bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amyloid fibrils derived from the apolipoprotein A1 Leu174Ser variant contain elements of ordered helical structure
Authors: Mangione Palma , Sunde Margaret , Giorgetti Sofia , Stoppini Monica , Esposito Gennaro , Gianelli Luca , Obici Laura , Asti Lia , Andreola Alessia , Viglino Paolo , Merlini Giampaolo , Bellotti Vittorio 
Published: July 2002

AbstractWe recently described a new apolipoprotein A1 variant presenting a Leu174Ser replacement mutation that is associated with a familial form of systemic amyloidosis displaying predominant heart involvement. We have now identified a second unrelated patient with very similar clinical presentation and carrying the identical apolipoprotein A1 mutation. In this new patient the main protein constituent of the amyloid fibrils is the polypeptide derived from the first 93 residues of the protein, the identical fragment to that found in the patient previously described to carry this mutation. The X‐ray fiber diffraction pattern obtained from preparations of partially aligned fibrils displays the cross‐β reflections characteristic of all amyloid fibrils. In addition to these cross‐β reflections, other reflections suggest the presence of well‐defined coiled‐coil helical structure arranged with a defined orientation within the fibrils. In both cases the fibrils contain a trace amount of full‐length apolipoprotein A1 with an apparent prevalence of the wild‐type species over the variant protein. We have found a ratio of full‐length wild‐type to mutant protein in plasma HDL of three to one. The polypeptide 1–93 purified from natural fibrils can be solubilized in aqueous solutions containing denaturants, and after removal of denaturants it acquires a monomeric state that, based on CD and NMR studies, has a predominantly random coil structure. The addition of phospholipids to the monomeric form induces the formation of some helical structure, thought most likely to occur at the C‐terminal end of the polypeptide.
Structure of a malaria parasite antigenic determinant displayed on filamentous bacteriophage determined by NMR spectroscopy: Implications for the structure of continuous peptide epitopes of proteins
Authors: Monette Martine , Opella Stanley J. , Greenwood Judith , Willis Anne E. , Perham Richard N. 
Published: July 2002

AbstractThe NANP repeating sequence of the circumsporozoite protein of Plasmodium falciparum was displayed on the surface of fd filamentous bacteriophage as a 12‐residue insert (NANP)3 in the N‐terminal region of the major coat protein (pVIII). The structure of the epitope determined by multidimensional solution NMR spectroscopy of the modified pVIII protein in lipid micelles was shown to be a twofold repeat of an extended and non‐hydrogen‐bonded loop based on the sequence NPNA, demonstrating that the repeating sequence is NPNA, not NANP. Further, high resolution solid‐state NMR spectra of intact hybrid virions containing the modified pVIII proteins demonstrate that the peptides displayed on the surface of the virion adopt a single, stable conformation; this is consistent with their pronounced immunogenicity as well as their ability to mimic the antigenicity of their native parent proteins.
A critical investigation of the Tanford‐Kirkwood shceme by means of Monte Carlo simulations
Authors: Da Silva Fernando LuífS B. , Jönsson Bo , Penfold Robert 
Published: July 2002

AbstractMonte Carlo simulations are used to assess the adequacy of the Tanford‐Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye‐Hückel theory, which forms the statistical mechanical basis for the Tanford‐Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye‐Hückel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford‐Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.
Modeling the Air-Cooled Gas Turbine: Part 1—General Thermodynamics
Authors: Young J. B. , Wilcock R. C. 
Published: July 2002

AbstractThis paper is Part I of a study concerned with developing a formal framework for modeling air-cooled gas turbine cycles and deals with basic thermodynamic issues. Such cycles involve gas mixtures with varying composition which must be modeled realistically. A possible approach is to define just two components, air and gas, the latter being the products of stoichiometric combustion of the fuel with air. If these components can be represented as ideal gases, the entropy increase due to compositional mixing, although a true exergy loss, can be ignored for the purpose of performance prediction. This provides considerable simplification. Consideration of three idealized simple cycles shows that the introduction of cooling with an associated thermal mixing loss does not necessarily result in a loss of cycle efficiency. This is no longer true when real gas properties and turbomachinery losses are included. The analysis clarifies the role of the cooling losses and shows the importance of assessing performance in the context of the complete cycle. There is a strong case for representing the cooling losses in terms of irreversible entropy production as this provides a formalized framework, clarifies the modeling difficulties, and aids physical interpretation. Results are presented that show the effects on performance of varying cooling flowrates and cooling losses. A comparison between simple and reheat cycles highlights the ro^le of the thermal mixing loss. Detailed modeling of the heat transfer and cooling losses is discussed in Part II of this paper.
Comparison of advanced plasma sources for etching applications. IV. Plasma induced damage in a helicon and a multipole electron cyclotron resonance source
Authors: Blayo N. , Tepermeister I. , Benton J. L. , Higashi G. S. , Boone T. , Onuoha A. , Klemens F. P. , Ibbotson D. E. , Lee J. T. C. , Sawin H. H. 
Published: July 2002

