bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multimodality segmentation framework for automatic target delineation in head and neck radiotherapy
Authors: Yang Jinzhong , Beadle Beth M. , Garden Adam S. , Schwartz David L. , Aristophanous Michalis 
Published: August 2015

Purpose:To develop an automatic segmentation algorithm integrating imaging information from computed tomography (CT), positron emission tomography (PET), and magnetic resonance imaging (MRI) to delineate target volume in head and neck cancer radiotherapy.Methods:Eleven patients with unresectable disease at the tonsil or base of tongue who underwent MRI, CT, and PET/CT within two months before the start of radiotherapy or chemoradiotherapy were recruited for the study. For each patient, PET/CT and T1‐weighted contrast MRI scans were first registered to the planning CT using deformable and rigid registration, respectively, to resample the PET and magnetic resonance (MR) images to the planning CT space. A binary mask was manually defined to identify the tumor area. The resampled PET and MR images, the planning CT image, and the binary mask were fed into the automatic segmentation algorithm for target delineation. The algorithm was based on a multichannel Gaussian mixture model and solved using an expectation–maximization algorithm with Markov random fields. To evaluate the algorithm, we compared the multichannel autosegmentation with an autosegmentation method using only PET images. The physician‐defined gross tumor volume (GTV) was used as the “ground truth” for quantitative evaluation.Results:The median multichannel segmented GTV of the primary tumor was 15.7 cm3 (range, 6.6–44.3 cm3), while the PET segmented GTV was 10.2 cm3 (range, 2.8–45.1 cm3). The median physician‐defined GTV was 22.1 cm3 (range, 4.2–38.4 cm3). The median difference between the multichannel segmented and physician‐defined GTVs was −10.7%, not showing a statistically significant difference (p‐value = 0.43). However, the median difference between the PET segmented and physician‐defined GTVs was −19.2%, showing a statistically significant difference (p‐value =0.0037). The median Dice similarity coefficient between the multichannel segmented and physician‐defined GTVs was 0.75 (range, 0.55–0.84), and the median sensitivity and positive predictive value between them were 0.76 and 0.81, respectively.Conclusions:The authors developed an automated multimodality segmentation algorithm for tumor volume delineation and validated this algorithm for head and neck cancer radiotherapy. The multichannel segmented GTV agreed well with the physician‐defined GTV. The authors expect that their algorithm will improve the accuracy and consistency in target definition for radiotherapy.
Darunavir and Ritonavir Total and Unbound Plasmatic Concentrations in HIV-HCV-Coinfected Patients with Hepatic Cirrhosis Compared to Those in HIV-Monoinfected Patients
Authors: Curran Adrian , Martí Ramon , López Rosa María , Pérez Mercè , Crespo Manel , Melià María Jesús , Navarro Jordi , Burgos Joaquín , Falcó Vicenç , Ocaña Inma , Ribera Esteban 
Published: August 2015

ABSTRACT

Our objective was to describe the pharmacokinetic (PK) parameters of total and unbound darunavir and ritonavir concentrations in HIV-hepatitis C virus (HCV)-coinfected patients with cirrhosis, as ritonavir-boosted darunavir is mainly metabolized in the liver, and hepatic cirrhosis might modify darunavir-ritonavir concentrations. This was a prospective, case-control, and unicenter study. HIV-HCV-coinfected patients with compensated cirrhosis (cases) and HIV-monoinfected patients with normal liver function (controls) were included. Darunavir-ritonavir was given at 800/100 mg once daily. Patients were followed for 24 weeks to assess safety and efficacy. A steady-state 12-h PK study was performed. Total and unbound concentrations were determined by liquid chromatography-tandem mass spectrometry. The unbound fraction was obtained by ultrafiltration. The plasma area under the concentration-time curve (AUC) and oral clearance (CL/F) were assessed by noncompartmental models. Thirty patients (20 cases and 10 controls) were included. Among cirrhotic patients, the Child-Pugh score was C in 4 cases, B in 1 case, and A in 15 cases; the median (interquartile range) transient elastography values were 20 kPa (14 to 26 kPa), and 5 patients had prior clinical decompensations. There were no significant differences in the darunavir PK parameters between cases and controls except for longer time to maximum plasma concentrations (
T
max
) and half-lives in the cirrhotic patients. There were no significant differences in ritonavir total concentrations, but the unbound concentrations were higher in cirrhotic patients. There were significant correlations between the darunavir total and unbound concentrations in both cirrhotic patients and controls. There were no differences in PK parameters based on Child-Pugh score, liver elasticity, gender, or use of concomitant medications. In conclusion, in HIV-HCV-coinfected patients with clinically compensated cirrhosis receiving darunavir-ritonavir at 800/100 mg once daily, the darunavir total and unbound concentrations are similar to those observed in noncirrhotic patients, and dose adjustments are not necessary.
Emergence of Raoultella ornithinolytica Coproducing IMP-4 and KPC-2 Carbapenemases in China
Authors: Zheng Beiwen , Zhang Jing , Ji Jinru , Fang Yunhui , Shen Ping , Ying Chaoqun , Lv Jifang , Xiao Yonghong , Li Lanjuan 
Published: August 2015

