Search

Stereotactic radiotherapy is a standard treatment option for patients with brain metastases. The planning target volume is based on gross tumor volume (GTV) segmentation. The aim of this work is to develop and validate a neural network for automatic GTV segmentation to accelerate clinical daily routine practice and minimize interobserver variability.We analyzed MRIs (T1-weighted sequence ± contrast-enhancement, T2-weighted sequence, and FLAIR sequence) from 348 patients with at least one brain metastasis from different cancer primaries treated in six centers. To generate reference segmentations, all GTVs and the FLAIR hyperintense edematous regions were segmented manually. A 3D-U-Net was trained on a cohort of 260 patients from two centers to segment the GTV and the surrounding FLAIR hyperintense region. During training varying degrees of data augmentation were applied. Model validation was performed using an independent international multicenter test cohort (n = 88) including four centers.Our proposed U-Net reached a mean overall Dice similarity coefficient (DSC) of 0.92 ± 0.08 and a mean individual metastasis-wise DSC of 0.89 ± 0.11 in the external test cohort for GTV segmentation. Data augmentation improved the segmentation performance significantly. Detection of brain metastases was effective with a mean F1-Score of 0.93 ± 0.16. The model performance was stable independent of the center (p = 0.3). There was no correlation between metastasis volume and DSC (Pearson correlation coefficient 0.07).Reliable automated segmentation of brain metastases with neural networks is possible and may support radiotherapy planning by providing more objective GTV definitions.

The development of strawberry (Fragaria × ananassa Duchesne ex Rozier) cultivars resistant to Phytophthora crown rot (PhCR), a devastating disease caused by the soil-borne pathogen Phytophthora cactorum (LebertCohn) J. Schröt., has been challenging partly because the resistance phenotypes are quantitative and only moderately heritable. To develop deeper insights into the genetics of resistance and build the foundation for applying genomic selection, a genetically diverse training population was screened for resistance to California isolates of the pathogen. Here we show that genetic gains in breeding for resistance to PhCR have been negligible (3% of the cultivars tested were highly resistant and none surpassed early 20th century cultivars). Narrow-sense genomic heritability for PhCR resistance ranged from 0.41 to 0.75 among training population individuals. Using multivariate genome-wide association studies (GWAS), we identified a large-effect locus (predicted to be RPc2) that explained 43.6-51.6% of the genetic variance, was necessary but not sufficient for resistance, and was associated with calcium channel and other candidate genes with known plant defense functions. The addition of underutilized gene bank resources to our training population doubled additive genetic variance, increased the accuracy of genomic selection, and enabled the discovery of individuals carrying favorable alleles that are either rare or not present in modern cultivars. The incorporation of an RPc2-associated single-nucleotide polymorphism (SNP) as a fixed effect increased genomic prediction accuracy from 0.40 to 0.55. Finally, we show that parent selection using genomic-estimated breeding values, genetic variances, and cross usefulness holds promise for enhancing resistance to PhCR in strawberry.

Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.

Many important traits in plants, animals, and microbes are polygenic and challenging to improve through traditional marker-assisted selection. Genomic prediction addresses this by incorporating all genetic data in a mixed model framework. The primary method for predicting breeding values is genomic best linear unbiased prediction, which uses the realized genomic relationship or kinship matrix (K) to connect genotype to phenotype. Genomic relationship matrices share information among entries to estimate the observed entries’ genetic values and predict unobserved entries’ genetic values. One of the main parameters of such models is genomic variance (σg2), or the variance of a trait associated with a genome-wide sample of DNA polymorphisms, and genomic heritability (hg2); however, the seminal papers introducing different forms of K often do not discuss their effects on the model estimated variance components despite their importance in genetic research and breeding. Here, we discuss the effect of several standard methods for calculating the genomic relationship matrix on estimates of σg2 and hg2. With current approaches, we found that the genomic variance tends to be either overestimated or underestimated depending on the scaling and centering applied to the marker matrix (Z), the value of the average diagonal element of K, and the assortment of alleles and heterozygosity (H) in the observed population. Using the average semivariance, we propose a new matrix, KASV, that directly yields accurate estimates of σg2 and hg2 in the observed population and produces best linear unbiased predictors equivalent to routine methods in plants and animals.

Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between sub-populations in a population as a result of non-random mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics it is an important confounding variable in genome wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this paper, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is either known a-priori through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to PCA, while neural network based methods fall behind.

Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria × ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and wild octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here we show that resistance to both races is widespread and that resistance to race 1 is mediated by dominant genes (FW1, FW2, FW3, FW4, and FW5) on three non-homoeologous chromosomes (1A, 2B, and 6B). The resistance proteins encoded by these genes are not yet known; however, plausible candidates were identified that encode pattern recognition receptor or other proteins known to mediate gene-for-gene resistance in plants.High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.Key MessageSeveral race-specific resistance genes were identified and rapidly deployed via marker-assisted selection to develop strawberry cultivars resistant to Fusarium wilt, a devastating soil-borne disease.

Key Message Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant toFusarium oxysporumf. sp.fragariae, a devastating soil-borne pathogen of strawberry. Abstract Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria$$\times$$ × ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

Gray mold, a disease of strawberry (Fragaria×ananassa) caused by the ubiquitous necrotrophBotrytis cinerea, renders fruit unmarketable and causes economic losses in the postharvest supply chain. To explore the feasibility of selecting for increased resistance to gray mold, we undertook genetic and genomic prediction studies in strawberry populations segregating for fruit quality and shelf life traits hypothesized to pleiotropically affect susceptibility. As predicted, resistance to gray mold was heritable but quantitative genetically complex. While every individual was susceptible, the speed of symptom progression and severity differed. Narrow-sense heritability ranged from 0.38-0.71 for lesion diameter (LD) and 0.39-0.44 for speed of emergence of external mycelium (EM). Even though significant additive genetic variation was genome wide observed for LD and EM, the phenotypic ranges were comparatively narrow and genome-wide analyses did not identify any large effect loci. Genomic selection accuracy ranged from 0.28-0.59 for LD and 0.37-0.47 for EM. Additive genetic correlations between fruit quality and gray mold resistance traits were consistent with prevailing hypotheses: LD decreased as titratable acidity increased, whereas EM increased as soluble solid whole genome content decreased and firmness increased. We concluded that phenotypic and genomic selection could be regression effective for reducing LD and increasing EM, especially in long shelf life populations, but that a significant fraction of the genetic variation for resistance to gray mold was caused by the pleiotropic effects of fruit quality traits that differ among market and shelf life classes.

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its wild progenitors are outbred octoploids (2n = 8x = 56) in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploid F. × ananassa hybrid ‘Royal Royce’ from the University of California. Our goal was to produce subgenome-and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a custom F. × ananassa repeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present ‘FaRR1’, a gold-standard reference genome of F. × ananassa cultivar ‘Royal Royce’ to assist future genomic research and molecular breeding of allo-octoploid strawberry.

Reliable phenotyping methods that are simple to operate and inexpensive to deploy are critical for studying quantitative traits in plants. Traditional fruit shape phenotyping relies on human raters or 2D analyses to assess form, e.g., size and shape. Systems for 3D imaging using multi-view stereo have been implemented, but frequently rely on commercial software and/or specialized hardware, which can lead to limitations in accessibility and scalability. We present a complete system constructed of consumer-grade components for capturing, calibrating, and reconstructing the 3D form of small-to-moderate sized fruits and tubers. Data acquisition and image capture sessions are 9 seconds to capture 60 images. The initial prototype cost was $1600 USD. We measured accuracy by comparing reconstructed models of 3D printed ground truth objects to the original digital files of those same ground truth objects. The R2 between length of the primary, secondary, and tertiary axes, volume, and surface area of the ground-truth object and the reconstructed models was > 0.97 and root-mean square error (RMSE) was <3mm for objects without locally concave regions. Measurements from 1mm and 2mm resolution reconstructions were consistent (R2> 0.99). Qualitative assessments were performed on 48 fruit and tubers, including 18 strawberries, 12 potatoes, 5 grapes, 7 peppers, and 4 Bosc and 2 red Anjou pears. Our proposed phenotyping system is fast, relatively low cost, and has demonstrated accuracy for certain shape classes, and could be used for the 3D analysis of fruit form.

