bluuebunny/crossref_metadata_2025_split huggingface dataset:
Web‐based, GPU‐accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance
Authors: Dong Han , Sharma Diksha , Badano Aldo 
Published: November 2014

Purpose:Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open‐source software packages. One such package, hybridmantis, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open‐source visualization interfaces, webmantis and visualmantis to facilitate the setup of computational experiments via hybridmantis.Methods:The visualization tools visualmantis and webmantis enable the user to control simulation properties through a user interface. In the case of webmantis, control via a web browser allows access through mobile devices such as smartphones or tablets. webmantis acts as a server back‐end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel.Results:The output consists of point response and pulse‐height spectrum, and optical transport statistics generated by hybridmantis. The users can download the output images and statistics through a zip file for future reference. In addition, webmantis provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons.Conclusions:The visualization tools visualmantis and webmantis provide features such as on the fly generation of pulse‐height spectra and response functions for microcolumnar x‐ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.
A GPU‐accelerated and Monte Carlo‐based intensity modulated proton therapy optimization system
Authors: Ma Jiasen , Beltran Chris , Seum Wan Chan Tseung Hok , Herman Michael G. 
Published: November 2014

Purpose:Conventional spot scanning intensity modulated proton therapy (IMPT) treatment planning systems (TPSs) optimize proton spot weights based on analytical dose calculations. These analytical dose calculations have been shown to have severe limitations in heterogeneous materials. Monte Carlo (MC) methods do not have these limitations; however, MC‐based systems have been of limited clinical use due to the large number of beam spots in IMPT and the extremely long calculation time of traditional MC techniques. In this work, the authors present a clinically applicable IMPT TPS that utilizes a very fast MC calculation.Methods:An in‐house graphics processing unit (GPU)‐based MC dose calculation engine was employed to generate the dose influence map for each proton spot. With the MC generated influence map, a modified least‐squares optimization method was used to achieve the desired dose volume histograms (DVHs). The intrinsic CT image resolution was adopted for voxelization in simulation and optimization to preserve spatial resolution. The optimizations were computed on a multi‐GPU framework to mitigate the memory limitation issues for the large dose influence maps that resulted from maintaining the intrinsic CT resolution. The effects of tail cutoff and starting condition were studied and minimized in this work.Results:For relatively large and complex three‐field head and neck cases, i.e., >100 000 spots with a target volume of ∼1000 cm3 and multiple surrounding critical structures, the optimization together with the initial MC dose influence map calculation was done in a clinically viable time frame (less than 30 min) on a GPU cluster consisting of 24 Nvidia GeForce GTX Titan cards. The in‐house MC TPS plans were comparable to a commercial TPS plans based on DVH comparisons.Conclusions:A MC‐based treatment planning system was developed. The treatment planning can be performed in a clinically viable time frame on a hardware system costing around 45 000 dollars. The fast calculation and optimization make the system easily expandable to robust and multicriteria optimization.
On the consistency of Monte Carlo track structure DNA damage simulations
Authors: Pater Piotr , Seuntjens Jan , El Naqa Issam , Bernal Mario A. 
Published: November 2014

Purpose:Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies.Methods:The MCTS code Geant4‐DNA was used to compare radial dose profiles in a nanometer‐scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV–220 keV were superimposed on a geometric DNA model composed of 2.7 × 106 nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy ETH. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter‐SB distances and on the number of affected strands.Results:Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer‐based SB definitions give similar SB yields as the one based on energy deposit when ETH ≈ 10.79 eV, but deviate significantly for higher ETH values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their implementations. The authors’ show that, for the four studied models, different yields are expected by up to 54% for SSBs and by up to 32% for DSBs, as a function of the incident electrons energy and of the models being compared.Conclusions:MCTS simulations allow to compare direct DNA damage types and complexities induced by ionizing radiation. However, simulation results depend to a large degree on user‐defined parameters, definitions, and algorithms such as: DNA model, dose distribution, SB definition, and the DNA damage clustering algorithm. These interdependencies should be well controlled during the simulations and explicitly reported when comparing results to experiments or calculations.
Potential Contribution of Anammox to Nitrogen Loss from Paddy Soils in Southern China
Authors: Yang Xiao-Ru , Li Hu , Nie San-An , Su Jian-Qiang , Weng Bo-Sen , Zhu Gui-Bing , Yao Huai-Ying , Gilbert Jack A. , Zhu Yong-Guan 
Published: November 2014

