Seedling root system adaptation to water availability during maize domestication and global expansion

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Genomic prediction within and across maize landrace derived populations using haplotypes

Genomic prediction (GP) using haplotypes is considered advantageous compared to GP solely reliant on single nucleotide polymorphisms (SNPs), owing to haplotypes' enhanced ability to capture ancestral information and their higher linkage disequilibrium with quantitative trait loci (QTL). Many empirical studies supported the advantages of haplotype-based GP over SNP-based approaches. Nevertheless, the performance of haplotype-based GP can vary significantly depending on multiple factors, including the traits being studied, the genetic structure of the population under investigation, and the particular method employed for haplotype construction. In this study, we compared haplotype and SNP based prediction accuracies in four populations derived from European maize landraces. Populations comprised either doubled haploid lines (DH) derived directly from landraces, or gamete capture lines (GC) derived from crosses of the landraces with an inbred line. For two different landraces, both types of populations were generated, genotyped with 600k SNPs and phenotyped as lines per se for five traits. Our study explores three prediction scenarios: (i) within each of the four populations, (ii) across DH and GC populations from the same landrace, and (iii) across landraces using either DH or GC populations. Three haplotype construction methods were evaluated: 1. fixed-window blocks (FixedHB), 2. LD-based blocks (HaploView), and 3. IBD-based blocks (HaploBlocker). In within population predictions, FixedHB and HaploView methods performed as well as or slightly better than SNPs for all traits. HaploBlocker improved accuracy for certain traits but exhibited inferior performance for others. In prediction across populations, the parameter setting from HaploBlocker which controls the construction of shared haplotypes between populations played a crucial role for obtaining optimal results. When predicting across landraces, accuracies were low for both, SNP and haplotype approaches, but for specific traits substantial improvement was observed with HaploBlocker. This study provides recommendations for optimal haplotype construction and identifies relevant parameters for constructing haplotypes in the context of genomic prediction.

Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks

The importance of accurate genomic prediction of phenotypes in plant breeding is undeniable, as higher prediction accuracy can increase selection responses. In this regard, epistasis models have shown to be capable of increasing the prediction accuracy while their high computational load is challenging. In this study, we investigated the predictive ability obtained in additive and epistasis models when utilizing haplotype blocks versus pruned sets of SNPs by including phenotypic information from the last growing season. This was done by considering a single biological trait in two growing seasons (2017 and 2018) as separate traits in a multi-trait model. Thus, bivariate variants of the Genomic Best Linear Unbiased Prediction (GBLUP) as an additive model, Epistatic Random Regression BLUP (ERRBLUP) and selective Epistatic Random Regression BLUP (sERRBLUP) as epistasis models were compared with respect to their prediction accuracies for the second year. The prediction accuracies of bivariate GBLUP, ERRBLUP and sERRBLUP were assessed with eight phenotypic traits for 471/402 doubled haploid lines in the European maize landrace Kemater Landmais Gelb/Petkuser Ferdinand Rot. The results indicate that the obtained prediction accuracies are similar when utilizing a pruned set of SNPs or haplotype blocks, while utilizing haplotype blocks reduces the computational load significantly compared to the pruned sets of SNPs. The number of interactions considered in the model was reduced from 323.5/456.4 million for the pruned SNP panel to 4.4/5.5 million in the haplotype block dataset for Kemater and Petkuser landraces, respectively. Since the computational load scales linearly with the number of parameters in the model, this leads to a reduction in computational time of 98.9% from 13.5 hours for the pruned set of markers to 9 minutes for the haplotype block dataset. We further investigated the impact of genomic correlation, phenotypic correlation and trait heritability as factors affecting the bivariate models' prediction accuracy, identifying the genomic correlation between years as the most influential one. As computational load is substantially reduced, while the accuracy of genomic prediction is unchanged, the here proposed framework to use haplotype blocks in sERRBLUP provided a solution for the practical implementation of sERRBLUP in real breeding programs. Furthermore, our results indicate that sERRBLUP is not only suitable for prediction across different locations, but also for the prediction across growing seasons.

Incidence and clinical outcome of primary carcinomas of the major salivary glands: 10-year data from a population-based state cancer registry in Germany

PURPOSE

The aim of this project was to provide an overview of the epidemiology of primary salivary gland carcinomas (SGC) in terms of incidence, distribution of clinicopathological features and survival in one of the largest cancer registries in Europe.

METHODS

Data were collected from patients with SGC of the major salivary glands registered in the population-based state cancer registry (Landeskrebsregister LKR) in North Rhine-Westphalia (NRW), Germany from 01/01/2009 to 12/31/2018. Age standardization of incidence was performed and relative survival estimates were computed by sex, histological group, age group and T-, N-, and M-stage.

RESULTS

A total of 1680 patients were included in this analysis. The most frequent tumor localization was the parotid gland (78%). Adenocarcinoma (not otherwise specified) was the most common tumor entity (18.5%). Most tumors were found in stages T1-T3 (29% T1; 29% T2; 28% T3). The age-standardized incidence rate (ASR) for SGC was 0.65/100,000 and remained stable during the observation period. There was an age-dependent incidence increasing especially from the age 70 years and onwards. The overall 5-year relative survival (RS) for all patients with SGC was 69.2%. RS was 80-95.6% for T1-2 stage tumors, 60.3% for T3, 47.3% for T4 stage, 87.4% for N0 and 51.2% for N1-2, 74.4% for M0 and 44.9% for M1.

