The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available datasets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism, and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.     

Reducing treatment machine downtime with a preventative MLC maintenance procedure

The persistent use of MLCs through VMAT and IMRT is causing additional wear and tear on these mechanical parts, leading to an increase in MLC interlocks, breakdowns and failures. This study investigates the effect of an MLC clean and service procedure on MLC performance and positional accuracy demonstrated through in-house service logbook reports, Varian MLC backlash test results, daily MLC position QC results and Varian TrueBeam trajectory log file data.A service and clean of each individual MLC leaf was carried out on 3 standard MLC and 2 high definition MLC (HDMLC) Varian TrueBeam linacs. In-house service logbook reports, Varian backlash test results, daily MLC picket fence QC results and beam hold data from patient delivery trajectory log files were analysed for up to 6 months pre and 2 years post the MLC service/clean to assess the impact on unplanned MLC maintenance work and MLC performance.The median (range) of hardware faults reduced from 12 (1–17) pre clean to 0 (0–1) and 4 (1–11) at 12 and 24 months respectively for all linacs with the exception of a HDMLC linac where faults increased from 4 pre-clean to 13 and 20 again at 12 and 24 months respectively. The reduction in faults in the alternative 4 linacs was consistent with the reduction in the number of MLCs reaching the 0.3 mm and the 0.4 mm backlash recommendations in the first 12 and 24 months following the service/clean. The increase in faults in the HDMLC linac was also consistent with the increase in MLCs reaching the 0.3 mm backlash recommendation in the first 12 and 24 months. The median (range) of MLCs reaching a daily picket fence QC position tolerance of 0.25 mm reduced from 14 (1–40) pre clean to 0 (0) at both 12 and 24 months post-clean. This demonstrates the improvement in MLC performance caused by the MLC service/clean but also reveals factors other than MLC position accuracy influence hardware faults. Additionally, the number of beam hold-offs determined from patient delivery trajectory log files were found to have no correlation with the MLC service/clean.The MLC service/clean improves MLC performance and MLC position accuracy, reducing reactive repair work for engineering and physics staff. The results were maintained for 1 year post the MLC service/clean, with a trend back towards pre-clean levels in the subsequent 12–24 months. This suggests this preventative maintenance work could be performed at a frequency of > 2 years. This period of reduced faults and improved performance is significant given the 10 year expected lifespan of a linac.     

Seed size,establishment sites and species coexistence in a Chilean rain forest

Abstract. Seedling densities on the forest floor and on elevated microsites (logs and stumps) were compared for eight woody species in a temperate rain forest in southern Chile. Degree of association with elevated microsites varied significantly between species, showed no systematic relationship with reported shade tolerance, but was significantly negatively correlated with seed mass. Large-seeded Podocarpus nubigena established preferentially on undisturbed forest floor sites, whereas seedlings of small-seeded species such as Nothofagus nitida and Laurelia philippiana were found mainly on fallen logs and stumps. The abundance of large seedlings and saplings of N. nitida on logs/stumps, and the growth forms of canopy trees, confirm that recruitment of this species occurs mainly on decaying wood. The relationship between seed size and microsite preferences may be caused by effects of seed size on (1) ability to establish in forest floor litter and (2) retention of seeds on logs. Seedling occupancy of logs and stumps varied with state of decay. Few seedlings of any species were present on logs in the early stages of decay. N. nitida established earlier than the other species, attaining maximum abundance on wood in the middle decay classes. Species richness and overall seedling abundance were highest on wood in advanced stages of decay. Seed size differences are suggested as a determinant of differential utilization of forest floor heterogeneity, and hence of plant species coexistence.     

Making up for lost time: Biophysical constraints on the temporal abundance of two fiddler crabs in wet–dry tropical mangroves

Biophysical models are used to predict the spatial distributions of organisms. Nevertheless, understanding factors influencing the temporal distributions of animals may often be additionally required. It is expected that intertidal macrofauna of the wet–dry tropics face a multitude of temporal challenges because there is not only seasonal drying but also variation in surface moisture over the circatidal cycle. Activities of fiddler crabs (Uca spp.) depend on adequate surface moisture being available for feeding and respiration. A recent study monitored crab abundance during spring tides and found that one Uca species in the mangroves of Darwin Harbour, Australia, U. flammula, is most abundant in the wet season, while another, U. elegans, is most abundant in the dry season. We hypothesized here that these seemingly contradictory abundance patterns are driven by temporal variation in the availability of soil moisture within each species habitat. We thus monitored crab abundance and measured soil moisture content across four types of habitat (low gap centres, low gap edges, mid‐height gap centres and high gap centres) seasonally and across the circatidal cycle. We found that crab abundance and soil moisture both varied over time among habitat types. We used a log‐linear model to show that habitat type influenced soil moisture and this in turn influenced crab abundance. Sampling across the circatidal cycle showed that U. flammula was more abundant in the wet season, as reported previously, while the abundance of U. elegans did not vary between seasons. Our model suggested that U. elegans ‘makes up for lost time’ in the dry season by undertaking all activities during spring tide low water as only at this time is the substratum moist enough for feeding and respiration. We highlight the importance of measuring multiple variables across habitats over small and large scales when assessing temporal abundance patterns of intertidal tropical organisms.     

