bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moving target irradiation with fast rescanning and gating in particle therapy
Authors: Furukawa Takuji , Inaniwa Taku , Sato Shinji , Shirai Toshiyuki , Mori Shinichiro , Takeshita Eri , Mizushima Kota , Himukai Takeshi , Noda Koji 
Published: August 2010

Purpose:In moving target irradiation with pencil beam scanning, the interplay effect between the target motion and the scanned beam is a problem because this effect causes over or under dosage in the target volume. To overcome this, we have studied rescanning using a gating technique.Methods:A simulation and experimental study was carried out. In the experiment, we used the fast scanning system developed at the HIMAC to verify the validity of phase controlled rescanning method, in which the time for rescanning irradiation of each slice is matched to the gating duration.Results:Simulation and experimental results showed that controlling the scan speed to match the respiration cycle with rescans can deliver the blurred dose distribution. In the comparison between the static measurements and the moving measurements with the phase controlled rescanning method, the dose difference was less than 2% for pinpoint chambers in the target volume.Conclusions:The simulation and experimental results demonstrated that the phase controlled rescanning method makes it possible to deliver the dose distribution close to the expected one. As an experimental result for 3D irradiation, it was estimated that blurring by the probability density function was not only for a lateral distribution, but also for a distal distribution, even in the lateral rescanning.
Assessment of normal tissue complications following prostate cancer irradiation: Comparison of radiation treatment modalities using NTCP models
Authors: Takam Rungdham , Bezak Eva , Yeoh Eric E. , Marcu Loredana 
Published: August 2010

Purpose:Normal tissue complication probability (NTCP) of the rectum, bladder, urethra, and femoral heads following several techniques for radiation treatment of prostate cancer were evaluated applying the relative seriality and Lyman models.Methods:Model parameters from literature were used in this evaluation. The treatment techniques included external (standard fractionated, hypofractionated, and dose‐escalated) three‐dimensional conformal radiotherapy (3D‐CRT), low‐dose‐rate (LDR) brachytherapy (I‐125 seeds), and high‐dose‐rate (HDR) brachytherapy (Ir‐192 source). Dose‐volume histograms (DVHs) of the rectum, bladder, and urethra retrieved from corresponding treatment planning systems were converted to biological effective dose‐based and equivalent dose‐based DVHs, respectively, in order to account for differences in radiation treatment modality and fractionation schedule.Results:Results indicated that with hypofractionated 3D‐CRT (20 fractions of 2.75 Gy/fraction delivered five times/week to total dose of 55 Gy), NTCP of the rectum, bladder, and urethra were less than those for standard fractionated 3D‐CRT using a four‐field technique (32 fractions of 2 Gy/fraction delivered five times/week to total dose of 64 Gy) and dose‐escalated 3D‐CRT. Rectal and bladder NTCPs (5.2% and 6.6%, respectively) following the dose‐escalated four‐field 3D‐CRT (2 Gy/fraction to total dose of 74 Gy) were the highest among analyzed treatment techniques. The average NTCP for the rectum and urethra were 0.6% and 24.7% for LDR‐BT and 0.5% and 11.2% for HDR‐BT.Conclusions:Although brachytherapy techniques resulted in delivering larger equivalent doses to normal tissues, the corresponding NTCPs were lower than those of external beam techniques other than the urethra because of much smaller volumes irradiated to higher doses. Among analyzed normal tissues, the femoral heads were found to have the lowest probability of complications as most of their volume was irradiated to lower equivalent doses compared to other tissues.
Phantom‐based experimental validation of computational fluid dynamics simulations on cerebral aneurysms
Authors: Sun Qi , Groth Alexandra , Bertram Matthias , Waechter Irina , Bruijns Tom , Hermans Roel , Aach Til 
Published: August 2010