CONCLUSION

Age-standardized incidence for SGC has been stable for the observed 10-year period. Smaller tumors and those without lymph node or distant metastases had a better RS than more advanced tumors.

Quantifying changes in ambient NOx, O3 and PM10 concentrations in Austria during the COVID-19 related lockdown in spring 2020

During spring 2020, unprecedented changes in local and regional emissions have occurred around the globe due to governmental restrictions associated with COVID-19. Many European countries including Austria issued partial curfews or stay-at-home order policies, which have impacted ambient air quality through reductions in non-essential transportation and energy consumption of industrial sites and work places. Here, we analyse the effect of these measures on ambient concentrations of nitrogen oxides (NO_x), ozone (O₃) and particulate matter (PM₁₀) during the first nationwide lockdown in Austria (16.03.2020 to 14.04.2020). To ensure a robust analysis, the Austrian domain is divided into four individual subsectors contingent on regional climate. For air quality analysis a novel method is applied for filtering days with comparable weather conditions during the 2020 lockdown and spring 2017 to 2019. In general, our analysis shows decreasing pollutant concentrations, although in magnitude dependent on pollutant and regional subdomain. Largest reductions are found for NO_x reaching up to −68% at traffic sites reflecting the substantial decrease in non-essential transport. Changes in the O₃ concentrations at background sites show a rather weak response to NO_x declines varying between roughly −18 to +8% for both the median and the upper tail of the distribution. Occasional site level increases in O₃ concentrations can be attributed to comparably weak titration during night-time. PM₁₀ concentrations show the smallest response among air pollutants, attributable to manifold precursor sources not affected by the lockdown measures. However, our analysis indicates also a shift of PM₁₀ distributions at traffic sites closer to distributions observed at background sites.

A-04 Acute Sports-Related Concussion Associations Between Cognitive Symptoms, Memory Performance, and Default Mode Network Hub Connectivity

Purpose: Disruptions in cognitive performance are commonly reported after a sports-related concussion (SRC) and may be related to brain network changes, particularly within the default mode network (DMN). Since well-connected brain regions across networks (hubs) play an important role in network organization, we hypothesize that DMN hubs will be disrupted after a SRC and associated with cognitive symptoms and cognitive performance. Methods: We collected resting-state fMRI, symptoms, and cognitive performance data from 44 student-athletes at baseline, after a SRC, and at recovery. Participation coefficient defined hubs for each athlete. We compared changes in functional connectivity between hubs and non-hubs within the DMN and between DMN hubs and non-hubs in the remaining networks. We used linear regression to examine the relationship between functional connectivity, cognitive symptoms, and cognitive performance while controlling for concussion history. Results: Functional connectivity between hubs and non-hubs within the DMN increased from baseline to post-injury and decreased from post-injury to recovery, but not to baseline connectivity levels. Post-injury functional connectivity was related to increased cognitive symptoms and decreased visual memory performance. Functional connectivity decreased between hubs in the DMN and non-hubs in the cingulo-opercular, salience, somatomotor, and visual networks from baseline to post-injury. Cognitive symptoms and visual memory performance were related to functional connectivity between DMN hubs and visual network non-hubs. Conclusions: Self-reported cognitive symptoms and cognitive performance were associated with changes in DMN hub connectivity. This relationship may suggest a decrease in efficiency between brain networks after a SRC and may provide insight into post-injury compensation during task performance.

Is Mini Beam Ready for Human Trials? Results of Randomized Study of Treating De-Novo Brain Tumors in Canines Using Linear Accelerator Generated Mini Beams

The main challenge in treating malignant brain neoplasms lies in eradicating the tumor while minimizing treatment-related damage. Conventional radiation treatments are associated with considerable side effects. Synchrotron generated micro-beam radiation (SMBRT) has shown to preserve brain architecture while killing tumor cells, however physical characteristics and limited facility access restrict its use. We have created a new clinical device which produces mini beams on a linear accelerator, to provide a new type of treatment called mini-beam radiation therapy (MBRT). The objective of this study is to compare the treatment outcomes of linear accelerator based MBRT versus standard radiation treatment (SRT), to evaluate the tumor response and the treatment-related changes in the normal brain with respect to each treatment type. Pet dogs with de-novo brain tumors were accrued for treatment. Dogs were randomized between standard fractionated stereotactic (9 Gy in 3 fractions) radiation treatment vs. a single fraction of MBRT (26 Gy mean dose). Dogs were monitored after treatment for clinical assessment and imaging. When the dogs were euthanized, a veterinary pathologist assessed the radiation changes and tumor response. We accrued 16 dogs, 8 dogs in each treatment arm. In the MBRT arm, 71% dogs achieved complete pathological remission. The radiation-related changes were all confined to the target region. Structural damage was not observed in the beam path outside of the target region. In contrast, none of the dogs in control group achieved remission and the treatment related damage was more extensive. Therapeutic superiority was observed with MBRT, including both tumor control and the normal structural preservation. The MBRT findings are suggestive of an immune related mechanism which is absent in standard treatment. These findings together with the widespread availability of clinical linear accelerators make MBRT a promising research topic to explore further treatment and clinical trial opportunities.

