bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acquisition of a Transposon Encoding Extended-Spectrum β-Lactamase SHV-12 by
Pseudomonas aeruginosa
Isolates during the Clinical Course of a Burn Patient
Authors: Uemura Shuji , Yokota Shin-ichi , Mizuno Hirotoshi , Sakawaki Eiji , Sawamoto Keigo , Maekawa Kunihiko , Tanno Katsutoshi , Mori Kazuhisa , Asai Yasufumi , Fujii Nobuhiro 
Published: June 2010

ABSTRACT

Three of seven clonally related
Pseudomonas aeruginosa
strains isolated from a burn patient produced the extended-spectrum β-lactamase (ESBL) SHV-12. Its gene was flanked by two IS
26
elements with a large transposon (>24 kb). The transposon also contained at least five IS
26
elements and a gene encoding the amikacin resistance determinant aminoglycoside 6′-
N
-acetyltransferase type Ib [
aac
(
6′
)
-Ib
]. It was inserted into the gene PA5317 in the
P. aeruginosa
chromosome.
Chromosomally Encoded
bla
CMY-2
Located on a Novel SXT/R391-Related Integrating Conjugative Element in a
Proteus mirabilis
Clinical Isolate
Authors: Harada Sohei , Ishii Yoshikazu , Saga Tomoo , Tateda Kazuhiro , Yamaguchi Keizo 
Published: June 2010

ABSTRACT

Integrating conjugative elements (ICEs) are mobile genetic elements that can transfer from the chromosome of a host to the chromosome of a new host through the process of excision, conjugation, and integration. Although SXT/R391-related ICEs, originally demonstrated in
Vibrio cholerae
O139 isolates, have become prevalent among
V. cholerae
isolates in Asia, the prevalence of the ICEs among Gram-negative bacteria other than
Vibrio
spp. remains unknown. In addition, SXT/R391-related ICEs carrying genes conferring resistance to extended-spectrum cephalosporins have never been described. Here we carried out a genetic analysis of a cefoxitin-resistant
Proteus mirabilis
clinical isolate, TUM4660, which revealed the presence of a novel SXT/R391-related ICE, ICE
Pmi
Jpn1. ICE
Pmi
Jpn1 had a core genetic structure showing high similarity to that of R391 and carried
xis
and
int
genes completely identical to those of R391, while an IS
10
-mediated composite transposon carrying
bla
CMY-2
was integrated into the ICE. A nucleotide sequence identical to the 3′ part of IS
Ecp1
was located upstream of the
bla
CMY-2
gene, and other genes observed around
bla
CMY-2
in earlier studies were also present. Furthermore, the nucleotide sequences of hot spot 2 and hot spot 4 in ICE
Pmi
Jpn1 showed high similarity to that of hot spot 2 in SXT
MO10
and with a part of the nucleotide sequence found in
P. mirabilis
ATCC 29906, respectively. ICE
Pmi
Jpn1 was successfully transferred to
Escherichia coli
,
Klebsiella pneumoniae
,
Salmonella enterica
serovar Typhimurium, and
Citrobacter koseri
in conjugation experiments. These observations suggest that ICEs may contribute to the dissemination of antimicrobial resistance genes among clinically relevant
Enterobacteriaceae
, which warrants careful observation of the prevalence of ICEs, including SXT/R391-related ICEs.
Investigations into the Role of the
Plasmodium falciparum
SERCA (PfATP6) L263E Mutation in Artemisinin Action and Resistance
Authors: Valderramos Stephanie Gaw , Scanfeld Daniel , Uhlemann Anne-Catrin , Fidock David A. , Krishna Sanjeev 
Published: June 2010