The effect of plasma induced damage on device yields becomes increasingly crucial as gate oxide thicknesses approach the 50–70 Å range for quarter micron design rules. To quantify plasma induced damage for new low pressure, high density plasma sources, inductively coupled carrier lifetime and photoluminescence are measured. Also, UV-visible spectroscopic ellipsometry is used to closely examine the wafer surface both during and after plasma exposure. This study is part of an ongoing research program that compares the etching performance of two commercially available, advanced plasma sources: a Lucas Labs helicon and a Wavemat multipole electron cyclotron resonance source. For n-type and p-type, nominally 100 μs lifetime wafers, plasma exposure in both sources under optimum polysilicon overetch conditions results in a degradation of carrier lifetimes of less than 5% for unprotected versus oxide protected crystalline silicon. For wafers with an initial carrier lifetime of 400 μs, exposure to plasmas in both sources leads to a decrease in carrier lifetimes to approximately 345 μs. The decrease in carrier lifetime, although measurable, is at least an order of magnitude smaller than measured in conventional reactive ion etching (RIE) processes.
To simulate an RIE etching process, rf-bias power is applied without source power so that both sources behave like highly asymmetric, parallel plate RIE reactors with the wafer platen acting as a driven electrode and the source wall acting as a grounded electrode. Under these conditions carrier lifetimes below 45 μs were measured in both sources with wafers that had initial lifetimes of 400 μs. Photoluminescence measurements indicate incorporation of hydrogen into the etched material, but no formation of interstitial defects associated with plasma induced damage. For samples exposed to a plasma at 25 and 50 W rf-bias, hydrogen produced from HBr dissociation readily incorporates into the sample. Exposure to a plasma at 200 W applied rf-bias results in a decrease in carrier lifetime and an increase in hydrogen incorporation. Under high rf-bias conditions, hydrogen incorporation is probably aided by ion surface damage. Ultraviolet-visible ellipsometry does not detect any morphological damage induced in silicon wafers, but as with carrier lifetime and photoluminescence measurements, significant damage is detected after exposure to rf-bias power without applied source power. Ellipsometry also detects a difference between real-time and post process spectra after HBr and Cl2 plasma exposure corresponding to the desorption of a film approximately 12 Å thick. This is not observed after Ar plasma exposure. Instead, the roughened surface remains stable which shows that the differences observed during and after plasma exposure for HBr and Cl2 are indeed the result of a chemically reacting layer.
Postantibiotic Leukocyte Enhancement of Meropenem against Gram-Positive and Gram-Negative Strains
Authors: Novelli Andrea , Fallani Stefania , Cassetta Maria Iris , Conti Silvia , Mazzei Teresita 
Published: July 2002

ABSTRACT
The postantibiotic leukocyte enhancement (PALE) of meropenem in vitro in comparison with that of imipenem was evaluated with 24 recently isolated gram-positive and gram-negative strains. In general, pre-exposure to carbapenems (at four times the MIC for 2 h) led to increased polymorphonuclear cell phagocytic killing. The PALE of imipenem was generally significantly less than that observed with meropenem.
Effect of Subinhibitory Antibiotic Concentrations on Polysaccharide Intercellular Adhesin Expression in Biofilm-Forming
Staphylococcus epidermidis
Authors: Rachid Shwan , Ohlsen Knut , Witte Wolfgang , Hacker Jörg , Ziebuhr Wilma 
Published: July 2002

