bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissemination and Persistence of
bla
CTX-M-9
Are Linked to Class 1 Integrons Containing CR1 Associated with Defective Transposon Derivatives from Tn
402
Located in Early Antibiotic Resistance Plasmids of IncHI2, IncP1-α, and IncFI Groups
Authors: Novais Ângela , Cantón Rafael , Valverde Aránzazu , Machado Elisabete , Galán Juan-Carlos , Peixe Luísa , Carattoli Alessandra , Baquero Fernando , Coque Teresa M. 
Published: July 2006

ABSTRACT

This study analyzes the diversity of In60, a class 1 integron bearing CR1 and containing
bla
CTX-M-9
, and its association with Tn
402
, Tn
21
, and classical conjugative plasmids among 45 CTX-M-9-producing clinical strains (41
Escherichia coli
strains, 2
Klebsiella pneumoniae
strains, 1
Salmonella enterica
strain, and 1
Enterobacter cloacae
strain). Forty-five patients in a Spanish tertiary care hospital were studied (1996 to 2003). The diversity of In60 and association of In60 with Tn
402
or mercury resistance transposons were investigated by overlapping PCR assays and/or hybridization. Plasmid characterization included comparison of restriction fragment length polymorphism patterns and determination of incompatibility group by PCR-based replicon typing, sequencing, and hybridization. CTX-M-9 plasmids belonged to IncHI2 (
n
= 26), IncP-1α (
n
= 10), IncFI (
n
= 4), and IncI (
n
= 1) groups. Genetic platforms containing
bla
CTX-M-9
were classified in six types in relation to the In60 backbone and in eight subtypes in relation to Tn
402
derivatives. They were associated with Tn
21
sequences when located in IncP-1α or IncHI2 plasmids. Our study identified
bla
CTX-M-9
in a high diversity of CR1-bearing class 1 integrons linked to different Tn
402
derivatives, often to Tn
21
, highlighting the role of recombination events in the evolution of antibiotic resistance plasmids. The presence of
bla
CTX-M-9
on broad-host-range IncP-1α plasmids might contribute to its dissemination to hosts that were not members of the family
Enterobacteriaceae
.
Crystal Structure and Activity Studies of the
Mycobacterium tuberculosis
β-Lactamase Reveal Its Critical Role in Resistance to β-Lactam Antibiotics
Authors: Wang Feng , Cassidy Craig , Sacchettini James C. 
Published: July 2006

ABSTRACT

β-Lactam antibiotics are extremely effective in disrupting the synthesis of the bacterial cell wall in both gram-positive and gram-negative bacteria. However, they are ineffective against
Mycobacterium tuberculosis
, due to the production of a β-lactamase enzyme encoded on the chromosome of
M. tuberculosis
that degrades these antibiotics. Indeed, recent studies have demonstrated that deletion of the
blaC
gene, the only gene encoding a β-lactamase in
M. tuberculosis
, or inhibition of the encoded enzyme resulted in significantly increased sensitivity to β-lactam antibiotics. In this paper we present a biochemical and structural characterization of
M. tuberculosis
BlaC. Recombinant BlaC shows a broad range of specificity with almost equal penicillinase and cepholothinase activity. While clavulanate is a mechanism-based inhibitor to class A β-lactamase with high potency (typically

K
i

< 0.1 μM), it is a relatively poor inhibitor of the
M. tuberculosis
BlaC (

K
i

= 2.4 μM). The crystal structure of the enzyme, determined at a resolution of 1.7 Å, shows that the overall fold of the
M. tuberculosis
enzyme is similar to other class A β-lactamases. There are, however, several distinct features of the active site, such as the amino acid substitutions N132G, R164A, R244A, and R276E, that explain the broad specificity of the enzyme, relatively low penicillinase activity, and resistance to clavulanate.
New Integron-Associated Gene Cassette Encoding a Trimethoprim-Resistant DfrB-Type Dihydrofolate Reductase
Authors: Levings Renee S. , Lightfoot Diane , Elbourne Liam D. H. , Djordjevic Steven P. , Hall Ruth M. 
Published: July 2006