ABSTRACT

We report here the emergence of seven IMP-4-producing
Raoultella ornithinolytica
isolates obtained from one patient. All isolates carried the
bla
IMP-4
carbapenemase gene, five isolates also carried
bla
SHV-12
, four contained
bla
TEM-1
, and one contained
bla
OXA-1
. Notably, the
R. ornithinolytica
isolate Ro25724 also expressed
Klebsiella pneumoniae
carbapenemase (KPC)-2. The
bla
KPC-2
gene was located on a Tn
3
-Tn
4401
integration structure on a plasmid of ∼450 kb. This is the first description of the coexistence of
bla
KPC-2
and
bla
IMP-4
from the genus
Raoultella
.
HIV Drug Resistance Testing by High-Multiplex “Wide” Sequencing on the MiSeq Instrument
Authors: Lapointe H. R. , Dong W. , Lee G. Q. , Bangsberg D. R. , Martin J. N. , Mocello A. R. , Boum Y. , Karakas A. , Kirkby D. , Poon A. F. Y. , Harrigan P. R. , Brumme C. J. 
Published: August 2015

ABSTRACTLimited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n= 759) and from a Ugandan study cohort (n= 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of <3.0 log10HIV RNA copies/ml. Overall, 99.3% nucleotide concordance between methods was observed. MiSeq sequencing achieved 97.4% sensitivity and 99.3% specificity in detecting resistance mutations identified by Sanger sequencing. Findings suggest that the Illumina MiSeq platform can yield high-quality data with a high-multiplex “wide” sequencing approach. This strategy can be used for multiple HIV subtypes, demonstrating the potential for widespread individual testing and annual population surveillance in resource-limited settings.
The Phosphoenolpyruvate:Sugar Phosphotransferase System Is Involved in Sensitivity to the Glucosylated Bacteriocin Sublancin
Authors: Garcia De Gonzalo C. V. , Denham E. L. , Mars R. A. T. , Stülke J. , van der Donk W. A. , van Dijl J. M. 
Published: August 2015

ABSTRACTThe mode of action of a group of glycosylated antimicrobial peptides known as glycocins remains to be elucidated. In the current study of one glycocin, sublancin, we identified the phosphoenolpyruvate:sugar phosphotransferase system (PTS) ofBacillusspecies as a key player in bacterial sensitivity. Sublancin kills several Gram-positive bacteria, such asBacillusspecies andStaphylococcus aureus, including methicillin-resistantS. aureus(MRSA). Unlike other classes of bacteriocins for which the PTS is involved in their mechanism of action, we show that the addition of PTS-requiring sugars leads to increased resistance rather than increased sensitivity, suggesting that sublancin has a distinct mechanism of action. Collectively, our present mutagenesis and genomic studies demonstrate that the histidine-containing phosphocarrier protein (HPr) and domain A of enzyme II (PtsG) in particular are critical determinants for bacterial sensitivity to sublancin.
Functional Analysis of a Bacitracin Resistance Determinant Located on ICE
Cp1
, a Novel Tn
916
-Like Element from a Conjugative Plasmid in Clostridium perfringens
Authors: Han Xiaoyan , Du Xiang-Dang , Southey Luke , Bulach Dieter M. , Seemann Torsten , Yan Xu-Xia , Bannam Trudi L. , Rood Julian I. 
Published: August 2015

