bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exonuclease-Deficient Polymerase Mutant of Herpes Simplex Virus Type 1 Induces Altered Spectra of Mutations
Authors: Hwang Ying T. , Hwang Charles B. C. 
Published: February 2003

ABSTRACT

The effect of exonuclease activity of the herpes simplex virus DNA polymerase (Pol) on DNA replication fidelity was examined by using the
supF
mutagenesis assay. The recombinants with exonuclease-deficient Pol, containing an integrated
supF
gene in the thymidine kinase locus (
tk
), exhibited
supF
mutation frequencies ranging from 0.14 to 5.6%, consistent with the
tk
mutation frequencies reported previously (Y. T. Hwang, B.-Y. Liu, D. M. Coen, and C. B. C. Hwang, J. Virol. 71:7791-7798, 1997). The increased mutation frequencies were 10- to 500-fold higher than those observed for wild-type Pol recombinants. The increased mutation frequencies also were significantly higher than those of
supF
mutant replicated by exonuclease-deficient Pols in the plasmid-borne assay. Furthermore, characterization of
supF
mutants demonstrated that recombinants with a defective exonuclease induced types and distributions of
supF
mutations different from those induced by wild-type Pol recombinants. The types of
supF
mutations induced by exonuclease-deficient recombinants differed between the plasmid- and genome-based assays. The spectra of
supF
mutations also differed between the two assays. In addition, exonuclease-defective viruses also induced different spectra of
supF
and
tk
mutations. Therefore, both the assay methods and the target genes used for mutagenesis studies can affect the repication fidelity of herpes simplex virus type 1 Pol with defective exonuclease activity.
An Antiviral Peptide Targets a Coiled-Coil Domain of the Human T-Cell Leukemia Virus Envelope Glycoprotein
Authors: Piñón Josefina D. , Kelly Sharon M. , Price Nicholas C. , Flanagan Jack U. , Brighty David W. 
Published: February 2003

ABSTRACT
Retrovirus entry into cells is mediated by the viral envelope glycoproteins which, through a cascade of conformational changes, orchestrate fusion of the viral and cellular membranes. In the absence of membrane fusion, viral entry into the host cell cannot occur. For human T-cell leukemia virus type 1 (HTLV-1), synthetic peptides that mimic a carboxy-terminal region of the transmembrane glycoprotein (TM) ectodomain are potent inhibitors of membrane fusion and virus entry. Here, we demonstrate that this class of inhibitor targets a fusion-active structure of HTLV-1 envelope. In particular, the peptides bind specifically to a core coiled-coil domain of envelope, and peptide variants that fail to bind the coiled-coil lack inhibitory activity. Our data indicate that the inhibitory peptides likely function by disrupting the formation of a trimer-of-hairpins structure that is required for membrane fusion. Importantly, we also show that peptides exhibiting dramatically increased potency can be readily obtained. We suggest that peptides or peptide mimetics targeting the fusion-active structures of envelope may be of therapeutic value in the treatment of HTLV-1 infections.
Synthesis and Characterization of Luminescent Rod–Coil Block Copolymers by Atom Transfer Radical Polymerization: Utilization of Novel End‐Functionalized Terfluorenes as Macroinitiators
Authors: Tsolakis Panagiotis K. , Kallitsis Joannis K. 
Published: February 2003

AbstractTwo novel, rigid, photoluminescent, substituted terfluorene derivatives were synthesized by utilizing direct bromination and Suzuki coupling reactions. These oligomers were used as initiators for the atom transfer radical polymerization (ATRP) of styrene andtert‐butyl acrylate. Thus, diblock and triblock rod–coil block copolymers were prepared with well‐defined structure, as far as their size and shape is concerned. Molecular weights up to approximately 21 000 and polydispersity indices not exceeding 1.5 in most cases were obtained. The copolymers emit blue light in solution, and their luminescence properties remain practically invariable when passing from solution to the solid state. No ground‐state aggregation or excimer formation were observed in the solid state, even after annealing at high temperatures.
Chemische Synthese in überkritischem Kohlendioxid: Die „bessere Lösung”︁?
Authors: Leitner Walter 
Published: February 2003

