Application of the phase-space distribution approach of Monte Carlo for radiation contamination dose estimation from the (n,γ), (γ,n) nuclear reactions and linac leakage photons in the megavoltage radiotherapy facility

AimThe aim of this study was to characterize the radiation contamination inside and outside the megavoltage radiotherapy room.BackgroundRadiation contamination components in the 18 MV linac room are the secondary neutron, prompt gamma ray, electron and linac leakage radiation.Materials and MethodsAn 18 MV linac modeled in a typical bunker employing the MCNPX code of Monte Carlo. For fast calculation, phase-space distribution (PSD) file modeling was applied and the calculations were conducted for the radiation contamination components dose and spectra at 6 locations inside and outside the bunker.ResultsThe results showed that the difference of measured and calculated percent depth-dose (PDD) and photo beam-profile (PBP) datasets were lower than acceptable values. At isocenter, the obtained photon dose and neutron fluence were 2.4 × 10⁻¹⁴ Gy/initial e° and 2.22 × 10^-8 n°/cm², respectively. Then, neutron apparent source strength (Q_N) value was found as 1.34 × 10¹² n°/Gy X at isocenter and the model verified to photon and neutron calculations. A surface at 2 cm below the flattening filter was modeled as phase-space (PS) file for PDD and PBP calculations. Then by use of a spherical cell in the center of the linac target as a PS surface, contaminant radiations dose, fluence and spectra were estimated at 6 locations in a considerably short time, using the registered history of all particles and photons in the 13GB PSD file as primary source in the second step.ConclusionDesigning the PSD file in MC modeling helps user to solve the problems with complex geometry and physics precisely in a shorter run-time.     

Does the setup of Monte Carlo simulations influence the calculated properties and effect of gold nanoparticles in radiation therapy?

PurposeTo investigate whether the dose-scoring process of Monte Carlo (MC) simulations of Gold nanoparticles (GNPs) in radiation therapy affects the results.MethodsThe GATE MC toolkit was used to simulate the irradiation of a water phantom containing a single solid or hollow GNP with 250 kVp and 6 MV photons. The dose was scored in 20 nm × 20 nm × 50 μm, 100 nm × 100 nm × 50 μm and 200 nm × 200 nm × 50 μm volumes using dose-scoring voxels of size 1 nm × 1 nm × 50 μm, 10 nm × 10 nm × 50 μm, 50 nm × 50 nm × 50 μm and 100 nm × 100 nm × 50 μm Εxcess dose depth-dose (EDDD) curves and lateral beam profiles were used to compare the dose-scoring voxels.ResultsIn a given volume, neither the EDDD curves nor the lateral beam profiles are affected by the size of the dose-scoring voxels, subject to noise and uncertainty. Certain features of the EDDD curves are clearly seen in larger volumes, but hidden within the uncertainty and noise levels in smaller volumes. For the lateral beam profiles, it is the larger volumes that result in misleading results and the smaller ones that give the expected results. However, the limited statistics result in asymmetries and skewness in the profiles.ConclusionFor a given volume, the dose curves are not affected by the size of the dose-scoring voxels. However, the voxel size may hide or reveal the finer structure of the dose curves and/or may result in misleading curves.     

Study of efficiency in five-field and field-by-field intensity modulated radiation therapy (IMRT) plan using DOSXYZnrc Monte Carlo code

