bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Note: Radiation dose reduction from computed tomography localizer radiographs using a tin spectral shaping filter
Authors: Saltybaeva Natalia , Krauss Andreas , Alkadhi Hatem 
Published: December 2018

PurposeTo evaluate the possibility of lowering radiation dose from a localizer radiograph (LR) using a tin spectral shaping filter and to investigate the effect of this adaptation on the radiation dose and image quality of subsequent computed tomography (CT) examination.MethodsThe study utilized a set of semianthropomorphic abdomen phantoms, representing small, medium, and large patients. The LR scans were performed with and without a tin spectral shaping filter using various kVp/mA settings. The tube current values of spiral CT examinations following the LR were assessed to evaluate the effect of LR settings on automatic exposure control (AEC). The image quality of CT examinations with various LRs was evaluated by measuring image noise in several regions‐of‐interest. Organ dose values from LR scans were derived from Monte Carlo simulations performed on a set of virtual anthropomorphic phantoms and the effective dose (ED) values were calculated.ResultsThe radiation dose from the LR can be strongly reduced by using a tin spectral shaping filter (P < 0.001). The optimal settings of the LR scan depend on the size of the scanned subject: for small and medium size subjects, the combination of a tin spectral shaping filter with 100 kVp and 20 mA resulted in the lowest possible radiation dose (ED = 0.007 mGy) without compromising the AEC and image quality of subsequent CT. In contrast, the LR settings of 100 kVp with a tin spectral shaping filter and the tube current values of 20 and 35 mA in large subject (47.4 cm in diameter) resulted in significant variation of the TCM values (11.1% and 8.4%, respectively) and the corresponding increase of noise by >5% in subsequent CT examination. For all investigated phantom sizes, the combination of 100 Sn kV with a tin spectral shaping filter and tube current values of 75 mA results in the lowest possible radiation dose, while still keeping the AEC function unchanged.ConclusionThe study indicated that tin spectral shaping filtration can be applied to LRs for radiation dose reduction, but such adaptation needs to take patient size into account.
Development and commissioning of a full‐size prototype fixed‐beam radiotherapy system with horizontal patient rotation
Authors: Liu Paul Zhi Yuan , O'Brien Ricky , Heng Soo‐Min , Newall Matthew , Downes Simon , Shieh Chun‐Chen , Corde Stephanie , Jackson Michael , Keall Paul 
Published: December 2018

PurposeCompared to conventional linacs with rotating gantries, a fixed‐beam radiotherapy system could be smaller, more robust and more cost‐effective. In this work, we developed and commissioned a prototype x‐ray radiotherapy system utilizing a fixed vertical radiation beam and horizontal patient rotation.MethodsThe prototype system consists of an Elekta Synergy linac with gantry fixed at 0° and a custom‐built patient rotation system (PRS). The PRS was designed to immobilize patients and safely rotate them about the horizontal axis. The interlocks and emergency stops of the linac and PRS were connected. Custom software was developed to monitor the system status, control the motion of the PRS and modify treatment plans for the fixed‐beam configuration. Following installation, the prototype system was commissioned for three‐dimensional (3D) conformal therapy based on guidelines specified in AAPM TG‐45 and TG‐142, with modifications for the fixed‐beam geometry made where necessary.ResultsThe system and control software was tested in a variety of machine states and executed motion, stop and beam gating commands as expected. Interlocks and emergency stops of the linac and PRS were found to correctly stop PRS motion and both kV and MV radiation beams when triggered. For 3D conformal treatments, the prototype system met all AAPM TG‐45 and TG‐142 specifications for geometric and dosimetric accuracy. Motion of the PRS was within 0.6 ± 0.3 mm and 0.10° ± 0.07° of input values for translation and rotation respectively. The axis of rotation of the PRS was coincident with the radiation beam axis to less than 1 mm. End‐to‐end treatment verification for 6 MV conformal treatments showed less than 2% difference between planned and delivered dose for all fields.ConclusionIn this work, we have developed and commissioned a radiotherapy system that utilizes a fixed vertical radiation beam and horizontal patient rotation. This system is a proof‐of‐concept prototype for a fixed‐beam treatment system without a rotating gantry. Fixed‐beam systems that are smaller and more cost‐effective could help in improving global access to radiotherapy.
Movement and Diel Habitat Use of Juvenile Neosho Smallmouth Bass in an Ozark Stream
Authors: Miller Andrew D. , Mollenhauer Robert , Brewer Shannon K. 
Published: December 2018