ABSTRACT

A sixth gene cassette containing a
dfrB
-type gene,
dfrB6
, was found in a
dfrB6-aadA1
cassette array in class 1 integrons. This array was isolated from several multiply antibiotic-resistant
Salmonella enterica
serovar Infantis strains that appear to be clonally related. The DfrB6 dihydrofolate reductase conferred resistance to trimethoprim.
Cysteine Proteinase Inhibitors in Murine Cysticercosis
Authors: Baig Salman , Damian Raymond T. , Morales-Montor Jorge , Thazhath Rupal , Ghaleb Amr , Welch Meredith , Talhouk Jamil , White A. Clinton 
Published: July 2006

ABSTRACT
We explored the prophylactic efficacies of two novel protease inhibitors in murine cysticercosis. Our results demonstrated a 95% and 80% reduction in parasite burden for mice injected with Z-LLL-FMK and Z-LLY-FMK, respectively. Further studies are merited on the role of cysteine proteinase inhibitors in treatment of cysticercosis.
Flow Cytometric Determination of the Effects of Antibacterial Agents on
Mycoplasma agalactiae
,
Mycoplasma putrefaciens
,
Mycoplasma capricolum
subsp.
capricolum
, and
Mycoplasma mycoides
subsp.
mycoides
Large Colony Type
Authors: Assunção Patricia , Antunes Nuno T. , Rosales Ruben S. , Poveda Carlos , Poveda Jose B. , Davey Hazel M. 
Published: July 2006

ABSTRACT
Flow cytometry together with SYBR green I and propidium iodide was used to study the effects of enrofloxacin, ciprofloxacin, gentamicin, chloramphenicol, oxytetracycline, and tylosin on four mycoplasma species. Inhibition of mycoplasma growth could be detected by as early as 3 h after the start of treatment. The strongest effect was observed with enrofloxacin- and ciprofloxacin-treated cells.
Impacts of Nucleating Aerosol on Florida Storms. Part I: Mesoscale Simulations
Authors: van den Heever Susan C. , Carrió Gustavo G. , Cotton William R. , DeMott Paul J. , Prenni Anthony J. 
Published: July 2006

Abstract
Toward the end of the Cirrus Regional Study of Tropical Anvils and Cirrus Layer–Florida Area Cirrus Experiment (CRYSTAL–FACE) field campaign held during July 2002, high concentrations of Saharan dust, which can serve as cloud condensation nuclei (CCN), giant CCN (GCCN), and ice-forming nuclei (IFN) were observed over the peninsula of Florida. To investigate the impacts of enhanced aerosol concentrations on the characteristics of convective storms and their subsequent anvil development, sensitivity tests are conducted using the Regional Atmospheric Modeling System (RAMS) model, in which the initialization profiles of CCN, GCCN, and IFN concentrations are varied. These variations are found to have significant effects on the storm dynamics and microphysical processes, as well as on the surface precipitation. Updrafts are consistently stronger as the aerosol concentrations are increased. The anvils cover a smaller area but are better organized and have larger condensate mixing ratio maxima in the cases with greater aerosol concentrations. Cloud water mass tends to increase with increasing aerosol concentrations, with enhanced GCCN concentrations having the most significant influence. Increasing either the GCCN or IFN concentrations produces the most rainfall at the surface whereas enhanced CCN concentrations reduce surface rainfall. Higher IFN concentrations produce ice at warmer temperatures and deeper anvils, but simultaneously increasing the concentrations of CCN and GCCN leads to more supercooled liquid water available for freezing and greater ice mixing ratios. Graupel mixing ratios decrease and hail mixing ratios increase with increasing aerosol concentrations. Higher concentrations of GCCN and IFN result in greater accumulated surface precipitation initially. By the end of the simulation period, however, the accumulated precipitation is the greatest for the case in which the aerosol concentrations are lowest. Such changes in the dynamical and microphysical characteristics of convective storms as a result of the variations in aerosol concentrations have potential climate consequences, both through cloud radiative effects and the hydrological cycle. The impacts of varying CCN, GCCN, and IFN concentrations on the anvils will be discussed more fully in Part II.
Dynamics of Synoptic Eddy and Low-Frequency Flow Interaction. Part II: A Theory for Low-Frequency Modes
Authors: Jin F-F. , Pan L-L. , Watanabe M. 
Published: July 2006