Implementation of a modern treatment technique, such as IMRT, has been improved. In line with that, Monte Carlo (MC) simulations of this technique require the ability of complex beam configurations modelling with respect to the patient. The source 20 DOSXYZnrc with the dynamic and step and shoot technique can be used to simulate the modality. However, they have a different process to obtain the dose distribution in a certain phantom. This study aimed to compare the simulation efficiency and isodose dose distribution in a water phantom from various beam angles and multileaf collimator (MLC) positions in an IMRT plan using source 20. The 30 × 30 × 30 cm³ phantom was irradiated by Varian Clinac iX10MV photon beam with various field sizes from 2 × 2 to 6 × 6 cm² using some beam angles 5°, 30°, 90°, 180°, and 300° and maintaining the source to surface distance (SSD) of 100 cm. The field-by-field and five-field methods were used to obtain the 3-dimensional (3D) dose distribution. The dose distribution of these methods was compared using the gamma index, DVH analysis, and simulation efficiency. Higher efficiency is better because it implies that it takes less time to reach a given uncertainty. The implementation of source 20 has been validated, with similar results, with validated source in DOSXYZnrc. The identical 3D-dimensions dose distributions using source 20 for dynamic and step and shoot were observed. Two simulations used the same number of histories with the statistical uncertainty of less than 3%. The step and shoot technique was more efficient than the dynamic simulation.     

Current status of the habitat and population of the black howler monkey (Alouatta pigra) in Balancán, Tabasco, Mexico

We evaluated the habitat and populations of the black howler monkey (Alouatta pigra) in the municipality of Balancán, Tabasco, southeastern Mexico, using a combination of field surveys and remotely sensed data. We identified 21,937 ha of remnant vegetation composed of 1,348 fragments. Fragments separated by up to 200 m were grouped into "clusters" of fragments in accordance with the maximum observed open distance crossed by A. pigra. A total of 11% or 84 of the 772 clusters identified through remote sensing were selected at random, and for these we determined the vegetation type, canopy height, area, and distance to the closest human settlement. In these same 84 clusters, which included a total area of 9,817 ha, from October to June of 2006 we located a total of 1,064 black howler monkeys, including 228 troops and 49 solitary monkeys. A. pigra was found in 62 (74.7%) of all clusters visited, with a cumulative area of 6,032 ha. Troops varied in size from 2 to 15 individuals (average 6.0+/-2.9 ind/troop). Adults were 67% (n=716) of detected individuals, whereas juveniles were 20.5% (n=218) and infants were 12.5% (n=133). We found black howlers to occur at an ecological density of 10.8 ind/km(2), which is low in comparison with A. pigra in other fragmented and conserved sites. We found a statistically significant relationship between the area of clusters and the abundance of howler monkeys (r(2)=0.2, F=10.47, gl=3, P=0.002). In addition, the probability of finding A. pigra was greater in secondary vegetation, riparian vegetation, tropical dry forest, undisturbed tropical oak forest, and palm forest (F=12, gl=3, P<0.0001), as compared with disturbed tropical oak forest. Our results provide data on the distribution, abundance, and population structure of black howler monkeys in a fragmented landscape in the southeast of Mexico. These data are a necessary prerequisite for conservation planning for this species.     

Do the high energy lifestyles of shorebirds result in high maximal metabolic rates? Basal and maximal metabolic rates in least and pectoral sandpipers during migration

Shorebirds have high resting and field metabolic rates relative to many other bird groups, and this is posited to be related to their high‐energy lifestyle. Maximum metabolic outputs for cold or exercise are also often high for bird groups with energetically demanding lifestyles. Moreover, shorebirds demonstrate flexible basal and maximal metabolic rates, which vary with changing energy demands throughout the annual cycle. Consequently, shorebirds might be expected to have high maximum metabolic rates, especially during migration periods. We captured least Calidris minutilla and pectoral C. melanotos sandpipers during spring and fall migration in southeastern South Dakota and measured maximal exercise metabolic rate (MMR; least sandpipers only), summit metabolic rate (M_sum, maximal cold‐induced metabolic rate) and basal metabolic rate (BMR, minimum maintenance metabolic rate) with open‐circuit respirometry. BMR for both least and pectoral sandpipers exceeded allometric predictions by 3–14%, similar to other shorebirds, but M_sum and MMR for both species were either similar to or lower than allometric predictions, suggesting that the elevated BMR in shorebirds does not extend to maximal metabolic capacities. Old World shorebirds show the highest BMR during the annual cycle on the Arctic breeding grounds. Similarly, least sandpiper BMR during migration was lower than on the Arctic breeding grounds, but this was not the case for pectoral sandpipers, so our data only partially support the idea of similar seasonal patterns of BMR variation in New World and Old World shorebirds. We found no correlations of BMR with either M_sum or MMR for either raw or mass‐independent data, suggesting that basal and maximum aerobic metabolic rates are modulated independently in these species.     

Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet

Key message

Linkage analysis confirmed the association in the region of PHYC in pearl millet. The comparison of genes found in this region suggests that PHYC is the best candidate.

Abstract

Major efforts are currently underway to dissect the phenotype–genotype relationship in plants and animals using existing populations. This method exploits historical recombinations accumulated in these populations. However, linkage disequilibrium sometimes extends over a relatively long distance, particularly in genomic regions containing polymorphisms that have been targets for selection. In this case, many genes in the region could be statistically associated with the trait shaped by the selected polymorphism. Statistical analyses could help in identifying the best candidate genes into such a region where an association is found. In a previous study, we proposed that a fragment of the PHYTOCHROME C gene (PHYC) is associated with flowering time and morphological variations in pearl millet. In the present study, we first performed linkage analyses using three pearl millet F₂ families to confirm the presence of a QTL in the vicinity of PHYC. We then analyzed a wider genomic region of ~100 kb around PHYC to pinpoint the gene that best explains the association with the trait in this region. A panel of 90 pearl millet inbred lines was used to assess the association. We used a Markov chain Monte Carlo approach to compare 75 markers distributed along this 100-kb region. We found the best candidate markers on the PHYC gene. Signatures of selection in this region were assessed in an independent data set and pointed to the same gene. These results foster confidence in the likely role of PHYC in phenotypic variation and encourage the development of functional studies.     

Beta-aminoisobutyric acid (BAIB) excretion in urine of residents of eight communities in the states of Michoacán and Oaxaca, Mexico

The ratio of β-aminoisobutyric acid to neutral amino acids (BAIB/N) in urine was determined in 474 Mexicans from three communities in the state of Michoacán and five in Oaxaca. The frequency curves vary significantly between the three communities in Michoacán and between the two states. The proportion of high excretors (BAIB/N 0.300) varies from 14 to 41% (all intermediate between European white and North American Indian values), but were generally higher in the more “Indian” communities.     

Effects of photoperiod and of ultraviolet radiation on the incidence of diapause in the Horn Fly, “Haematobia Irritans (L.) (Diptera: Muscidae)”

The horn fly, HAEMATOBIA IRRITANS (L.), is a bloodsucking pest of cattle found in almost all cattle-raising areas of the northern hemisphere.Predisposition to diapause in the pupal stage was determined in the adult parent. The predisposition was influenced by photoperiod which may have its effect either directly on the insect or indirectly by influencing the host blood. The percentage of the pupae that entered diapause varied inversely with the length of the photoperiod between 12 and 20 hours. Light in the visible range (7,800 to 4,000 A.U.) was provided byCool-whitefluorescent tubes. The addition of ultraviolet radiation (3,900 to 2,800 A.U.) in the 16- and 20-hour photoperiods further decreased the percentage of diapause.

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Zusammenfassung Die Hornfliege, HAEMATOBIA IRRITANS (L.), ist ein blutsaugender Parasit in fast allen Rinderzuchtgebieten der nördlichen Hemisphäre.Die Prädisposition zur Diapause im Puppenstadium wurde in den erwachsenen Eltern determiniert.Sie wurde durch Belichtung beeinflusst, die entweder direkt auf das Insekt oder indirekt über das Blut des Wirtes wirkte. Die Prozentzahl an Puppen in Diapause fiel ab, wenn die periodischen Belichtungszeiten von 12 bis 20 Stunden verlängert wurden. Das sichtbare Licht (7800–4000 Å) stammte von cool-white fluoreszierenden Röhren. Durch die periodische Zugabe einer Ultraviolett- (3900 – 2800 Å) Bestrahlung fiel der Anteil an Diapausen noch weiter.