AbstractDie in dieser kurzen Übersicht angeführten Beispiele verdeutlichen das Potenzial von überkritischem Kohlendioxid als Reaktionsmedium für nachhaltige Syntheseverfahren („Green Chemistry”︁). Die Forschung auf diesem Gebiet vereint in besonderer Weise anwendungsbezogene Fragestellungen mit dem grundlegenden Studium molekularer und reaktionstechnischer Zusammenhänge. Dabei zeigt sich bereits heute, dass scCO2 aufgrund seiner einzigartigen physikalisch‐chemischen Eigenschaften für die Synthesechemie weit mehr ist als nur ein „Ersatzlösungsmittel”︁ und beispielsweise gänzlich neue Methoden für die Kontrolle von Aktivität, Selektivität und Prozessdesign mit heterogenen Katalysatoren, metallorganischen Katalysatoren und Biokatalysatoren eröffnet. Besonders spannend bleibt für die Zukunft gerade auch die Suche nach neuen, in „konventionellen”︁ Lösungsmitteln nicht durchführbaren Reaktionen.
In Situ Observation of the Surface Processes Involved in Dissolution from the Cleavage Surface of Calcite in Aqueous Solution Using Combined Scanning Electrochemical–Atomic Force Microscopy (SECM‐AFM)
Authors: Jones Claire E. , Unwin Patrick R. , Macpherson Julie V. 
Published: February 2003

AbstractThe surface processes involved in the initial stages of the proton‐assisted dissolution of the calcite single crystal cleavage plane (10$\bar 1$4) have been identified using a combined scanning electrochemical–atomic force microscope (SECM‐AFM). This instrument employs a platinum‐coated AFM probe, which functions as an electrode as well as a high‐resolution topographical sensor. Dissolution in this arrangement is effected by the local electrogeneration of protons, produced by oxidation of water at the probe electrode. By careful control of the applied potential, it is possible to vary the magnitude of the electrogenerated flux of protons from the probe towards the calcite surface. Crucially, by generating a small proton flux for short time periods (0.5 s) it is possible to observe and monitor the initial sites in the dissolution process. Topographical images were recorded in the same area of the surface both prior to and after inducing dissolution, as a function of the proton flux. At low proton fluxes, of the order of 1 nmol cm−2 s−1 or less, the surface was observed to dissolve by the nucleation of monolayer deep pits, with densities of about 108 cm−2. These pits are likely to be formed at point vacancies or atomic (impurity, for example) defects in the crystal lattice. As the proton flux was increased (over two orders of magnitude), these same etch pits were found to open into wider macro‐pits, with an outline morphology that reflected the crystallographic orientation of the surface. At the highest proton fluxes, dissolution from macroscopic step edges became significant.
A Microscopic, Continous, Optical Monitor for Interstitial Electrolytes and Glucose
Authors: Tohda Koji , Gratzl Miklós 
Published: February 2003

AbstractIons, such as hydrogen (pH), sodium, or potassium, as well as metabolites, such as glucose or lactate, diffuse easily between blood in the capillaries and the interstitial fluid (ISF) residing between cells and tissues. This work represents a synthesis of several unique concepts to achieve accurate, continuous, in vivo monitoring of critical ions and glucose in the ISF under the human skin. Ionic levels are monitored using optode technology that translates the respective concentrations into variable colors of ionophore/dye/polymeric liquid membranes. Glucose is monitored indirectly, by coupling through immobilized glucose oxidase with pH, that is then detected using a similar color scheme. The monitor consists of a tiny plastic bar (“sliver sensor”), 100–300 μm wide and 1–1.5 mm long, placed just under the skin, with optical spots or stripes for each analyte as well as blanks for calibration. The colors are read and translated into concentration values by a watchlike device placed above the skin. Direct optical coupling between the in vivo sensing bar and the ex vivo detector device requires negligible power, and eliminates the need for wires or optical fibers crossing the skin. The microminiature sliver penetrates the skin easily and painlessly, so that the user could insert it him‐ or herself. No risk of track infection exists. We are reporting here on the first successful in vitro tests of this approach.
Mechanistic Aspects of On‐Line Electrochemical Tagging of Free L‐Cysteine Residues during Electrospray Ionisation for Mass Spectrometry in Protein Analysis
Authors: Roussel Christophe , Rohner Tatiana C. , Jensen Henrik , Girault Hubert H. 
Published: February 2003