ABSTRACT

The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N
2
production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to “
Candidatus
Brocadia” and “
Candidatus
Kuenenia” and two novel unidentified clusters were detected, with “
Candidatus
Brocadia” comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (
hzsB
) genes, which showed that the abundance ranged from 1.16 × 10
4
to 9.65 × 10
4
copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N
2
production. It is estimated that a total loss of 2.50 × 10
6
Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of
hzsB
genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.
Interactions between Head Blight Pathogens: Consequences for Disease Development and Toxin Production in Wheat Spikes
Authors: Siou Dorothée , Gélisse Sandrine , Laval Valérie , Elbelt Sonia , Repinçay Cédric , Bourdat-Deschamps Marjolaine , Suffert Frédéric , Lannou Christian 
Published: November 2014

ABSTRACT

Head blight (HB) is one of the most damaging diseases on wheat, inducing significant yield losses and toxin accumulation in grains. Fungal pathogens responsible for HB include the genus
Microdochium
, with two species, and the toxin producer genus
Fusarium
, with several species. Field studies and surveys show that two or more species can coexist within a same field and coinfect the same plant or the same spike. In the current study, we investigated how the concomitant presence of
F. graminearum
and another of the HB complex species influences the spike colonization and the toxin production by the fungi. To study these interactions, 17 well-characterized isolates representing five species were inoculated alone or in pairs on wheat spikes in greenhouse and field experiments. The fungal DNA in the grains was estimated by quantitative PCR and toxin contents (deoxynivalenol and nivalenol) by ultraperformance liquid chromatography-UV detection-tandem mass spectrometry. The responses of the different isolates to the presence of a competitor were variable and isolate specific more than species specific. The development of the most aggressive isolates was either unchanged or a slightly increased, while the development of the less aggressive isolates was reduced. The main outcome of the study was that no trend of increased toxin production was observed in coinoculations compared to single inoculations. On the contrary, the amount of toxin produced was often lower than expected in coinoculations. We thus conclude against the hypothesis that the co-occurrence of several HB-causing species in the same field might aggravate the risk linked to fusarium toxins in wheat production.
Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents
Authors: Kawato Yasuhiko , Yasuike Motoshige , Nakamura Yoji , Shigenobu Yuya , Fujiwara Atushi , Sano Motohiko , Nakai Toshihiro 
Published: November 2014

ABSTRACT

Pseudomonas plecoglossicida
is a lethal pathogen of ayu (
Plecoglossus altivelis
) in Japan and is responsible for substantial economic costs to ayu culture. Previously, we demonstrated the efficacy of phage therapy against
P. plecoglossicida
infection using two lytic phages (PPpW-3 and PPpW-4) (S. C. Park, I. Shimamura, M. Fukunaga, K. Mori, and T. Nakai, Appl Environ Microbiol 66:1416–1422, 2000,
http://dx.doi.org/10.1128/AEM.66.4.1416-1422.2000
; S. C. Park and T. Nakai, Dis Aquat Org 53:33–39, 2003,
http://dx.doi.org/10.3354/dao053033
). In the present study, the complete genome sequences of these therapeutic
P. plecoglossicida
phages were determined and analyzed for deleterious factors as therapeutic agents. The genome of PPpW-3 (myovirus) consisted of 43,564 bp with a GC content of 61.1% and 66 predicted open reading frames (ORFs). Approximately half of the genes were similar to the genes of the
Escherichia coli
phage vB_EcoM_ECO1230-10 (myovirus). The genome of PPpW-4 (podovirus) consisted of 41,386 bp with a GC content of 56.8% and 50 predicted ORFs. More than 70% of the genes were similar to the genes of
Pseudomonas fluorescens
phage ϕIBB-PF7A and
Pseudomonas putida
phage ϕ15 (podoviruses). The whole-genome analysis revealed that no known virulence genes were present in PPpW-3 and PPpW-4. An integrase gene was found in PPpW-3, but other factors used for lysogeny were not confirmed. The PCR detection of phage genes in phage-resistant variants provided no evidence of lysogenic activity in PPpW-3 and PPpW-4. We conclude that these two lytic phages qualify as therapeutic agents.
Effects of Eliminating Pyruvate Node Pathways and of Coexpression of Heterogeneous Carboxylation Enzymes on Succinate Production by Enterobacter aerogenes
Authors: Tajima Yoshinori , Yamamoto Yoko , Fukui Keita , Nishio Yousuke , Hashiguchi Kenichi , Usuda Yoshihiro , Sode Koji 
Published: November 2014

