Towards real-time 4D radiation dosimetry on an MRI-Linac.

4D radiation dosimetry using a highly radiation-sensitive polymer gel dosimeter with real-time quantitative magnetic resonance imaging (MRI) readout is presented as a technique to acquire the accumulated radiation dose distribution during image-guided radiotherapy on an MRI-Linac. Optimized T 2-weighted Turbo-Spin-Echo (TSE) scans are converted into quantitative ΔR 2 maps and subsequently to radiation dose maps. The concept of temporal uncertainty is introduced as a metric of effective temporal resolution. A mathematical framework is presented to optimize the echo time of the TSE sequence in terms of dose resolution, and the trade-off between temporal resolution and dose resolution is discussed. The current temporal uncertainty achieved with the MAGAT gel dosimeter on a 1 T MRI-Linac is 3.8 s which is an order of magnitude better than what has been achieved until now. The potential of real-time 4D radiation dosimetry in a theragnostic MRI-Linac is demonstrated for two scenarios: an irradiation with three coplanar beams on a head phantom and a dynamic arc treatment on a cylindrical gel phantom using a rotating couch. The dose maps acquired on the MRI-Linac are compared with a treatment plan and with dose maps acquired on a clinical 3 T MRI scanner. 3D gamma map evaluations for the different modalities are provided. While the presented method demonstrates the potential of gel dosimetry for tracking the dose delivery during radiotherapy in 4D, a shortcoming of the MAGAT gel dosimeter is a retarded dose response. The effect of non-ideal radiofrequency pulses resulting from limitations in the specific absorption rate or B1-field inhomogeneity on the TSE acquired ΔR 2 values is analysed experimentally and by use of computational modelling with a Bloch simulator.

Quantification of the effects of audible rattle and source type on the human response to environmental vibration.

The present research quantifies the influence of source type and the presence of audible vibration-induced rattle on annoyance caused by vibration in residential environments. The sources of vibration considered are railway and the construction of a light rail system. Data were measured in the United Kingdom using a socio-vibration survey (N = 1281). These data are analyzed using ordinal logit models to produce exposure-response relationships describing community annoyance as a function of vibration exposure. The influence of source type and the presence of audible vibration-induced rattle on annoyance are investigated using dummy variable analysis, and quantified using odds-ratios and community tolerance levels. It is concluded that the sample population is more likely to express higher levels of annoyance if the vibration source is construction compared to railway, and if vibration-induced rattle is audible.

Human annoyance, acceptability and concern as responses to vibration from the construction of Light Rapid Transit lines in residential environments.

The aim of this paper is to investigate the use of different self-reported measures for assessing the human response to environmental vibration from the construction of an urban LRT (Light Rapid Transit) system. The human response to environmental stressors such as vibration and noise is often expressed in terms of exposure-response relationships that describe annoyance as a function of the magnitude of the vibration. These relationships are often the basis of noise and vibration policy and the setting of limit values. This paper examines measures other than annoyance by expressing exposure-response relationships for vibration in terms of self-reported concern about property damage and acceptability. The exposure-response relationships for concern about property damage and for acceptability are then compared with those for annoyance. It is shown that concern about property damage occurs at vibration levels well below those where there is any risk of damage. Earlier research indicated that concern for damage is an important moderator of the annoyance induced. Acceptability, on the other hand, might be influenced by both annoyance and concern, as well as by other considerations. It is concluded that exposure-response relationships expressing acceptability as a function of vibration exposure could usefully complement existing relationships for annoyance in future policy decisions regarding environmental vibration. The results presented in this paper are derived from data collected through a socio-vibration survey (N=321) conducted for the construction of an urban LRT in the United Kingdom.

Design of measurement methodology for the evaluation of human exposure to vibration in residential environments.

Exposure-response relationships are important tools for policy makers to assess the impact of an environmental stressor on the populace. Their validity lies partly in their statistical strength which is greatly influenced by the size of the sample from which the relationship is derived. As such, the derivation of meaningful exposure-response relationships requires estimates of vibration exposure at a large number of receiver locations. In the United Kingdom a socio-vibrational survey has been conducted with the aim of deriving exposure-response relationships for annoyance due to vibration from (a) railway traffic and (b) the construction of a new light rail system. Response to vibration was measured via a questionnaire conducted face-to-face with residents in their own homes and vibration exposure was estimated using data from a novel measurement methodology. In total, 1281 questionnaires were conducted: 931 for vibration from railway traffic and 350 for vibration from construction sources. Considering the interdisciplinary nature of this work along with the volume of experimental data required, a number of significant technical and logistical challenges needed to be overcome through the planning and implementation of the fieldwork. Four of these challenges are considered in this paper: the site identification for providing a robust sample of the residents affected, the strategies used for measuring both exposure and response and the coordination between the teams carrying out the social survey and the vibration measurements.