Abstract
Documenting fish movement patterns and examining relationships with both fish and habitat characteristics are essential aspects of sound conservation and management. Stream fish movement and habitat use have been associated with a myriad of factors, and variability among individuals is common. Movement and habitat use patterns of juvenile Smallmouth Bass Micropterus dolomieu in streams are poorly understood, particularly for the Neosho subspecies M. dolomieu velox. Our study objective was to determine diel movement patterns and microhabitat use by juvenile Neosho Smallmouth Bass during late autumn. In 2016, we surgically implanted radio transmitters into 13 juvenile Smallmouth Bass in Honey Creek, Oklahoma. We tracked the fish by using radiotelemetry on 41 occasions over the 26-d tag life and located fish throughout the diel cycle to characterize movement and habitat use. Movement patterns varied among individual fish, with cumulative movements ranging from 33 to 1,302 m. Incremental displacement (the distance moved between two consecutive relocations) increased slightly with warmer water temperatures and increasing fish size. Although there was also considerable individual variation in habitat use patterns, deeper habitats were associated with larger juvenile Smallmouth Bass and daytime. Fish also tended to use higher-velocity habitats during the day, and this trend increased over the duration of the study. Our results suggest high individual variation in both movement and habitat use by juvenile Neosho Smallmouth Bass across the diel cycle. We show that juvenile Smallmouth Bass move among microhabitats and would benefit from management actions that maintain and promote instream habitat complexity. Future efforts focused on juvenile Smallmouth Bass movement over longer time periods would be beneficial for understanding movement and habitat use dynamics across a greater range of seasonal and environmental variability.
Fetal akinesia deformation sequence, arthrogryposis multiplex congenita, and bilateral clubfeet: Is motor assessment of additional value for in utero diagnosis? A 10‐year cohort study
Authors: Tjon Jill K. , Tan‐Sindhunata Gita M. , Bugiani Marianna , Witbreuk Melinda M. , van der Sluijs Johannes A. , Weiss Marjan M. , van de Pol Laura A. , van Weissenbruch Mirjam M. , van der Knoop Bloeme J. , de Vries Johanna I. 
Published: December 2018

AbstractObjectiveThe diagnosis of fetal akinesia deformation sequence (FADS) is a challenge. Motor assessment is of additional value to advanced ultrasound examinations (AUE) for in utero FADS diagnosis before 24 weeks of gestation.MethodsAll consecutive fetuses with greater than or equal to two contractures on the 20 week structural anomaly scan (2007–2016) were included. Findings at AUE, including motor assessment were analysed and related to outcome.ResultsSixty‐six fetuses fulfilled the inclusion criteria. On the basis of the first AUE, FADS was suspected in 13 of 66, arthrogryposis multiplex congenita (AMC) in 12 of 66, bilateral pes equinovares (BPEV) in 40 of 66, and Holt‐Oram syndrome in one of 66. On the basis of the first motor assessment, the suspected diagnosis changed in 19 of 66, in 13 of 66 worsening to FADS, six of 66 amelioration from FADS, and confirmed FADS in seven of 13. The result was 20 FADS, seven AMC, and 38 BPEV. Second AUE in 44 fetuses showed additional contractures in two of eight FADS, and one intrauterine fetal death (IUFD). The second motor assessment changed the diagnosis in three of 43, one worsening from BPEV into FADS, two ameliorations from FADS, and confirmed FADS in seven by deterioration of motility. The result was nine FADS, six AMC, and 29 BPEV.ConclusionThe results suggest that motor assessment has additional value to distinguish between FADS, AMC, and BPEV.
Intact Glycopeptide Analysis of Influenza A/H1N1/09 Neuraminidase Revealing the Effects of Host and Glycosite Location on Site‐Specific Glycan Structures
Authors: Zhu Bojing , Shen Jiechen , Zhao Ting , Jiang Haihai , Ma Tianran , Zhang Jie , Dang Liuyi , Gao Ni , Hu Yingwei , Shi Yi , Sun Shisheng 
Published: December 2018