ABSTRACT

Lowering the pH in bacterium-based succinate fermentation is considered a feasible approach to reduce total production costs. Newly isolated
Enterobacter aerogenes
strain AJ110637, a rapid carbon source assimilator under weakly acidic (pH 5.0) conditions, was selected as a platform for succinate production. Our previous work showed that the Δ
adhE/
PCK strain, developed from AJ110637 with inactivated ethanol dehydrogenase and introduced
Actinobacillus succinogenes
phosphoenolpyruvate carboxykinase (PCK), generated succinate as a major product of anaerobic mixed-acid fermentation from glucose under weakly acidic conditions (pH <6.2). To further improve the production of succinate by the Δ
adhE
/PCK strain, metabolically engineered strains were designed based on the elimination of pathways that produced undesirable products and the introduction of two carboxylation pathways from phosphoenolpyruvate and pyruvate to oxaloacetate. The highest production of succinate was observed with strain ES04/PCK+PYC, which had inactivated ethanol, lactate, acetate, and 2,3-butanediol pathways and coexpressed PCK and
Corynebacterium glutamicum
pyruvate carboxylase (PYC). This strain produced succinate from glucose with over 70% yield (gram per gram) without any measurable formation of ethanol, lactate, or 2,3-butanediol under weakly acidic conditions. The impact of lowering the pH from 7.0 to 5.5 on succinate production in this strain was evaluated under pH-controlled batch culture conditions and showed that the lower pH decreased the succinate titer but increased its yield. These findings can be applied to identify additional engineering targets to increase succinate production.
Guidelines for chest drain insertion may not prevent damage to abdominal viscera
Authors: Bowness J , Kilgour P M , Whiten S , Parkin I , Mooney J , Driscoll P 
Published: November 2014

ObjectivesGuidelines to improve the ease and safety of chest drain insertion recommend using the fifth intercostal space, around the midaxillary line (MAL). This study aimed to assess whether compliance with published guidelines reliably ensured such placement and avoided the potentially serious complications of subdiaphragmatic insertion and peripheral nerve injury.MethodsThree international guidelines were assessed by identifying the intercostal space for chest drain insertion using 16 cadavers (32 sides) at a point 1 cm anterior to MAL. The European Trauma Course method was compared with the British Thoracic Society's ‘safe triangle’ and the ATLS course technique.ResultsThe level most commonly found was the sixth intercostal space (43%; 41 of 96 sides). Overall the sixth space or below was found in 83% of insertions (80 of 96 sides). In the fifth intercostal space, the long thoracic nerve ran posterior to the marker placed in all cases and the lateral cutaneous branches of intercostal nerves arose anteriorly to the marker in all but one case.ConclusionsThe results suggest these guidelines may result in insertion of chest drains below the fifth intercostal space, potentially risking injury to subdiaphragmatic structures. Peripheral nerves of the lateral thoracic wall appear safe from incisions 1 cm anterior to MAL.
Causal analysis of H1N1pdm09 influenza infection risk in a household cohort
Authors: Mansiaux Yohann , Salez Nicolas , Lapidus Nathanael , Setbon Michel , Andreoletti Laurent , Leruez-Ville Marianne , Cauchemez Simon , Gougeon Marie-Lise , Vély Frédéric , Schwarzinger Michael , Abel Laurent , Delabre Rosemary Markovic , Flahault Antoine , de Lamballerie Xavier , Carrat Fabrice 
Published: November 2014

BackgroundObtaining a comprehensive quantitative figure of the determinants of influenza infection will help identify priority targets for future influenza mitigation interventions. We developed an original causal model integrating highly diverse factors and their dependencies, to identify the most critical determinants of pandemic influenza infection (H1N1pdm09) during the 2010–2011 influenza season.MethodsWe used data from 601 households (1450 participants) included in a dedicated cohort. Structural equations were used to model direct and indirect relationships between infection and risk perception, compliance with preventive behaviours, social contacts, indoor and outdoor environment, sociodemographic factors and pre-epidemic host susceptibility. Standardised estimates (βstd) were used to assess the strength of associations (ranging from −1 for a completely negative association to 1 for a completely positive association).ResultsHost susceptibility to H1N1pdm09 and compliance with preventive behaviours were the only two factors directly associated with the infection risk (βstd=0.31 and βstd=−0.21). Compliance with preventive behaviours was influenced by risk perception and preventive measures perception (βstd=0.14 and βstd=0.27). The number and duration of social contacts were not associated with H1N1pdm09 infection.ConclusionsOur findings suggest that influenza vaccination in addition to public health communication campaigns focusing on personal preventive measures should be prioritised as potentially efficient interventions to mitigate influenza epidemics.
Renormalized-generalized solutions for the KPZ equation
Authors: Catuogno Pedro , Olivera Christian 
Published: November 2014