Abstract
Amidst stormy atmospheric circulation, there are prominent recurrent patterns of variability in the planetary circulation, such as the Antarctic Oscillation (AAO), Arctic Oscillation (AO) or North Atlantic Oscillation (NAO), and the Pacific–North America (PNA) pattern. The role of the synoptic eddy and low-frequency flow (SELF) feedback in the formation of these dominant low-frequency modes is investigated in this paper using the linear barotropic model with the SELF feedback proposed in Part I. It is found that the AO-like and AAO-like leading singular modes of the linear dynamical system emerge from the stormy background flow as the result of a positive SELF feedback. This SELF feedback also prefers a PNA-like singular vector as well among other modes under the climatological conditions of northern winters.
A model with idealized conditions of basic mean flow and activity of synoptic eddy flow and a prototype model are also used to illustrate that there is a natural scale selection for the AAO- and AO-like modes through the positive SELF feedback. The zonal scale of the localized features in the Atlantic (southern Indian Ocean) for AO (AAO) is largely related to the zonal extent of the enhanced storm track activity in the region. The meridional dipole structures of AO- and AAO-like low-frequency modes are favored because of the scale-selective positive SELF feedback, which can be heuristically understood by the tilted-trough mechanism.
Solar Semidiurnal Tide in the Dusty Atmosphere of Mars
Authors: Forbes Jeffrey M. , Miyahara Saburo 
Published: July 2006

Abstract
Vertical coupling due to the solar semidiurnal tide in Mars's atmosphere, and effects on zonal mean temperature and wind structures, are investigated using a numerical model. The model provides self-consistent solutions to the coupled zonal mean and tidal equations from the surface to 250 km. Breaking (convective instability) of the semidiurnal tide is parameterized using a linear saturation scheme with associated eddy diffusivities. Thermal forcing in the model gives rise to surface pressure perturbations and middle-atmosphere zonal mean winds and temperatures that are consistent with available measurements and general circulation models. Results presented here primarily focus on globally elevated dust levels during Southern Hemisphere summer, conditions similar to those experienced by the Viking 1 and Viking 2 landers during the 1977 global dust storms. Semidiurnal temperature and wind amplitudes maximize in the winter hemisphere and exceed 50 K and 100 m s−1 above 150 km and are typically 10–20 K and 10–20 m s−1 at 50 km. Perturbation densities are of order 50%–70% between 90 and 150 km, and thus contribute significantly to variability of the aerobraking regime in Mars's atmosphere.
Eddy diffusivities associated with the breaking parameterization reach values of order 103–104 m2 s−1 between 100 and 150 km, and can be of order 1–10 m2 s−1 between 0 and 50 km. Dissipation of the semidiurnal tide induces zonal mean westward winds of order 10–30 m s−1 below 100 km, and in excess of 200 m s−1 above 150 km. The corresponding temperature perturbations range between −20 and −70 K over most of the thermosphere, with 10–20-K increases in temperature at high winter latitudes between 50 and 100 km. All of the wave and zonal mean perturbations noted above represent very significant modifications to the thermal and dynamical structure of Mars's atmosphere.
Estimates are also provided for the eastward-propagating diurnal tides with zonal wavenumbers s = −1 and s = −2. These waves also have long vertical wavelengths and hence are capable of effectively coupling the lower and upper atmospheres of Mars. However, the perturbation and zonal mean effects of these waves are a factor of 2 or more smaller than those cited above for the semidiurnal tide under dusty conditions.
A Mass-Flux Scheme View of a High-Resolution Simulation of a Transition from Shallow to Deep Cumulus Convection
Authors: Kuang Zhiming , Bretherton Christopher S. 
Published: July 2006

Abstract
In this paper, an idealized, high-resolution simulation of a gradually forced transition from shallow, nonprecipitating to deep, precipitating cumulus convection is described; how the cloud and transport statistics evolve as the convection deepens is explored; and the collected statistics are used to evaluate assumptions in current cumulus schemes. The statistical analysis methodologies that are used do not require tracing the history of individual clouds or air parcels; instead they rely on probing the ensemble characteristics of cumulus convection in the large model dataset. They appear to be an attractive way for analyzing outputs from cloud-resolving numerical experiments. Throughout the simulation, it is found that 1) the initial thermodynamic properties of the updrafts at the cloud base have rather tight distributions; 2) contrary to the assumption made in many cumulus schemes, nearly undiluted air parcels are too infrequent to be relevant to any stage of the simulated convection; and 3) a simple model with a spectrum of entraining plumes appears to reproduce most features of the cloudy updrafts, but significantly overpredicts the mass flux as the updrafts approach their levels of zero buoyancy. A buoyancy-sorting model was suggested as a potential remedy. The organized circulations of cold pools seem to create clouds with larger-sized bases and may correspondingly contribute to their smaller lateral entrainment rates. Our results do not support a mass-flux closure based solely on convective available potential energy (CAPE), and are in general agreement with a convective inhibition (CIN)-based closure. The general similarity in the ensemble characteristics of shallow and deep convection and the continuous evolution of the thermodynamic structure during the transition provide justification for developing a single unified cumulus parameterization that encompasses both shallow and deep convection.
Structure, Propagation, and Mixing of Energetic Baroclinic Tides in Mamala Bay, Oahu, Hawaii
Authors: Alford Matthew H. , Gregg Michael C. , Merrifield Mark A. 
Published: July 2006