AbstractInfluenza H1N1 virus has posed a serious threat to human health. The glycosylation of neuraminidase (NA) could affect the infectivity and virulence of the influenza virus, but detailed site‐specific glycosylation information of NA is still missing. In this study, intact glycopeptide analysis is performed on an influenza NA (A/H1N1/California/2009) that is expressed in human 293T and insect Hi‐5 cells. The data indicate that three of four potential N‐linked glycosylation sites are glycosylated, including one partial glycosylation site from both cell lines. The NA expressed in human cells has more complex glycans than that of insect cells, suggesting the importance of selecting an appropriate expression system for the production of functional glycoproteins. Different types of glycans are identified from different glycosites of NA expressed in human cells, which implies the site‐dependence of glycosylation on NA. This study provides valuable information for the research of influenza virus as well as the functions of viral protein glycosylation.
MS‐Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments
Authors: Andreatta Massimo , Nicastri Annalisa , Peng Xu , Hancock Gemma , Dorrell Lucy , Ternette Nicola , Nielsen Morten 
Published: December 2018

AbstractLC–MS/MS has become the standard platform for the characterization of immunopeptidomes, the collection of peptides naturally presented by major histocompatibility complex molecules to the cell surface. The protocols and algorithms used for immunopeptidomics data analysis are based on tools developed for traditional bottom‐up proteomics that address the identification of peptides generated by tryptic digestion. Such algorithms are generally not tailored to the specific requirements of MHC ligand identification and, as a consequence, immunopeptidomics datasets suffer from dismissal of informative spectral information and high false discovery rates. Here, a new pipeline for the refinement of peptide‐spectrum matches (PSM) is proposed, based on the assumption that immunopeptidomes contain a limited number of recurring peptide motifs, corresponding to MHC specificities. Sequence motifs are learned directly from the individual peptidome by training a prediction model on high‐confidence PSMs. The model is then applied to PSM candidates with lower confidence, and sequences that score significantly higher than random peptides are rescued as likely true ligands. The pipeline is applied to MHC class I immunopeptidomes from three different species, and it is shown that it can increase the number of identified ligands by up to 20–30%, while effectively removing false positives and products of co‐precipitation. Spectral validation using synthetic peptides confirms the identity of a large proportion of rescued ligands in the experimental peptidome.
Direct synthesis of tetrazine functionalities on polymer backbones
Authors: Kara Sinem Sipahioglu , Ateş Mustafa Yasin , Deveci Gozde , Cetinkaya Ahmet , Kahveci Muhammet U. 
Published: December 2018

ABSTRACTTetrazine mediated inverse Electron Demand Diels–Alder Reaction (IEDDA) is an important modification technique due to its high selectivity and super‐fast kinetics. Incorporation of tetrazine moieties on polymer chains requires multistep synthetic pathways and a post‐polymerization step leading to functional polymeric materials. Such approaches involve separate syntheses of polymer and the molecule which will be employed in modification. Herein, we introduce a straightforward synthetic approach for direct synthesis of tetrazine groups on polymers as side chains. As model systems, tetrazine functional poly(N‐isopropylacrylamide)‐and poly(ethylene glycol)‐based polymers from corresponding precursor polymers with nitrile moieties as pendant groups are prepared and IEDDA Click Reaction is achieved with trans‐cyclooctene derivatives. The click reaction is monitored by both NMR and UV–vis spectroscopies. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 673–680
Photopolymerization of maleimide perfluoropolyalkylethers without a photoinitiator
Authors: Bonneaud Céline , Burgess Julia M. , Bongiovanni Roberta , Joly‐Duhamel Christine , Friesen Chadron M. 
Published: December 2018