This work introduces a new notion of solution for the KPZ equation, in particular, our approach encompasses the Cole–Hopf solution. We set in the context of the distribution theory the proposed results by Bertini and Giacomin from the mid '90s. This new approach provides a pathwise notion of solution as well as a structured approximation theory. The developments are based on regularization arguments from the theory of distributions.
Contributions to Drug Resistance in Glioblastoma Derived from Malignant Cells in the Sub-Ependymal Zone
Authors: Piccirillo Sara G.M. , Spiteri Inmaculada , Sottoriva Andrea , Touloumis Anestis , Ber Suzan , Price Stephen J. , Heywood Richard , Francis Nicola-Jane , Howarth Karen D. , Collins Vincent P. , Venkitaraman Ashok R. , Curtis Christina , Marioni John C. , Tavaré Simon , Watts Colin 
Published: November 2014

Abstract
Glioblastoma, the most common and aggressive adult brain tumor, is characterized by extreme phenotypic diversity and treatment failure. Through fluorescence-guided resection, we identified fluorescent tissue in the sub-ependymal zone (SEZ) of patients with glioblastoma. Histologic analysis and genomic characterization revealed that the SEZ harbors malignant cells with tumor-initiating capacity, analogous to cells isolated from the fluorescent tumor mass (T). We observed resistance to supramaximal chemotherapy doses along with differential patterns of drug response between T and SEZ in the same tumor. Our results reveal novel insights into glioblastoma growth dynamics, with implications for understanding and limiting treatment resistance. Cancer Res; 75(1); 194–202. ©2014 AACR.
Solid Tumors of Childhood Display Specific Serum microRNA Profiles
Authors: Murray Matthew J. , Raby Katie L. , Saini Harpreet K. , Bailey Shivani , Wool Sophie V. , Tunnacliffe Jane M. , Enright Anton J. , Nicholson James C. , Coleman Nicholas 
Published: November 2014

Abstract
Background: Serum biomarkers for diagnosis and risk stratification of childhood solid tumors would improve the accuracy/timeliness of diagnosis and reduce the need for invasive biopsies. We hypothesized that differential expression and/or release of microRNAs (miRNAs) by such tumors may be detected as altered serum miRNA profiles.
Methods: We undertook global quantitative reverse transcription PCR (qRT-PCR) miRNA profiling (n = 741) on RNA from 53 serum samples, representing 33 diagnostic cases of common childhood cancers plus 20 controls. Technical confirmation was performed in a subset of 21 cases, plus four independent samples.
Results: We incorporated robust quality control steps for RNA extraction, qRT-PCR efficiency and hemolysis quantification. We evaluated multiple methods to normalize global profiling data and identified the ‘global mean’ approach as optimal. We generated a panel of six miRNAs that were most stable in pediatric serum samples and therefore most suitable for normalization of targeted miRNA qRT-PCR data. Tumor-specific serum miRNA profiles were identified for each tumor type and selected miRNAs underwent confirmatory testing. We identified a panel of miRNAs (miR-124-3p/miR-9-3p/miR-218-5p/miR-490-5p/miR-1538) of potential importance in the clinical management of neuroblastoma, as they were consistently highly overexpressed in MYCN-amplified high-risk cases (MYCN-NB). We also derived candidate miRNA panels for noninvasive differential diagnosis of a liver mass (hepatoblastoma vs. combined MYCN-NB/NB), an abdominal mass (Wilms tumor vs. combined MYCN-NB/NB), and sarcoma subtypes.
Conclusions: This study describes a pipeline for robust diagnostic serum miRNA profiling in childhood solid tumors, and has identified candidate miRNA profiles for prospective testing.
Impact: We propose a new noninvasive method with the potential to diagnose childhood solid tumors. Cancer Epidemiol Biomarkers Prev; 24(2); 350–60. ©2014 AACR.