bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple anatomy optimization of accumulated dose
Authors: Watkins W. Tyler , Moore Joseph A. , Gordon James , Hugo Geoffrey D. , Siebers Jeffrey V. 
Published: October 2014

Purpose:To investigate the potential advantages of multiple anatomy optimization (MAO) for lung cancer radiation therapy compared to the internal target volume (ITV) approach.Methods:MAO aims to optimize a single fluence to be delivered under free‐breathing conditions such that the accumulated dose meets the plan objectives, where accumulated dose is defined as the sum of deformably mapped doses computed on each phase of a single four dimensional computed tomography (4DCT) dataset. Phantom and patient simulation studies were carried out to investigate potential advantages of MAO compared to ITV planning. Through simulated delivery of the ITV‐ and MAO‐plans, target dose variations were also investigated.Results:By optimizing the accumulated dose, MAO shows the potential to ensure dose to the moving target meets plan objectives while simultaneously reducing dose to organs at risk (OARs) compared with ITV planning. While consistently superior to the ITV approach, MAO resulted in equivalent OAR dosimetry at planning objective dose levels to within 2% volume in 14/30 plans and to within 3% volume in 19/30 plans for each lung V20, esophagus V25, and heart V30. Despite large variations in per‐fraction respiratory phase weights in simulated deliveries at high dose rates (e.g., treating 4/10 phases during single fraction beams) the cumulative clinical target volume (CTV) dose after 30 fractions and per‐fraction dose were constant independent of planning technique. In one case considered, however, per‐phase CTV dose varied from 74% to 117% of prescription implying the level of ITV‐dose heterogeneity may not be appropriate with conventional, free‐breathing delivery.Conclusions:MAO incorporates 4DCT information in an optimized dose distribution and can achieve a superior plan in terms of accumulated dose to the moving target and OAR sparing compared to ITV‐plans. An appropriate level of dose heterogeneity in MAO plans must be further investigated.
Antibiotic Use before Chlamydia and Gonorrhea Genital and Extragenital Screening in the Sexually Transmitted Infection Clinical Setting
Authors: Dukers-Muijrers Nicole H. T. M. , van Liere Genevieve A. F. S. , Wolffs Petra F. G. , Den Heijer Casper , Werner Marita I. L. S. , Hoebe Christian J. P. A. 
Published: October 2014

ABSTRACT

Background antibiotic use (i.e., administration of antibiotics not directly related to
Chlamydia trachomatis
or
Neisseria gonorrhoeae
infections) has been associated with a lower prevalence of genital
C. trachomatis
infection in a clinical setting. Associations with specific antibiotic types or with
N. gonorrhoeae
are lacking. Here, we assessed the prevalence of antibiotic use, the different classes and agents used, and their association with a subsequent sexually transmitted infection (STI) clinic
C. trachomatis
and
N. gonorrhoeae
test result. At our STI clinic, we systematically registered whether antibiotics were used in the past month (in 29% of the cases, the specific antibiotic agent was named). Patients were screened for urogenital
C. trachomatis
and
N. gonorrhoeae
; a third of them were also screened for anorectal and oropharyngeal
C. trachomatis
and
N. gonorrhoeae
. The proportion of antibiotics used and their association with
C. trachomatis
and
N. gonorrhoeae
prevalence were assessed for heterosexual men, men who have sex with men (MSM), and women. During 14,775 clinic consultations, antibiotic use was reported by 12.2% (95% confidence interval [CI], 11.7% to 12.7%), i.e., 14.8% of women, 8.6% of heterosexual men, and 11.6% of MSM. The most reported antibiotics were penicillins, tetracyclines, and macrolides, respectively. The prevalence was 11.0% (95% CI, 10.3% to 11.3%) for
C. trachomatis
and 1.9% (95% CI, 1.7% to 2.1%) for
N. gonorrhoeae
. Only tetracycline use was associated with a lower
C. trachomatis
prevalence (3%). Overall antibiotic use was associated with lower anorectal
C. trachomatis
prevalence in MSM only (odds ratio, 0.4; 95% CI, 0.2 to 0.8). STI clinic visitors commonly report recent antibiotic use. Even in a country with low antibiotic consumption, tetracycline use impacted
C. trachomatis
prevalence, while there was a notable absence of association with azithromycin.
Genome-Wide Evaluation of the Interplay between Caenorhabditis elegans and Yersinia pseudotuberculosis during
In Vivo
Biofilm Formation
Authors: Joshua George W. P. , Atkinson Steve , Goldstone Robert J. , Patrick Hannah L. , Stabler Richard A. , Purves Joanne , Cámara Miguel , Williams Paul , Wren Brendan W. 
Published: October 2014