ABSTRACTPerfluoropolyalkylethers derived from hexafluoropropylene oxide were functionalized with maleimide groups. Irradiated by UV‐light, the new maleimide macromonomers demonstrated very fast polymerization kinetics with a curing time as fast as 8 s. The effect on photopolymerization of different features such as the molecular weight of the fluorinated chain and the chain length of the hydrogenated spacer were studied, as well as the influence of the type of photoinitiator and the presence of air. Thermal and surface properties of the UV‐cured polymers were examined and were typical to fluoropolymers in view of water–oil repellent coatings. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 699–707
Interaction of NKX3.1 and SELENOP genotype with prostate cancer recurrence
Authors: Donadio Janaina L. S. , Liu Li , Freeman Vincent L. , Ekoue Dede N. , Diamond Alan M. , Bermano Giovanna 
Published: December 2018

Background: NKX3.1 is a tumor suppressor frequently lost in prostate cancer. Previous studies by others indicated that the risks associated with reduced NKX3.1 levels can be enhanced by anti‐oxidant supplementation. Selenium is an essential component of several proteins with anti‐oxidant functions and lower levels of selenium have been associated with greater risk of prostate cancer. In contrast, participants of the select prostate cancer prevention trial were at increased risk of prostate cancer when supplemented with selenium when their baseline selenium levels were high.Methods: In order to investigate whether there was an interaction between a functional polymorphism in NKX3.1 that results in less protein and selenium status with prostate cancer grade or outcome, plasma selenium levels and the genotypes of NKX3.1 and the selenium carrier protein SELENOP were determined from a cohort of men who underwent radical protatectomy.Results: NKX3.1 and SELENOP genotypes were associated with a more aggressive prostate tumor grade at the time of prostatectomy, but there were no significant interactions of NKX3.1 genotype with either selenium status or SELENOP genotype. There was also a significant association between NKX3.1 genotype and prostate cancer recurrence, however this association was modified by SELENOP genotype, but not with plasma selenium levels.Conclusions: These data indicate that the impact of selenium status on prostate cancer may be influenced by factors other than the amount of selenium in circulation.
A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone
Authors: da Silva Neto Antonio Marinho , Silva Samuel Reghim , Vendruscolo Michele , Camilloni Carlo , Montalvão Rinaldo Wander 
Published: December 2018

AbstractHere a differential geometry (DG) representation of protein backbone is explored on the analyses of protein conformational ensembles. The protein backbone is described by curvature, κ, and torsion, τ, values per residue and we propose 1) a new dissimilarity and protein flexibility measurement and 2) a local conformational clustering method. The methods were applied to Ubiquitin and c‐Myb‐KIX protein conformational ensembles and results show that κ\τ metric space allows to properly judge protein flexibility by avoiding the superposition problem. The dmax measurement presents equally good or superior results when compared to RMSF, especially for the intrinsically unstructured protein. The clustering method is unique as it relates protein global to local dynamics by providing a global clustering solutions per residue. The methods proposed can be especially useful to the analyses of highly flexible proteins. The software written for the analyses presented here is available at https://github.com/AMarinhoSN/FleXgeo for academic usage only.
Raspberry ketone accelerates sexual maturation and improves mating performance of sterile male Queensland fruit fly, Bactrocera tryoni (Froggatt)
Authors: Khan Mohammed Abul Monjur , Shuttleworth Lucas A , Osborne Terry , Collins Damian , Gurr Geoff M , Reynolds Olivia L 
Published: December 2018

AbstractBACKGROUNDTephritid fruit flies are recognized as the most economically important insect pest group, causing significant losses to horticultural crops globally. The sterile insect technique (SIT) is used to suppress or eradicate pest fruit flies in many countries. The provisioning of adult dietary or olfactory supplementation pre‐release is commonly used to improve the mating performance of sterile male flies in SIT. This study on a major pest species, Queensland fruit fly, Bactrocera tryoni (Froggatt), focused on improving mating performance by providing a semiochemical, raspberry ketone (RK), in the pre‐release adult diet.RESULTSSurvival was numerically higher for RK‐supplemented males. Sexual maturity occurred 1 day earlier (from 7 to 6 days) in RK‐supplemented sterile males. The mating latency period decreased with maturation age and was lower for RK‐fed males. RK‐supplemented sterile males increasingly mated with fertile females as they aged (10–19 days). The mating competitiveness of both RK‐supplemented sterile males and RK‐denied sterile males was greater than that of wild males.CONCLUSIONThe early sexual maturity and increased mating performance of RK‐supplemented sterile males indicate that the effectiveness of SIT programmes can be increased through dietary supplementation with RK during the pre‐release period. © 2018 Society of Chemical Industry
Zoophytophagous mites can trigger plant‐genotype specific defensive responses affecting potential prey beyond predation: the case of Euseius stipulatus and Tetranychus urticae in citrus
Authors: Cruz‐Miralles Joaquín , Cabedo‐López Marc , Pérez‐Hedo Meritxell , Flors Víctor , Jaques Josep A 
Published: December 2018

