopes in diatom silica
Authors: Hernández Armand , Bao Roberto , Giralt Santiago , Leng Melanie J. , Barker Philip A. , Sáez Alberto , Pueyo Juan J. , Moreno Ana , Valero‐Garcés Blas L. , Sloane Hilary J. 
Published: April 2008

AbstractOxygen isotopes of diatom silica and petrographical characterisation of diatomaceous laminated sediments of Lago Chungará (northern Chilean Altiplano) have allowed us to establish its palaeohydrological evolution during the Lateglacial–early Holocene (ca. 12 000–9400 cal. yr BP). These laminated sediments are composed of light and dark pluriannual couplets of diatomaceous ooze formed by different processes. Light sediment laminae accumulated during short‐term diatom blooms whereas dark sediment laminae represent the baseline limnological conditions during several years of deposition. Oxygen isotope analysis of the dark diatom laminae show a generalδ18O enrichment trend during the studied period. Comparison of theseδ18Odiatomvalues with the previously published lake‐level evolution suggests a correlation betweenδ18Odiatomand the precipitation:evaporation ratio, but also with the evolution of other local hydrological factors as changes in the groundwater outflow as well as shifts in the surface:volume ratio of Lago Chungará. The lake expanded (probably increasing this ratio) during the rising lake‐level trend due to changes in its morphology, enhancing evaporation. Furthermore, the lake's hydrology was probably modified as the groundwater outflow became sealed by sediments, increasing lake water residence time and potential evaporation. Both factors could cause isotope enrichment. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons, Ltd.
Combined oxygen and silicon isotope analysis of biogenic silica
Authors: Leng Melanie J. , Sloane Hilary J. 
Published: April 2008

AbstractThere is increasing interest in the use of biogenic silica O and Si isotope ratios to understand climate and environmental processes. Virtually all of the fairly substantial body of literature deals with either oxygen or silicon. This is partly because measurement of oxygen isotope composition is done using either vacuum dehydration, isotope exchange or stepped fluorination techniques, while increasingly researchers are turning to multicollector inductively coupled plasma mass spectrometry (MC‐ICP‐MS) for Si isotope analysis, even though Si isotope analysis can be done using fluorination methods used for the oxygen isotope measurements. Here we describe a procedure for simultaneous determination of isotopic abundances of oxygen and silicon from the same aliquot of biogenic silica. Pure silica is dissociated into O and Si compounds using a fluorination technique, in which reaction with bromine pentafluoride (BrF5) produces oxygen (O2, subsequently converted to CO2), silicon tetrafluoride (SiF4) and other fluorine by‐products (e.g. BrF3). These compounds are cryogenically separated using cold traps. Yields for oxygen and silicon recovery are 70–80% for biogenic silica depending on the nature of the hydrous layer and 97–99% for pure quartz. Reproducibility of the oxygen isotopic composition is ca. 0.3‰ and silicon between 0.06–0.12‰. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons, Ltd.
Isotopes in Biogenic Silica (IBiS)
Authors: Leng Melanie J. , Street‐Perrott F. Alayne , Barker Philip A. 
Published: April 2008

AbstractThis special issue of the Journal of Quaternary Science comprises a selection of papers from the third meeting of a series on ‘ISOtopes in PALaeoenvironmental reconstruction’ (ISOPAL), themed around Isotopes and Biogenic silica (IBiS). The meeting was held at the British Geological Survey (Nottingham, UK) in April 2007, and consisted of a series of presentations giving methodological approaches to using isotopes in biogenic silica but also specific examples of the application, the majority of which are presented in this issue. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons Ltd.
Raman characterization of painted mortar in Republican Roman mosaics
Authors: Boschetti Cristina , Corradi Anna , Baraldi Pietro 
Published: April 2008

AbstractIn several Italian archaeological sites, the presence of the so‐called emblemata has been attested to the Republican Roman Age (2nd to 1st century B.C.). They are small mosaics made on a stone or terracotta tray using the opus vermiculatum. This particular technique, which originated in Egypt and/or in Greece during the Hellenistic period (3rd century B.C.), uses very small tesserae (of size less than 0.5 cm) producing a pictorial effect. In the literature, this type of mosaic has been studied from a technical approach only for a small group of mosaics from Greece (Delos, Samos and Rhodes island), while for the Italian area, a project on their archaeometrical and archaeological study is in progress. In a few cases, by observing the surface of the mosaics, it was possible to detect the presence of a painting layer on the mortar. This feature was never reported in the literature, probably because the painted details have survived only in traces, and they are visible only by direct observation. A mosaic from Rome (preserved in site, under the church of St. Susanna), was sampled and analyzed by Raman spectrometry, while two vermiculata mosaics from Privernum (LT) were observed in situ by a portable instrument. Thanks to the characterization, it was possible to observe the use of a luxurious palette of pigments, including cinnabar and Egyptian Blue. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of adsorption mechanism on colloidal silver surface of alafosfalin and its analogs
Authors: Podstawka Edyta , Andrzejak Marcin , Kafarski Paweł , Proniewicz Leonard M. 
Published: April 2008