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Résumé La mouche, HAEMATOBIA IRRITANS (L.), est un parasite hématophage du bétail répandu dans presque toutes les zones d'élevagê de l'hémisphère nord. La prédisposition à la diapause au stade de pupe a été déterminée chez les parents adultes. La prédisposition est influencée par une période d'éclairage qui peut agir soit directement sur l'insecte soit indirectement par l'intermédiaire du sang de l'hôte. Le pourcentage des pupes entrant en diapause varie inversement à la durée d'un éclairage de 12 à 20 heures. La lumière blanche (7800 – 4000 Å) est produite par des tubes fluorescents froids. L'addition de rayonnement ultra-violet (3900 à 2800 Å) dans les périodes d'éclairage de 16 et de 20 heures réduit encore le pourcentage de diapauses.

     

Raman Spectroscopy Study of the B-Z Transition in (dG-dC)n · (dG-dC)n and a DNA Restriction Fragment

Abstract

The B to Z conformational transition of (dG-dC)_n·(dG-dC)_n and a 157 bp DNA restriction fragment were followed using Raman spectroscopy. The 157 bp DNA has a 95 bp segment from the E. coli lactose operon sandwiched between 26 and 32 bp of (dC-dG) sequences. Raman spectra of the DNAs were obtained at varying sodium chloride concentrations through the region of the transition. A data analysis procedure was developed to subtract the background curves and quantify Raman vibrational bands. Profiles of relative intensity vs. sodium chloride concentration are shown for bands at 626, 682, 831–833 and 1093 cm^?1. Both (dG-dC)_n·(dG-dC)_n and the 157 bp DNA show changes in the guanine vibration at 682 cm^?1 and backbone band at 831–3 cm^?1 preceeding a highly cooperative change in the 1093 cm^?1 PO 7 vibration. This result indicates that there are at least two conformational steps in the B to Z conformational pathway.

We review the effect of the (dC-dG) portion of the 157 bp DNA on the 95 bp segment. Comparison of Raman spectra of the 157 bp DNA, the 95 bp fragment and (dG-dC)_n·(dG- dC)_n indicate that in 4.5 M NaC/the (dC-dG) segments are in a Z-conformation. Base stacking in the 95 bp portion of the 157 bp DNA appears to maintain a B-type conformation. However, a substantial portion of this region no longer has a B-type backbone vibration.     

A procedure for the Cherenkov counting of high energy β and γ emitting radionuclides in coloured plant extracts

Summary Elimination of count rate variations caused by the absorption of Cherenkov radiation by pigments in coloured solutions was achieved by placing these solutions in opaque walled cylinders immersed in colourless liquids contained in standard counting vials. Good counting efficiencies for a range of and emitting radionuclides were obtained by selecting colourless liquids with high refractive index.     

Study of the inclusion of the (R)- and (S)-camphor enantiomers in α-cyclodextrin by X-ray crystallography and molecular dynamics

The inclusion of (R)- and (S)-camphor compounds in α-cyclodextrin has been studied by X-ray crystallography. The crystal structures of the complexes reveal that one guest molecule is accommodated inside the cavity formed by a head-to-head cyclodextrin dimer. In the crystal lattice, the dimers form layers which are successively shifted by half a dimer. In both (R)- and (S)-cases, the camphor molecule exhibits disorder and occupies three major sites with orientations that can be described as either ‘polar’ or ‘equatorial’. Molecular dynamics simulations performed for the observed complexes indicate that although the carbonyl oxygen of both (R)- and (S)-camphor switches between different hydrogen bonding partners, it maintains the observed mode of ‘polar’ or ‘equatorial’ alignment.     

