12 research outputs found

    An inverse oblique effect in human vision

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    AbstractIn the classic oblique effect contrast detection thresholds, orientation discrimination thresholds, and other psychophysical measures are found to be smallest for vertical or horizontal stimuli and significantly higher for stimuli near the ±45° obliques. Here we report a novel inverse oblique effect in which thresholds for detecting translational structure in random dot patterns [Glass, L. (1969). Moiré effect from random dots. Nature, 223, 578–580] are lowest for obliquely oriented structure and higher for either horizontal or vertical structure. Area summation experiments provide evidence that this results from larger pooling areas for oblique orientations in these patterns. The results can be explained quantitatively by a model for complex cells in which the final filtering stage in a filter–rectify–filter sequence is of significantly larger area for oblique orientations

    Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

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    Background The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with similar to 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesiiMirb. (Franco)) and Interior spruce (Picea glauca(Moench) Voss xPicea engelmanniiParry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200-50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F(1)families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada. Results As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000-15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size. Conclusions Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits

    Data from: Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform

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    Background Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, we used: 1) exome capture as a genotyping platform for 1372 Douglas-fir trees representing 37 full-sib families growing on three sites in British Columbia, Canada and 2) height growth and wood density (EBVs), and deregressed estimated breeding values (DEBVs) as phenotypes. Representing models with (EBVs) and without (DEBVs) pedigree structure. Ridge regression best linear unbiased predictor (RR-BLUP) and generalized ridge regression (GRR) were used to assess their predictive accuracies over space (within site, cross-sites, multi-site, and multi-site to single site) and time (age-age/ trait-trait). Results The RR-BLUP and GRR models produced similar predictive accuracies across the studied traits. Within-site GS prediction accuracies with models trained on EBVs were high (RR-BLUP: 0.79–0.91 and GRR: 0.80–0.91), and were generally similar to the multi-site (RR-BLUP: 0.83–0.91, GRR: 0.83–0.91) and multi-site to single-site predictive accuracies (RR-BLUP: 0.79–0.92, GRR: 0.79–0.92). Cross-site predictions were surprisingly high, with predictive accuracies within a similar range (RR-BLUP: 0.79–0.92, GRR: 0.78–0.91). Height at 12 years was deemed the earliest acceptable age at which accurate predictions can be made concerning future height (age-age) and wood density (trait-trait). Using DEBVs reduced the accuracies of all cross-validation procedures dramatically, indicating that the models were tracking pedigree (family means), rather than marker-QTL LD. Conclusions While GS models’ prediction accuracies were high, the main driving force was the pedigree tracking rather than LD. It is likely that many more markers are needed to increase the chance of capturing the LD between causal genes and markers

    validation genotypes

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    SNP data for 136 samples from Jordan River validation population (69951 SNPs)

    Data from: Genomic selection of juvenile height across a single generational gap in Douglas-fir

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    Here we perform cross-generational GS analysis on coastal Douglas-fir (Pseudotsuga menziesii), reflecting trans-generational selective breeding application. 1,321 trees, representing 37 full-sib F1 families from 3 environments in British Columbia, Canada, were used as the training population for 1) EBVs (estimated breeding values) of juvenile height (HTJ) in the F1 generation predicting genomic EBVs of HTJ of 136 individuals in the F2 generation, 2) deregressed EBVs of F1 HTJ predicting deregressed genomic EBVs of F2 HTJ, 3) F1 mature height (HT35) predicting HTJ EBVs in F2, and 4) deregressed F1 HT35 predicting genomic deregressed HTJ EBVs in F2. Ridge regression best linear unbiased predictor (RR-BLUP), generalized ridge regression (GRR), and Bayes-B GS methods were used and compared to pedigree-based (ABLUP) predictions. GS accuracies for scenarios 1 (0.92, 0.91, and 0.91) and 3 (0.57, 0.56, and 0.58) were similar to their ABLUP counterparts (0.92 and 0.60 respectively) (using RR-BLUP, GRR, and Bayes-B). Results using deregressed values fell dramatically for both scenarios 2 and 4 which approached zero in many cases. Cross-generational GS validation of juvenile height in Douglas-fir produced predictive accuracies almost as high as that of ABLUP. Without capturing LD, GS cannot surpass the prediction of ABLUP. Here we tracked pedigree relatedness between training and validation sets. More markers or improved distribution of markers are required to capture LD in Douglas-fir. This is essential for accurate forward selection among siblings as markers that track pedigree are of little use for forward selection of individuals within controlled pollinated families

    Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform

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    Background: Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, we used: 1) exome capture as a genotyping platform for 1372 Douglas-fir trees representing 37 full-sib families growing on three sites in British Columbia, Canada and 2) height growth and wood density (EBVs), and deregressed estimated breeding values (DEBVs) as phenotypes. Representing models with (EBVs) and without (DEBVs) pedigree structure. Ridge regression best linear unbiased predictor (RR-BLUP) and generalized ridge regression (GRR) were used to assess their predictive accuracies over space (within site, cross-sites, multi-site, and multi-site to single site) and time (age-age/ trait-trait). Results: The RR-BLUP and GRR models produced similar predictive accuracies across the studied traits. Within-site GS prediction accuracies with models trained on EBVs were high (RR-BLUP: 0.79–0.91 and GRR: 0.80–0.91), and were generally similar to the multi-site (RR-BLUP: 0.83–0.91, GRR: 0.83–0.91) and multi-site to single-site predictive accuracies (RR-BLUP: 0.79–0.92, GRR: 0.79–0.92). Cross-site predictions were surprisingly high, with predictive accuracies within a similar range (RR-BLUP: 0.79–0.92, GRR: 0.78–0.91). Height at 12 years was deemed the earliest acceptable age at which accurate predictions can be made concerning future height (age-age) and wood density (trait-trait). Using DEBVs reduced the accuracies of all cross-validation procedures dramatically, indicating that the models were tracking pedigree (family means), rather than marker-QTL LD. Conclusions: While GS models’ prediction accuracies were high, the main driving force was the pedigree tracking rather than LD. It is likely that many more markers are needed to increase the chance of capturing the LD between causal genes and markers.Forestry, Faculty ofNon UBCForest and Conservation Sciences, Department ofReviewedFacult

    Douglas-fir exomic SNP file

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    Exomic genotype file for Douglas-fir produced by RAPiD Genomics© , containing 74199 biallelic SNPs with less than 40% missing data and minQ=10

    Douglas-fir phenotypes

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    Phenotypic measurements from Douglas-fir trial over 3 sites in British Columbia, Canada. Courtesy of Forests, Lands and Natural Resource Operations, BC, Canada

    Primum non nocere: Shared informed decision making in low back pain - A pilot cluster randomised trial

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    Background: Low back pain is a common and disabling condition leading to large health service and societal costs. Although there are several treatment options for back pain little is known about how to improve patient choice in treatment selection. The purpose of this study was to pilot a decision support package to help people choose between low back pain treatments. Methods: This was a single-centred pilot cluster randomised controlled trial conducted in a community physiotherapy service. We included adults with non-specific low back pain referred for physiotherapy. Intervention participants were sent an information booklet prior to their first consultation. Intervention physiotherapists were trained to enhance their skills in shared informed decision making. Those in the control arm received care as usual. The primary outcome was satisfaction with the treatment received at four months using a five-point Likert Scale dichotomised into "satisfaction" (very satisfied or somewhat satisfied) and "non-satisfaction" (neither satisfied nor dissatisfied, somewhat dissatisfied or very dissatisfied). Results: We recruited 148 participants. In the control arm 67% of participants were satisfied with their treatment and in the intervention arm 53%. The adjusted relative risk of being satisfied was 1.28 (95% confidence interval 0.79 to 2.09). For most secondary outcomes the trend was towards worse outcomes in the intervention group. For one measure; the Roland Morris Disability Questionnaire, this difference was clinically important (2.27, 95% confidence interval 0.08 to 4.47). Mean healthcare costs were slightly lower (£38 saving per patient) within the intervention arm but health outcomes were also less favourable (0.02 fewer QALYs); the estimated probability that the intervention would be cost-effective at an incremental threshold of £20,000 per QALY was 16%. Conclusion: We did not find that this decision support package improved satisfaction with treatment; it may have had a substantial negative effect on clinical outcome, and is very unlikely to prove cost-effective. That a decision support package might have a clinically important detrimental effect is of concern. To our knowledge this has not been observed previously. Decision support packages should be formally tested for clinical and cost-effectiveness, and safety before implementation. Trial registration: Current Controlled Trials ISRCTN46035546 registered on 11/02/10
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