bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of diffusion models in breast cancer
Authors: Panek Rafal , Borri Marco , Orton Matthew , O'Flynn Elizabeth , Morgan Veronica , Giles Sharon L. , deSouza Nandita , Leach Martin O. , Schmidt Maria A. 
Published: July 2015

Purpose:The purpose of this study is to investigate whether the microvascular pseudodiffusion effects resulting with non‐monoexponential behavior are present in breast cancer, taking into account tumor spatial heterogeneity. Additionally, methodological factors affecting the signal in low and high diffusion‐sensitizing gradient ranges were explored in phantom studies.Methods:The effect of eddy currents and accuracy of b‐value determination using a multiple b‐value diffusion‐weighted MR imaging sequence were investigated in test objects. Diffusion model selection and noise were then investigated in volunteers (n = 5) and breast tumor patients (n = 21) using the Bayesian information criterion.Results:54.3% of lesion voxels were best fitted by a monoexponential, 26.2% by a stretched‐exponential, and 19.5% by a biexponential intravoxel incoherent motion (IVIM) model. High correlation (0.92) was observed between diffusion coefficients calculated using mono‐ and stretched‐exponential models and moderate (0.59) between monoexponential and IVIM (medians: 0.96/0.84/0.72 × 10−3 mm2/s, respectively). Distortion due to eddy currents depended on the direction of the diffusion gradient and displacement varied between 1 and 6 mm for high b‐value images. Shift in the apparent diffusion coefficient due to intrinsic field gradients was compensated for by averaging diffusion data obtained from opposite directions.Conclusions:Pseudodiffusion and intravoxel heterogeneity effects were not observed in approximately half of breast cancer and normal tissue voxels. This result indicates that stretched and IVIM models should be utilized in regional analysis rather than global tumor assessment. Cross terms between diffusion‐sensitization gradients and other imaging or susceptibility‐related gradients are relevant in clinical protocols, supporting the use of geometric averaging of diffusion‐weighted images acquired with diffusion‐sensitization gradients in opposite directions.
A Novel Y319H Substitution in CYP51C Associated with Azole Resistance in Aspergillus flavus
Authors: Paul R. A. , Rudramurthy S. M. , Meis J. F. , Mouton J. W. , Chakrabarti A. 
Published: July 2015

ABSTRACT

This study aimed to explore any mutation in the
CYP51
gene conferring azole resistance in
Aspergillus flavus
. Two voriconazole-resistant and 45 voriconazole-susceptible isolates were included in the study. Sequence analysis demonstrated a T1025C nucleotide change in
CYP51C
, resulting in the Y319H amino acid substitution in one resistant isolate. However, the earlier described T788G mutation in
CYP51C
conferring voriconazole resistance in
A. flavus
isolates was present in all isolates, irrespective of their susceptibility status.
Bactericidal Activity of Ceragenin CSA-13 in Cell Culture and in an Animal Model of Peritoneal Infection
Authors: Bucki Robert , Niemirowicz Katarzyna , Wnorowska Urszula , Byfield Fitzroy J. , Piktel Ewelina , Wątek Marzena , Janmey Paul A. , Savage Paul B. 
Published: July 2015

ABSTRACTCeragenins constitute a novel family of cationic antibiotics characterized by a broad spectrum of antimicrobial activities, which have mostly been assessedin vitro. Using a polarized human lung epithelial cell culture system, we evaluated the antibacterial activities of the ceragenin CSA-13 against two strains ofPseudomonas aeruginosa(PAO1 and Xen5). Additionally, the biodistribution and bactericidal activity of a CSA-13–IRDye 800CW derivate were assessed using an animal model of peritoneal infection after PAO1 challenge. In cell culture, CSA-13 bactericidal activities against PAO1 and Xen5 were higher than the activities of the human cathelicidin peptide LL-37. Increased CSA-13 activity was observed in polarized human lung epithelial cell cultures subjected to butyric acid treatment, which is known to increase endogenous LL-37 production. Eight hours after intravenous or intraperitoneal injection, the greatest CSA-13–IRDye 800CW accumulation was observed in mouse liver and kidneys. CSA-13–IRDye 800CW administration resulted in decreased bacterial outgrowth from abdominal fluid collected from animals subjected to intraperitoneal PAO1 infection. These observations indicate that CSA-13 may synergistically interact with antibacterial factors that are naturally present at mucosal surfaces and it maintains its antibacterial activity in the infected abdominal cavity. Cationic lipids such as CSA-13 represent excellent candidates for the development of new antibacterial compounds.
Fluconazole and Voriconazole Resistance in Candida parapsilosis Is Conferred by Gain-of-Function Mutations in
MRR1
Transcription Factor Gene
Authors: Branco Joana , Silva Ana P. , Silva Raquel M. , Silva-Dias Ana , Pina-Vaz Cidália , Butler Geraldine , Rodrigues Acácio G. , Miranda Isabel M. 
Published: July 2015