ABSTRACT

Artemisinin-based combination therapies (ACTs) are highly effective for the treatment of
Plasmodium falciparum
malaria, yet their sustained efficacy is threatened by the potential spread of parasite resistance. Recent studies have provided evidence that artemisinins can inhibit the function of PfATP6, the
P. falciparum
ortholog of the ER calcium pump SERCA, when expressed in
Xenopus laevis
oocytes. Inhibition was significantly reduced in an L263E variant, which introduced the mammalian residue into a putative drug-binding pocket. To test the hypothesis that this single mutation could decrease
P. falciparum
susceptibility to artemisinins, we implemented an allelic-exchange strategy to replace the wild-type
pfatp6
allele by a variant allele encoding L263E. Transfected
P. falciparum
clones were screened by PCR analysis for disruption of the endogenous locus and introduction of the mutant L263E allele under the transcriptional control of a
calmodulin
promoter. Expression of the mutant allele was demonstrated by reverse transcriptase (RT) PCR and verified by sequence analysis. Parasite clones expressing wild-type or L263E variant PfATP6 showed no significant difference in 50% inhibitory concentrations (IC
50
s) for artemisinin or its derivatives dihydroartemisinin and artesunate. Nonetheless, hierarchical clustering analysis revealed a trend toward reduced susceptibility that neared significance (artemisinin,
P
≈ 0.1; dihydroartemisinin,
P
= 0.053 and
P
= 0.085; and artesunate,
P
= 0.082 and
P
= 0.162 for the D10 and 7G8 lines, respectively). Notable differences in the distribution of normalized IC
50
s provided evidence of decreased responsiveness to artemisinin and dihydroartemisinin (
P
= 0.02 for the D10 and 7G8 lines), but not to artesunate in parasites expressing mutant PfATP6.
In
Vitro
Synergism of Ciprofloxacin and Cefotaxime against Nalidixic Acid-Resistant
Salmonella enterica
Serotypes Paratyphi A and Paratyphi B
Authors: Neupane Ganesh Prasad , Kim Dong-Min , Kim Sung Hun , Lee Bok Kwon 
Published: June 2010

ABSTRACT

Paratyphoid fever is considered an emerging systemic intracellular infection caused by
Salmonella enterica
serotypes Paratyphi A, B, and C. We performed
in vitro
time-kill studies on three clinical isolates of nalidixic acid-resistant
Salmonella
serotype Paratyphi (NARSP) with different concentrations of ciprofloxacin and cefotaxime to identify combinations of antibiotics with synergistic activity against paratyphoid fever. Furthermore, we identify the frequency of mutations to ciprofloxacin, cefotaxime, and rifampin resistance and also sequenced the
gyrA
,
gyrB
,
parC
, and
parE
genes to identify the cause of resistance in NARSP. When the activity of ciprofloxacin at 0.75× MIC (0.012 to 0.38 μg/ml) with cefotaxime at the MIC (0.125 to 0.25 μg/ml) against all three NARSP isolates was investigated, synergy was observed at 24 h, and the bacterial counts were reduced by >3 log
10
CFU/ml. This synergy was elongated for up to 72 h in two out of three isolates. When ciprofloxacin at 0.75× MIC (0.012 to 0.38 μg/ml) was combined with cefotaxime at 2× MIC (0.25 to 0.50 μg/ml), synergy was prolonged for up to 72 h in all three isolates. Both
Salmonella
serotype Paratyphi A isolates carried single mutations in codon 83 of the
gyrA
gene and codon 84 of the
par
C gene that were responsible for their reduced susceptibility to ciprofloxacin, while no mutations were found in the
gyrB
or
parE
gene. The ciprofloxacin-plus-cefotaxime regimen was very effective in reducing the bacterial counts at 24 h for all three isolates, and this combination therapy may be helpful in reducing the chance of the emergence of fluoroquinolone-resistant mutants in patients with severe paratyphoid fever.
Fusidic Acid Resistance Rates and Prevalence of Resistance Mechanisms among
Staphylococcus
spp. Isolated in North America and Australia, 2007-2008
Authors: Castanheira Mariana , Watters Amy A. , Bell Jan M. , Turnidge John D. , Jones Ronald N. 
Published: June 2010