Genetic diversity of European maize landraces: Dataset on the molecular and phenotypic variation of derived doubled-haploid populations

Genetic variation is the basis of selection, evolution and breeding. Maize landraces represent a rich source of allelic diversity, but their efficient utilization in breeding and research has been hampered by their heterogeneous and heterozygous nature and insufficient information about most accessions. While molecular inventories of germplasm repositories are growing steadily, linking these data to meaningful phenotypes for quantitative traits is challenging.

Here, we present comprehensive molecular and phenotypic data for ∼1,000 doubled-haploid (DH) lines derived from three pre-selected European maize landraces. Due to their full homozygosity, the DH lines can be multiplied ad libitum and represent a powerful biological resource available to the community. The DH lines allow high-precision phenotyping in repeated experiments and reveal the full additive genetic variance of the population. The DH lines were evaluated for nine agronomically important, quantitative traits in multi-environment field trials comprising seven locations and two years. The DH populations revealed high genetic variance and high heritability for the analysed traits. The DH lines were genotyped with 600k SNP markers. After stringent quality filtering 500k markers remained for further analyses.

This is the largest resource of landrace derived DH material in maize, unprecedented in its structure and dimension. The presented data are ideal for linking molecular variation to meaningful phenotypes. They can be used for genome-wide association studies, genomic prediction, and population genetic analyses as well as for developing and testing statistical methods. All plant material is available to the community for conducting additional experiments, extending the panel of traits and environments, and for testing the landrace-derived lines in combination with other genetic material.

Expression of Mucins in Different Entities of Salivary Gland Cancer: Highest Expression of Mucin-1 in Salivary Duct Carcinoma : Mucin-1 - highest expression in Salivary Duct Carcinoma

Therapeutic options for advanced salivary gland cancer (SGC) are rare. Therefore, it was the aim of this study to investigate the extent and intensity of Mucin-1 (MUC1), Mucin-16 (MUC16), and Mucin-5AC (MUC5AC) as potential molecular targets using immunohistochemistry. The medical records of all patients who underwent primary surgery for salivary gland cancer with curative intent in a tertiary referral center between 1990 and 2018 were reviewed. Immunohistochemical staining for MUC1, MUC16, and MUC5AC was performed for all patients with sufficient formalin-fixed paraffin-embedded material, and a semi-quantitative combined score derived from the H-score for the cytoplasmatic, the membranous and the apical membrane was built for the most common entities of SGC. 107 patients with malignancies of the parotid (89.7%) and the submandibular gland (10.3%) were included. The most common entities were mucoepidermoid carcinoma (MuEp; n = 23), adenoid cystic carcinoma (AdCy; n = 22), and salivary duct carcinoma (SaDu; n = 21). The highest mean MUC1 combined score was found in SaDu with 223.6 (±91.7). The highest mean MUC16 combined score was found in MuEp with 177.0 (±110.0). The mean MUC5AC score was low across all entities. A higher MUC1 combined score was significantly associated with male gender (p = 0.03), lymph node metastasis (p < 0.01), lymphovascular invasion (p = 0.045), and extracapsular extension (p = 0.03). SaDu patients with MUC16 expression showed a significantly worse 5-year progression-free survival than those without MUC16 expression (p = 0.02). This is the first study to give a comprehensive overview of the expression of MUC1, MUC16, and MUC5AC in SGC. Since advanced SGCs lack therapeutic options in many cases, these results warrant in vitro research on therapeutic targets against MUC1 in SaDu cell lines and xenograft models.

[Project report on fostering scientific competencies in pain medicine in the context of student education]

AIM

The training of scientific skills and competencies is an essential part of academic medical studies. As part of the MaReCuM model study program at Heidelberg University's Mannheim Medical School, a fifth-year rotation on scientific skills in the field of pain medicine was implemented. This paper describes this competence-oriented rotation as well as the investigation of the educational effect.

METHOD

A total of 114 fifth-year medical students participated in the survey (response rate: 83%). The control group completed the fifth year prior to the implementation of the rotation. The experimental group was required to participate in the rotation and the real healthcare research study "Case management program: low back pain". A survey of both groups was conducted on the first day of the rotation and at the end of the module.

RESULTS

The innovative and competency-based learning unit was successfully implemented as part of the MaReCuM model study program and carried out with partners in general practice as well as the Mannheim Institute of Public Health. The participating students accepted the rotation well. There was no measurable effect on the subjective learning success of the rotation in the evaluation.

DISCUSSION

To the authors' knowledge, this educational approach has never been tested before in a German study program. The presented rotation offers an additional option for the training of scientific competencies as part of medical studies. The missing of a measurable effect could be due to the extensive experience of the medical students as well as the limitations on participation in a real healthcare study. An additional learning opportunity could be created by connecting the preexisting lectures to a longitudinal module on scholarly competencies. The implementation of the program also offers a unique opportunity for educational research on the acquisition of scientific competencies in medical students.

Global perspective of familial hypercholesterolaemia: a cross-sectional study from the EAS Familial Hypercholesterolaemia Studies Collaboration (FHSC)

BACKGROUND

The European Atherosclerosis Society Familial Hypercholesterolaemia Studies Collaboration (FHSC) global registry provides a platform for the global surveillance of familial hypercholesterolaemia through harmonisation and pooling of multinational data. In this study, we aimed to characterise the adult population with heterozygous familial hypercholesterolaemia and described how it is detected and managed globally.

METHODS

Using FHSC global registry data, we did a cross-sectional assessment of adults (aged 18 years or older) with a clinical or genetic diagnosis of probable or definite heterozygous familial hypercholesterolaemia at the time they were entered into the registries. Data were assessed overall and by WHO regions, sex, and index versus non-index cases.