The effect of (NH4)2Sx passivation on the (311)A GaAs surface and its use in AlGaAs/GaAs heterostructure devices.

We have studied the efficacy of (NH4)2Sx surface passivation on the (311)A GaAs surface. We report XPS studies of simultaneously-grown (311)A and (100) heterostructures showing that the (NH4)2Sx solution removes surface oxide and sulfidizes both surfaces. Passivation is often characterized using photoluminescence measurements; we show that while (NH4)2Sx treatment gives a 40-60 ×  increase in photoluminescence intensity for the (100) surface, an increase of only 2-3 ×  is obtained for the (311)A surface. A corresponding lack of reproducible improvement in the gate hysteresis of (311)A heterostructure transistor devices made with the passivation treatment performed immediately prior to gate deposition is also found. We discuss possible reasons why sulfur passivation is ineffective for (311)A GaAs, and propose alternative strategies for passivation of this surface.

Genetic variation in eggshell crystal size and orientation is large and these traits are correlated with shell thickness and are associated with eggshell matrix protein markers.

The size and orientation of calcium carbonate crystals influence the structure and strength of the eggshells of chickens. In this study, estimates of heritability were found to be high (0.6) for crystal size and moderate (0.3) for crystal orientation. There was a strong positive correlation (0.65) for crystal size and orientation with the thickness of the shell and, in particular, with the thickness of the mammillary layer. Correlations with shell breaking strength were positive but with a high standard error. This was contrary to expectations, as in man-made materials smaller crystals would be stronger. We believe the results of this study support the hypothesis that the structural organization of shell, and in particular the mammillary layer, is influenced by crystal size and orientation, especially during the initial phase of calcification. Genetic associations for crystal measurements were observed between haplotype blocks or individual markers for a number of eggshell matrix proteins. Ovalbumin and ovotransferrin (LTF) markers for example were associated with crystal size, while ovocleidin-116 and ovocalyxin-32 (RARRES1) markers were associated with crystal orientation. The location of these proteins in the eggshell is consistent with different phases of the shell-formation process. In conclusion, the variability of crystal size, and to a lesser extent orientation, appears to have a large genetic component, and the formation of calcite crystals are intimately related to the ultrastructure of the eggshell. Moreover, this study also provides evidence that proteins in the shell influence the variability of crystal traits and, in turn, the shell's thickness profile. The crystal measurements and/or the associated genetic markers may therefore prove to be useful in selection programs to improve eggshell quality.

Complex traits analysis of chicken growth using targeted genetical genomics.

Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.

New hypotheses on the function of the avian shell gland derived from microarray analysis comparing tissue from juvenile and sexually mature hens.

Activation of the shell gland region of the avian oviduct is mediated by ovarian steroids. To understand more extensively how shell glands are maintained and function, we have compared gene expression in the shell glands from juvenile and laying hens using a chicken cDNA microarray. Average expression profiles of juvenile and sexually mature shell glands were compared resulting in the identification of 266 differentially regulated genes. Reverse transcription quantitative polymerase chain reaction confirmed expression differences. The differentially expressed genes included several with known involvement in shell gland function, including ion transport and shell matrix proteins. There were also many unpredicted differentially expressed genes, and for some we propose hypotheses for their functions. These include those encoding (a) osteoprotegerin, a decoy death receptor for receptor activator of nuclear factor NFkB ligand (RANKL) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), that in the shell gland, may prevent apoptosis and/or may have an endocrine effect by preventing RANKL's action on bone osteoclasts that mobilize stored calcium; (b) prostatic acid phosphatase (ACPP) and prostate stem cell antigen (PSCA) that could play a role in sperm physiology within the shell gland; (c) urea transporter (SLC14A2) that could provide a novel anti-microbial defence; (d) bactericidal/permeability-increasing protein-like 2 (BPIL2), and other potential anti-microbials that have not previously been documented in the chicken. These new hypotheses, if borne out experimentally, will lead to a greater understanding of shell gland function including the processes involved in eggshell formation and anti-microbial activity.