AbstractThe mechanistic details behind an electrochemically induced tagging of L‐cysteine residues in peptides and proteins have been unravelled using cyclic voltammetry. It was found that when hydroquinone is oxidised in the medium used in electrospray ionisation mass spectrometry (ESI‐MS) a protonated form of benzoquinone is produced that acts as an efficient electrophile for free L‐cysteine residues. Upon substitution of L‐cysteine the reduced form of the adduct is formed, which may be further oxidised leading to further substitution of L‐cysteine. Digital simulations of the cyclic voltammograms corroborated the mechanism and allowed a determination of the homogeneous second order rate constant corresponding to the addition of L‐cysteine onto the protonated form of benzoquinone. The selectivity of the tagging process was confirmed using ESI‐MS, which showed that a protein without L‐cysteine residues does not react with benzoquinone dissolved in the medium. Finally, the kinetic information obtained in this investigation is used to discuss the optimal parameters for a nanospray capable of quantitative tagging of L‐cysteine residues.
Etched Electrochemical Detection for Electrophoresis in Nanometer Inner Diameter Capillaries
Authors: Woods Lori A. , Ewing Andrew G. 
Published: February 2003

AbstractCapillary electrophoresis in nanometer inner diameter capillaries allows for the analysis of extremely small volume samples, such as the contents of single cells. However, the utilization of these ultrasmall capillaries requires a very sensitive and low volume detector. An improved method for end‐column amperometric detection for capillary electrophoresis in nanometer inner diameter (i.d.) capillaries is presented. This new method involves etching both the electrode and the detection end of the capillary. These design improvements allow for better alignment between the capillary bore and the electrode. As a result, dead volume in the detector is minimized. The etched method for electrochemical detection in ultrasmall capillaries provides average coulometric efficiencies of 70±10 % for dopamine and 40±20 % for catechol in 770 nm i.d. capillaries. Furthermore, this technique provides peak efficiencies as high as 100 000 theoretical plates and detection limits as low as 340 zmol for both dopamine and catechol.
Synthesis and Pyrolytic and Kinetic Behaviour of β,δ′‐Dioxo‐Stabilised Phosphorus Ylides: Convenient Preparation of γ,δ‐Alkynyl Ketones and 2,3‐Functionalised Butadienes
Authors: Aitken R. Alan , Al‐Awadi Nouria A. , Balkovich Mark E. , Bestmann Hans Jürgen , Clem Oliver , Gibson Scott , Groß Andreas , Kumar Ajith , Röder Thomas 
Published: February 2003

AbstractBoth ketone‐ and ester‐stabilised phosphorus ylides undergo Michael addition to vinyl ketones to give the β,δ′‐dioxo ylides 3 and 5, respectively, although in the latter case careful temperature control is required to avoid an undesired side‐reaction. Under conditions of flash vacuum pyrolysis at 650 °C the ylides 3 generally undergo Ph3PO extrusion to afford the γ,δ‐alkynyl ketones 14, although these are found to partly undergo a secondary fragmentation. In contrast, the ylides 5 react under the same conditions to give the synthetically useful 1,3‐dienes 20 by way of cyclobutenes. Rate constants for the reaction of selected ylides 3 and 5 are reported. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Measuring the impact of US research consortia
Authors: Sakakibara Mariko , Branstetter Lee 
Published: February 2003

AbstractThis paper empirically evaluates the impact of the US Advanced Technology Program‐sponsored consortia on the ex‐post research productivity of participating firms. We find that there is a positive association between the intensity of participation in research consortia and the overall research productivity of participants. We also find a positive impact of consortia on the research productivity of participants in the technological areas targeted by the consortia. This positive impact is higher when the average technological proximity of participants is high. There is evidence that large, R&D intensive firms tend to benefit more from participation in consortia. Copyright © 2003 John Wiley & Sons, Ltd.
Sulphur isotopes in palaeodietary studies: a review and results from a controlled feeding experiment
Authors: Richards M. P. , Fuller B. T. , Sponheimer M. , Robinson T. , Ayliffe L. 
Published: February 2003