FINDINGS

Of the 61 612 individuals in the registry, 42 167 adults (21 999 [53·6%] women) from 56 countries were included in the study. Of these, 31 798 (75·4%) were diagnosed with the Dutch Lipid Clinic Network criteria, and 35 490 (84·2%) were from the WHO region of Europe. Median age of participants at entry in the registry was 46·2 years (IQR 34·3-58·0); median age at diagnosis of familial hypercholesterolaemia was 44·4 years (32·5-56·5), with 40·2% of participants younger than 40 years when diagnosed. Prevalence of cardiovascular risk factors increased progressively with age and varied by WHO region. Prevalence of coronary disease was 17·4% (2·1% for stroke and 5·2% for peripheral artery disease), increasing with concentrations of untreated LDL cholesterol, and was about two times lower in women than in men. Among patients receiving lipid-lowering medications, 16 803 (81·1%) were receiving statins and 3691 (21·2%) were on combination therapy, with greater use of more potent lipid-lowering medication in men than in women. Median LDL cholesterol was 5·43 mmol/L (IQR 4·32-6·72) among patients not taking lipid-lowering medications and 4·23 mmol/L (3·20-5·66) among those taking them. Among patients taking lipid-lowering medications, 2·7% had LDL cholesterol lower than 1·8 mmol/L; the use of combination therapy, particularly with three drugs and with proprotein convertase subtilisin-kexin type 9 inhibitors, was associated with a higher proportion and greater odds of having LDL cholesterol lower than 1·8 mmol/L. Compared with index cases, patients who were non-index cases were younger, with lower LDL cholesterol and lower prevalence of cardiovascular risk factors and cardiovascular diseases (all p<0·001).

INTERPRETATION

Familial hypercholesterolaemia is diagnosed late. Guideline-recommended LDL cholesterol concentrations are infrequently achieved with single-drug therapy. Cardiovascular risk factors and presence of coronary disease were lower among non-index cases, who were diagnosed earlier. Earlier detection and greater use of combination therapies are required to reduce the global burden of familial hypercholesterolaemia.

FUNDING

Pfizer, Amgen, Merck Sharp & Dohme, Sanofi-Aventis, Daiichi Sankyo, and Regeneron.

Measurements of Argon-39 from locations near historic underground nuclear explosions

Measurement of radioactive gas seepage from an underground nuclear explosion is one of the primary methods to confirm whether an event was nuclear in nature. Radioactive noble gas indicators that are commonly targeted by such measurements (e.g. ¹³³Xe, ³⁷Ar) have half-lives of 35 days or less. Argon-39, an activation product similar to ³⁷Ar, is produced by the interaction between neutrons and potassium in the surrounding geology and has a half-life of 269 years. Measurements taken at three sites near three historic underground nuclear test locations at the Nevada National Security Site have all shown highly elevated levels of ³⁹Ar in soil gas decades after the test events. Elevated levels of ³⁹Ar were also detected in atmospheric air collected near two of these sites, and outside the entrance of the one tunnel site. These measurements demonstrate that ³⁹Ar has the potential to be a long-term signature of an underground nuclear event which can be reliably detected at the surface or in the shallow subsurface. This radionuclide detection of an underground nuclear event decades after the event takes place is in contrast to the commonly held assumption that detecting underground nuclear events via radionuclides at the surface needs to be done in a matter of months. Depending upon what further studies show about the robustness of this signature in a variety of geological settings, it may in fact be easy to detect underground nuclear events at the surface for a very long time post-detonation.

Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments

The accuracy of genomic prediction of phenotypes can be increased by including the top-ranked pairwise SNP interactions into the prediction model. We compared the predictive ability of various prediction models for a maize dataset derived from 910 doubled haploid lines from two European landraces (Kemater Landmais Gelb and Petkuser Ferdinand Rot), which were tested at six locations in Germany and Spain. The compared models were Genomic Best Linear Unbiased Prediction (GBLUP) as an additive model, Epistatic Random Regression BLUP (ERRBLUP) accounting for all pairwise SNP interactions, and selective Epistatic Random Regression BLUP (sERRBLUP) accounting for a selected subset of pairwise SNP interactions. These models have been compared in both univariate and bivariate statistical settings for predictions within and across environments. Our results indicate that modeling all pairwise SNP interactions into the univariate/bivariate model (ERRBLUP) is not superior in predictive ability to the respective additive model (GBLUP). However, incorporating only a selected subset of interactions with the highest effect variances in univariate/bivariate sERRBLUP can increase predictive ability significantly compared to the univariate/bivariate GBLUP. Overall, bivariate models consistently outperform univariate models in predictive ability. Across all studied traits, locations and landraces, the increase in prediction accuracy from univariate GBLUP to univariate sERRBLUP ranged from 5.9 to 112.4 percent, with an average increase of 47 percent. For bivariate models, the change ranged from -0.3 to + 27.9 percent comparing the bivariate sERRBLUP to the bivariate GBLUP, with an average increase of 11 percent. This considerable increase in predictive ability achieved by sERRBLUP may be of interest for "sparse testing" approaches in which only a subset of the lines/hybrids of interest is observed at each location.