ABSTRACT

Candida parapsilosis
is the second most prevalent fungal agent causing bloodstream infections. Nevertheless, there is little information about the molecular mechanisms underlying azole resistance in this species. Mutations (G1747A, A2619C, and A3191C) in the
MRR1
transcription factor gene were identified in fluconazole- and voriconazole-resistant strains. Independent expression of
MRR1
genes harboring these mutations showed that G1747A (G583R) and A2619C (K873N) are gain-of-function mutations responsible for azole resistance, the first described in
C. parapsilosis
.
Antimicrobial Susceptibility and SOS-Dependent Increase in Mutation Frequency Are Impacted by Escherichia coli Topoisomerase I C-Terminal Point Mutation
Authors: Yang Jenny , Annamalai Thirunavukkarasu , Cheng Bokun , Banda Srikanth , Tyagi Rakhi , Tse-Dinh Yuk-Ching 
Published: July 2015

ABSTRACT

Topoisomerase functions are required in all organisms for many vital cellular processes, including transcription elongation. The C terminus domains (CTD) of
Escherichia coli
topoisomerase I interact directly with RNA polymerase to remove transcription-driven negative supercoiling behind the RNA polymerase complex. This interaction prevents inhibition of transcription elongation from hypernegative supercoiling and R-loop accumulation. The physiological function of bacterial topoisomerase I in transcription is especially important for a rapid network response to an antibiotic challenge. In this study,
Escherichia coli
with a
topA66
single nucleotide deletion mutation, which results in a frameshift in the TopA CTD, was shown to exhibit increased sensitivity to trimethoprim and quinolone antimicrobials. The topoisomerase I-RNA polymerase interaction and the SOS response to the antimicrobial agents were found to be significantly reduced by this
topA66
mutation. Consequently, the mutation frequency measured by rifampin selection following SOS induction was diminished in the
topA66
mutant. The increased antibiotic sensitivity for the
topA66
mutant can be reversed by the expression of recombinant
E. coli
topoisomerase I but not by the expression of recombinant
Mycobacterium tuberculosis
topoisomerase I that has a nonhomologous CTD even though the recombinant
M. tuberculosis
topoisomerase I can restore most of the plasmid DNA linking number deficiency caused by the
topA66
mutation. Direct interactions of
E. coli
topoisomerase I as part of transcription complexes are likely to be required for the rapid network response to an antibiotic challenge. Inhibitors of bacterial topoisomerase I functions and interactions may sensitize pathogens to antibiotic treatment and limit the mutagenic response.
A Simple, Efficient, and Sensitive Method for Simultaneous Detection of Anti-HIV Drugs Atazanavir, Ritonavir, and Tenofovir by Use of Liquid Chromatography-Tandem Mass Spectrometry
Authors: Koehn Josefin , Ding Yue , Freeling Jennifer , Duan Jinghua , Ho Rodney J. Y. 
Published: July 2015

ABSTRACT
In the treatment of HIV infection, a combination of anti-HIV drugs is commonly used in highly active antiretroviral therapy (HAART). One such combination recommended for clinical therapy consists of the two HIV protease inhibitors atazanavir and ritonavir and the HIV nucleotide reverse transcriptase inhibitor tenofovir. The detection of plasma and cell drug concentrations provides an assessment of actual drug exposure and patient compliance. We thus developed a simple, efficient, and sensitive method to simultaneously extract and detect these three drugs in plasma and peripheral blood mononuclear cells. The use of a liquid-liquid extraction followed by protein precipitation provided a simple process, yielding a high recovery rate for all three drugs in plasma (>92%) and in cells (>86%). The liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was able to detect 0.01, 0.25, and 2.5 pg (2, 50, and 500 pg/ml, respectively) in 5 μl for atazanavir, ritonavir, and tenofovir, respectively. Validation of the method exhibited high precision and accuracy. This method was subsequently applied to a primate study to determine the concentrations of all three drugs in both plasma and cell samples. This validated method can be useful for an evaluation of drug concentrations in biological samples in an efficient and sensitive manner.
Persister Development by Borrelia burgdorferi Populations
In Vitro
Authors: Caskey John R. , Embers Monica E. 
Published: July 2015