ABSTRACTBackgroundZoophytophagous predators can trigger plant defenses affecting prey populations beyond predation. Euseius stipulatus is a presumed zoophytophagous phytoseiid common in citrus. The response of citrus to one of its potential prey, Tetranychus urticae, is genotype dependent, with Citrus reshni and C. aurantium exhibiting extreme susceptibility and resistance, respectively. Volatile blends produced upon infestation affected the behavior of these two mites. We wondered whether E. stipulatus could trigger similar responses.ResultsEuseius stipulatus triggered genotype‐dependent defense responses in citrus. Whereas C. aurantium upregulated the Jasmonic Acid, Salicylic Acid and flavonoids defensive pathways, C. reshni upregulated JA only. Likewise, different volatile blends were induced. These blends were exploited by E. stipulatus to select less‐defended plants (i.e., those in which higher pest densities are expected) and, interestingly, did not prevent T. urticae from choosing E. stipulatus‐infested plants. To the best of our knowledge, this is the first time that this type of response has been described for a zoophytophagous phytoseiid.ConclusionThe observed responses could affect herbivore populations through plant‐mediated effects. Although further research is needed to fully characterize them and include other arthropods in the system, these results open opportunities for more sustainable and effective pest control methods (i.e., combining semiochemicals and biological control). © 2018 Society of Chemical Industry
Statistics of convective cloud turbulence from a comprehensive turbulence retrieval method for radar observations
Authors: Feist Matthew M. , Westbrook Chris D. , Clark Peter A. , Stein Thorwald H.M. , Lean Humphrey W. , Stirling Alison J. 
Published: December 2018

Turbulent mixing processes are important in determining the evolution of convective clouds, and the production of convective precipitation. However, the exact nature of these impacts remains uncertain due to limited observations. Model simulations show that assumptions made in parametrizing turbulence can have a marked effect on the characteristics of simulated clouds. This leads to significant uncertainty in forecasts from convection‐permitting numerical weather prediction (NWP) models. This contribution presents a comprehensive method to retrieve turbulence using Doppler weather radar to investigate turbulence in observed clouds. This method involves isolating the turbulent component of the Doppler velocity spectrum width, expressing turbulence intensity as an eddy dissipation rate, ϵ. By applying this method throughout large datasets of observations collected over the southern United Kingdom using the (0.28° beam‐width) Chilbolton Advanced Meteorological Radar (CAMRa), statistics of convective cloud turbulence are presented. Two contrasting case days are examined: a shallow “shower” case, and a “deep convection” case, exhibiting stronger and deeper updraughts. In our observations, ϵ generally ranges from 10−3 to 10−1 m2/s3, with the largest values found within, around and above convective updraughts. Vertical profiles of ϵ suggest that turbulence is much stronger in deep convection; 95th percentile values increase with height from 0.03 to 0.1 m2/s3, compared to approximately constant values of 0.02–0.03 m2/s3 throughout the depth of shower cloud. In updraught regions on both days, the 95th percentile of ϵ has significant (p < 10−3) positive correlations with the updraught velocity, and the horizontal shear in the updraught velocity, with weaker positive correlations with updraught dimensions. The ϵ‐retrieval method presented considers a very broad range of conditions, providing a reliable framework for turbulence retrieval using high‐resolution Doppler weather radar. In applying this method across many observations, the derived turbulence statistics will form the basis for evaluating the parametrization of turbulence in NWP models.