Calibration and validation of predicted genomic breeding values in an advanced cycle maize population

Model training on data from all selection cycles yielded the highest prediction accuracy by attenuating specific effects of individual cycles. Expected reliability was a robust predictor of accuracies obtained with different calibration sets. The transition from phenotypic to genome-based selection requires a profound understanding of factors that determine genomic prediction accuracy. We analysed experimental data from a commercial maize breeding programme to investigate if genomic measures can assist in identifying optimal calibration sets for model training. The data set consisted of six contiguous selection cycles comprising testcrosses of 5968 doubled haploid lines genotyped with a minimum of 12,000 SNP markers. We evaluated genomic prediction accuracies in two independent prediction sets in combination with calibration sets differing in sample size and genomic measures (effective sample size, average maximum kinship, expected reliability, number of common polymorphic SNPs and linkage phase similarity). Our results indicate that across selection cycles prediction accuracies were as high as 0.57 for grain dry matter yield and 0.76 for grain dry matter content. Including data from all selection cycles in model training yielded the best results because interactions between calibration and prediction sets as well as the effects of different testers and specific years were attenuated. Among genomic measures, the expected reliability of genomic breeding values was the best predictor of empirical accuracies obtained with different calibration sets. For grain yield, a large difference between expected and empirical reliability was observed in one prediction set. We propose to use this difference as guidance for determining the weight phenotypic data of a given selection cycle should receive in model retraining and for selection when both genomic breeding values and phenotypes are available.

Generalized gametic relationships for flexible analyses of parent-of-origin effects

A class of epigenetic inheritance patterns known as genomic imprinting allows alleles to influence the phenotype in a parent-of-origin-specific manner. Various pedigree-based parent-of-origin analyses of quantitative traits have attempted to determine the share of genetic variance that is attributable to imprinted loci. In general, these methods require four random gametic effects per pedigree member to account for all possible types of imprinting in a mixed model. As a result, the system of equations may become excessively large to solve using all available data. If only the offspring have records, which is frequently the case for complex pedigrees, only two averaged gametic effects (transmitting abilities) per parent are required (reduced model). However, the parents may have records in some cases. Therefore, in this study, we explain how employing single gametic effects solely for informative individuals (i.e., phenotyped individuals), and only average gametic effects otherwise, significantly reduces the complexity compared with classical gametic models. A generalized gametic relationship matrix is the covariance of this mixture of effects. The matrix can also make the reduced model much more flexible by including observations from parents. Worked examples are present to illustrate the theory and a realistic body mass data set in mice is used to demonstrate its utility. We show how to set up the inverse of the generalized gametic relationship matrix directly from a pedigree. An open-source program is used to implement the rules. The application of the same principles to phased marker data leads to a genomic version of the generalized gametic relationships.

Exploiting genetic diversity in two European maize landraces for improving Gibberella ear rot resistance using genomic tools

KEY MESSAGE

High genetic variation in two European maize landraces can be harnessed to improve Gibberella ear rot resistance by integrated genomic tools. Fusarium graminearum (Fg) causes Gibberella ear rot (GER) in maize leading to yield reduction and contamination of grains with several mycotoxins. This study aimed to elucidate the molecular basis of GER resistance among 500 doubled haploid lines derived from two European maize landraces, "Kemater Landmais Gelb" (KE) and "Petkuser Ferdinand Rot" (PE). The two landraces were analyzed individually using genome-wide association studies and genomic selection (GS). The lines were genotyped with a 600-k maize array and phenotyped for GER severity, days to silking, plant height, and seed-set in four environments using artificial infection with a highly aggressive Fg isolate. High genotypic variances and broad-sense heritabilities were found for all traits. Genotype-environment interaction was important throughout. The phenotypic (r) and genotypic ([Formula: see text]) correlations between GER severity and three agronomic traits were low (r =  - 0.27 to 0.20; [Formula: see text]=  - 0.32 to 0.22). For GER severity, eight QTLs were detected in KE jointly explaining 34% of the genetic variance. In PE, no significant QTLs for GER severity were detected. No common QTLs were found between GER severity and the three agronomic traits. The mean prediction accuracies ([Formula: see text]) of weighted GS (wRR-BLUP) were higher than [Formula: see text] of marker-assisted selection (MAS) and unweighted GS (RR-BLUP) for GER severity. Using KE as the training set and PE as the validation set resulted in very low [Formula: see text] that could be improved by using fixed marker effects in the GS model.

Metastases of Cutaneous Squamous Cell Carcinoma Seem to be the Most Frequent Malignancies in the Parotid Gland: A Hospital-Based Study From a Salivary Gland Center

Malignant parotid tumors account for approximately 20% of all parotid lesions. In addition to the various primary parotid lesions there are secondary parotid malignancies, such as metastases or lymphomas. Data on histopathological distribution of all malignancies-including secondary parotid lesions-is limited. Recent evidence indicated a rising surgical incidence of secondary parotid malignancies. This study aims to review the distribution of malignancies in parotid resections from a salivary gland center. A retrospective review of prospectively collected data for all patients who had received parotidectomy between 2014 and 2019 was performed. Histopathological distribution was displayed separately for all parotid malignancies and for primary parotid malignancies. Further, patients` characteristics were compared between benign and malignant parotid lesions and between the two most common malignant parotid lesions. Out of 777 patients, 614 (78.9%) patients had a benign and 164 (21.1%) patients had a malignant parotid lesion. The most common parotid malignancy was metastatic cutaneous squamous cell carcinoma (cSCC) accounting for 35.4% of all parotid malignancies. 71.5% of all malignant lesions were secondary malignancies. Patients with metastatic cSCC were significantly older (p < 0.001) and significantly more likely to be male (p < 0.001) than patients with primary parotid malignancies. No significant difference was found when the lesion size of metastatic cSCC was compared to primary parotid malignancies (p = 0.216). The present study shows the high prevalence of secondary parotid malignancies in patients who had received parotidectomy. Furthermore, it confirms a rising surgical incidence of metastatic cSCC to the parotid gland in a series from a salivary gland center. At this time, parotid surgery for malignant lesions is more likely to be performed for metastases than for primary parotid malignancies.