ABSTRACT

Among 4,167
Staphylococcus aureus
and 790 coagulase-negative
Staphylococcus
(CoNS; not
S. saprophyticus
) isolates collected consecutively from North American and Australian hospitals, only 87 (1.7% overall) isolates displayed a fusidic acid (FA; also known as CEM-102) MIC of ≥2 μg/ml (FA resistance). These strains were further evaluated with a multiplex PCR to amplify the acquired resistance genes
fusB
,
fusC
, and
fusD.
Mutations in
fusA
and
fusE
were evaluated in all isolates showing an absence of acquired resistance genes and/or showing FA MIC values of ≥64 μg/ml.
S. aureus
resistance rates were very low in the United States (0.3%) and were higher in Canada and Australia (7.0% for both countries). Among CoNS isolates, FA resistance rates were significantly more elevated than that for
S. aureus
(7.2 to 20.0%; the highest rates were in Canada). All 52 (41 CoNS) FA-resistant isolates from the United States showed FA MIC results of ≤64 μg/ml, and 7 of 11
S. aureus
isolates carried
fusC
. CoNS strains from the United States carried
fusB
or
fusC
. In Canada,
fusB
and
fusC
occurrences were similar among
S. aureus
and CoNS isolates, and modestly elevated FA MIC values were observed (all MIC results were ≤32 μg/ml). Isolates from Australia showed MIC values ranging from 2 to 32 μg/ml, and
S. aureus
isolates were predominantly
fusC
positive.
fusA
mutations were detected in only three
S. aureus
isolates, conferring FA MIC values of 2 to 8 μg/ml. Target mutations have been considered the primary FA resistance mechanism among
Staphylococcus
spp.; however, acquired resistance genes appear to have a dominant role in resistance against this older antimicrobial agent. In summary, this study shows that acquired genes are highly prevalent among FA-resistant strains (>90%) in three nations with distinct or absence (United States) of fusidic acid clinical use.
Leishmania donovaniAmastigotes Impair Gamma Interferon-Induced STAT1α Nuclear Translocation by Blocking the Interaction between STAT1α and Importin-α5
Authors: Matte Christine , Descoteaux Albert 
Published: June 2010

ABSTRACTThe protozoan parasiteLeishmania donovani, the etiological agent of visceral leishmaniasis, is renowned for its capacity to sabotage macrophage functions and signaling pathways stimulated by activators such as gamma interferon (IFN-γ). Our knowledge of the strategies utilized byL. donovanito impair macrophage responsiveness to IFN-γ remains fragmentary. In the present study, we investigated the impact of an infection by the amastigote stage ofL. donovanion IFN-γ responses and signaling via the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway in mouse bone marrow-derived macrophages. The levels of IFN-γ-induced expression of major histocompatibility complex class II and inducible nitric oxide synthase (iNOS) were strongly reduced inL. donovaniamastigote-infected macrophages. As the expression of those genes is mediated by the transcription factors STAT1α and IFN regulatory factor 1 (IRF-1), we investigated their activation in amastigote-infected macrophages treated with IFN-γ. We found that whereas STAT1α protein levels and the levels of phosphorylation on Tyr701 and Ser727 were normal, IRF-1 expression was inhibited in infected macrophages. This inhibition of IRF-1 expression correlated with a defective nuclear translocation of STAT1α, and further analyses revealed that the IFN-γ-induced STAT1α association with the nuclear transport adaptor importin-α5 was compromised inL. donovaniamastigote-infected macrophages. Taken together, our results provide evidence for a novel mechanism used byL. donovaniamastigotes to interfere with IFN-γ-activated macrophage functions and provide a better understanding of the strategies deployed by this parasite to ensure its intracellular survival.
Global Gene Expression Profiling ofYersinia pestisReplicating inside Macrophages Reveals the Roles of a Putative Stress-Induced Operon in Regulating Type III Secretion and Intracellular Cell Division
Authors: Fukuto Hana S. , Svetlanov Anton , Palmer Lance E. , Karzai A. Wali , Bliska James B. 
Published: June 2010

ABSTRACTYersinia pestis, the causative agent of plague, is a facultative intracellular pathogen. Previous studies have indicated that the ability ofY. pestisto survive inside macrophages may be critical during the early stages of plague pathogenesis. To gain insights into the biology of intracellularY. pestisand its environment following phagocytosis, we determined the genome-wide transcriptional profile ofY. pestisKIM5 replicating inside J774.1 macrophage-like cells using DNA microarrays. At 1.5, 4, and 8 h postinfection, a total of 801, 464, and 416Y. pestisgenes were differentially regulated, respectively, compared to the level of gene expression of control bacteria grown in tissue culture medium. A number of stress-response genes, including those involved in detoxification of reactive oxygen species, as well as several metabolic genes involved in macromolecule synthesis, were significantly induced in intracellularY. pestis, consistent with the presence of oxidative stress and nutrient starvation insideYersinia-containing vacuoles. A putative stress-induced operon consisting of y2313, y2315, and y2316 (y2313-y2316), and a previously unidentified open reading frame,orfX, was studied further on the basis of its high level of intracellular expression. Mutant strains harboring either deletion, Δy2313-y2316 or ΔorfX, exhibited diverse phenotypes, including reduced effector secretion by the type III secretion system, increased intracellular replication, and filamentous morphology of the bacteria growing inside macrophages. The results suggest a possible role for these genes in regulating cell envelope characteristics in the intracellular environment.
Developing injury indicators for Canadian children and youth: a modified-Delphi approach
Authors: Pike Ian , Piedt Shannon , Warda Lynne , Yanchar Natalie , Macarthur Colin , Babul Shelina , Macpherson Alison K 
Published: June 2010