ABSTRACT

Biofilm production is an important step in the pathogenesis of
Staphylococcus epidermidis
polymer-associated infections and depends on the expression of the
ica
ADBC operon leading to the synthesis of a polysaccharide intercellular adhesin. A chromosomally encoded reporter gene fusion between the
ica
promoter and the beta-galactosidase gene
lac
Z from
Escherichia coli
was constructed and used to investigate the influence of both environmental factors and subinhibitory concentrations of different antibiotics on
ica
expression in
S. epidermidis
. It was shown that
S. epidermidis
biofilm formation is induced by external stress (i.e., high temperature and osmolarity). Subinhibitory concentrations of tetracycline and the semisynthetic streptogramin antibiotic quinupristin-dalfopristin were found to enhance
ica
expression 9- to 11-fold, whereas penicillin, oxacillin, chloramphenicol, clindamycin, gentamicin, ofloxacin, vancomycin, and teicoplanin had no effect on
ica
expression. A weak (i.e., 2.5-fold) induction of
ica
expression was observed for subinhibitory concentrations of erythromycin. The results were confirmed by Northern blot analyses of
ica
transcription and quantitative analyses of biofilm formation in a colorimetric assay.
New Gene Cassettes for Trimethoprim Resistance,
dfr13
, and Streptomycin-Spectinomycin Resistance,
aadA4
, Inserted on a Class 1 Integron
Authors: Adrian Peter V. , Thomson Christopher J. , Klugman Keith P. , Amyes Sebastian G. B. 
Published: July 2002

ABSTRACT

In a previous survey of 357 trimethoprim-resistant isolates of aerobic gram-negative bacteria from commensal fecal flora, hybridization experiments showed that 25% (90 of 357) of the isolates failed to hybridize to specific oligonucleotide probes for dihydrofolate reductase types 1, 2b, 3, 5, 6, 7, 8, 9, 10, and 12. Subsequent cloning and sequencing of a plasmid-borne trimethoprim resistance gene from one of these isolates revealed a new dihydrofolate reductase gene,
dfr13
, which occurred as a cassette integrated in a site-specific manner in a class 1 integron. The gene product shared 84% amino acid identity with
dfr12
and exhibited a trimethoprim inhibition profile similar to that of
dfr12
. Gene probing experiments with an oligonucleotide probe specific for this gene showed that 12.3% (44 of 357) of the isolates which did not hybridize to probes for other dihydrofolate reductases hybridized to this probe. Immediately downstream of
dfr13
, a new cassette, an aminoglycoside resistance gene of the class AADA [ANT(3")(9)-I], which encodes streptomycin-spectinomycin resistance, was identified. This gene shares 57% identity with the consensus
aadA1
(
ant(3")-Ia
) and has been called
aadA4
(
ant(3")-Id). The 3′ end of the aadA4
cassette was truncated by IS
26
, which was contiguous with a truncated form of Tn
3
. On the same plasmid, pUK2381, a second copy of IS
26
was associated with
sul2
, which suggests that both integrase and transposase activities have played major roles in the arrangement and dissemination of antibiotic resistance genes
dfr13
,
aadA4
,
bla
TEM-1
, and
sul2
.
Mechanisms of Resistance to Quinupristin-Dalfopristin among Isolates of
Enterococcus faecium
from Animals, Raw Meat, and Hospital Patients in Western Europe
Authors: Soltani Mehnam , Beighton David , Philpott-Howard John , Woodford Neil 
Published: July 2002

ABSTRACT

Twenty-eight quinupristin-dalfopristin-resistant isolates of
Enterococcus faecium
from hospital patients and nonhuman sources in European countries were studied. High-level resistance (MICs, ≥32 μg/ml) was associated with the presence of
vat
(E) (
satG
) (14 isolates [50%]) or
vat
(D) (
satA
) (6 isolates [21%]). These genes were not detected in eight (29%) isolates with lower levels of quinupristin-dalfopristin resistance (MICs, 4 to 16 μg/ml). This suggests the presence of further mechanisms of resistance to quinupristin-dalfopristin in
E. faecium
.
Multiparameter Flow Cytometric Analysis of Antibiotic Effects on Membrane Potential, Membrane Permeability, and Bacterial Counts of
Staphylococcus aureus
and
Micrococcus luteus
Authors: Novo David J. , Perlmutter Nancy G. , Hunt Richard H. , Shapiro Howard M. 
Published: July 2002