ABSTRACT

The formation of an incapacitating biofilm on
Caenorhabditis elegans
by
Yersinia pseudotuberculosis
represents a tractable model for investigating the genetic basis for host-pathogen interplay during the biofilm-mediated infection of a living surface. Previously we established a role for quorum sensing (QS) and the master motility regulator, FlhDC, in biofilm formation by
Y. pseudotuberculosis
on
C. elegans
. To obtain further genome-wide insights, we used transcriptomic analysis to obtain comparative information on
C. elegans
in the presence and absence of biofilm and on wild-type
Y. pseudotuberculosis
and
Y. pseudotuberculosis
QS mutants. Infection of
C. elegans
with the wild-type
Y. pseudotuberculosis
resulted in the differential regulation of numerous genes, including a distinct subset of nematode C-lectin (
clec
) and fatty acid desaturase (
fat
) genes. Evaluation of the corresponding
C. elegans
clec-49
and
fat-3
deletion mutants showed delayed biofilm formation and abolished biofilm formation, respectively. Transcriptomic analysis of
Y. pseudotuberculosis
revealed that genes located in both of the histidine utilization (
hut
) operons were upregulated in both QS and
flhDC
mutants. In addition, mutation of the regulatory gene
hutC
resulted in the loss of biofilm, increased expression of
flhDC
, and enhanced swimming motility. These data are consistent with the existence of a regulatory cascade in which the Hut pathway links QS and
flhDC
. This work also indicates that biofilm formation by
Y. pseudotuberculosis
on
C. elegans
is an interactive process during which the initial attachment/recognition of
Yersinia
to/by
C. elegans
is followed by bacterial growth and biofilm formation.
Ethanol-Induced Alcohol Dehydrogenase E (AdhE) Potentiates Pneumolysin in Streptococcus pneumoniae
Authors: Luong Truc Thanh , Kim Eun-Hye , Bak Jong Phil , Nguyen Cuong Thach , Choi Sangdun , Briles David E. , Pyo Suhkneung , Rhee Dong-Kwon 
Published: October 2014

ABSTRACTAlcohol impairs the host immune system, rendering the host more vulnerable to infection. Therefore, alcoholics are at increased risk of acquiring serious bacterial infections caused byStreptococcus pneumoniae, including pneumonia. Nevertheless, how alcohol affects pneumococcal virulence remains unclear. Here, we showed that theS. pneumoniaetype 2 D39 strain is ethanol tolerant and that alcohol upregulates alcohol dehydrogenase E (AdhE) and potentiates pneumolysin (Ply). Hemolytic activity, colonization, and virulence ofS. pneumoniae, as well as host cell myeloperoxidase activity, proinflammatory cytokine secretion, and inflammation, were significantly attenuated inadhEmutant bacteria (ΔadhEstrain) compared to D39 wild-type bacteria. Therefore, AdhE might act as a pneumococcal virulence factor. Moreover, in the presence of ethanol,S. pneumoniaeAdhE produced acetaldehyde and NADH, which subsequently led Rex (redox-sensing transcriptional repressor) to dissociate from theadhEpromoter. An increase in AdhE level under the ethanol condition conferred an increase in Ply and H2O2levels. Consistently,S. pneumoniaeD39 caused higher cytotoxicity to RAW 264.7 cells than the ΔadhEstrain under the ethanol stress condition, and ethanol-fed mice (alcoholic mice) were more susceptible to infection with the D39 wild-type bacteria than with the ΔadhEstrain. Taken together, these data indicate that AdhE increases Ply under the ethanol stress condition, thus potentiating pneumococcal virulence.
Expression of Enteropathogenic Escherichia coli Map Is Significantly Different than That of Other Type III Secreted Effectors
In Vivo
Authors: Nguyen Mai , Rizvi Jason , Hecht Gail 
Published: October 2014