AbstractRecent advances in mass spectrometry now allow relatively routine measurements of sulphur isotopes (δ34S) in small samples (>10 mg) of tissue from archaeological human, plant, and faunal samples. δ34S values of human and faunal bone collagen can indicate residence or migration and can provide palaeodietary information. Here we present a review of applications of sulphur isotopes to archaeological materials, and we also present preliminary results from one of the few controlled feeding experiments undertaken for sulphur isotopes. This study indicates that there is relatively little fractionation (−1‰ ) between diet and body protein (keratin) δ34S values for modern horses on a protein adequate C3 plant diet. In contrast, horses fed a possible low protein C4 feed have a diet to hair fractionation of +4‰ that could be the result of the input of endogenous sulphur from the recycling of body proteins. Copyright © 2003 John Wiley & Sons, Ltd.
Polyethylene cross‐linking by two different methods reduces acetabular liner wear in a hip joint wear simulator
Authors: D'Lima Darryl D. , Hermida Juan C. , Chen Peter C. , Colwell Clifford W. 
Published: February 2003

AbstractAdvances in cross‐linking have led to the development of wear resistant ultrahigh molecular weight polyethylene for total joint replacement. This study compared wear reduction by two different cross‐linking methods as measured in a hip wear simulator. One highly cross‐linked polyethylene was treated with 7.5 Mrad gamma irradiation with post‐irradiation annealing and a sterilization dose of 2.5 Mrad (10 Gamma), while the other used 9.5 Mrad warm irradiation with 10 MeV electron‐beam (9.5 EB). Liners of the same design, made from nominally cross‐linked (gamma sterilized) polyethylene were also tested. Gravimetric wear analysis was performed every 500,000 cycles for 5,000,000 cycles. After correcting for weight gain due to water absorption, the nominally cross‐linked liners demonstrated mean wear rates of 15.7 (±1.7) and 12.5 (±1.0) mg/million cycles. Both highly cross‐linked polyethylene liners demonstrated significantly less wear than their respective controls (with mean wear rates of 1.5 (±1.2) and –1.4 (±1.5) mg/million cycles). The 9.5 EB liners gained weight presumably due to increased fluid absorption, in addition to that measured in loaded–soaked control implants. Any wear occurring was therefore assumed to have been more than offset by weight gain. Highly cross‐linked polyethylene was significantly more wear resistant than non‐ or nominally cross‐linked polyethylene. The differences in wear rates between the two highly cross‐linked polyethylene designs (9.5 EB or 10 Gamma) are probably too small to be clinically significant. © 2003 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved.
Central hemodynamic responses during serial exercise tests in heart failure patients using implantable hemodynamic monitors
Authors: Ohlsson Å. , Steinhaus D. , Kjellström B. , Ryden L. , Bennett T. 
Published: February 2003

AbstractIntroduction:Exercise testing is commonly used in patients with congestive heart failure for diagnostic and prognostic purposes. Such testing may be even more valuable if invasive hemodynamics are acquired. However, this will make the test more complex and expensive and only provides information from isolated moments. We studied serial exercise tests in heart failure patients with implanted hemodynamic monitors allowing recording of central hemodynamics.Methods:Twenty‐one NYHA Class II–III heart failure patients underwent maximal exercise tests and submaximal bike or 6‐min hall walk tests to quantify their hemodynamic responses and to study the feasibility of conducting exercise tests in patients with such devices.Results:Patients were followed for 2–3 years with serial exercise tests. During maximal tests (n=70), heart rate increased by 52±19 bpm while SvO2 decreased by 35±10% saturation units. RV systolic and diastolic pressure increased 29±11 and 11±6 mmHg, respectively, while pulmonary artery diastolic pressure increased 21±8 mmHg. Submaximal bike (n=196) and hall walk tests (n=172) resulted in SvO2 changes of 80 and 91% of the maximal tests, while RV pressures ranged from 72 to 79% of maximal responses.Conclusions:An added potential value of implantable hemodynamic monitors in heart failure patients may be to quantitatively determine the true hemodynamic profile during standard non‐invasive clinical exercise tests and to compare that to hemodynamic effects of regular exercise during daily living. It would be of interest to study whether such information could improve the ability to predict changes in a patient's clinical condition and to improve tailoring patient management.
Multifactor dimensionality reduction software for detecting gene–gene and
gene–environment interactions
Authors: Hahn Lance W. , Ritchie Marylyn D. , Moore Jason H. 
Published: February 2003

