Patient preferences for timing and access to radiation therapy

PURPOSE

Patient preferences for radiation therapy (rt) access were investigated.

METHODS

Patients completing a course of rt at 6 centres received a 17-item survey that rated preferences for time of day; day of week; actual, ideal, and reasonable travel times for rt; and actual, ideal, and reasonable times between referral and first oncologic consultation. Patients receiving single-fraction rt or brachytherapy alone were excluded.

RESULTS

Of the respondents who returned surveys (n = 1053), 54% were women, and 74% had received more than 15 rt fractions. With respect to appointment times, 88% agreed or strongly agreed that rt between 08h00 and 16h30 was preferred; 14%-15% preferred 07h30-08h00 or 16h30-17h00; 10% preferred 17h00-18h00; and 6% or fewer preferred times before 07h30 or after 18h00. A preference not to receive rt before 07h30 or after 18h00 was expressed by 30% or more of the respondents. When days of the week were considered, 18% and 11% would have preferred to receive rt on a Saturday or Sunday respectively; 52% and 55% would have preferred not to receive rt on those days. A travel time of 1 hour or less for rt was reported by 82%, but 61% felt that a travel time of 1 hour or more was reasonable. A first consultation within 2 weeks of referral was felt to be ideal or reasonable by 88% and 73% of patients respectively.

CONCLUSIONS

An rt service designed to meet patient preferences would make most capacity available between 08h00 and 16h30 on weekdays and provide 10%-20% of rt capacity on weekends and during 07h30-08h00 and 16h30-18h00 on weekdays. Approximately 80%, but not all, of the responding patients preferred a 2-week or shorter interval between referral and first oncologic consultation.

Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes

Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.

The locus of sexual selection: moving sexual selection studies into the post-genomics era

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.

A multivariate view of the evolution of sexual dimorphism

Sexual differences are often dramatic and widespread across taxa. Their extravagance and ubiquity can be puzzling because the common underlying genome of males and females is expected to impede rather than foster phenotypic divergence. Widespread dimorphism, despite a shared genome, may be more readily explained by considering the multivariate, rather than univariate, framework governing the evolution of sexual dimorphism. In the univariate formulation, differences in genetic variances and a low intersexual genetic correlation (rMF) can facilitate the evolution of sexual dimorphism. However, studies that have analysed sex-specific differences in heritabilities or genetic variances do not always find significant differences. Furthermore, many of the reported estimates of rMF are very high and positive. When monomorphic heritabilities and a high rMF are present together, the evolution of sexual dimorphism on a trait-by-trait basis is severely constrained. By contrast, the multivariate formulation has greater generality and more flexibility. Although the number of multivariate sexual dimorphism studies is low, almost all support sex-specific differences in the G (variance-covariance) matrix; G matrices can differ with respect to size and/or orientation, affecting the response to selection differently between the sexes. Second, whereas positive values of the univariate quantity rMF only hinder positive changes in sexual dimorphism, positive covariances in the intersexual covariance B matrix can either help or hinder. Similarly, the handful of studies reporting B matrices indicate that it is often asymmetric, so that B can affect the evolution of single traits differently between the sexes. Multivariate approaches typically demonstrate that genetic covariances among traits can strongly constrain trait evolution when compared with univariate approaches. By contrast, in the evolution of sexual dimorphism, a multivariate view potentially reveals more opportunities for sexual dimorphism to evolve by considering the effect sex-specific selection has on sex-specific G matrices and an asymmetric B matrix.

A hybrid approach for the automated finishing of bacterial genomes

Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.

Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa

A strain from Haiti shares genetic ancestry with those from Asia and Africa.

Cholera was absent from the island of Hispaniola at least a century before an outbreak that began in Haiti in the fall of 2010. Pulsed-field gel electrophoresis (PFGE) analysis of clinical isolates from the Haiti outbreak and recent global travelers returning to the United States showed indistinguishable PFGE fingerprints. To better explore the genetic ancestry of the Haiti outbreak strain, we acquired 23 whole-genome Vibriocholerae sequences: 9 isolates obtained in Haiti or the Dominican Republic, 12 PFGE pattern-matched isolates linked to Asia or Africa, and 2 nonmatched outliers from the Western Hemisphere. Phylogenies for whole-genome sequences and core genome single-nucleotide polymorphisms showed that the Haiti outbreak strain is genetically related to strains originating in India and Cameroon. However, because no identical genetic match was found among sequenced contemporary isolates, a definitive genetic origin for the outbreak in Haiti remains speculative.