ObjectiveTo develop a set of national injury indicators for Canadian children and youth which will eventually be used to reflect and monitor identified prevention priorities.MethodsThe Canadian Injury Indicators Development Team brought together injury researchers, policy makers, and practitioners to develop injury indicators in the following areas: overall health services implications; motor vehicle occupant; sports, recreation, and leisure; violence; and trauma care, quality, and outcomes. A modified-Delphi process was used to establish a set of indicators that met evidence-based criteria, were useful, and that would prompt action. Each indicator was rated by 132 respondent injury experts and stakeholders on itsusefulnessand ability toprompt actionto reduce injury among Canadian children and youth.ResultsFrom an initial list of 51 indicators, a refined set of 34 indicators was established. Indicators were grouped into three categories related to: policies; risk and protective factors; and outcomes. Indicators related to motor vehicle injury were rated as mostusefuland most able toprompt action. Injury mortality rate and injury hospitalisation rate were also rated highly for bothusefulnessand ability toprompt action. Policy, violence, sport and recreation, and trauma indicators were all rated higher forusefulness, but somewhat lower for ability toprompt action.ConclusionResults suggest that a broad-based modified-Delphi process is an important first step in developing useful and relevant indicators for injury prevention activity focused on Canadian children and youth.
Low-temperature thermochronology in the Peruvian Central Andes: implications for long-term continental denudation, timing of plateau uplift, canyon incision and lithosphere dynamics
Authors: Gunnell Yanni , Thouret Jean-Claude , Brichau Stéphanie , Carter Andy , Gallagher Kerry 
Published: June 2010

Abstract:

In Peru, the western edge of the 4.5 km high Western Cordillera is cut by a >3 km deep canyon. To understand incision by the Cotahuasi–Ocoña River and the regional uplift history of this orogenic plateau capped by volcanic rocks, 26 crystalline rock samples were collected for low-temperature thermochronology from vertical profiles parallel and perpendicular to the canyon. Rock cooling histories confirm that most plateau denudation had occurred prior to 24 Ma but plateau incision peaked after
c
. 14–9 Ma in response to rapid surface uplift. The abrupt occurrence of a rock heating event is also detected during middle Miocene time. This was either a response to the emplacement of low-conductivity, regionally extensive ignimbritic caprock or a response to crustal-scale fluid circulation caused by wet melting of the overriding plate when magmatism resumed
c
. 24 Ma. The potential for thermochronology to provide information on past geothermal gradients is discussed, showing how it can be used as a proxy for understanding change in subducting slab dynamics, with oscillations in subduction angle having perhaps been the main on–off switch for magmatism in this Cordilleran setting.

Supplementary material:

Fission-track and apatite (U–Th)/He results and apatite chemistry indicators are available at
http://www/geolsoc.org.uk/SUP18405
.
Exceptionally preserved ostracodes from a Middle Miocene palaeolake, California, USA
Authors: Wilkinson I.P. , Wilby P.R. , Williams M. , Siveter D.J. , Page A.A. , Leggitt L. , Riley D.A. 
Published: June 2010

Abstract:

Exceptionally well-preserved specimens of a new cypridid ostracode (Crustacea),
Raepula ira
sp. nov., are described from palaeolake sediments of the Middle Miocene Barstow Formation of the Mud Hills, southern California. This is only the second occurrence of exceptionally preserved ostracodes from the Miocene. Based on ages obtained from associated volcanic tuffs the palaeolake sediments were deposited between 16.3 and 15.8 Ma. The ostracodes form one element of a diverse lake community dominated by fairy shrimps, copepods, diatoms, larvae of diving beetles, flies and mosquitoes, and body fossils and ephippia of branchiopods and anomopods. The ostracodes are preserved three dimensionally with their soft anatomy replicated in microcrystalline silica. Submicron-scale details such as sensory setae are preserved, surpassing the resolution of most other ostracode-bearing lagerstätten and allowing their biology to be compared with extant taxa.