Abstract
Motivation: Polymorphisms in human genes are being described in remarkable numbers. Determining which polymorphisms and which environmental factors are associated with common, complex diseases has become a daunting task. This is partly because the effect of any single genetic variation will likely be dependent on other genetic variations (gene–gene interaction or epistasis) and environmental factors (gene–environment interaction). Detecting and characterizing interactions among multiple factors is both a statistical and a computational challenge. To address this problem, we have developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe the MDR approach and an MDR software package.
Results: We developed a program that integrates MDR with a cross-validation strategy for estimating the classification and prediction error of multifactor models. The software can be used to analyze interactions among 2–15 genetic and/or environmental factors. The dataset may contain up to 500 total variables and a maximum of 4000 study subjects.
Availability: Information on obtaining the executable code, example data, example analysis, and documentation is available upon request.
Contact: moore@phg.mc.vanderbilt.edu
Supplementary information: All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR.
* To whom correspondence should be addressed.
WiGID: wireless genome information database
Authors: Ursing Björn M. 
Published: February 2003

Abstract
Summary: WiGID, wireless genome information database, is a new application for mobile internet and can be reached through wireless application protocol (WAP). The main purpose of WiGID is to give easy access to information on completely sequenced genomes. Genome entries in WiGID can be queried by the number of open reading frames (ORFs), genus and species name and year published. Initial search results are linked to information on the full entry.
Availability: WiGID can be accessed through WAP at http://wigid.cgb.ki.se/index.wml and through the regular internet at http://wigid.cgb.ki.se.
Contact: bjorn.ursing@cgb.ki.se
* To whom correspondence should be addressed.
A literature-based method for assessing the functional
coherence of a gene group
Authors: Raychaudhuri Soumya , Altman Russ B. 
Published: February 2003

Abstract
Motivation: Many experimental and algorithmic approaches in biology generate groups of genes that need to be examined for related functional properties. For example, gene expression profiles are frequently organized into clusters of genes that may share functional properties. We evaluate a method, neighbor divergence per gene (NDPG), that uses scientific literature to assess whether a group of genes are functionally related. The method requires only a corpus of documents and an index connecting the documents to genes.
Results: We evaluate NDPG on 2796 functional groups generated by the Gene Ontology consortium in four organisms: mouse, fly, worm and yeast. NDPG finds functional coherence in 96, 92, 82 and 45% of the groups (at 99.9% specificity) in yeast, mouse, fly and worm respectively.
Availability: Contact authors.
Contact: russ.altman@stanford.edu
* To whom correspondence should be addressed.
Leader Proteinase of
Beet Yellows Virus
Functions in Long-Distance Transport
Authors: Peng Chih-Wen , Napuli Alberto J. , Dolja Valerian V. 
Published: February 2003

ABSTRACT

The 66-kDa leader proteinase (L-Pro) of the
Beet yellows virus
(BYV) possesses a nonconserved N-terminal domain and a conserved, papain-like C-terminal domain. Previous work revealed that the N-terminal domain functions in RNA amplification, whereas the C-terminal domain is required for autoproteolysis. Alanine-scanning mutagenesis was applied to complete the functional analysis of L-Pro throughout the virus life cycle. This analysis indicated that the C-terminal domain of L-Pro, in addition to being required for proteolysis, also functions in RNA amplification and that these two functions are genetically separable. Examination of the role of L-Pro in BYV cell-to-cell movement revealed that none of the 20 examined replication-competent mutants was movement defective. In contrast, six of the L-Pro mutations affected the long-distance transport of BYV to various degrees, whereas three mutations completely abolished the transport. Because these mutations were located throughout the protein molecule, both domains of L-Pro function in virus transport. We conclude that in addition to previously identified functions of L-Pro, it also serves as the BYV long-distance transport factor.