Many important traits in plants, animals, and microbes are polygenic and are therefore difficult to improve through traditional marker-assisted selection. Genomic prediction addresses this by enabling the inclusion of all genetic data in a mixed model framework. The main method for predicting breeding values is genomic best linear unbiased prediction (GBLUP), which uses the realized genomic relationship or kinship matrix (K) to connect genotype to phenotype. The use of relationship matrices allows information to be shared for estimating the genetic values for observed entries and predicting genetic values for unobserved entries. One of the key parameters of such models is genomic heritability , or the variance of a trait associated with a genome-wide sample of DNA polymorphisms. Here we discuss the relationship between several common methods for calculating the genomic relationship matrix and propose a new matrix based on the average semivariance that yields accurate estimates of genomic variance in the observed population regardless of the focal population quality as well as accurate breeding value predictions in unobserved samples. Notably, our proposed method is highly similar to the approach presented by Legarra (2016) despite different mathematical derivations and statistical perspectives and only deviates from the classic approach presented in VanRaden (2008) by a scaling factor. With current approaches, we found that the genomic heritability tends to be either over- or underestimated depending on the scaling and centering applied to the marker matrix (Z), the value of the average diagonal element of K, and the assortment of alleles and heterozygosity (H) in the observed population and that, unlike its predecessors, our newly proposed kinship matrix KASV yields accurate estimates of in the observed population, generalizes to larger populations, and produces BLUPs equivalent to common methods in plants and animals.

The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible-pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.

The development of genome-informed methods for identifying quantitative trait loci (QTL) and studying the genetic basis of quantitative variation in natural and experimental populations has been driven by advances in high-throughput genotyping. For many complex traits, the underlying genetic variation is caused by the segregation of one or more ‘large-effect’ loci, in addition to an unknown number of loci with effects below the threshold of statistical detection. The large-effect loci segregating in populations are often necessary but not sufficient for predicting quantitative phenotypes. They are, nevertheless, important enough to warrant deeper study and direct modelling in genomic prediction problems. We explored the accuracy of statistical methods for estimating the fraction of marker-associated genetic variance (p) and heritability (HM2) for large-effect loci underlying complex phenotypes. We found that commonly used statistical methods overestimate p and HM2. The source of the upward bias was traced to inequalities between the expected values of variance components in the numerators and denominators of these parameters. Algebraic solutions for bias-correcting estimates of p and HM2 were found that only depend on the degrees of freedom and are constant for a given study design. We discovered that average semivariance methods, which have heretofore not been used in complex trait analyses, yielded unbiased estimates of p and HM2, in addition to best linear unbiased predictors of the additive and dominance effects of the underlying loci. The cryptic bias problem described here is unrelated to selection bias, although both cause the overestimation of p and HM2. The solutions we described are predicted to more accurately describe the contributions of large-effect loci to the genetic variation underlying complex traits of medical, biological, and agricultural importance., Author summary The contributions of individual genes to the phenotypic variation observed for genetically complex traits has been an ongoing and important challenge in biology, medicine, and agriculture. While many genes have statistically undetectable effects, those with large effects often warrant in-depth study and can be important predictors of complex phenotypes such as disease risk in humans or disease resistance in domesticated plants and animals. The genes identified through associations with genetic markers in complex trait analyses typically account for a fraction of the heritable variation, a genetic parameter we called ‘marker heritability’. We discovered that textbook statistical methods systematically overestimate marker heritability and thus overestimate the contributions of specific genes to the phenotypic variation observed for complex traits in natural and experimental populations. We describe the source of the upward bias, validate our findings through computer simulation, describe methods for bias-correcting estimates of marker heritability, and illustrate their application through empirical examples. The statistical methods we describe supply investigators with more accurate estimates of the contributions of specific genes or networks of interacting genes to the heritable variation observed in complex trait studies.