Purpose:Recently, image‐based computational fluid dynamics (CFD) simulation has been applied to investigate the hemodynamics inside human cerebral aneurysms. The knowledge of the computed three‐dimensional flow fields is used for clinical risk assessment and treatment decision making. However, the reliability of the application specific CFD results has not been thoroughly validated yet.Methods:In this work, by exploiting a phantom aneurysm model, the authors therefore aim to prove the reliability of the CFD results obtained from simulations with sufficiently accurate input boundary conditions. To confirm the correlation between the CFD results and the reality, virtual angiograms are generated by the simulation pipeline and are quantitatively compared to the experimentally acquired angiograms. In addition, a parametric study has been carried out to systematically investigate the influence of the input parameters associated with the current measuring techniques on the flow patterns.Results:Qualitative and quantitative evaluations demonstrate good agreement between the simulated and the real flow dynamics. Discrepancies of less than 15% are found for the relative root mean square errors of time intensity curve comparisons from each selected characteristic position. The investigated input parameters show different influences on the simulation results, indicating the desired accuracy in the measurements.Conclusions:This study provides a comprehensive validation method of CFD simulation for reproducing the real flow field in the cerebral aneurysm phantom under well controlled conditions. The reliability of the CFD is well confirmed. Through the parametric study, it is possible to assess the degree of validity of the associated CFD model based on the parameter values and their estimated accuracy range.
Technical Note: Calculation of normal tissue complication probability using Gaussian error function model
Authors: Chow James C. L. , Markel Daniel , Jiang Runqing 
Published: August 2010

Purpose:The Gaussian error function was first used and verified in normal tissue complication probability (NTCP) calculation to reduce the dose‐volume histogram (DVH) database by replacing the dose‐volume bin set with the error function parameters for the differential DVH (dDVH).Methods:Seven‐beam intensity modulated radiation therapy (IMRT) treatment planning was performed in three patients with small, medium , and large prostate volume, selected from a group of 20 patients. Rectal dDVH varying with the interfraction prostate motion along the anterior‐posterior direction was determined by the treatment planning system (TPS) and modeled by the Gaussian error function model for the three patients. Rectal NTCP was then calculated based on the routine dose‐volume bin set of the rectum by the TPS and the error function model. The variations in the rectal NTCP with the prostate motion and volume were studied.Results:For the ranges of prostate motion of 8–2, 4–8, and 4–3 mm along the anterior‐posterior direction for the small, medium, and large prostate patient, the rectal NTCP was determined varying in the ranges of 4.6%–4.8%, 4.5%–4.7%, and 4.6%–4.7%, respectively. The deviation of the rectal NTCP calculated by the TPS and the Gaussian error function model was within ±0.1%.Conclusions:The Gaussian error function was successfully applied in the NTCP calculation by replacing the dose‐volume bin set with the model parameters. This provides an option in the NTCP calculation using a reduced size of dose‐volume database. Moreover, the rectal NTCP was found varying in about ±0.2% with the interfraction prostate motion along the anterior‐posterior direction in the radiation treatment. The dependence of the variation in the rectal NTCP with the interfraction prostate motion on the prostate volume was found to be more significant in the patient with larger prostate.
Dosimetric evaluation of the OneDose™ MOSFET for measuring kilovoltage imaging dose from image‐guided radiotherapy procedures
Authors: Ding George X. , Coffey Charles W. 
Published: August 2010

Purpose:The purpose of this study is to investigate the feasibility of using a single‐use dosimeter, OneDose™ MOSFET designed for in vivo patient dosimetry, for measuring the radiation dose from kilovoltage (kV) x rays resulting from image‐guided procedures.Methods:The OneDose™ MOSFET dosimeters were precalibrated by the manufacturer using Co‐60 beams. Their energy response and characteristics for kV x rays were investigated by using an ionization chamber, in which the air‐kerma calibration factors were obtained from an Accredited Dosimetry Calibration Laboratory (ADCL). The dosimetric properties have been tested for typical kV beams used in image‐guided radiation therapy (IGRT).Results:The direct dose reading from the OneDose™ system needs to be multiplied by a correction factor ranging from 0.30 to 0.35 for kilovoltage x rays ranging from 50 to 125 kVp, respectively. In addition to energy response, the OneDose™ dosimeter has up to a 20% reduced sensitivity for beams (70–125 kVp) incident from the back of the OneDose™ detector.Conclusions:The uncertainty in measuring dose resulting from a kilovoltage beam used in IGRT is approximately 20%; this uncertainty is mainly due to the sensitivity dependence of the incident beam direction relative to the OneDose™ detector. The ease of use may allow the dosimeter to be suitable for estimating the dose resulting from image‐guided procedures.
Thr202Ala in
thyA
Is a Marker for the Latin American Mediterranean Lineage of the
Mycobacterium tuberculosis
Complex Rather than
Para
-Aminosalicylic Acid Resistance
Authors: Feuerriegel Silke , Köser Claudio , Trübe Leona , Archer John , Rüsch Gerdes Sabine , Richter Elvira , Niemann Stefan 
Published: August 2010