ABSTRACT

Although flow cytometry has been used to study antibiotic effects on bacterial membrane potential (MP) and membrane permeability, flow cytometric results are not always well correlated to changes in bacterial counts. Using new, precise techniques, we simultaneously measured MP, membrane permeability, and particle counts of antibiotic-treated and untreated
Staphylococcus aureus
and
Micrococcus luteus
cells. MP was calculated from the ratio of red and green fluorescence of diethyloxacarbocyanine [DiOC
2
(3)]. A normalized permeability parameter was calculated from the ratio of far red fluorescence of the nucleic acid dye TO-PRO-3 and green DiOC
2
(3) fluorescence. Bacterial counts were calculated by the addition of polystyrene beads to the sample at a known concentration. Amoxicillin increased permeability within 45 min. At concentrations of <1 μg/ml, some organisms showed increased permeability but normal MP; this population disappeared after 4 h, while bacterial counts increased. At amoxicillin concentrations above 1 μg/ml, MP decreased irreversibly and the particle counts did not increase. Tetracycline and erythromycin caused smaller, dose- and time-dependent decreases in MP. Tetracycline concentrations of <1 μg/ml did not change permeability, while a tetracycline concentration of 4 μg/ml permeabilized 50% of the bacteria; 4 μg of erythromycin per ml permeabilized 20% of the bacteria. Streptomycin decreased MP substantially, with no effect on permeability; chloramphenicol did not change either permeability or MP. Erythromycin pretreatment of bacteria prevented streptomycin and amoxicillin effects. Flow cytometry provides a sensitive means of monitoring the dynamic cellular events that occur in bacteria exposed to antibacterial agents; however, it is probably simplistic to expect that changes in a single cellular parameter will suffice to determine the sensitivities of all species to all drugs.
A Rapid Phenotypic Assay for Detection of Acyclovir-Resistant Varicella-Zoster Virus with Mutations in the Thymidine Kinase Open Reading Frame
Authors: Sahli Roland , Andrei Graciela , Estrade Christine , Snoeck Robert , Meylan Pascal R. A. 
Published: July 2002

ABSTRACTSusceptibility assays by cell culture methods are time-consuming and are particularly difficult to perform with varicella-zoster virus (VZV). To overcome this limitation, we have adapted a functional test of the viral thymidine kinase (TK) in TK-deficient (tdkmutant) bacteria to detect ACV-resistant VZV in clinical samples. After PCR amplification, the complete viral TK open reading frame (ORF) is purified from PCR primers, digested with two restriction enzymes, and ligated in an oriented fashion into a bacterial expression vector. The ligation products are then used to transformtdkmutant bacteria. After transformation, an aliquot of the bacteria is plated onto a plate with minimal medium containing (i) ampicillin to select for plasmids carrying the viral TK ORF and (ii) isopropyl β-d-thiogalactopyranoside (IPTG) to induce its expression. An identical aliquot of bacteria is also plated onto a medium containing, in addition to the components described above, 5-fluorodeoxyuridine (FUdR). Compared to the number of transformants on FUdR-free medium, the number of colonies carrying TK derived from susceptible strains was reduced by 86%, on average, in the presence of FUdR. In contrast, the number of transformants carrying TK from resistant strains with a mutant TK were reduced by only 4%, on average, on FUdR-containing plates. We have assessed the validity of this assay with cell culture isolates and several clinical samples including two cerebrospinal fluid samples from which no virus could be isolated. This colony reduction assay allowed the correct identification of the TK phenotype of each VZV isolate tested and can be completed within 3 days of receipt of the sample.
Activities of Trovafloxacin and Ampicillin-Sulbactam Alone or in Combination versus Three Strains of Vancomycin- Intermediate
Staphylococcus aureus
in an In Vitro Pharmacodynamic Infection Model
Authors: Aeschlimann Jeffrey R. , Hershberger Ellie , Rybak Michael J. 
Published: July 2002