ABSTRACT

Bacitracins are mixtures of structurally related cyclic polypeptides with antibiotic properties. They act by interfering with the biosynthesis of the bacterial cell wall. In this study, we analyzed an avian necrotic enteritis strain of
Clostridium perfringens
that was resistant to bacitracin and produced NetB toxin. We identified a bacitracin resistance locus that resembled a bacitracin resistance determinant from
Enterococcus faecalis
. It contained the structural genes
bcrABD
and a putative regulatory gene,
bcrR
. Mutagenesis studies provided evidence that both
bcrA
and
bcrB
are essential for bacitracin resistance, and that evidence was supported by the results of experiments in which the introduction of both the
bcrA
and
bcrB
genes into a bacitracin-susceptible
C. perfringens
strain was required to confer bacitracin resistance. The wild-type strain was shown to contain at least three large, putatively conjugative plasmids, and the
bcrRABD
locus was localized to an 89.7-kb plasmid, pJIR4150. This plasmid was experimentally shown to be conjugative and was sequenced. The sequence revealed that it also carries a
tpeL
toxin gene and is related to the pCW3 family of conjugative antibiotic resistance and toxin plasmids from
C. perfringens
. The
bcr
genes were located on a genetic element, ICE
Cp1
, which is related to the Tn
916
family of integrative conjugative elements (ICEs). ICE
Cp1
appears to be the first Tn
916
-like element shown to confer bacitracin resistance. In summary, we identified in a toxin-producing
C. perfringens
strain a novel mobile bacitracin resistance element which was experimentally shown to be essential for bacitracin resistance and is carried by a putative ICE located on a conjugative plasmid.
Lack of Mutational Hot Spots during Decitabine-Mediated HIV-1 Mutagenesis
Authors: Rawson Jonathan M. O. , Landman Sean R. , Reilly Cavan S. , Bonnac Laurent , Patterson Steven E. , Mansky Louis M. 
Published: August 2015

ABSTRACT
Decitabine has previously been shown to induce lethal mutagenesis of human immunodeficiency virus type 1 (HIV-1). However, the factors that determine the susceptibilities of individual sequence positions in HIV-1 to decitabine have not yet been defined. To investigate this, we performed Illumina high-throughput sequencing of multiple amplicons prepared from proviral DNA that was recovered from decitabine-treated cells infected with HIV-1. We found that decitabine induced an ≈4.1-fold increase in the total mutation frequency of HIV-1, primarily due to a striking ≈155-fold increase in the G-to-C transversion frequency. Intriguingly, decitabine also led to an ≈29-fold increase in the C-to-G transversion frequency. G-to-C frequencies varied substantially (up to ≈80-fold) depending upon sequence position, but surprisingly, mutational hot spots (defined as upper outliers within the mutation frequency distribution) were not observed. We further found that every single guanine position examined was significantly susceptible to the mutagenic effects of decitabine. Taken together, these observations demonstrate for the first time that decitabine-mediated HIV-1 mutagenesis is promiscuous and occurs in the absence of a clear bias for mutational hot spots. These data imply that decitabine-mediated G-to-C mutagenesis is a highly effective antiviral mechanism for extinguishing HIV-1 infectivity.
Interplay among Membrane-Bound Lytic Transglycosylase D1, the CreBC Two-Component Regulatory System, the AmpNG-AmpD
I
-NagZ-AmpR Regulatory Circuit, and L1/L2 β-Lactamase Expression in Stenotrophomonas maltophilia
Authors: Huang Yi-Wei , Wu Chao-Jung , Hu Rouh-Mei , Lin Yi-Tsung , Yang Tsuey-Ching 
Published: August 2015