ABSTRACT

Single nucleotide polymorphisms (SNPs) involved in the development of resistance represent powerful markers for the rapid detection of first- and second-line resistance in clinical
Mycobacterium tuberculosis
complex (MTBC) isolates. However, the association between particular mutations and phenotypic resistance is not always clear-cut, and phylogenetic SNPs have been misclassified as resistance markers in the past. In the present study, we investigated the utility of a specific polymorphism in
thyA
(Thr202Ala) as a marker for resistance to
para
-aminosalicyclic acid (PAS). Sixty-three PAS-susceptible MTBC strains comprising all major phylogenetic lineages, reference strain H37Rv, and 135 multidrug-resistant (MDR) strains from Germany (comprising 8 PAS-resistant isolates) were investigated for the presence of Thr202Ala. In both strain collections, the Thr202Ala SNP was found exclusively in strains of the Latin American Mediterranean (LAM) lineage irrespective of PAS resistance. Furthermore, PAS MICs (0.5 mg/liter) for selected LAM strains (all containing the SNP) and non-LAM strains (not containing the SNP), as well as the results of growth curve analyses performed in liquid 7H9 medium in the presence of increasing PAS concentrations (0 to 2.0 mg/liter), were identical. In conclusion, our data demonstrate that the Thr202Ala polymorphism in
thyA
is not a valid marker for PAS resistance but, instead, represents a phylogenetic marker for the LAM lineage of the
M. tuberculosis
complex. These findings challenge some of the previous understanding of PAS resistance and, as a consequence, warrant further in-depth investigations of the genetic variation in PAS-resistant clinical isolates and spontaneous mutants.
In Vitro
and
In Vivo
Antifungal Susceptibilities of the Mucoralean Fungus
Cunninghamella
Authors: Pastor F. Javier , Ruíz-Cendoya Mery , Pujol Isabel , Mayayo Emilio , Sutton Deanna A. , Guarro Josep 
Published: August 2010

ABSTRACT

We have determined the
in vitro
activities of amphotericin B (AMB), voriconazole, posaconazole (PSC), itraconazole (ITC), ravuconazole, terbinafine, and caspofungin against five strains of
Cunninghamella bertholletiae
and four of
Cunninghamella echinulata
. The best activity was shown by terbinafine against both species (MIC range = 0.3 to 0.6 μg/ml) and PSC against
Cunninghamella bertholletiae
(MIC = 0.5 μg/ml). We have also evaluated the efficacies of PSC, ITC, and AMB in neutropenic and diabetic murine models of disseminated infection by
Cunninghamella bertholletiae
. PSC at 40, 60, or 80 mg/kg of body weight/day was as effective as AMB at 0.8 mg/kg/day in prolonging survival and reducing the fungal tissue burden in neutropenic mice. PSC at 80 mg/kg/day was more effective than AMB at 0.8 mg/kg/day in reducing the fungal load in brain and lung of diabetic mice. Histological studies revealed an absence of fungal elements in organs of mice treated with either AMB at 0.8 mg/kg/day or PSC at 60 or 80 mg/kg/day in both models. ITC showed limited efficacy in both models. PSC could be a therapeutic option for the treatment of systemic infections caused by
Cunninghamella bertholletiae
.
Distinct Mutation Pathways of Non-Subtype B HIV-1 duringIn VitroResistance Selection with Nonnucleoside Reverse Transcriptase Inhibitors
Authors: Lai Ming-Tain , Lu Meiqing , Felock Peter J. , Hrin Renee C. , Wang Ying-Jie , Yan Youwei , Munshi Sanjeev , McGaughey Georgia B. , Tynebor Robert M. , Tucker Thomas J. , Williams Theresa M. , Grobler Jay A. , Hazuda Daria J. , McKenna Philip M. , Miller Michael D. 
Published: August 2010