Intramuscular oxytocin versus Syntometrine® versus carbetocin for prevention of primary postpartum haemorrhage after vaginal birth: a randomised double-blinded clinical trial of effectiveness, side effects and quality of life

OBJECTIVE

To compare intramuscular oxytocin, Syntometrine^® and carbetocin for prevention of postpartum haemorrhage after vaginal birth.

DESIGN

Randomised double-blinded clinical trial.

SETTING

Six hospitals in England.

POPULATION

A total of 5929 normotensive women having a singleton vaginal birth.

METHODS

Randomisation when birth was imminent.

MAIN OUTCOME MEASURES

Primary: use of additional uterotonic agents. Secondary: weighed blood loss, transfusion, manual removal of placenta, adverse effects, quality of life.

RESULTS

Participants receiving additional uterotonics: 368 (19.5%) oxytocin, 298 (15.6%) Syntometrine and 364 (19.1%) carbetocin. When pairwise comparisons were made: women receiving carbetocin were significantly more likely to receive additional uterotonics than those receiving Syntometrine (odds ratio [OR] 1.28, 95% CI 1.08-1.51, P = 0.004); the difference between carbetocin and oxytocin was non-significant (P = 0.78); Participants receiving Syntometrine were significantly less likely to receive additional uterotonics than those receiving oxytocin (OR 0.75, 95% CI 0.65-0.91, P = 0.002). Non-inferiority between carbetocin and Syntometrine was not shown. Use of Syntometrine reduced non-drug PPH treatments compared with oxytocin (OR 0.64, 95% CI 0.42-0.97) but not carbetocin (P = 0.64). Rates of PPH and blood transfusion were not different. Syntometrine was associated with an increase in maternal adverse effects and reduced ability of the mother to bond with her baby.

CONCLUSIONS

Non-inferiority of carbetocin to Syntometrine was not shown. Carbetocin is not significantly different to oxytocin for use of additional uterotonics. Use of Syntometrine reduced use of additional uterotonics and need for non-drug PPH treatments compared with oxytocin. Increased maternal adverse effects are a disadvantage of Syntometrine.

TWEETABLE ABSTRACT

IM carbetocin does not reduce additional uterotonic use compared with IM Syntometrine or oxytocin.

Burden of Spinal Muscular Atrophy (SMA) on Patients and Caregivers in Canada

BACKGROUND

Spinal muscular atrophy (SMA) is a rare neurodegenerative disease characterized by progressive muscular weakness, which occurs in one in 6,000 to 10,000 live births. The burden of SMA on Canadian patients and caregivers is not known.

OBJECTIVE

To characterize the burden of SMA in Canada as reported by patients and caregivers, including disease and treatment impacts, indirect costs, and caregiver burden.

METHODS

Surveys were distributed by Cure SMA Canada and Muscular Dystrophy Canada to individuals with SMA and their caregivers. The online surveys were anonymous and completed between January 28 and February 21, 2020.

RESULTS

965 patient and 962 caregiver responses met the eligibility criteria. Patients reported SMA subtypes as: type I (25.0%), type II (41.3%), type III (29.3%). Using the EQ-5D, patients were shown to have impaired quality of life with an average health utility index of 0.49 (SD: 0.26). The median expenditure was $4,500 CAD (IQR: $1,587 - $11,000) for assistive devices; $6,800 CAD (IQR: $3,900-$13,000) on health professional services; and $1,200 CAD (IQR: $600 -$3,100) on SMA-related travel and accommodation in the past 12 months. Caregivers reported needing respite care (45.7%), physiotherapy for an injury from a lift/transfer (45.7%), or other health impacts (63.3%). Caregivers reported changes to personal plans, sleep disturbances, and work adjustments, with a mean Caregiver Strain Index score of 7.5 [SD: 3.3].

CONCLUSION

SMA in Canada is associated with a significant burden for patients and their caregivers.

Genomic imprinting analyses identify maternal effects as a cause of phenotypic variability in type 1 diabetes and rheumatoid arthritis

Imprinted genes, giving rise to parent-of-origin effects (POEs), have been hypothesised to affect type 1 diabetes (T1D) and rheumatoid arthritis (RA). However, maternal effects may also play a role. By using a mixed model that is able to simultaneously consider all kinds of POEs, the importance of POEs for the development of T1D and RA was investigated in a variance components analysis. The analysis was based on Swedish population-scale pedigree data. With P = 0.18 (T1D) and P = 0.26 (RA) imprinting variances were not significant. Explaining up to 19.00% (± 2.00%) and 15.00% (± 6.00%) of the phenotypic variance, the maternal environmental variance was significant for T1D (P = 1.60 × 10-24) and for RA (P = 0.02). For the first time, the existence of maternal genetic effects on RA was indicated, contributing up to 16.00% (± 3.00%) of the total variance. Environmental factors such as the social economic index, the number of offspring, birth year as well as their interactions with sex showed large effects.