AbstractLarge semidiurnal vertical displacements (≈100 m) and strong baroclinic currents (≈0.5 m s−1; several times as large as barotropic currents) dominate motions in Mamala Bay, outside the mouth of Pearl Harbor, Hawaii. During September 2002, the authors sought to characterize them with a 2-month McLane moored profiler deployment and a 4-day intensive survey with a towed CTD/ADCP and the Research Vessel (R/V) Revelle hydrographic sonar. Spatial maps and time series of turbulent dissipation rate ε, diapycnal diffusivity Kρ, isopycnal displacement η, velocity u, energy E, and energy flux F are presented. Dissipation rate peaks in the lower 150 m during rising isopycnals and high strain and shows a factor-of-50 spring–neap modulation. The largest Kρ values, in the western bay near a submarine ridge, exceed 10−3 m2 s−1. The M2 phases of η and u increase toward the west, implying a westward phase velocity cp ≈ 1 m s−1 and horizontal wavelength ≈60 km, consistent with theoretical mode-1 values. These phases vary strongly (≈±45°) in time relative to astronomical forcing, implying remotely generated signals. Energy and energy flux peak 1–3 days after spring tide, supporting this interpretation. The group velocity, computed as the ratio F/E, is near ≈1 m s−1, also in agreement with theoretical mode-1 values. Spatial maps of energy flux agree well with results from the Princeton Ocean Model, indicating converging fluxes in the western bay from waves generated to the east and west. The observations indicate a time-varying interference pattern between these waves that is modulated by background stratification between their sources and Mamala Bay.
Baroclinic Energy Flux at the Hawaiian Ridge: Observations from the R/P FLIP
Authors: Rainville Luc , Pinkel Robert 
Published: July 2006

Abstract
Estimates of baroclinic energy flux are made in the immediate “Nearfield” (September–October 2002) and 450 km offshore (“Farfield”; October–November 2001) of the Kaena Ridge, an active barotropic-to-baroclinic conversion site. The flux estimates are based on repeated profiles of velocity and density obtained from the Research Platform Floating Instrument Platform (FLIP) as an aspect of the Hawaii Ocean Mixing Experiment. Energetic beams associated with both semidiurnal and diurnal internal waves are observed in the Kauai Channel. Beam depths and orientations are consistent with generation along the upper flanks of the ridge. At the far-field site, the baroclinic energy flux is borne primarily by first-mode semidiurnal waves. The energy flux associated with the entire spectrum of internal waves is computed by cross-spectral analysis. Significant energy fluxes are found in the inertial, diurnal, semidiurnal, and twice-semidiurnal frequency bands. The semidiurnal energy flux strongly dominates the spectrum at both sites. The flux magnitude follows the spring–neap cycle of the semidiurnal barotropic tide. The averaged depth-integrated mode-1 semidiurnal energy flux (over the entire water column) in the Farfield is found to be 1.7 ± 0.3 kW m−1 away from the ridge, with peak values up to 4 kW m−1. Small fluxes toward the ridge are occasionally seen at neap tide. At both sites, energy fluxes in the diurnal frequency band represent 15%–20% of the semidiurnal energy flux. In the Farfield, the magnitude of the diurnal energy flux varies in accord with the fortnightly cycle of the barotropic semidiurnal tide, rather than with the diurnal forcing, suggesting that energy for those waves is supplied by a cross-frequency transfer from the low-vertical-mode M2 internal tide to higher-mode internal waves at frequencies ½M2. In the Nearfield, the diurnal flux varies with fluctuations in both diurnal and semidiurnal forcing.
Flow and Mixing around a Small Seamount on Kaena Ridge, Hawaii
Authors: Carter Glenn S. , Gregg Michael C. , Merrifield Mark A. 
Published: July 2006