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

Understanding the genetic basis of plant traits requires comprehensive and quantitative descriptions of the phenotypic variation that exists within populations. Cameras and other sensors have made high‐throughput phenotyping possible, but image‐based phenotyping procedures involve a step where a researcher selects the traits to be measured. This feature selection step is inherently prone to human biases. Recently, a set of phenotyping approaches, which are referred to collectively as latent phenotyping techniques, have arisen in the literature. Latent phenotyping techniques isolate a latent source of variance in the data, such as stress or genotype, and then quantify the effect of this latent source of variance using latent variables without defining any conventional traits. In this review, we discuss the differences between, and challenges of, both traditional and latent phenotyping.

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.

With the proliferation of ultrahigh-speed mobile networks and internet-connected devices, along with the rise of artificial intelligence (AI)

The allo-octoploid cultivated strawberry (Fragaria×ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploidFragariaspecies harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM inF. chiloensissubsp.lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM inF. ×ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information, and unifying existing chromosome nomenclatures. Through comparative genetic mapping, we show that the genomes of geographically diverse wild octoploids are effectively diploidized and completely collinear. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported both its origin and domestication through repeated cycles of interspecific hybridization.

BackgroundShape is a critical element of the visual appeal of strawberry fruit and determined by both genetic and non-genetic factors. Current fruit phenotyping approaches for external characteristics in strawberry rely on the human eye to make categorical assessments. However, fruit shape is multi-dimensional, continuously variable, and not adequately described by a single quantitative variable. Morphometric approaches enable the study of complex forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the principal progression of k clusters (PPKC). We use these human-recognizable shape categories to select features extracted from multiple morphometric analyses that are best fit for genome-wide and forward genetic analyses.ResultsWe transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered four principal shape categories, and inferred progression using PPKC. We extracted 67 quantitative features from digital images of strawberries using a suite of morphometric analyses and multi-variate approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68.9 – 99.3% for the newly created, genetically correlated phenotypic variables describing a shape.ConclusionsOur results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches we applied in strawberry should apply to other fruits, vegetables, and specialty crops.

Herbivorous insects exhibit strong feeding preferences when choosing among plant genotypes, yet experiments to map loci mediating plant susceptibility to herbivory rarely incorporate host choice. To address this gap, we applied genome-wide association (GWA) mapping to uncover genetic polymorphisms mediating damage from foraging insects (two populations ofScaptomyza flava) across a mixture ofArabidopsis thalianagenotypes in experimental enclosures. The effect of chemical defenses (glucosinolates) on herbivory depended on herbivore genotype. Unlike many studies that minimize the effects of host choice behavior, we also found a large effect of plant size on herbivory—likely through its effect on plant apparency—that was independent of herbivore genotype. These herbivory-associated loci are polymorphic at fine spatial scales, and thus have potential to shape variation in herbivory within natural populations. We also show that the polymorphism with the largest effect on herbivory underlies adaptive latitudinal variation inArabidopsisplant size across Europe. Overall, our results provide genetic support for ecological observations that variation in both chemical defenses and non-canonical defense traits (e.g., plant size and phenology) jointly shapes plant-herbivore interactions.