Fear the reaper: ungulate carcasses may generate an ephemeral landscape of fear for rodents

Animal carcasses provide an ephemeral pulse of nutrients for scavengers that use them. Carcass sites can increase species interactions and/or ephemeral, localized landscapes of fear for prey within the vicinity. Few studies have applied the landscape of fear to carcasses. Here, we use a mass die-off of reindeer caused by lightning in Norway to test whether rodents avoided larger scavengers (e.g. corvids and fox). We used the presence and abundance of faeces as a proxy for carcass use over the course of 2 years and found that rodents showed the strongest avoidance towards changes in raven abundance (β = -0.469, s.e. = 0.231, p-value = 0.0429), but not fox, presumably due to greater predation risk imposed by large droves of raven. Moreover, the emergence of rodent occurrence within the carcass area corresponded well with the disappearance of raven during the second year of the study. We suggest that carcasses have the potential to shape the landscape of fear for prey, but that the overall effects of carcasses on individual fitness and populations of species ultimately depend on the carcass regime, e.g. carcass size, count, and areal extent, frequency and the scavenger guild. We discuss conservation implications and how carcass provisioning and landscapes of fear could be potentially used to manage populations and ecosystems, but that there is a gap in understanding that must first be bridged.

Improving Imputation Quality in BEAGLE for Crop and Livestock Data

Imputation is one of the key steps in the preprocessing and quality control protocol of any genetic study. Most imputation algorithms were originally developed for the use in human genetics and thus are optimized for a high level of genetic diversity. Different versions of BEAGLE were evaluated on genetic datasets of doubled haploids of two European maize landraces, a commercial breeding line and a diversity panel in chicken, respectively, with different levels of genetic diversity and structure which can be taken into account in BEAGLE by parameter tuning. Especially for phasing BEAGLE 5.0 outperformed the newest version (5.1) which in turn also lead to improved imputation. Earlier versions were far more dependent on the adaption of parameters in all our tests. For all versions, the parameter ne (effective population size) had a major effect on the error rate for imputation of ungenotyped markers, reducing error rates by up to 98.5%. Further improvement was obtained by tuning of the parameters affecting the structure of the haplotype cluster that is used to initialize the underlying Hidden Markov Model of BEAGLE. The number of markers with extremely high error rates for the maize datasets were more than halved by the use of a flint reference genome (F7, PE0075 etc.) instead of the commonly used B73. On average, error rates for imputation of ungenotyped markers were reduced by 8.5% by excluding genetically distant individuals from the reference panel for the chicken diversity panel. To optimize imputation accuracy one has to find a balance between representing as much of the genetic diversity as possible while avoiding the introduction of noise by including genetically distant individuals.

European maize landraces made accessible for plant breeding and genome-based studies

KEY MESSAGE

Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.

HaploBlocker: Creation of Subgroup-Specific Haplotype Blocks and Libraries

The concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach ("HaploBlocker") for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium. We define a haplotype block as a sequence of genetic markers that has a predefined minimum frequency in the population, and only haplotypes with a similar sequence of markers are considered to carry that block, effectively screening a dataset for group-wise identity-by-descent. From these haplotype blocks, we construct a haplotype library that represents a large proportion of genetic variability with a limited number of blocks. Our method is implemented in the associated R-package HaploBlocker, and provides flexibility not only to optimize the structure of the obtained haplotype library for subsequent analyses, but also to handle datasets of different marker density and genetic diversity. By using haplotype blocks instead of single nucleotide polymorphisms (SNPs), local epistatic interactions can be naturally modeled, and the reduced number of parameters enables a wide variety of new methods for further genomic analyses such as genomic prediction and the detection of selection signatures. We illustrate our methodology with a dataset comprising 501 doubled haploid lines in a European maize landrace genotyped at 501,124 SNPs. With the suggested approach, we identified 2991 haplotype blocks with an average length of 2685 SNPs that together represent 94% of the dataset.

Exploring the Structure of the Bound Proton with Deeply Virtual Compton Scattering

In the past two decades, deeply virtual Compton scattering of electrons has been successfully used to advance our knowledge of the partonic structure of the free proton and investigate correlations between the transverse position and the longitudinal momentum of quarks inside the nucleon. Meanwhile, the structure of bound nucleons in nuclei has been studied in inclusive deep-inelastic lepton scattering experiments off nuclear targets, showing a significant difference in longitudinal momentum distribution of quarks inside the bound nucleon, known as the EMC effect. In this Letter, we report the first beam spin asymmetry (BSA) measurement of exclusive deeply virtual Compton scattering off a proton bound in ^{4}He. The data used here were accumulated using a 6 GeV longitudinally polarized electron beam incident on a pressurized ^{4}He gaseous target placed within the CLAS spectrometer in Hall-B at the Thomas Jefferson National Accelerator Facility. The azimuthal angle (ϕ) dependence of the BSA was studied in a wide range of virtual photon and scattered proton kinematics. The Q^{2}, x_{B}, and t dependencies of the BSA on the bound proton are compared with those on the free proton. In the whole kinematical region of our measurements, the BSA on the bound proton is smaller by 20% to 40%, indicating possible medium modification of its partonic structure.

Care management intervention to strengthen self-care of multimorbid patients with type 2 diabetes in a German primary care network: A randomized controlled trial

Purpose

This study aimed to assess the effectiveness of a care management intervention in improving self-management behavior in multimorbid patients with type 2 diabetes; care was delivered by medical assistants in the context of a primary care network (PCN) in Germany.