ABSTRACT

Lytic transglycosylases (LTs) are an important class of enzymes involved in peptidoglycan (PG) cleavage, with the concomitant formation of an intramolecular 1,6-anhydromuramoyl reaction product. There are six annotated LT genes in the
Stenotrophomonas maltophilia
genome, including genes for five membrane-bound LTs (
mltA
,
mltB1
,
mltB2
,
mltD1
, and
mltD2
) and a gene for soluble LT (
slt
). Six LTs of
S. maltophilia
KJ were systematically mutated, yielding the Δ
mltA
, Δ
mltB1
, Δ
mltB2
, Δ
mltD1
, Δ
mltD2
, and Δ
slt
mutants. Inactivation of
mltD1
conferred a phenotype of elevated uninduced β-lactamase activity. The underlying mechanism responsible for this phenotype was elucidated by the construction of several mutants and determination of β-lactamase activity. The expression of the genes assayed was assessed by quantitative reverse transcriptase PCR and a promoter transcription fusion assay. The results demonstrate that Δ
mltD1
mutant-mediated L1/L2 β-lactamase expression involved the
creBC
two-component regulatory system (TCS) and the
ampNG-ampD
I
-
nagZ-ampR
regulatory circuit. The inactivation of
mltD1
resulted in
mltB1
and
mltD2
upexpression in a
creBC
- and
ampNG
-dependent manner. The overexpressed MltB1 and MltD2 activity contributed to the expression of the L1/L2 β-lactamase genes via the
ampNG-ampD
I
-
nagZ-ampR
regulatory circuit. These findings reveal, for the first time, a linkage between LTs, the CreBC TCS, the
ampNG-ampD
I
-
nagZ-ampR
regulatory circuit, and L1/L2 β-lactamase expression in
S. maltophilia
.
Gingipains from the Periodontal Pathogen Porphyromonas gingivalis Play a Significant Role in Regulation of Angiopoietin 1 and Angiopoietin 2 in Human Aortic Smooth Muscle Cells
Authors: Zhang Boxi , Khalaf Hazem , Sirsjö Allan , Bengtsson Torbjörn 
Published: August 2015

ABSTRACT

Angiopoietin 1 (Angpt1) and angiopoietin 2 (Angpt2) are the ligands of tyrosine kinase (Tie) receptors, and they play important roles in vessel formation and the development of inflammatory diseases, such as atherosclerosis.
Porphyromonas gingivalis
is a Gram-negative periodontal bacterium that is thought to contribute to the progression of cardiovascular disease. The aim of this study was to investigate the role of
P. gingivalis
infection in the modulation of Angpt1 and Angpt2 in human aortic smooth muscle cells (AoSMCs). We exposed AoSMCs to wild-type (W50 and 381), gingipain mutant (E8 and K1A), and fimbrial mutant (DPG-3 and KRX-178)
P. gingivalis
strains and to different concentrations of tumor necrosis factor (TNF). The atherosclerosis risk factor TNF was used as a positive control in this study. We found that
P. gingivalis
(wild type, K1A, DPG3, and KRX178) and TNF upregulated the expression of Angpt2 and its transcription factor ETS1, respectively, in AoSMCs. In contrast, Angpt1 was inhibited by
P. gingivalis
and TNF. However, the RgpAB mutant E8 had no effect on the expression of Angpt1, Angpt2, or ETS1 in AoSMCs. The results also showed that ETS1 is critical for
P. gingivalis
induction of Angpt2. Exposure to Angpt2 protein enhanced the migration of AoSMCs but had no effect on proliferation. This study demonstrates that gingipains are crucial to the ability of
P. gingivalis
to markedly increase the expressed Angpt2/Angpt1 ratio in AoSMCs, which determines the regulatory role of angiopoietins in angiogenesis and their involvement in the development of atherosclerosis. These findings further support the association between periodontitis and cardiovascular disease.
MdsABC-Mediated Pathway for Pathogenicity in Salmonella enterica Serovar Typhimurium
Authors: Song Saemee , Lee Boeun , Yeom Ji-Hyun , Hwang Soonhye , Kang Ilnam , Cho Jang-Cheon , Ha Nam-Chul , Bae Jeehyeon , Lee Kangseok , Kim Yong-Hak 
Published: August 2015