ABSTRACT

The recent isolation of clinical strains of methicillin-resistant
Staphylococcus aureus
(MRSA) with intermediate susceptibility (MICs, 8 μg/ml) to vancomycin (vancomycin-intermediate
S. aureus
[VISA]) emphasizes the importance of developing novel antimicrobial regimens and/or agents for future treatment. We studied the activities of ampicillin-sulbactam and trovafloxacin alone or in combination against three unique strains of VISA in an in vitro infection model. Two VISA strains were trovafloxacin susceptible (MICs, ≤2 μg/ml); one VISA strain was trovafloxacin resistant (MIC, 4 μg/ml). Trovafloxacin was administered to simulate a dose of 200 or 400 mg every 24 h. Ampicillin-sulbactam was administered to simulate a dose of 3 g every 6 h. Samples were removed from the infection models over 48 h, and reductions in colony counts were compared between regimens. Trovafloxacin (200 mg) produced rapid killing of a control MRSA strain over the 48-h experiment but produced only slight killing of all three VISA strains. The higher dose of trovafloxacin improved killing but did not produce bactericidal activity at 48 h. Ampicillin-sulbactam produced rapid bactericidal activity against all four strains tested, and colony counts at 8 h were at the limits of detection. However, regrowth occurred by 48 h for each strain. The combination of ampicillin-sulbactam and trovafloxacin provided additive activity against two of the three VISA strains. In conclusion, trovafloxacin or ampicillin-sulbactam alone did not provide adequate activity against the VISA strains for the 48-h evaluation period, but the combination could help improve activity against some strains of VISA.
Pharmacokinetics and Safety of AMD-3100, a Novel Antagonist of the CXCR-4 Chemokine Receptor, in Human Volunteers
Authors: Hendrix Craig W. , Flexner Charles , MacFarland Ronald T. , Giandomenico Christen , Fuchs Edward J. , Redpath Ella , Bridger Gary , Henson Geoffrey W. 
Published: July 2002

ABSTRACT

AMD-3100, a bicyclam, is a novel agent that uniquely inhibits the entry of human immunodeficiency virus type 1 (HIV-1) into CD4
+
T cells via selective blockade of the chemokine CXCR-4 receptor. Twelve healthy volunteers were given AMD-3100 as a single 15-min intravenous infusion at 10, 20, 40, or 80 μg/kg. Five subjects also received a single subcutaneous injection of AMD-3100 (40 or 80 μg/kg). Three subjects received two escalating oral doses each (80 and 160 μg/kg). All subjects tolerated their dose(s) well without any grade 2 toxicity or dose adjustment. Six subjects experienced mild, transient symptoms, primarily gastrointestinal in nature and not dose related. All subjects experienced a dose-related elevation of the white blood cell count, from 1.5 to 3.1 times the baseline, which returned to the baseline 24 h after dosing. AMD-3100 demonstrated dose proportionality for the maximum drug concentration in serum (
C
max
) and the area under the concentration-time curve from 0 h to ∞ (AUC
0–∞
) over the entire dose range. At the highest intravenous dose (80 μg/kg), the median
C
max
was 515 (range, 470 to 521) ng/ml and the AUC
0–∞
was 1,044 (range, 980 to 1,403) ng-h/ml. The median systemic absorption after subcutaneous dosing was 87% (range, 67 to 106%). No drug was detectable in the blood following oral dosing. Using a two-compartment model, the median pharmacokinetic parameter estimates (ranges) were as follows: volume of distribution, 0.34 (0.27 to 0.36) liter/kg; clearance, 1.30 (0.97 to 1.34) liters/h; elimination half-life, 3.6 (3.5 to 4.9) h. After a single, well-tolerated intravenous dose of AMD-3100, concentrations were sustained for 12 h above the in vitro antiretroviral 90% inhibitory concentrations and for 8 h above antiviral concentrations identified in the SCID-hu Thy/Liv mouse model of HIV infection.
Prevalence of β-Lactamases among 1,072 Clinical Strains of
Proteus mirabilis
: a 2-Year Survey in a French Hospital
Authors: Chanal C. , Bonnet R. , De Champs C. , Sirot D. , Labia R. , Sirot J. 
Published: July 2002

ABSTRACT

β-Lactam resistance was studied in 1,072 consecutive
P. mirabilis
clinical strains isolated at the Clermont-Ferrand teaching hospital between April 1996 and March 1998. The frequency of amoxicillin resistance was 48.5%. Among the 520 amoxicillin-resistant isolates, three resistance phenotypes were detected: penicillinase (407 strains [78.3%]), extended-spectrum β-lactamase (74 strains [14.2%]), and inhibitor resistance (39 strains [7.5%]). The penicillinase phenotype isolates were divided into three groups according to the level of resistance to β-lactams, which was shown to be related to the strength of the promoter. The characterization of the different β-lactamases showed that amoxicillin resistance in
P. mirabilis
was almost always (97%) associated with TEM or TEM-derived β-lactamases, most of which evolved via TEM-2.