Effects of Forest Type and Disturbance on Diversity of Coarse Woody Debris in Boreal Forest

Coarse woody debris (CWD) volume and diversity are vital attributes of forest ecosystems. However, despite their importance, their long-term dynamics associated with fire- or logging-origin and overstory type have not been examined in boreal forest. We hypothesize that (1) CWD compositional diversity increases with stand development whereas CWD volume follows a U-shaped pattern. Furthermore, we attempted to test if (2) CWD volume and compositional diversity converge for postlogged and postfire stands through stand development, and (3) mixedwoods have more CWD volume and greater compositional diversity than conifer or broadleaf overstory types. We sampled 72 stands ranging in age from 7 to 201 years in fire-origin stands and 7–31 years in managed stands with conifer, mixedwood, and broadleaf overstory types in central boreal Canada. For fire-origin stands, snag volume was 100–260 m³/ha in 7-year-old stands, 5–20 m³/ha in 25-year-old stands, and 25–60 m³/ha in older stands; downed woody debris (DWD) volume decreased from 7 to 72–90 year-old stands, increased in 124- to 139-year-old stands, then either decreased or increased in 201-year-old stands depending on overstory type. CWD diversity increased from 25 to 124–139 year-old and plateaued, but in 7-year-old stands, CWD diversity was as high as that in the 124 and up year-old age classes. Logging resulted in a smaller amount and lower size variability of CWD in 7-year-old stands, with a larger portion being fast-decomposing Betula papyrifera. Most CWD characteristics had not converged by approximately 30 years since disturbance between the two stand origins. More diverse CWD occurred in mixedwoods, but conifer stands contained the greatest CWD volume except in 7 year-old postfire stands. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. B. W. Brassard collected and analyzed data and wrote the paper. H. Y. H. Chen conceived and designed the study, analyzed data, and critiqued earlier drafts of the paper.     

兴安落叶松老龄林落叶松林木死亡格局以及倒木对更新的影响

对兴安落叶松老龄林落叶松林木死亡格局和死亡木对更新的影响进行了研究 .结果表明 ,丛桦落叶松林和杜香落叶松林的枯立木以中径木占多数 ,赤杨落叶松林主要为中、大径木 ,草类落叶松林主要是中、小径木 .落叶松枯立木主要因火烧、受压和老死而形成 .丛桦落叶松林和赤杨落叶松林掘根倒木较多 .杜香落叶松林和草类落叶松林的倒木以风折为主 .地形、山体走向和盛行风向对树倒方向影响很大 .丛桦落叶松林倒木方向杂乱 ,赤杨落叶松林林木均向东倒下 ,杜香落叶松林和草类落叶松林的掘根木分别向南、东北方倒下 ,两者的风折木倒向随机性较大 .草类落叶松和赤杨落叶松老龄林内 ,倒木更新为 1 8和 40株·m- 2 ,远远高于矿物土基质上 2株·m- 2 的水平 .丛桦落叶松林内倒木和林地上更新均相当好 ,约为 2 8株·m- 2 .杜香落叶松林倒木更新效果不突出 .     

QSAR and docking studies of anthraquinone derivatives by similarity cluster prediction

Forty anthraquinone derivatives have been downloaded from PubChem database and investigated in a quantitative structure-activity relationships (QSAR) study. The models describing log P and LD50 of this set were built up on the hypermolecule scheme that mimics the investigated receptor space; the models were validated by the leave-one-out procedure, in the external test set and in a new version of prediction by using similarity clusters. Molecular docking approach using Lamarckian Genetic Algorithm was made on this class of anthraquinones with respect to 3Q3B receptor. The best scored molecules in the docking assay were used as leaders in the similarity clustering procedure. It is demonstrated that the LD50 data of this set of anthraquinones are related to the binding energies of anthraquinone ligands to the 3Q3B receptor.     

The effect of beam interruption during VMAT delivery on the delivered dose distribution

PurposeThe aim of this study is to investigate the effect of beam interruptions during delivery of volumetric modulated arc therapy (VMAT) on delivered dose distributions.MethodsTen prostate and ten head and neck (H&N) VMAT plans were retrospectively selected. Each VMAT plan was delivered using Trilogy™ without beam interruption, and with 4 and 8 intentional beam interruptions per a single arc. Two-dimensional global and local gamma evaluations with a diode array were performed with gamma criteria of 3%/3 mm, 2%/2 mm, 1%/2 mm and 2%/1 mm for each VMAT plan with and without beam interruptions. The VMAT plans were reconstructed with log files recorded during delivery and the dose-volumetric parameters were calculated for each reconstructed plan. The differences among dose-volumetric parameters due to the beam interruptions were calculated.ResultsThe changes in global gamma passing rates with various gamma criteria were less than 1.6% on average, while the changes in local gamma passing rates were less than 5.3% on average. The dose-volumetric parameter changes for the target volumes of prostate and H&N VMAT plans due to beam interruptions were less than 0.72% and 1.5% on average, respectively.ConclusionThe delivered dose distributions with up to 8 beam interruptions per an arc were clinically acceptable, showing minimal changes in both gamma passing rates and dose-volumetric parameters.