Polymorphisms in eggshell organic matrix genes are associated with eggshell quality measurements in pedigree Rhode Island Red hens.

Novel and traditional eggshell quality measurements were made from up to 2000 commercial pedigree hens for a candidate gene association analysis with organic eggshell matrix genes: ovocleidin-116, osteopontin (SPP1), ovocalyxin-32 (RARRES1), ovotransferrin (LTF), ovalbumin and ovocalyxin-36, as well as key genes in the maintenance and function of the shell gland [estrogen receptor (ESR1) and carbonic anhydrase II (CAII)]. Associations were found for (i) ovalbumin with breaking strength and shell thickness; (ii) ovocleidin-116 with elastic modulus, shell thickness and egg shape; (iii) RARRES1 with mammillary layer thickness; (iv) ESR1 with dynamic stiffness; (v) SPP1 with fracture toughness and (vi) CAII with egg shape. The marker effects are as large as 17% of trait standard deviations and could be used to improve eggshell quality.

Structural analysis and haplotype diversity in swine LEP and MC4R genes.

Knowledge about structural variation of candidate genes could be important to improve breeding selection scheme and preserve genetic variability in livestock species. Leptin (LEP) and melanocortin-4 receptor (MC4R) genes are involved in the energetic pathway and are obvious candidate genes for fatness. By sequencing LEP and MC4R genes in 72 pigs belonging to lean (Large White and Duroc), fat (Meishan and Casertana) breeds and also Wild Boar, 98 polymorphic sites, of which 91 were novel, were found in the Leptin sequence while only the previously described mutation was found in the MC4R gene. A total of 18 LEP haplotypes were observed and their distribution was unequal among the breeds. The phylogenetic analysis showed two haplotype branches distinguishing between lean and fat breeds.

Probability of an egg cracking during packing can be predicted using a simple non-destructive acoustic test.

1. The aim of this investigation was to test the predictive power of the dynamic stiffness measurement to identify eggs which are most likely to crack under field conditions. 2. A representative sample of eggs (n = 1660) was collected from the front of the cages in a commercial battery unit. Egg weight, % damping and dynamic stiffness (Kdyn) were recorded using an acoustic crack detection device. Intact eggs were marked and replaced in the front of the cages. These eggs were subsequently passed through online collection, grading and packing machinery, along with a volume of unmarked eggs. At the end of packing the acoustic test was repeated on the marked eggs, and these were subsequently categorised as being either intact (0) or cracked (1). 3. A logistic regression of the probability of cracking vs Kdyn revealed that as the Kdyn measurement decreases below 15,000 N/m there is a rapid increase in the probability that an egg will crack during routine handling. 4. Additional variables (visit, egg weight,% damping and position in the house (battery [1 to 7], side [1, 2] and tier [1 to 8]) were also fitted to the model but only egg weight, visit and tier effects significantly improved the model fit. 5. This study confirms that the dynamic stiffness measurement can predict the probability of an egg cracking in the field and with high precision. As this measurement also has a high heritability, it could be incorporated into breeding programmes, where it would offer an excellent method to improve eggshell quality and reduce the incidence of cracked eggs.

Heritability and genetic correlation of measurements derived from acoustic resonance frequency analysis; a novel method of determining eggshell quality in domestic hens.

Cracked eggshells result in economic loss and provide a route for pathogenic organisms to enter the egg. Genetic factors that contribute to shell strength are likely to decrease the risk that an egg will crack when subject to insult. A novel measurement, the dynamic stiffness of the eggshell (Kdyn) was examined to determine if it might be used in the genetic selection of hens with improved eggshell characteristics. The measurement is determined from acoustic resonance frequency analysis. The estimates of heritability for the novel measurement of Kdyn were moderately high and ranged from 0.33 to 0.53 depending on the model used for the estimation. The estimates of genetic correlation of Kdyn with eggshell breaking strength (0.49) and static stiffness (0.57) were positive and relatively large as expected. There was a small negative genetic correlation between Kdyn and egg production from 26 to 50 weeks of age (-0.19) and a moderate one from 58 to 74 weeks of age (-0.36). The moderate heritability and relative independence of Kdyn indicates that this measurement could be used successfully in a breeding programme to improve shell quality and to reduce the incidence of cracks.

Application of AFLP technology to radiation hybrid mapping.