ABSTRACTStudies were conducted to investigate mutation pathways among subtypes A, B, and C of human immunodeficiency virus type 1 (HIV-1) during resistance selection with nonnucleoside reverse transcriptase inhibitors (NNRTIs) in cell culture under low-multiplicity of infection (MOI) conditions. The results showed that distinct pathways were selected by different virus subtypes under increasing selective pressure of NNRTIs. F227C and Y181C were the major mutations selected by MK-4965 in subtype A and C viruses during resistance selection. With efavirenz (EFV), F227C and V106M were the major mutations responsible for viral breakthrough in subtype A viruses, whereas a single pathway (G190A/V106M) accounted for mutation development in subtype C viruses. Y181C was the dominant mutation in the resistance selection with etravirine (ETV) in subtype A, and E138K/H221Y were the mutations detected in the breakthrough viruses from subtype C viruses with ETV. In subtype B viruses, on the other hand, known NNRTI-associated mutations (e.g., Y181C, P236L, L100I, V179D, and K103N) were selected by the NNRTIs. The susceptibility of the subtype A and B mutant viruses to NNRTIs was determined in order to gain insight into the potential mechanisms of mutation development. Collectively, these results suggest that minor differences may exist in conformation of the residues within the NNRTI binding pocket (NNRTIBP) of reverse transcriptase (RT) among the three subtypes of viruses. Thus, the interactions between NNRTIs and the residues in the NNRTIBPs of different subtypes may not be identical, leading to distinct mutation pathways during resistance selection in cell culture.
GES Extended-Spectrum β-Lactamases in
Acinetobacter baumannii
Isolates in Belgium
Authors: Bogaerts Pierre , Naas Thierry , El Garch Farid , Cuzon Gaelle , Deplano Ariane , Delaire Tugba , Huang Te-Din , Lissoir Benedicte , Nordmann Patrice , Glupczynski Youri 
Published: August 2010

ABSTRACT

During a PCR-based surveillance study of β-lactam resistance, 125 multidrug-resistant (MDR)
Acinetobacter baumannii
isolates were obtained from 18 hospitals in Belgium from January 2008 to December 2009. Nine GES-positive
A. baumannii
isolates were detected at 6 Belgian hospitals. DNA sequencing of the
bla
GES
genes identified GES-11, GES-12, and a novel variant GES-14, which differs from GES-11 by a single amino acid substitution (Gly170Ser). All index isolates were travel associated and originated from patients transferred from Turkey (
n
= 2), Egypt (
n
= 2), and Palestinian territories (Gaza) (
n
= 2). A nosocomial outbreak involving three additional patients occurred in a burn unit at a single hospital. No clonal relatedness could be established between the 6 index isolates by pulsed-field gel electrophoresis (PFGE) analysis. Three different alleles (the plasmid-located
bla
GES-11
and
bla
GES-12
and a likely chromosomally located novel variant
bla
GES-14
) were detected as part of a class 1 integron, also including the
aac6
′
Ib
and
dfrA7
genes. Restriction analysis of plasmids suggests a common origin for the plasmids bearing
bla
GES-11
and
bla
GES-12
. Cloning of the
bla
GES
genes in
E
scherichia
coli
identified GES-14 as hydrolyzing imipenem, while GES-12 showed the highest specific activity against ceftazidime. This report highlights the emergence of various
bla
GES-like
genes, especially those conferring carbapenem resistance in
A. baumannii
and its importation in Western Europe from Middle Eastern countries.
Characterization of the CpxRA Regulon in
Haemophilus ducreyi
Authors: Labandeira-Rey Maria , Brautigam Chad A. , Hansen Eric J. 
Published: August 2010

ABSTRACT

The
H
aemophilus
ducreyi
35000HP genome encodes a homolog of the CpxRA two-component cell envelope stress response system originally characterized in
E
scherichia
coli
. CpxR, the cytoplasmic response regulator, was shown previously to be involved in repression of the expression of the
lspB-lspA2
operon (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402-3411, 2009). In the present study, the
H. ducreyi
CpxR and CpxA proteins were shown to closely resemble those of other well-studied bacterial species. A
cpxA
deletion mutant and a CpxR-overexpressing strain were used to explore the extent of the CpxRA regulon. DNA microarray and real-time reverse transcriptase (RT) PCR analyses indicated several potential regulatory targets for the
H. ducreyi
CpxRA two-component regulatory system. Electrophoretic mobility shift assays (EMSAs) were used to prove that
H. ducreyi
CpxR interacted with the promoter regions of genes encoding both known and putative virulence factors of
H. ducreyi
, including the
lspB-lspA2
operon, the
flp
operon, and
dsrA.
Interestingly, the use of EMSAs also indicated that
H. ducreyi
CpxR did not bind to the promoter regions of several genes predicted to encode factors involved in the cell envelope stress response. Taken together, these data suggest that the CpxRA system in
H. ducreyi
, in contrast to that in
E. coli
, may be involved primarily in controlling expression of genes not involved in the cell envelope stress response.
Interaction of
Candida albicans
Cell Wall Als3 Protein with
Streptococcus gordonii
SspB Adhesin Promotes Development of Mixed-Species Communities
Authors: Silverman Richard J. , Nobbs Angela H. , Vickerman M. Margaret , Barbour Michele E. , Jenkinson Howard F. 
Published: August 2010