ABSTRACT

The enteropathogenic
Escherichia coli
(EPEC) locus of enterocyte effacement (LEE)-encoded effectors EspF and Map are multifunctional and have an impact on the tight junction barrier while the non-LEE-encoded proteins NleH1 and NleH2 possess significant anti-inflammatory activity. In order to address the temporal expression of these important genes
in vivo
, their promoters were cloned upstream of the
luxCDABE
operon, and luciferase expression was measured in EPEC-infected mice by bioluminescence using an
in vivo
imaging system (IVIS). Bioluminescent images of living mice, of excised whole intestines, and of whole intestines longitudinally opened and washed were assessed. The majority of bioluminescent bacteria localized in the cecum by 3 h postinfection, indicating that the cecum is not only a major colonization site of EPEC but also a site of EPEC effector gene expression in mice.
espF
,
nleH1
, and
nleH2
were abundantly expressed over the course of infection. In contrast,
map
expression was suppressed at 2 days postinfection, and at 4 days postinfection it was totally abolished. After 2 to 4 days postinfection, when
map
is suppressed, EPEC colonization is significantly reduced, indicating that
map
may be one of the factors required to maintain EPEC colonization. This was confirmed in a competitive colonization study and in two models of chronic infection, repeated exposure to ketamine and
Citrobacter rodentium
infection. Our data suggest that
map
expression contributes to the maintenance of EPEC colonization.
Transgenic Expression of CXCR3 on T Cells Enhances Susceptibility to Cutaneous Leishmania major Infection by Inhibiting Monocyte Maturation and Promoting a Th2 Response
Authors: Oghumu Steve , Stock James C. , Varikuti Sanjay , Dong Ran , Terrazas Cesar , Edwards Jessica A. , Rappleye Chad A. , Holovatyk Ariel , Sharpe Arlene , Satoskar Abhay R. 
Published: October 2014

ABSTRACTCutaneous leishmaniasis, caused mainly byLeishmania major, an obligate intracellular parasite, is a disfiguring disease characterized by large skin lesions and is transmitted by a sand fly vector. We previously showed that the chemokine receptor CXCR3 plays a critical role in mediating resistance to cutaneous leishmaniasis caused byLeishmania major. Furthermore, T cells fromL. major-susceptible BALB/c but notL. major-resistant C57BL/6 mice fail to efficiently upregulate CXCR3 upon activation. We therefore examined whether transgenic expression of CXCR3 on T cells would enhance resistance toL. majorinfection in susceptible BALB/c mice. We generated BALB/c and C57BL/6 transgenic mice, which constitutively overexpressed CXCR3 under a CD2 promoter, and then examined the outcomes withL. majorinfection. Contrary to our hypothesis, transgenic expression of CXCR3 (CXCR3Tg) on T cells of BALB/c mice resulted in increased lesion sizes and parasite burdens compared to wild-type (WT) littermates afterL. majorinfection. Restimulated lymph node cells fromL. major-infected BALB/c-CXCR3Tgmice produced more interleukin-4 (IL-4) and IL-10 and less gamma interferon (IFN-γ). Cells in draining lymph nodes from BALB/c-CXCR3Tgmice showed enhanced Th2 and reduced Th1 cell accumulation associated with increased neutrophils and inflammatory monocytes. However, monocytes displayed an immature phenotype which correlated with increased parasite burdens. Interestingly, transgenic expression of CXCR3 on T cells did not impact the outcome ofL. majorinfection in C57BL/6 mice, which mounted a predominantly Th1 response and spontaneously resolved their infection similar to WT littermates. Our findings demonstrate that transgenic expression of CXCR3 on T cells increases susceptibility of BALB/c mice toL. major.
Persistence and Toxin Production by Clostridium difficile within Human Intestinal Organoids Result in Disruption of Epithelial Paracellular Barrier Function
Authors: Leslie Jhansi L. , Huang Sha , Opp Judith S. , Nagy Melinda S. , Kobayashi Masayuki , Young Vincent B. , Spence Jason R. 
Published: October 2014