Ontogenetic change in genetic variance in size depends on growth environment

Within populations, the amount of environmental and genetic variation present may differ greatly among traits measured at multiple times over ontogeny. Brief periods of food deprivation are often followed by a period of accelerated (compensatory) growth. Early laboratory studies likewise reported a contraction of genetic variance in size as maturation approached. However, studies of wild populations often contradict these laboratory results. One possibility is that environmentally imposed stress is exposing genetic variance not seen in the laboratory. We tested the effect of rearing environment (high or low food) on genetic variance in size traits measured at two ages in the ladybird beetle Harmonia axyridis. A substantial amount of genetic variance was present in all combinations of rearing environment by ontogenetic stage among males. The pattern of change in male variance in mass over ontogeny was of opposite sign in the two food treatments, which may reflect cryptic genetic variance that is apparent only under stress. The proportion of overall variance that was due to additive genetic effects was much lower in females than in males, which suggests that the underlying genetics of female growth trajectories differs from that males. Our experimental design afforded an initial exploration of the genetics of compensatory growth.

A simplified method for deriving shunt and reduced VA/Q in infants

BACKGROUND

Right to left shunt and regional hypoventilation (reduced ventilation/perfusion ratio (V(A)/Q)) have different effects on the curve relating inspired oxygen (P(I)O(2)) to oxygen saturation measured by pulse oximetry (SpO(2)) and can be derived non-invasively from measurements of SpO(2) and inspired oxygen pressure (P(I)O(2)) using complex models of gas exchange. We developed a simpler computerised "slide-rule" method of making these derivations.

AIMS

To describe the slide-rule method and determine agreement between measurements derived with this and a more complex algorithm.

METHODS

Series of P(I)O(2) versus SpO(2) data points obtained during 43 studies in 16 preterm infants with bronchopulmonary dysplasia were analysed. Percentage shunt and the degree of right shift (kPa) of the P(I)O(2) versus SpO(2) curve compared with the oxyhaemoglobin dissociation curve (a measure of V(A)/Q) were determined for each dataset with both methods, and the results were compared using the method of Bland and Altman.

RESULTS

The computer slide-rule method produced results for all 43 datasets. The more complex model could derive results for 40/43 datasets. The mean differences (95% limits of agreement) between the two methods for measurements of shunt were -1.7% (-6.5 to +3.5%) and for measurements of right shift were 0.3 kPa (-2.9 to +3.6 kPa).

CONCLUSION

The slide-rule method was reliable for deriving shunt and right shift (reduced V(A)/Q) of the P(I)O(2) versus SpO(2) curve when compared with the more complex algorithm. The new method should enable wider clinical application of these measurements of oxygen exchange.

Effects of early growth conditions on body composition, allometry, and survival in the ladybird beetle Harmonia axyridis

During both the larval and adult stages, the ladybird beetles Harmonia axyridis (Pallas, 1773) feed primarily on aphids, populations of which may fluctuate dramatically in time and space. Harmonia axyridis were reared under three resource treatments: high, low, and improving. We predicted that beetles experiencing consistently poor larval conditions would allocate limited resources to dispersal traits (by increasing relative wing surface area and fat storage), whereas larvae facing good or improving conditions were predicted to allocate preferentially to reproductive traits. As predicted, beetles reared at low food had lower wing loading and stored more fat than individuals reared at consistently high food. When conditions were initially poor but improved during development, body size was reduced relative to the high food treatment, though wing area scaled similarly. Allocation of fat and protein was dependent on both sex and treatment. Females in improving conditions stored less fat, and males less protein, relative to low food conditions. This is suggestive of a trade-off between reproduction and dispersal that is resolved differently between the sexes. Unexpectedly, adult survival under starvation was not appreciably affected by larval growth conditions, although males lived about 10 days longer, on average.

Aequorin variants with improved bioluminescence properties

The photoprotein aequorin has been widely used as a bioluminescent label in immunoassays, for the determination of calcium concentrations in vivo, and as a reporter in cellular imaging. It is composed of apoaequorin (189 amino acid residues), the imidazopyrazine chromophore coelenterazine and molecular oxygen. The emission characteristics of aequorin can be changed by rational design of the protein to introduce mutations in its structure, as well as by substituting different coelenterazine analogues to yield semi-synthetic aequorins. Variants of aequorin were created by mutating residues His16, Met19, Tyr82, Trp86, Trp108, Phe113 and Tyr132. Forty-two aequorin mutants were prepared and combined with 10 different coelenterazine analogues in a search for proteins with different emission wavelengths, altered decay kinetics and improved stability. This spectral tuning strategy resulted in semi-synthetic photoprotein mutants with significantly altered bioluminescent properties.