ABSTRACT

Doxycycline is an antibiotic commonly used to treat Lyme disease and other bacterial infections. The MIC and minimum bactericidal concentration (MBC) for
Borrelia burgdorferi
have been investigated by different groups but were experimentally established in this study as a function of input cell density. We demonstrated that
B. burgdorferi
treated in the stationary phase has a higher probability of regrowth following removal of antibiotic. In addition, we determined experimentally and mathematically that the spirochetes which persist posttreatment do not have a longer lag phase but exhibit a lower growth rate than untreated spirochetes. Finally, we found that treating the spirochetes by pulse-dosing did not eliminate growth or reduce the persister population
in vitro
. From these data, we propose that
B. burgdorferi
persister development is stochastic and driven by slowed growth.
The Flavonoid Isoliquiritigenin Reduces Lung Inflammation and Mouse Morbidity during Influenza Virus Infection
Authors: Traboulsi Hussein , Cloutier Alexandre , Boyapelly Kumaraswamy , Bonin Marc-André , Marsault Éric , Cantin André M. , Richter Martin V. 
Published: July 2015

ABSTRACTThe host response to influenza virus infection is characterized by an acute lung inflammatory response in which intense inflammatory cell recruitment, hypercytokinemia, and a high level of oxidative stress are present. The sum of these events contributes to the virus-induced lung damage that leads to high a level of morbidity and mortality in susceptible infected patients. In this context, we identified compounds that can simultaneously reduce the excessive inflammatory response and the viral replication as a strategy to treat influenza virus infection. We investigated the anti-inflammatory and antiviral potential activities of isoliquiritigenin (ILG). Interestingly, we demonstrated that ILG is a potent inhibitor of influenza virus replication in human bronchial epithelial cells (50% effective concentration [EC50] = 24.7 μM). In addition, our results showed that this molecule inhibits the expression of inflammatory cytokines induced after the infection of cells with influenza virus. We demonstrated that the anti-inflammatory activity of ILG in the context of influenza virus infection is dependent on the activation of the peroxisome proliferator-activated receptor gamma pathway. Interestingly, ILG phosphate (ILG-p)-treated mice displayed decreased lung inflammation as depicted by reduced cytokine gene expression and inflammatory cell recruitment. We also demonstrated that influenza virus-specific CD8+effector T cell recruitment was reduced up to 60% in the lungs of mice treated with ILG-p (10 mg/kg) compared to that in saline-treated mice. Finally, we showed that administration of ILG-p reduced lung viral titers and morbidity of mice infected with the PR8/H1N1 virus.
In Vitro
and
In Vivo
Effects of the Bumped Kinase Inhibitor 1294 in the Related Cyst-Forming Apicomplexans Toxoplasma gondii and Neospora caninum
Authors: Winzer Pablo , Müller Joachim , Aguado-Martínez Adriana , Rahman Mahbubur , Balmer Vreni , Manser Vera , Ortega-Mora Luis Miguel , Ojo Kayode K. , Fan Erkang , Maly Dustin J. , Van Voorhis Wesley C. , Hemphill Andrew 
Published: July 2015