ABSTRACT

Clostridium difficile
is the leading cause of infectious nosocomial diarrhea. The pathogenesis of
C. difficile
infection (CDI) results from the interactions between the pathogen, intestinal epithelium, host immune system, and gastrointestinal microbiota. Previous studies of the host-pathogen interaction in CDI have utilized either simple cell monolayers or
in vivo
models. While much has been learned by utilizing these approaches, little is known about the direct interaction of the bacterium with a complex host epithelium. Here, we asked if human intestinal organoids (HIOs), which are derived from pluripotent stem cells and demonstrate small intestinal morphology and physiology, could be used to study the pathogenesis of the obligate anaerobe
C. difficile
. Vegetative
C. difficile
, microinjected into the lumen of HIOs, persisted in a viable state for up to 12 h. Upon colonization with
C. difficile
VPI 10463, the HIO epithelium is markedly disrupted, resulting in the loss of paracellular barrier function. Since similar effects were not observed when HIOs were colonized with the nontoxigenic
C. difficile
strain F200, we directly tested the role of toxin using TcdA and TcdB purified from VPI 10463. We show that the injection of TcdA replicates the disruption of the epithelial barrier function and structure observed in HIOs colonized with viable
C. difficile
.
Lon-Mediated Proteolysis of the FeoC Protein Prevents Salmonella enterica from Accumulating the Fe(II) Transporter FeoB under High-Oxygen Conditions
Authors: Kim Hyunkeun , Lee Hwiseop , Shin Dongwoo 
Published: October 2014

ABSTRACT

The
Salmonella
Feo system consists of the FeoA, FeoB, and FeoC proteins and mediates ferrous iron [Fe(II)] import. FeoB is an inner membrane protein that, along with contributions from two small hydrophilic proteins, FeoA and FeoC, transports Fe(II). We previously reported that FeoC binds to and protects the FeoB transporter from FtsH-mediated proteolysis. In the present study, we report proteolytic regulation of FeoC that occurs in an oxygen-dependent fashion. While relatively stable under low-oxygen conditions, FeoC was rapidly degraded by the Lon protease under high-oxygen conditions. The putative Fe-S cluster of FeoC seemed to function as an oxygen sensor to control FeoC stability, as evidenced by the finding that mutation of the putative Fe-S cluster-binding site greatly increased FeoC stability under high-oxygen conditions.
Salmonella
ectopically expressing the
feoB
and
feoC
genes was able to accumulate FeoB and FeoC only under low-oxygen conditions, suggesting that FeoC proteolysis prevents
Salmonella
from accumulating the FeoB transporter under high-oxygen conditions. Finally, we propose that Lon-mediated FeoC proteolysis followed by FtsH-mediated FeoB proteolysis helps
Salmonella
to avoid uncontrolled Fe(II) uptake during the radical environmental changes encountered when shifting from low-iron anaerobic conditions to high-iron aerobic conditions.
Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH
Authors: Christensen G. A. , Zane G. M. , Kazakov A. E. , Li X. , Rodionov D. A. , Novichkov P. S. , Dubchak I. , Arkin A. P. , Wall J. D. 
Published: October 2014

ABSTRACT

Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbe
Desulfovibrio vulgaris
Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction in
D. vulgaris
Hildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putative
rex
gene was made in
D. vulgaris
Hildenborough, and transcript expression studies of
sat
, encoding sulfate adenylyl transferase, showed increased levels in the
D. vulgaris
Hildenborough Rex (Rex
DvH
) mutant relative to the parental strain. The Rex
DvH
-binding site upstream of
sat
was identified, confirming Rex
DvH
to be a repressor of
sat
. We established
in vitro
that the presence of elevated NADH disrupted the interaction between Rex
DvH
and DNA. Examination of the 5′ transcriptional start site for the
sat
mRNA revealed two unique start sites, one for respiring cells that correlated with the Rex
DvH
-binding site and a second for fermenting cells. Collectively, these data support the role of Rex
DvH
as a transcription repressor for
sat
that senses the redox status of the cell.
Inactivation of the Organic Hydroperoxide Stress Resistance Regulator OhrR Enhances Resistance to Oxidative Stress and Isoniazid in Mycobacterium smegmatis
Authors: Saikolappan Sankaralingam , Das Kishore , Dhandayuthapani Subramanian 
Published: October 2014