Supplementary material:

Red–blue anaglyphs of the exceptionally preserved ostracodes are available at
http://www.geolsoc.org.uk/SUP18407
.
Singleton types here, singleton types there, singleton types everywhere
Authors: Monnier Stefan , Haguenauer David 
Published: June 2010

Singleton types are often considered a poor man's substitute for dependent types. But their generalization in the form of GADTs has found quite a following. The main advantage of singleton types and GADTs is to preserve the so-called phase distinction, which seems to be so important to make use of the usual compilation techniques. Of course, they considerably restrict the programmers, which often leads them to duplicate code at both the term and type levels, so as to reflect at the type level what happens at the term level, in order to be able to reason about it.
In this article, we show how to automate such a duplication while eliminating the problematic dependencies. More specifically, we show how to compile the Calculus of Constructions into ?H, a non-dependently-typed language, while still preserving all the typing information. Since ?H has been shown to be amenable to type preserving CPS and closure conversion, it shows a way to preserve types when doing code extraction and more generally when using all the common compiler techniques.
Strong Convergence Theorems by Hybrid Methods for Strict Pseudocontractions and Equilibrium Problems
Authors: Duan Peichao , Zhao Jing 
Published: June 2010

AbstractLet "Equation missing" be N strict pseudocontractions defined on a closed convex subset "Equation missing" of a real Hilbert space "Equation missing". Consider the problem of finding a common element of the set of fixed point of these mappings and the set of solutions of an equilibrium problem with the parallel and cyclic algorithms. In this paper, we propose new iterative schemes for solving this problem and prove these schemes converge strongly by hybrid methods.
Influence of Sea Surface Warming on Environmental Factors Affecting Long-Term Changes of Atlantic Tropical Cyclone Formation
Authors: Wu Liguang , Tao Li , Ding Qinghua 
Published: June 2010

Abstract
Despite the observed high correlation between the Atlantic sea surface temperature (SST) and the Atlantic tropical cyclone (TC) activity, interpretation of this relationship remains uncertain. This study suggests that the tropical Atlantic sea surface warming induces a pair of anomalous low-level cyclones on each side of the equator, providing favorable conditions for enhancing TC formation east of 45°W, while the effect of SST warming in the tropical Indian Ocean and Pacific Ocean tends to suppress the TC formation.
Over the past 30 years (1978–2007), the TC activity in the Atlantic basin is characterized with significant enhancement of TC formation east of 45°W, where the total TC number increased significantly compared to the period 1948–77. Despite the possible undercount of TCs, this study shows that the recently enhanced TC formation may not be totally accounted for by the poor TC observing network prior to the satellite era. The Atlantic sea surface warming that occurred in recent decades might have allowed more TCs to form, to form earlier, and to take a longer track, while the effect is partially offset by the SST warming in Indian and Pacific Oceans. This study suggests that the close relationship between the Atlantic SST and TC activity over the past 30 years, including basinwide increases in the average lifetime, annual frequency, proportion of intense hurricanes, and annual accumulated power dissipation index (PDI), as reported in previous studies, is mainly a result of the SST warming in the tropical Atlantic exceeding that in the tropical Indian and Pacific Oceans. The results agree with recent argument that the relative Atlantic SST change or the SST difference between the tropical Atlantic and other oceans play an important role in controlling long-term TC activity in the Atlantic basin.
On the Reasons for the Formation and Variability of the Azores Current
Authors: Volkov Denis L. , Fu Lee-Lueng 
Published: June 2010

Abstract
Recent studies have shown that the formation of the well-defined, zonally oriented Azores Current may be the result of water mass transformation associated with the Mediterranean outflow in the Gulf of Cadiz. As the denser Mediterranean water descends down the continental slope, it entrains overlying North Atlantic Central Water. It is believed that the Azores Current then forms as part of the horizontal recirculating gyre generated through the β-plume mechanism. In this study, the authors further explore this hypothesis by performing a series of numerical experiments. These experiments are based on a high-resolution general circulation model that includes the Mediterranean Sea and that realistically simulates the water mass exchange through the Strait of Gibraltar and the transport and variability of the Azores Current. The authors show that the divergence of the relative vorticity flux and the planetary vorticity flux, associated with planetary waves, are the main factors determining the variability of the Azores Current. It is shown experimentally that the closure of the Strait of Gibraltar leads to a complete disappearance of the Azores Current. On the other hand, with the open Strait of Gibraltar, the Azores Current persists even when the wind forcing over the region is turned off. The atmospheric forcing is thus not responsible for the formation of the Azores Current, but it affects the variability of the current with a minor effect on its magnitude. Numerical experiments suggest that the strength and the variability of the Azores Current depend on the magnitude of the water mass exchange through the Strait of Gibraltar but not on its seasonal variability.