ABSTRACT

We report on the
in vitro
effects of the bumped kinase inhibitor 1294 (BKI-1294) in cultures of virulent
Neospora caninum
isolates Nc-Liverpool (Nc-Liv) and Nc-Spain7 and in two strains of
Toxoplasma gondii
(RH and ME49), all grown in human foreskin fibroblasts. In these parasites, BKI-1294 acted with 50% inhibitory concentrations (IC
50
s) ranging from 20 nM (
T. gondii
RH) to 360 nM (
N. caninum
Nc-Liv), and exposure of intracellular stages to 1294 led to the nondisjunction of newly formed tachyzoites, resulting in the formation of multinucleated complexes similar to complexes previously observed in BKI-1294-treated
N. caninum
beta-galactosidase-expressing parasites. However, such complexes were not seen in a transgenic
T. gondii
strain that expressed CDPK1 harboring a mutation (G to M) in the gatekeeper residue. In
T. gondii
ME49 and
N. caninum
Nc-Liv, exposure of cultures to BKI-1294 resulted in the elevated expression of mRNA coding for the bradyzoite marker BAG1. Unlike in bradyzoites, SAG1 expression was not repressed. Immunofluorescence also showed that these multinucleated complexes expressed SAG1 and BAG1 and the monoclonal antibody CC2, which binds to a yet unidentified bradyzoite antigen, also exhibited increased labeling. In a pregnant mouse model, BKI-1294 efficiently inhibited vertical transmission in BALB/c mice experimentally infected with one of the two virulent isolates Nc-Liv or Nc-Spain7, demonstrating proof of concept that this compound protected offspring from vertical transmission and disease. The observed deregulated antigen expression effect may enhance the immune response during BKI-1294 therapy and will be the subject of future studies.
Legionella pneumophila Effector LpdA Is a Palmitoylated Phospholipase D Virulence Factor
Authors: Schroeder Gunnar N. , Aurass Philipp , Oates Clare V. , Tate Edward W. , Hartland Elizabeth L. , Flieger Antje , Frankel Gad 
Published: July 2015

ABSTRACT

Legionella pneumophila
is a bacterial pathogen that thrives in alveolar macrophages, causing a severe pneumonia. The virulence of
L. pneumophila
depends on its Dot/Icm type IV secretion system (T4SS), which delivers more than 300 effector proteins into the host, where they rewire cellular signaling to establish a replication-permissive niche, the
Legionella
-containing vacuole (LCV). Biogenesis of the LCV requires substantial redirection of vesicle trafficking and remodeling of intracellular membranes. In order to achieve this, several T4SS effectors target regulators of membrane trafficking, while others resemble lipases. Here, we characterized LpdA, a phospholipase D effector, which was previously proposed to modulate the lipid composition of the LCV. We found that ectopically expressed LpdA was targeted to the plasma membrane and Rab4- and Rab14-containing vesicles. Subcellular targeting of LpdA required a C-terminal motif, which is posttranslationally modified by S-palmitoylation. Substrate specificity assays showed that LpdA hydrolyzed phosphatidylinositol, -inositol-3- and -4-phosphate, and phosphatidylglycerol to phosphatidic acid (PA)
in vitro
. In HeLa cells, LpdA generated PA at vesicles and the plasma membrane. Imaging of different phosphatidylinositol phosphate (PIP) and organelle markers revealed that while LpdA did not impact on membrane association of various PIP probes, it triggered fragmentation of the Golgi apparatus. Importantly, although LpdA is translocated inefficiently into cultured cells, an
L. pneumophila
Δ
lpdA
mutant displayed reduced replication in murine lungs, suggesting that it is a virulence factor contributing to
L. pneumophila
infection
in vivo
.
Chlamydia trachomatis Type III Secretion Proteins Regulate Transcription
Authors: Hanson Brett R. , Slepenkin Anatoly , Peterson Ellena M. , Tan Ming 
Published: July 2015

ABSTRACT

The Scc4 protein (CT663) of the pathogenic bacterium
Chlamydia
has been described as a type III secretion (T3S) chaperone as well as an inhibitor of RNA polymerase. To examine if these roles are connected, we first investigated physical interactions between
Chlamydia trachomatis
Scc4 and the T3S chaperone Scc1 and a T3S substrate, CopN. In a yeast 3-hybrid assay, Scc4, Scc1, and CopN were all required to detect an interaction, which suggests that these proteins form a trimolecular complex. We also detected interactions between any two of these three T3S proteins in a pulldown assay using only recombinant proteins. We next determined whether these interactions affected the function of Scc4 as an inhibitor of RNA transcription. Using
Escherichia coli
as a heterologous
in vivo
system, we demonstrated that expression of
C. trachomatis
Scc4 led to a drastic decrease in transcript levels for multiple genes. However, coexpression of Scc4 with Scc1, CopN, or both alleviated Scc4-mediated inhibition of transcription. Scc4 expression also severely impaired
E. coli
growth, but this growth defect was reversed by coexpression of Scc4 with Scc1, CopN, or both, suggesting that the inhibitory effect of Scc4 on transcription and growth can be antagonized by interactions between Scc4, Scc1, and CopN. These findings suggest that the dual functions of Scc4 may serve as a bridge to link T3S and the regulation of gene expression in
Chlamydia
.