An account of the taxonomy and distribution of Syllidae (Annelida, Polychaetes) in the eastern Mediterranean, with notes on the genus Prosphaerosyllis San Martín, 1984 in the Mediterranean

The syllid fauna of three locations in Crete and Israel (eastern Mediterranean Sea) was studied, yielding 82 syllid species, many of which were found for the first time in the respective areas: Seventeen species were recorded for the first time on the Israeli coasts and 20 in Greek waters. Perkinsyllis augeneri (Hartmann-Schröder, 1979) and Prosphaerosyllis chauseyensis Olivier et al., 2011 are new records for the Mediterranean Sea. Detailed information is given on the morphology, ecology and distribution of the species recorded for the first time in the studied areas. In addition, an update on the distribution of the genus Prosphaerosyllis San Martín, 1984 in the Mediterranean is given and an identification key to the Mediterranean species is provided.     

Density functional calculations for a high energy density compound of formula C6H6?n (NO2) n

A series of polynitroprismanes, C(6)H(6-n )(NO(2))(n) (n?=?1-6) intended for use as high energy density compounds (HEDCs) were designed computationally. Their electronic structures, heats of formation, interactions between nitro groups, specific enthalpies of combustion, bond dissociation energies, and explosive performances (detonation velocities and detonation pressures) were calculated using density functional theory (DFT) with the 6-311 G** basis set. The results showed that all of the polynitroprismanes had high positive heats of formation that increased with the number of substitutions for the prismane derivatives, while the specific enthalpy of combustion decreased as the number of nitro groups increased. In addition, the range of enthalpy of combustion reducing is getting smaller. Interactions between ortho (vicinal) groups deviate from the group additivity rule and decrease as the number of nitro groups increases. In terms of thermodynamic stability, all of the polynitroprismanes had higher bond dissociation energies (BDEs) than RDX and HMX. Detonation velocities and detonation pressures were estimated using modified Kamlet-Jacobs equations based on the heat of detonation (Q) and the theoretical density of the molecule (ρ). It was found that ρ, D, and P are strongly linearly related to the number of nitro groups. Taking both their energetic properties and thermal stabilities into account, pentanitroprismane and hexanitroprismane are potential candidate HEDCs.     

Chilling and heat requirements for the prediction of the beginning of the pollen season of Alnus glutinosa (L.) Gaertner in Ponferrada (León, Spain)

Winter-flowering trees such as the alder (Alnus glutinosa (L.) Gaertner) can survive periods of adverse climatic conditions, entering a period of dormancy in the early fall. The end of dormancy and the start of the pollen season require a period of low temperatures followed by another of warm temperatures. These requirements were studied from 1995 to 2002, in order to develop a model to predict the onset of the alder pollen season in Ponferrada (Spain). Chilling accumulation took place from late October to late December or early January. The best result was obtained with a threshold temperature of 6.5 °C and an average of 848 chilling hours (CH). Heat requirements were calculated at maximum temperature, an average 143 growth degree days (GDD) were needed, with a threshold temperature of 0 °C. In order to validate models, predicted values were compared with real values for 2002–2003, 2003–2004 and 2004–2005, years not used in developing the models. Predictions for the pollen-season start-date differed only slightly from observed dates: in 2002–2003 predicted and observed dates were the same, in 2003–2004 there was a difference of 7 days and in 2004–2005 a difference of 3 days.     

Application of kinetic Monte Carlo method to the vapour–liquid equilibria of associating fluids and their mixtures

Canonical kinetic Monte Carlo (C-kMC) simulations have been carried out to assess their feasibility and potential for calculating the vapour–liquid equilibria of various pure components with increasingly strong electrostatic interactions (carbon dioxide, methanol, ammonia and water) over a wide range of temperatures and for methanol/water mixtures at 298 K. The simulation results show that C-kMC is successful as a method for studying phase equilibria and thermodynamic properties. For all the examples investigated, the performance of the C-kMC method is at least as good as that of the conventional Monte Carlo (MC) methods and is efficient at low temperature where these fail. It also provides a route that is superior to the Widom method for the calculation of chemical potential. We recommend this method for this purpose and as an alternative to conventional MC for simulations of strongly associating fluids and at low temperatures.