BACKGROUND: Injuries to the physis are common in children with a subset resulting in an osseous bar and potential growth disturbance. Magnetic resonance imaging allows for detailed assessment of the physis with the ability to generate 3-dimensional physeal models from volumetric data. The purpose of this study was to assess the interrater reliability of physeal bar area measurements generated using a validated semiautomated segmentation technique and to highlight the clinical utility of quantitative 3-dimensional (3D) physeal mapping in pediatric orthopaedic practice. METHODS: The Radiology Information System/Picture Archiving Communication System (PACS) at our institution was searched to find consecutive patients who were imaged for the purpose of assessing a physeal bar or growth disturbance between December 2006 and October 2011. Physeal segmentation was retrospectively performed by 2 independent operators using semiautomated software to generate physeal maps and bar area measurements from 3-dimensional spoiled gradient recalled echo sequences. Inter-reliability was statistically analyzed. Subsequent surgical management for each patient was recorded from the patient notes and surgical records. RESULTS: We analyzed 24 patients (12M/12F) with a mean age of 11.4 years (range, 5-year to 15-year olds) and 25 physeal bars. Of the physeal bars: 9 (36%) were located in the distal tibia; 8 (32%) in the proximal tibia; 5 (20%) in the distal femur; 1 (4%) in the proximal femur; 1 (4%) in the proximal humerus; and 1 (4%) in the distal radius. The independent operator measurements of physeal bar area were highly correlated with a Pearson correlation coefficient (r) of 0.96 and an intraclass correlation coefficient for average measures of 0.99 (95% confidence interval, 0.97-0.99). Four patients underwent resection of the identified physeal bars, 9 patients were treated with epiphysiodesis, and 1 patient underwent bilateral tibial osteotomies. CONCLUSIONS: Semiautomated segmentation of the physis is a reproducible technique for generating physeal maps and accurately measuring physeal bars, providing quantitative and anatomic information that may inform surgical management and prognosis in patients with physeal injury.

Vitamin and mineral composition in the raw material for all diets used in this study. (PDF 61Â kb)

List of transcripts showing the highest change in the HK of fish injected with poly(I:C) and dependent on prior feeding regime. The selection was based on the results of the GO analysis (Fig. 7). All the genes with corresponding microarray feature code1 found involved in a biological process significantly altered by the experimental diet in the HK were selected. If the transcripts were significantly modulated also in fish fed the experimental diet enriched with 4 mg Se Kg−1 by adding Sel-Plex and injected with poly(I:C)3, or in the same tissue of fish fed the control diet and injected with poly(I:C)4 , these values are given. Also the fold change of the expression of the same targets between these last two groups is reported, as given from Genespring software5. All the transcripts shown were significantly modulated at p

Real time qPCR analysis of genes selected for confirmation of microarray data. Candidate transcripts expression in HK (A) and liver (B) RNA isolated from rainbow trout fed a control diet (CTRL) or a diet enriched with 4 mg Se Kg −1 (Sel-Plex), and injected with either PBS or poly(I:C). The expression of gene transcripts was quantified by qPCR and normalized against the geometric mean of three housekeeping genes (ef-1α, drpII, hprt) from the same samples, and then used for statistical analysis. The transcript expression is reported as a fold change, calculated as the average expression level of stimulated samples divided by that of the controls. The results represent the mean ± SEM from five pools of HK or liver RNA extracted from 3 individuals from 3 different tanks. The letters above the columns indicate values that are statistically significant vs the controls (p

Principal component analysis of the expression patterns of the four distinct conditions analyzed. Clustering of diets (control diet and Sel-Plex supplementation) and treatments (PBS or poly(I:C)) groups based on the three (left) and two principal components (right), in HK (A) and liver (B). The colours and shapes of the data points indicate diet group and treatment. The x-, y- and z-axes represent PC1, PC2 and PC3, respectively. (PDF 753Â kb)

List of selenoprotein transcripts significantly modulated. All the selenoprotein transcripts modulated in the HK and liver of fish fed the experimental diet enriched with 2 g Kg−1 Sel-Plex and injected with PBS, of fish injected with poly(I:C) and fed the experimental diet enriched with 2 g Kg−1 Sel-Plex and the control diet respectively, are given. All the transcripts shown were significantly modulated (p