Methods

This study is an 18-month, multi-center, two-armed, open-label, patient-randomized parallel-group superiority trial (ISRCTN 83908315). The intervention group received the care management intervention in addition to the usual care. The control group received usual care only. The primary outcome was the change in self-care behavior at month 9 compared to baseline. The self-care behavior was measured with the German version of the Summary of Diabetes Self-Care Activities Measure (SDSCA-G). A multilevel regression analysis was applied.

Results

We assigned 495 patients to intervention (n = 252) and control (n = 243). At baseline, the mean age was 68 ±11 years, 47.8% of the patients were female and the mean HbA1c was 7.1±1.2%. The primary analysis showed no statistically significant effect, but a positive trend was observed (p = 0.206; 95%-CI = -0.084; 0.384). The descriptive analysis revealed a significantly increased sum score of the SDSCA-G in the intervention group over time (P = 0.012) but not in the control group (p = 0.1973).

Conclusion

The sum score for self-care behavior markedly improved in the intervention group over time. However, the results of our primary analysis showed no statistically significant effect.

Possible reasons are the high baseline performance in our sample and the low intervention fidelity. The implementation of this care management intervention in PCNs has the potential to improve self-care behavior of multimorbid patients with type 2 diabetes.

Testcross performance of doubled haploid lines from European flint maize landraces is promising for broadening the genetic base of elite germplasm

Selected doubled haploid lines averaged similar testcross performance as their original landraces, and the best of them approached the yields of elite inbreds, demonstrating their potential to broaden the narrow genetic diversity of the flint germplasm pool. Maize landraces represent a rich source of genetic diversity that remains largely idle because the high genetic load and performance gap to elite germplasm hamper their use in modern breeding programs. Production of doubled haploid (DH) lines can mitigate problems associated with the use of landraces in pre-breeding. Our objective was to assess in comparison with modern materials the testcross performance (TP) of the best 89 out of 389 DH lines developed from six landraces and evaluated in previous studies for line per se performance (LP). TP with a dent tester was evaluated for the six original landraces, ~ 15 DH lines from each landrace selected for LP, and six elite flint inbreds together with nine commercial hybrids for grain and silage traits. Mean TP of the DH lines rarely differed significantly from TP of their corresponding landrace, which averaged in comparison with the mean TP of the elite flint inbreds ~ 20% lower grain yield and ~ 10% lower dry matter and methane yield. Trait correlations of DH lines closely agreed with the literature; correlation of TP with LP was zero for grain yield, underpinning the need to evaluate TP in addition to LP. For all traits, we observed substantial variation for TP among the DH lines and the best showed similar TP yields as the elite inbreds. Our results demonstrate the high potential of landraces for broadening the narrow genetic base of the flint heterotic pool and the usefulness of the DH technology for exploiting idle genetic resources from gene banks.

Meeting the needs of multimorbid patients with Type 2 diabetes mellitus - A randomized controlled trial to assess the impact of a care management intervention aiming to improve self-care

AIMS

This study explored the impact of a care management intervention aiming to improve self-care behavior in multimorbid individuals with Type 2 diabetes mellitus on health-related quality of life (HRQoL).

METHODS

A patient-level randomized parallel-group superiority trial with 32 primary care practice teams, 11 care managers and 495 patients was conducted. The intervention was delivered as add-on to an already implemented disease management program and embedded in a network of primary care practices. Hierarchical linear modeling was used to analyze impacts of the care management approach on HRQoL.

RESULTS

Small improvements of HRQoL in the intervention arm were found after nine months (r = 0.024; 95%CI = [0.000, 0.047]). However, compared to standard care no significant differences of HRQoL changes were observed (r = 0.022; 95%CI = [-0.011, 0.054]). Subgroup analyses showed effects for female participants favoring the intervention arm (r = 0.059; 95%CI = [0.010, 0.108]). No significant differences between intervention and control arm for several other subgroups were observed, including subgroups defined by comorbidities.

CONCLUSION

Additional care management did not influence HRQoL over and above standard disease management. Improving diabetes patients' self-care behavior in the context of structured disease management programs may be difficult to achieve. Women might benefit from additional care management, but this finding needs to be confirmed in future research.

Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny

Depending on their parental origin, alleles at imprinted loci are fully or partially inactivated through epigenetic mechanisms. Their effects contribute to the broader class of parent-of-origin effects. Standard methodology for mapping imprinted quantitative trait loci in association studies requires phenotypes and parental origin of marker alleles (ordered genotypes) to be simultaneously known for each individual. As such, many phenotypes are known from un-genotyped offspring in ongoing breeding programmes (e.g. meat animals), while their parents have known genotypes but no phenotypes. By theoretical considerations and simulations, we showed that the limitations of standard methodology can be overcome in such situations. This is achieved by first estimating parent-of-origin effects, which then serve as dependent variables in association analyses, in which only imprinted loci give a signal. As a theoretical foundation, the regression of parent-of-origin effects on the number of B-alleles at a biallelic locus — representing the un-ordered genotype — equals the imprinting effect. The applicability to real data was demonstrated for about 1800 genotyped Brown Swiss bulls and their un-genotyped fattening progeny. Thus, this approach unlocks vast data resources in various species for imprinting analyses and offers valuable clues as to what extent imprinted loci contribute to genetic variability.