We have investigated the use of AFLP technology as a tool for the high throughput enrichment of Radiation Hybrid (RH) maps. The 3000 rad TM112 bovine RH panel was assayed with 37 EcoRI/TaqI AFLP primer combinations. The number of selective nucleotides used during PCR was increased to seven, to reduce the complexity of the AFLP profile and minimise the overlap between hamster and bovine bands co-amplified from hybrid cell clones. Seven-hundred-forty-seven bovine AFLP bands were amplified that could be distinguished following electrophoresis. Repeatability was tested within and between laboratories on independent template preparations and an error rate of 1.3% found. Two-point linkage analysis clustered 428 AFLP fragments in 39 linkage groups of at least 4 markers. Multi-point maps were constructed for 5 sample linkage groups. The study demonstrated that the AFLP approach could be used to rapidly screen for the most informative clones during panel construction and to increase the number of markers on RH maps, which could be useful for joining linkage groups formed by other markers. The use of AFLP markers as anchor points between existing RH maps and other physical maps, such as BAC contigs, is also discussed.

A study of association between genetic markers in candidate genes and reproductive traits in one generation of a commercial broiler breeder hen population.

Markers of alleles for three physiological candidate genes for reproductive traits, growth hormone (GHR), gonadotropin-releasing hormone receptor (GNRHR) and neuropeptide Y (NPY) were assessed for the association with the total egg production, number of double-yolked eggs and age at first egg in a single generation of a broiler breeder (Gallus gallus) pedigree dam line. Single-nucleotide polymorphisms and deletions were detected in the GHR, GNRHR and NPY genes. Genotypes were identified using a PCR-RFLP assay. The frequency of restriction enzyme+/-alleles in the population was for GHR 0.68 (NspI-) and 0.32 (NspI+), for NPY 0.78 (DraI+) and 0.22 (DraI-) and for GNRHR 0.54 (Bpu1102I+) and 0.46 (Bpu1102I-). Trait data from a total of 772 hens in 67 sire families from one generation of the pedigree dam line were recorded. However, the analysis used only the offspring of heterozygous sires to reduce the influence of selection and genetic background (n=33 sire families for GHR; n=14 sire families for NPY; n=36 sire families for GNRHR). A dominance effect of NPY on age at first egg and an additive effect of GNRHR on the number of double-yolked eggs were found (P<0.05).

Bone strength during growth: influence of growth rate on cortical porosity and mineralization.

Although it is well accepted that bone architecture adapts to withstand the loads placed on it, the manner in which this occurs in the immature growing skeleton is not fully understood. To investigate the possible mechanisms, we have compared morphometric differences between tibiae from chickens with fast and those with slow growth potential and also distinguished between the effects of genetic potential and growth rate on their impact on bone quality. Two different fast-growing (ad lib modern) strains, one additionally feed-restricted and one slow-growing (control) strain of chicken, were compared at 15 and 42 days of age. The ad lib modern strains had similar final body weights and were approximately twice the weight of the control and restricted-fed birds. Tibiae from the control and restricted birds had a higher ash content and lower porosity than the ad lib modern strain at 42 days. The porosity was a result of rapid primary osteon formation at the periosteal surface and incomplete infilling of the resultant canal by osteoblasts. When adjusted to average body weight of contemporaries, bones from the control strain and the restricted-fed modern birds were stiffer and at least as strong as those from the fast growing ad lib-fed birds. In conclusion, rapid bone deposition at the periosteal surface was associated with decreased mineralization, increased cortical porosity, and altered biomechanical properties. Our results also indicate that growth rate, and not genetic potential, of the fast growing birds was responsible for the rapid periosteal bone deposition.

Age-related changes in fear, sociality and pecking behaviours in two strains of laying hen.