ABSTRACT

MdsABC is a
Salmonella
-specific tripartite efflux pump that has been implicated in the virulence of
Salmonella enterica
serovar Typhimurium; however, little is known about the virulence factors associated with this pump. We observed MdsABC expression-dependent alterations in the degree of resistance to extracellular oxidative stress and macrophage-mediated killing. Thin-layer chromatography and tandem mass spectrometry analyses revealed that overexpression of MdsABC led to increased secretion of 1-palmitoyl-2-stearoyl-phosphatidylserine (PSPS), affecting the ability of the bacteria to invade and survive in host cells. Overexpression of MdsABC and external addition of PSPS similarly rendered the
mdsABC
deletion strain resistant to diamide. Diagonal gel analysis showed that PSPS treatment reduced the diamide-mediated formation of disulfide bonds, particularly in the membrane fraction of the bacteria.
Salmonella
infection of macrophages induced the upregulation of MdsABC expression and led to an increase of intracellular bacterial number and host cell death, similar to the effects of MdsABC overexpression and PSPS pretreatment on the
mdsABC
deletion strain. Our study shows that MdsABC mediates a previously uncharacterized pathway that involves PSPS as a key factor for the survival and virulence of
S
. Typhimurium in phagocytic cells.
Campylobacter hyointestinalis Isolated from Pigs Produces Multiple Variants of Biologically Active Cytolethal Distending Toxin
Authors: Kamei Kazumasa , Hatanaka Noritoshi , Asakura Masahiro , Somroop Srinuan , Samosornsuk Worada , Hinenoya Atsushi , Misawa Naoaki , Nakagawa Shinsaku , Yamasaki Shinji 
Published: August 2015

ABSTRACTCampylobacter hyointestinalisisolated from swine with proliferative enteritis often is considered to be pathogenic. While the precise virulence mechanisms of this species remain unclear, we have recently identified a cytolethal distending toxin (cdt) gene cluster inC. hyointestinalisisolated from a patient with diarrhea (W. Samosornsuk et al., J Med Microbiol, 27 July 2015,http://dx.doi.org/10.1099/jmm.0.000145). However, the sequences of thecdtgenes inC. hyointestinaliswere found to be significantly different and the gene products are immunologically distinct from those of otherCampylobacterspecies. In this study, we demonstrate the presence of a second variant of thecdtgene cluster inC. hyointestinalis, designatedcdt-II, while the former is namedcdt-I. Sequencing of thecdt-IIgene cluster and deduced amino acid sequences revealed that homologies between the subunits CdtA, CdtB, and CdtC of ChCDT-I and ChCDT-II are 25.0, 56.0, and 24.8%, respectively. Furthermore, the CdtB subunit of ChCDT-II was found to be immunologically unrelated to that of ChCDT-I by Ouchterlony double gel diffusion test. Recombinant ChCDT-II also induced cell distention and death of HeLa cells by blocking the cell cycle at G2/M phase. Interestingly, thecdt-IIgenes were detected in all 23 animal isolates and in 1 human isolate ofC. hyointestinalis, and 21 of these strains carried bothcdt-Iandcdt-IIgene clusters. Altogether, our results indicate that ChCDT-II is an important virulence factor ofC. hyointestinalisin animals.
Role of Inflammatory Monocytes in Vaccine-Induced Reduction of Helicobacter felis Infection
Authors: Moyat Mati , Mack Matthias , Bouzourene Hanifa , Velin Dominique 
Published: August 2015

ABSTRACT

Despite the proven ability of immunization to reduce
Helicobacter
infection in mouse models, the precise mechanism of protection has remained elusive. In this study, we evaluated the role of inflammatory monocytes in the vaccine-induced reduction of
Helicobacter felis
infection. We first showed by using flow cytometric analysis that Ly6C
low
major histocompatibility complex class II-positive chemokine receptor type 2 (CCR2)-positive CD64
+
inflammatory monocytes accumulate in the stomach mucosa during the vaccine-induced reduction of
H. felis
infection. To determine whether inflammatory monocytes played a role in the protection, these cells were depleted with anti-CCR2 depleting antibodies. Indeed, depletion of inflammatory monocytes was associated with an impaired vaccine-induced reduction of
H. felis
infection on day 5 postinfection. To determine whether inflammatory monocytes had a direct or indirect role, we studied their antimicrobial activities. We observed that inflammatory monocytes produced tumor necrosis factor alpha and inducible nitric oxide synthase (iNOS), two major antimicrobial factors. Lastly, by using a
Helicobacter
in vitro
killing assay, we showed that mouse inflammatory monocytes and activated human monocytes killed
H. pylori
in an iNOS-dependent manner. Collectively, these data show that inflammatory monocytes play a direct role in the immunization-induced reduction of
H. felis
infection from the gastric mucosa.