ABSTRACT

Candida albicans
colonizes human mucosa and prosthetic surfaces associated with artificial joints, catheters, and dentures. In the oral cavity,
C. albicans
coexists with numerous bacterial species, and evidence suggests that bacteria may modulate fungal growth and biofilm formation.
Streptococcus gordonii
is found on most oral cavity surfaces and interacts with
C. albicans
to promote hyphal and biofilm formation. In this study, we investigated the role of the hyphal-wall protein Als3p in interactions of
C. albicans
with
S. gordonii
. Utilizing an
ALS3
deletion mutant strain, it was shown that cells were not affected in initial adherence to the salivary pellicle or in hyphal formation in the planktonic phase. However, the Als3
−
mutant was unable to form biofilms on the salivary pellicle or deposited
S. gordonii
DL1 wild-type cells, and after initial adherence,
als3
Δ
/als3
Δ (Δ
ALS3
) cells became detached concomitant with hyphal formation. In coaggregation assays,
S. gordonii
cells attached to, and accumulated around, hyphae formed by
C. albicans
wild-type cells. However, streptococci failed to attach to hyphae produced by the Δ
ALS3
mutant.
Saccharomyces cerevisiae
S150-2B cells expressing Als3p, but not control cells, supported binding of
S. gordonii
DL1. However,
S. gordonii
Δ(
sspA sspB
) cells deficient in production of the surface protein adhesins SspA and SspB showed >50% reduced levels of binding to
S. cerevisiae
expressing Als3p.
Lactococcus lactis
cells expressing SspB bound avidly to
S. cerevisiae
expressing Als3p, but not to S150-2B wild-type cells. These results show that recognition of
C. albicans
by
S. gordonii
involves Als3 protein-SspB protein interaction, defining a novel mechanism in fungal-bacterial communication.
“Please keep an eye on your younger sister”: sibling supervision and young children's risk of unintentional injury
Authors: Morrongiello Barbara A , Schell Stacey L , Schmidt Sarah 
Published: August 2010

ObjectivesParental supervision reduces young children's risk of unintentional injuries, but supervision by older siblings has been shown to increase risk. The current study explored how this differential risk of injury may arise.MethodsThe supervision behaviours of mothers were compared to those of their older children when each was the designated supervisor of a young child in their family in a setting having ‘contrived hazards’.ResultsMothers engaged in more proactive safety behaviours by removing hazards, whereas older siblings more often modelled injury-risk behaviours by interacting with hazards, and supervisees were likely to interact with hazards the older sibling touched. Supervisees displayed more injury-risk behaviours when supervised by a sibling, yet sibling supervisors were less attentive to supervisee risk behaviours than mothers. Supervisees also were more non-compliant with older siblings than mothers when requested to stop risk taking.ConclusionsBoth supervisor and supervisee behaviour patterns contribute to increase the risk of injury when older siblings supervise younger ones.
Nonblocking real-time garbage collection
Authors: Schoeberl Martin , Puffitsch Wolfgang 
Published: August 2010

A real-time garbage collector has to fulfill two basic properties: ensure that programs with bounded allocation rates do not run out of memory and provide short blocking times. Even for incremental garbage collectors, two major sources of blocking exist, namely, root scanning and heap compaction. Finding root nodes of an object graph is an integral part of tracing garbage collectors and cannot be circumvented. Heap compaction is necessary to avoid probably unbounded heap fragmentation, which in turn would lead to unacceptably high memory consumption. In this article, we propose solutions to both issues.
Thread stacks are local to a thread, and root scanning, therefore, only needs to be atomic with respect to the thread whose stack is scanned. This fact can be utilized by either blocking only the thread whose stack is scanned, or by delegating the responsibility for root scanning to the application threads. The latter solution eliminates blocking due to root scanning completely. The impact of this solution on the execution time of a garbage collector is shown for two different variants of such a root scanning algorithm.
During heap compaction, objects are copied. Copying is usually performed atomically to avoid interference with application threads, which could render the state of an object inconsistent. Copying of large objects and especially large arrays introduces long blocking times that are unacceptable for real-time systems. In this article, an interruptible copy unit is presented that implements nonblocking object copy. The unit can be interrupted after a single word move.
We evaluate a real-time garbage collector that uses the proposed techniques on a Java processor. With this garbage collector, it is possible to run high-priority hard real-time tasks at 10 kHz parallel to the garbage collection task on a 100 MHz system.