IMPORTANCE
This study investigates a novel mechanism for regulating gene expression in the pathogenic bacterium
Chlamydia
. The
Chlamydia
type III secretion (T3S) chaperone Scc4 has been shown to inhibit transcription by RNA polymerase. This study describes physical interactions between Scc4 and the T3S proteins Scc1 and CopN. Furthermore,
Chlamydia
Scc1 and CopN antagonized the inhibitory effects of Scc4 on transcription and growth in a heterologous
Escherichia coli
system. These results provide evidence that transcription in
Chlamydia
can be regulated by the T3S system through interactions between T3S proteins.
CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants
Authors: Bao Yun-Juan , Liang Zhong , Mayfield Jeffrey A. , Lee Shaun W. , Ploplis Victoria A. , Castellino Francis J. 
Published: July 2015

ABSTRACTThe two-componentcontrolofvirulence (Cov) regulator (R)-sensor (S) (CovRS) regulates the virulence ofStreptococcus pyogenes(group AStreptococcus[GAS]). Inactivation of CovS during infection switches the pathogenicity of GAS to a more invasive form by regulating transcription of diverse virulence genes via CovR. However, the manner in which CovRS controls virulence through expression of extended gene families has not been fully determined. In the current study, the CovS-regulated gene expression profiles of a hypervirulentemm23GAS strain (M23ND/CovS negative [M23ND/CovS−]) and a noninvasive isogenic strain (M23ND/CovS+), under different growth conditions, were investigated. RNA sequencing identified altered expression of ∼349 genes (18% of the chromosome). The data demonstrated that M23ND/CovS−achieved hypervirulence by allowing enhanced expression of genes responsible for antiphagocytosis (e.g.,hasABC), by abrogating expression of toxin genes (e.g.,speB), and by compromising gene products with dispensable functions (e.g.,sfb1). Among these genes, several (e.g.,parEandparC) were not previously reported to be regulated by CovRS. Furthermore, the study revealed that CovS also modulated the expression of a broad spectrum of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination, where the bacteria encounter large variations in available nutrients, thus restructuring metabolism of GAS for adaption to diverse growth environments. From constructing a genome-scale metabolic model, we identified 16 nonredundant metabolic gene modules that constitute unique nutrient sources. These genes were proposed to be essential for pathogen growth and are likely associated with GAS virulence. The genome-wide prediction of genes associated with virulence identifies new candidate genes that potentially contribute to GAS virulence.IMPORTANCEThe CovRS system modulates transcription of ∼18% of the genes in theStreptococcus pyogenesgenome. Mutations that inactivate CovR or CovS enhance the virulence of this bacterium. We determined complete transcriptomes of a naturally CovS-inactivated invasive deep tissue isolate of anemm23strain ofS. pyogenes(M23ND) and its complemented avirulent variant (CovS+). We identified diverse virulence genes whose altered expression revealed a genetic switching of a nonvirulent form of M23ND to a highly virulent strain. Furthermore, we also systematically uncovered for the first time the comparative levels of expression of a broad spectrum of metabolic genes, which reflected different metabolic needs of the bacterium as it invaded deeper tissue of the human host.
A Sham-Controlled Trial of Acupressure on the Quality of Sleep and Life in Haemodialysis Patients
Authors: Arab Zahra , Shariati Ali Reza , Asayesh Hamid , Vakili Mohammad Ali , Bahrami-Taghanaki Hamidreza , Azizi Hoda 
Published: July 2015

Background Sleep disorder in haemodialysis patients can lead to disturbance in their psychosocial function and interpersonal relations, and reduced quality of life. The aim of the present study was to investigate the effect of acupressure on the quality of sleep of haemodialysis patients. Methods In a randomised controlled trial, 108 haemodialysis patients were randomly divided into three groups: true acupressure, placebo acupressure, and no treatment. The two acupressure groups received treatment three times a week for 4 weeks during dialysis. Routine care only was provided for the no treatment group. The main study outcome was sleep quality. Results The total Pittsburgh Sleep Quality Index score decreased significantly from 11.9±3.13 to 6.2±1.93 in the true acupressure group, from 11.3±3.69 to 10.6±3.82 in the sham acupressure group, and from 10.9±4.10 to 10.7±3.94 in the no treatment group. There was a significant difference between groups (p<0.001). Conclusions Acupressure seems to have a positive effect on the sleep quality in haemodialysis patients. Clinical Trial Registration IRCT201106145864N2.