Condition dependence of sexually dimorphic colouration and longevity in the ambush bug Phymata americana

Sexually selected traits that are costly are predicted to be more condition dependent than nonsexually selected traits. Assuming resource limitation, increased allocation to a sexually selected trait may also come at a cost to other fitness components. To test these predictions, we varied adult food ration to manipulate condition in the colour dimorphic bug, Phymata americana. We compared the degree of condition dependence in a sexually selected trait expressed in males to a nonsexually selected trait expressed in males and females. We also evaluated the effects of condition on longevity of both sexes. We found that the expression of these colour pattern traits was strongly influenced by both diet and age. As expected, the strength of condition dependence was much more pronounced in the sexually selected, male-limited trait but the nonsexual trait also exhibited significant condition dependence in both sexes. The sexually selected male trait also exhibited a higher coefficient of phenotypic variation than the nonsexually selected trait in males and females. Diet had contrasting effects on male and female longevity; increased food availability had positive effects on female lifespan but these effects were not detected in males, suggesting that males allocated limited resources preferentially to sexually selected traits. These results are consistent with the expectation that optimal allocation to various fitness components differs between the sexes.

Effects of early resource limitation and compensatory growth on lifetime fitness in the ladybird beetle (Harmonia axyridis)

Acceleration of growth following a period of diet restriction may result in either complete or partial catch-up in size. The existence of such compensatory growth indicates that organisms commonly grow at rates below their physiological maxima and this implies a cost for accelerated growth. We examined patterns of accelerated growth in response to temporary resource limitation, and assayed both short and long-term costs of this growth in the ladybird beetle Harmonia axyridis. Subsequent to the period of food restriction, accelerated growth resulted in complete compensation for body sizes, although we observed greater larval mortality during the period of compensation. There were no effects on female fecundity or survivorship within 3 months of maturation. Females did not discriminate against males that had undergone compensatory growth, nor did we observe effects on male mating behaviour. However, individuals that underwent compensatory growth died significantly sooner when deprived of food late in adult life, suggesting that longer-term costs of compensatory growth may be quite mild and detectable only under stressful conditions.

Effects of early resource-limiting conditions on patterns of growth, growth efficiency, and immune function at emergence in a damselfly (Odonata: Coenagrionidae)

Periods of restricted growth during early development are expected to have detrimental effects on subsequent metrics of fitness, most prominently increases in age and decreases in size at maturity. However, in some cases, animals may compensate by altering foraging effort, growth efficiency, or patterns of resource allocation between critical traits prior to maturation. Yet, even when compensation for age and size is complete, brief periods of restricted growth may carry costs persisting in the long term, and compensatory tactics may themselves be costly. We investigated the long-term costs of early growth restriction and mechanisms of compensatory growth in the damselfly Ischnura verticalis (Say, 1839). Larvae were temporarily exposed to one of three feeding regimes in the early stages of development, after which food levels were restored. In the period of unrestricted growth prior to emergence, partial compensation for structural size in the lowest food treatment was observed, while both resource-limited groups accelerated mass gain relative to controls. Changes in food consumption and food conversion efficiency were ruled out as mechanisms for accelerating growth following diet restriction. We tested for changes in resource allocation patterns that could explain the observed compensatory growth and found that adult body shape may depend on early growth conditions in females. There was no evidence of detrimental effects on immune function at emergence, although males tended to have higher phenoloxidase activity (a measure of immunocompetence) than females.

A comparison of parasite loads on asexual and sexual Phoxinus (Pisces: Cyprinidae)

In light of the inherent disadvantages of sexual reproduction, the existence of sex is often seen as a paradox. There are a variety of hypothetical benefits of sexual reproduction that may balance its disadvantages. The Red Queen hypothesis proposes that sexually reproducing species are better able to evolve resistance to parasites than asexually reproducing species. A prediction of the Red Queen hypothesis is that a parasite should evolve to preferentially exploit an asexual species over a sexual species. To test this central prediction of the Red Queen hypothesis, intensity of infection by the parasite Gyrodactylus eos Mayes, 1977 (Monogenea) was compared between sympatric asexual and sexual fish species in the genus Phoxinus Rafinesque, 1820. In each lake where these species coexist, the asexual fish should suffer higher intensities of infection than the sexual fish. In the majority of lakes sampled, there were more parasites on asexual than sexual fish.