1. Two lines of commercial hybrid layers (Tetra and ISA Brown) were reared from hatch to 30 weeks of age in groups of 8. The objectives of the experiment were to evaluate the significance of the different selection practices involved in the development of the lines and to assess the potential association between selected behavioural states and the potential for feather damage and cannibalism. 2. Behavioural tests related to fear (tonic immobility, novel object, open field), sociality (runway, proximity in the home pen) and pecking (feather bunch and focal observations of inter-bird and environmental pecking) were conducted at 0 to 2, 5 to 7, 12 to 14, 19 to 21 and 29 to 31 weeks of age. Scan sampling of general behaviour was also conducted at these ages. 3. Underlying sociality was greater in Tetras than in ISA Brown hens. 4. There were no apparent overall strain differences in fearfulness although ISA Brown hens showed significantly longer tonic immobility fear reactions than Tetras at 31 weeks of age. 5. ISA Brown hens gave and received more gentle pecks than Tetra hens whereas preening was commoner among Tetras. There were no strain differences in the number of pecks at litter or food. 6. As birds aged they showed less avoidance of novel objects and Tetras, though not ISA Browns, showed progressively shorter tonic immobility responses. Birds of both strains spent less time resting, more foraging (pecking and scratching) and pecked more at the feather bunch at older ages. 7. Measures taken in the TI, open field, runway (social affiliation) and feather bunch tests were stable over time whereas focal observations of pecking at hens and the environment were not. 8. Factor Analysis showed that 3 factors defined by the novel object test, environmental pecking and pecking ata feather bunch explained most of the variation in the correlation matrix between summary measures for the 8 behavioural traits.

Proinflammatory cytokine expression by Theileria annulata infected cell lines correlates with the pathology they cause in vivo.

Control of Theileria annulata is currently best achieved by the use of live attenuated cell line vaccines. However, the mechanisms underlying attenuation are unclear and there is a need to rapidly produce new cell line vaccines, which could safely and effectively vaccinate cattle against tropical theileriosis. There is increasing evidence to suggest that proinflammatory cytokines produced by T. annulata infected cells play a central role in both pathology and immune evasion. This study aimed to test this hypothesis and to evaluate cytokine expression as a marker of virulence. The pathogenicity and protective efficacy of cloned T. annulata cell lines that expressed different levels of proinflammatory cytokines were compared. In two independent trials using different stocks of T. annulata, cell lines that expressed higher levels of proinflammatory cytokines induced severe reactions, and in some cases death, when used to vaccinate groups of cattle. In contrast, low cytokine expressing lines induced low post-vaccinal reactions. The results clearly demonstrated that cytokine expression by T. annulata infected cells could be used as a marker of virulence and provided strong evidence to support a role for cytokines in the induction of pathology. Both high and low cytokine expressing cell lines protected cattle against heterologous challenge infection, offering the possibility of using cytokine expression to rapidly select new safe, potent vaccines against tropical theileriosis without the need for culture attenuation.

Dietary effects on bone quality and turnover, and Ca and P metabolism in chickens.

The responses of skeletal health and blood calcium (Ca) and phosphorus (P) status to different dietary calcium and available P (avP) contents were examined in 2-week-old chickens. High avP content resulted in more inorganic P (P(i)) and less ionised Ca (Ca(2+)) in the blood. Birds on low Ca and high avP diets showed a higher incidence of tibial dyschondroplasia and hypocalcaemic rickets and were therefore assumed to be hypocalcaemic. However the molar Ca:P ratio in bone was closer to the expected 1.67:1 in diets high in avP. No significant dietary mineral content effect was found on bone mineral content, or breaking strength, within the range of diets used. Results suggest that variations in molar Ca:P ratios in bone have little effect on mechanical competence, and that diets for this strain should be higher in Ca, and could be lower in avP, than current recommendations.

Skeletal development in the meat-type chicken.

1. This study ascertained how bone of modern meat-type chickens develops under typical commercial conditions and compares development with that in genetic precursor stock. 2. A modern fast-growing selected strain and a slower-growing control strain were used. Birds were weighed weekly. A random sample was taken from each population at a range of ages up to 39 d. 3. A tibiotarsus from each bird was X-rayed and its dimensions and estimated resistance to bending were determined. Cortical bone samples were ashed to measure total mineral, calcium and phosphorus content. Cortical samples were also taken for porosity assessment. 4. As expected, the selected strain grew faster and heavier than the control strain. Despite this, both strains demonstrated similar periods of rapid bone formation (days 4 to 18) and mineralisation (days 4 to 11), and achieved similar estimates of resistance to bending. 5. However, cortical bone of the selected strain was less well mineralised and more porous than that of the control strain and showed a significant increase in the molar Ca:P ratios above the expected range of values during the first 2 to 3 weeks of life. 6. Despite production of bones with the correct dimensions for load support, the relatively poor density and mineral content of bone in the selected strain is likely to reduce effective breaking strength of the tibiotarsus. Possible reasons may be either inadequate dietary supply of Ca and P or impaired utilisation of the minerals due to a rapid growth rate or genetic factors.