AbstractThis study reports the Raman (FT‐RS) and absorption infrared (FT‐IR) spectra, based on calculated wavenumbers and normal modes of vibrations, of the following compounds: L‐Ala‐L‐NH‐CH(Me)‐PO3H2 (alafosfalin, A1), L‐Ala‐D‐NH‐CH(Me)‐PO3H2 (A2), L‐Ala‐L‐NH‐CH(Et)‐PO3H2 (A3), D,L‐Ala‐D,L‐NH‐CH(Et)‐PO3H2 (A4), L‐Ala‐D‐NH‐CH(iPr)‐PO3H2 (A5), L‐Ala‐D,L‐NH‐CH(iPr)‐PO3H2 (A6), L‐Ala‐D,L‐NH‐CH(tBu)‐PO3H2 (A7), L‐Ala‐D,L‐NH‐CH(iBu)‐PO3H2 (A8), L‐Ala‐D,L‐NH‐CH(cBu)‐PO3H2 (A9), L‐Ala‐D,L‐NH‐CH(nPA)‐PO3H2 (A10), β‐Ala‐D‐NH‐CH(Me)‐PO3H2 (A11), and D,L‐Ala‐NH‐C(Me,Me)‐PO3H2 (A12). The equilibrium geometries and vibrational wavenumbers are calculated using density functional theory (DFT) at the B3LYP; 6–31 + + G** level of theory using Gaussian'03, GaussSum 0.8, and GAR2PED software. We briefly compare and analyze the experimental and calculated vibrational wavenumbers in the range of 3600–400 cm−1. In addition, Raman wavenumbers are compared to those from surface‐enhanced Raman scattering (SERS) for the phosphonodipeptides of alanine (Ala) adsorbed on a colloidal silver surface. The geometry of these molecules etched on the silver surface is deduce from the observed changes in both the intensity and breadth of Raman bands in the spectra of the bound vs free species. For example, A7, A8, A1, A3, and A4 appear to adsorb onto the colloidal silver particles mainly through the phosphonate terminus, and for A3 and A4, through the C‐NH2 and CONH fragments. The most dominant SERS bands of A5, A6, A9, A10, and A11 are due to the amide bond vibrations, as well as to the vibrations of the C‐NH2 group (A9 and A10) and the CC group (A6 and A11). The differences recorded for the A5, A6, A9, A10, and A11 and those of A2 and A12 are due to interactions between the amine and methyl groups with the silver surface, and they reflect vibrational characteristic of these groups. Copyright © 2008 John Wiley & Sons, Ltd.
High pressure Raman spectra of L‐methionine crystal
Authors: Lima J. A. , Freire P. T. C. , Melo F. E. A. , Lemos V. , Mendes Filho J. , Pizani P. S. 
Published: April 2008

AbstractRaman spectra of an L‐methionine (C5H11NO2S) crystal were obtained in the spectral region between 50 and 3200 cm−1 for pressures up to 5 GPa. Pronounced changes of the Raman spectra were observed for bands associated to rocking of CO2−; wagging of CO2−; deformations of CO2−, CH3, and NH3+; and stretching vibrations of SC, CC, CH, CH2, and CH3. Upon decompression to ambient pressure the original Raman spectrum prior to compression is recovered. These modifications were associated to a reversible phase transition undergone by the L‐methionine crystal at about 2.2 GPa, with a hysteresis of ∼0.8 GPa. Pressure coefficients for most of the internal modes of the crystal are given. Copyright © 2008 John Wiley & Sons, Ltd.
Laser Markets in the USA
Authors: Belforte David 
Published: April 2008

AbstractThe world market for industrial laser materials processing systems in 2007 was in excess of $6.1 billion (Figure 1). An additional $2.5 billion is attributable to excimer lasers for photolithography applications, which will not be discussed in this paper. The market covered in this report is that for which lasers produce a physical or visual change in a material that is being processed in a manufacturing environment by automated or semi‐automated systems typically operated by semi‐skilled workers, on a routine production schedule.
Robot Supported Laser System Technology
Authors: Kroth Eberhard 
Published: April 2008

AbstractIt took more than two decades to introduce the combination of lasers and robot technology to the industry, but today this combination is a must‐have for any technology leader in mechanical engineering. From CO2 lasers towards Fiber lasers and from a bare addition of laser and robot towards integrated system technology – it is interesting to have a look at the steps of this development and to think about the future.
Innovative Laser Welding Processes
Authors: Olowinsky Alexander , Boglea Andrei , Gedicke Jens 
Published: April 2008

AbstractLaser beam micro joining is known as one of the most promising applications of laser technology. The paper will give an overview of new applications in microtechnology using laser beams with high beam quality such as fiber lasers. Hence two new processes will be reported. The combination of small focus dimensions with high feed rates for scanning has advantages for metal welding as well as for polymer welding. Advanced Microsystems with complicated welding contours especially from the medical and biotechnological applications are challenging the limits of laser welding of polymers.
Large Scale Laser Microstructuring in the Printing Industry
Authors: Hennig Guido , Selbmann Karl‐Heinz , Brüning Stephan 
Published: April 2008

AbstractApplying lasers in gravure print form fabrication is getting more and more important due to a high machining rate, high spatial resolution and the ability of digital modulation. Direct laser engraving into the metallic surface is the fastest and most versatile process for gravure cylinder imaging (ablation rate up to 1 cm3/min). High power Q‐switch Nd:YAG and fiber lasers up to repetition rates of 100 kHz are used, tuned for high reproducibility and stability. A fast modulation of the laser beam profile for each single pulse allows for optimization of the cell shape to get the best ink transfer interaction on a specific print substrate. Highest screen resolutions are made with single mode cw fiber lasers > 100 W.