ABSTRACT

The organic hydroperoxide stress resistance regulator (OhrR) is a MarR type of transcriptional regulator that primarily regulates the expression of organic hydroperoxide reductase (Ohr) in bacteria. In mycobacteria, the genes encoding these proteins exist in only a few species, which include the fast-growing organism
Mycobacterium smegmatis
. To delineate the roles of Ohr and OhrR in defense against oxidative stress in
M. smegmatis
, strains lacking the expression of these proteins were constructed by deleting the
ohrR
and
ohr
genes, independently and together, through homologous recombination. The OhrR mutant strain (MSΔohrR) showed severalfold upregulation of Ohr expression, which could be observed at both the transcript and protein levels. Similar upregulation of Ohr expression was also noticed in an
M. smegmatis
wild-type strain (MSWt) induced with cumene hydroperoxide (CHP) and
t
-butyl hydroperoxide (
t
-BHP). The elevated Ohr expression in MSΔohrR correlated with heightened resistance to oxidative stress due to CHP and
t
-BHP and to inhibitory effects due to the antituberculosis drug isoniazid (INH). Further, this mutant strain exhibited significantly enhanced survival in the intracellular compartments of macrophages. In contrast, the strains lacking either Ohr alone (MSΔohr) or both Ohr and OhrR (MSΔohr-ohrR) displayed limited or no resistance to hydroperoxides and INH. Additionally, these strains showed no significant differences in intracellular survival from the wild type. Electrophoretic mobility shift assays (EMSAs) revealed that the overexpressed and purified OhrR interacts with the
ohr-ohrR
intergenic region with a greater affinity and this interaction is contingent upon the redox state of the OhrR. These findings suggest that Ohr-OhrR is an important peroxide stress response system in
M. smegmatis
.
FlgM Is Secreted by the Flagellar Export Apparatus in Bacillus subtilis
Authors: Calvo Rebecca A. , Kearns Daniel B. 
Published: October 2014

ABSTRACT

The bacterial flagellum is assembled from over 20 structural components, and flagellar gene regulation is morphogenetically coupled to the assembly state by control of the anti-sigma factor FlgM. In the Gram-negative bacterium
Salmonella enterica
, FlgM inhibits late-class flagellar gene expression until the hook-basal body structural intermediate is completed and FlgM is inhibited by secretion from the cytoplasm. Here we demonstrate that FlgM is also secreted in the Gram-positive bacterium
Bacillus subtilis
and is degraded extracellularly by the proteases Epr and WprA. We further demonstrate that, like in
S. enterica
, the structural genes required for the flagellar hook-basal body are required for robust activation of σ
D
-dependent gene expression and efficient secretion of FlgM. Finally, we determine that FlgM secretion is strongly enhanced by, but does not strictly require, hook-basal body completion and instead demands a minimal subset of flagellar proteins that includes the FliF/FliG basal body proteins, the flagellar type III export apparatus components FliO, FliP, FliQ, FliR, FlhA, and FlhB, and the substrate specificity switch regulator FliK.
Long QT Syndrome Complicating Atrioventricular Block
Authors: Rosso Raphael , Adler Arnon , Strasberg Boris , Guevara-Valdivia Milton E. , Somani Riyaz , Baranchuk Adrian , Halkin Amir , Márquez Manlio F. , Scheinman Melvin , Steinvil Arie , Belhassen Bernard , Kazatsker Mark , Katz Amos , Viskin Sami 
Published: October 2014

Background—
The magnitude of QT prolongation in response to bradycardia, rather than the bradycardia per se, determines the risk for torsade de pointes during atrioventricular block (AVB). However, we do not know why some patients develop more QT prolongation than others, despite similar bradycardia. We hypothesized that in patients who develop significant QRS vector changes during AVB, the effects of cardiac memory lead to excessive QT prolongation.

Methods and Results—

We studied 91 patients who presented with AVB and who also had an ECG predating the bradyarrhythmia for comparison. We correlated changes in QRS morphology and axis taking place during AVB with the bradycardia-induced QT prolongation. Patients with and without QRS morphology changes at the time of AVB were of similar age and sex. Moreover, despite similar R-R interval during AVB, cases with a QRS morphology change had significantly longer QT (648±84 versus 561±84;
P
<0.001) than those without. Patients who developed a change in QRS morphology at the time of AVB had a 7-fold higher risk of developing long QT. This risk nearly doubled when the change in QRS morphology was accompanied by a change in QRS axis.

Conclusions—
Cardiac memory resulting from a change in QRS morphology during AVB is independently associated with QT prolongation and may be arrhythmogenic during AVB.