Diagram outlining the experimental setup and hybridization strategy for microarray analysis. For each experimental group five pools of HK or liver RNA extracted from three individuals were used. For the microarray experiment, the effect of the 4 mg Se Kg−1 diet (SeC), plus the effect of poly(I:C) stimulation on fish fed either a control diet (CP) or the 4 mg Se Kg−1 enriched diet (SeP) was investigated, in both liver and head kidney. One-way ANOVA was used to compare differences among groups, whilist two-way ANOVA analysis was applied to determine differential responses to poly(I:C) between the two diet groups. The pooled control was an equal mixture of RNA pools from each group. All hybridizations were between experimental groups and the pooled control. (PDF 317 kb)

Rationale and Objectives This study was designed to evaluate the performance of radiology residents in interpreting emergency department (ED) chest radiographs for congestive heart failure and to characterize the factors associated with a subsequent amended interpretation by an attending radiologist. Materials and Methods We retrospectively reviewed all amended reports for ED chest radiographs between January 2004 and July 2005 and identified those with discrepant interpretations regarding the diagnosis of congestive heart failure. A total of 1.9% (476 of 24,600) of chest radiographs were amended over the study period. Forty-eight patients (75% female, mean age 66 years) whose chest radiograph was amended for the diagnosis of congestive heart failure and were available for review formed the study population. A control group of 35 patients (69% female, mean age 67 years) were individually matched to a convenience subset of patients by age, gender, clinical indication, and radiographic projection. Chest radiographs were in the anteroposterior projection in 62% (30 of 48) of study patients and 60% (21 of 35) of controls. A blinded expert panel of three board-certified cardiothoracic radiologists jointly reviewed each chest radiograph for the presence or absence of congestive heart failure and its specific radiographic findings. Results The expert panel diagnosed congestive heart failure in 19% (9 of 48) of study patients and in 23% (8 of 35) of controls (P = .65). When present, congestive heart failure was mild to moderate in severity in both the study and control groups (P = 1.00). There was a significant difference in the expert panel agreement between the attending versus the resident interpretation (65% versus 35%, P = .008), for the study group. This resulted in fair agreement (κ = 0.29) between the expert panel and the attending interpretation and no agreement (κ = −0.29) between the expert panel and the resident interpretation. In contrast, the expert panel agreed with the joint resident/attending interpretation in 83% (29 of 35) of controls, yielding substantial agreement (κ = 0.72). Conclusion Interpretation of chest radiographs for congestive heart failure by radiology residents has a low error rate. The majority of chest radiographs with discrepant resident and attending interpretations were portable films of female patients with subtle radiographic findings of congestive heart failure, and were inherently difficult to interpret.

(2001). Classroom Civility is Another of Our Instructor Responsibilities. College Teaching: Vol. 49, No. 4, pp. 137-140.

Das “Ubersteuerungskriterium” von 19×99 dB(A), das von seinem Begrunder Gerd Jansen als gesicherte Erkenntnis der Larmwirkungsforschung bezeichnet wird und vielfach zur Festlegung von “Larmbelastungsgebieten” fur den wachen Menschen herangezogen wurde, ist durch eine fehlerhafte physikalisch-mathematische Datenaufbereitung entstanden. Das ist das Ergebnis einer umfangreichen Revision der Originalliteratur. Basierend auf den von Jansen 1967 durchgefuhrten Laboruntersuchungen, ergibt sich bei physikalisch korrektem Vorgehen eine “vegetative Ubersteuerung” fur breitbandige Gerausche ab Schallpegeln von Leq, 30s=88–89 dB(A) und nicht ab Pegeln von 99 dB(A). Bis zum Vorliegen uberlegenerer wissenschaftlicher Erkenntnisse sollte daher fur den wachen Menschen diese korrigierte “Ubersteuerungsgrenze” zur Pravention akuter Fehlregulationen herangezogen werden. Jede Veranderung der “Ubersteuerungsgrenze” wirkt sich auch auf die Anzahl der bisher 19 zulassigen Uberschreitungen aus. Die im Rahmen der Revision durchgefuhrten neuen Berechnungen fuhren zwar formal auf eine Anzahl von 36 zulassigen Ubersteuerungen und damit auf ein korrigiertes “Ubersteuerungskriterium” von “36×88 dB(A)”, das Ergebnis bleibt aber letztendlich unbefriedigend, weil der methodische Ansatz der von Jansen zur Bestimmung der zulassigen Ubersteuerungen gewahlt wurde, keinen ausreichenden praventivmedizinischen Schutz bietet. Die Anwendung des Ubersteuerungskriteriums von “19×99 dB(A)” fuhrt zu einer erheblichen Unterschatzung der Gesundheitsgefahren durch Fluglarm und ist zur praventivmedizinischen Festlegung von Larmbelastungsgebieten nicht geeignet.