AbstractMicrostructure observations over a small seamount on the Kaena Ridge, Hawaii, showed asymmetry in the along- and across-ridge directions. The ∼400-m-high seamount is on the southern edge of the ridge (centered at 21°43′49″N, 158°38′48″W), 42 km northwest of Oahu. A 1-km-resolution numerical simulation shows that the flow within the depth range of the seamount tends to be accelerated around the seamount rather than going up and over it. The flow patterns, however, are more complicated than for an isolated seamount because of the influence of the ∼3000-m-high Kaena Ridge. Comparison with the numerical simulations indicates that the across-ridge asymmetry, in which dissipation on the north-northeastern side of the seamount was higher and more concentrated toward the bed than on the south-southwestern side, is consistent with an M2 tidal beam generated at the northern edge of the ridge. The along-ridge asymmetry, with higher dissipation on the east-southeastern flank than on the west-northwestern flank, is in qualitative agreement with M2 shear variance from the model simulation. The average observed dissipation rate over the seamount was ɛ = 6.2 × 10−8 W kg−1, and diapycnal diffusivity was Kρ = 1.3 × 10−3 m2 s−1. Dissipation measurements following the 1000-m isobath south-southwest of the seamount suggest along-ridge internal tide generation caused by topographic steering that creates an along-ridge current over critical topography northwest of the seamount.
Histone acetylation is associated with differential gene expression in the rapid and robust memory CD8+ T-cell response
Authors: Fann Monchou , Godlove Jason M. , Catalfamo Marta , Wood William H. , Chrest Francis J. , Chun Nicholas , Granger Larry , Wersto Robert , Madara Karen , Becker Kevin , Henkart Pierre A. , Weng Nan-ping 
Published: July 2006

AbstractTo understand the molecular basis for the rapid and robust memory T-cell responses, we examined gene expression and chromatin modification by histone H3 lysine 9 (H3K9) acetylation in resting and activated human naive and memory CD8+ T cells. We found that, although overall gene expression patterns were similar, a number of genes are differentially expressed in either memory or naive cells in their resting and activated states. To further elucidate the basis for differential gene expression, we assessed the role of histone H3K9 acetylation in differential gene expression. Strikingly, higher H3K9 acetylation levels were detected in resting memory cells, prior to their activation, for those genes that were differentially expressed following activation, indicating that hyperacetylation of histone H3K9 may play a role in selective and rapid gene expression of memory CD8+ T cells. Consistent with this model, we showed that inducing high levels of H3K9 acetylation resulted in an increased expression in naive cells of those genes that are normally expressed differentially in memory cells. Together, these findings suggest that differential gene expression mediated at least in part by histone H3K9 hyperacetylation may be responsible for the rapid and robust memory CD8+ T-cell response.
The effects of lestaurtinib (CEP701) and PKC412 on primary AML blasts: the induction of cytotoxicity varies with dependence on FLT3 signaling in both FLT3-mutated and wild-type cases
Authors: Knapper Steven , Mills Kenneth I. , Gilkes Amanda F. , Austin Steve J. , Walsh Val , Burnett Alan K. 
Published: July 2006

AbstractThe receptor tyrosine kinase FLT3 is a promising molecular therapeutic target in acute myeloid leukemia (AML). Activating mutations of FLT3 are present in approximately one-third of patients, while many nonmutants show evidence of FLT3 activation, which appears to play a significant role in leukemogenesis. We studied the effects of lestaurtinib (CEP701) and PKC412, 2 small molecule inhibitors of FLT3, on 65 diagnostic AML blast samples. Both agents induced concentration-dependent cytotoxicity in most cases, although responses to PKC412 required higher drug concentrations. Cytotoxic responses were highly heterogeneous and were only weakly associated with FLT3 mutation status and FLT3 expression. Importantly, lestaurtinib induced cytotoxicity in a synergistic fashion with cytarabine, particularly in FLT3 mutant samples. Both lestaurtinib and PKC412 caused inhibition of FLT3 phosphorylation in all samples. Translation of FLT3 inhibition into cytotoxicity was influenced by the degree of residual FLT3 phosphorylation remaining and correlated with deactivation of STAT5 and MAP kinase. FLT3 mutant and wild-type cases both varied considerably in their dependence on FLT3 signaling for survival. These findings support the continued clinical assessment of FLT3 inhibitors in combination with cytotoxic chemotherapy: Entry to future clinical trials should include FLT3 wild-type patients and should remain unrestricted by FLT3 expression level.