Using low temperature single molecule spectroscopy on rigid-rod conjugated polymers we are able to identify homogeneously broadened, strongly polarized emission from individual chromophore units on a single chain. Gated fluorescence spectroscopy allows real time imaging of intramolecular energy transfer as the chain behaves as a series of weakly interacting chromophores. Energy transfer is controlled by the chromophoric spectral linewidth, which depends on temperature. Linewidths exceeding intramolecular disorder lead to incoherent chromophore coupling and collective fluorescence phenomena.

Single crystals of Ba2(VO)V2O8 have been prepared by solid state reactions of Ba2V2O7, V2O3 and V2O5 in sealed silica tubes. This compound crystallizes with monoclinic symmetry, space group C2 2 -P21, a = 8.1174(9), b = 5.9699(9), c = 9.2903(9) Å , β = 113.94(1)°, Z = 2. V 5+ shows tetrahedral coordination. V 4+ inside 1 ∞ [V (3)O4] chains is characterized by a square pyramidal coordination with a short apical V-O distance of 1.6 Å typically for vanadyl groups. Ba2(VO)V2O8 represents a new structure type and is not isotypic to Sr2(VO)V2O8.

Single crystals of Bi1.9Cu4V4O16 have been prepared by quenching of CO2-LASER heated samples. They were investigated by X-ray techniques. The compound crystallizes with tetragonal symmetry, space group C5 4h-I4 /m , a = 9.945(2) Å , c = 2.915(3) Å, Z = 1, and is isotypic to the mineral Hollandite. Bi1.9Cu4V4O16 is the first Hollandite with a statistical distribution of vanadium and copper in the network of octahedra. Calculations of the Coulomb terms of lattice energy led to a distance of bismuth to the lone pair of 1.07 Å. Considering the lone pair as part of the coordination sphere of Bi3+ a square pyramidal polyhedron is obtained.

Single crystals of CuCdVO4 have been prepared by CO2-LASER techniques. X -ray investigations of the black single crystals led to orthorhombic symmetry, space group D2h 17-Cmcm , a = 5.921(1), b = 9.065(4), c = 6.633(2) Å, Z = 4. CuCdVO4 represents the first example of a quaternary oxide containing cadmium and copper(I). Compared to AgCdVO4, CuCdVO4 shows a different linkage of the VO4 and CuO4 tetrahedra, explaining the missing isotypy of these com pounds.

Single crystals of Sr2(VO)V2O8 have been prepared by quenching melts from higher temperatures. This compound represents a new structure type and crystallizes with monoclinic symmetry, space group C6 2h–I2/a, a = 6.929, b = 16.246, c = 7.260 Å, β = 115.82°, Z = 4. The point positions occupied by V5+ show tetrahedral coordination. The refinement of the V4+ position led to split positions with acentric orientations of V4+ in the octahedral O2- surrounding. It results in a square pyramidal coordination with one short V–O distance typically for vanadyl groups.