Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently... Show moreBackground: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk. Show less
Forslund, T.; Granqvist, P.; IJzendoorn, M.H. van; Sagi-Schwartz, A.; Glaser, D.; Steele, M.; ... ; Duschinsky, R. 2022
Attachment theory and research are drawn upon in many applied settings, including family courts, but misunderstandings are widespread and sometimes result in misapplications. The aim of this... Show moreAttachment theory and research are drawn upon in many applied settings, including family courts, but misunderstandings are widespread and sometimes result in misapplications. The aim of this consensus statement is, therefore, to enhance understanding, counter misinformation, and steer family-court utilisation of attachment theory in a supportive, evidence-based direction, especially with regard to child protection and child custody decision-making. This article is divided into two parts. In the first part, we address problems related to the use of attachment theory and research in family courts, and discuss reasons for these problems. To this end, we examine family court applications of attachment theory in the current context of the best-interest-of-the-child standard, discuss misunderstandings regarding attachment theory, and identify factors that have hindered accurate implementation. In the second part, we provide recommendations for the application of attachment theory and research. To this end, we set out three attachment principles: the child's need for familiar, non-abusive caregivers; the value of continuity of good-enough care; and the benefits of networks of attachment relationships. We also discuss the suitability of assessments of attachment quality and caregiving behaviour to inform family court decision-making. We conclude that assessments of caregiver behaviour should take center stage. Although there is dissensus among us regarding the use of assessments of attachment quality to inform child custody and child-protection decisions, such assessments are currently most suitable for targeting and directing supportive interventions. Finally, we provide directions to guide future interdisciplinary research collaboration. Show less
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million... Show moreA major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology. Show less
Wang, Z.Y.; Virgolin, M.; Balgobind, B.V.; Dijk, I.W.E.M. van; Smith, S.A.; Howell, R.M.; ... ; Alderliesten, T. 2022
Purpose: Our purpose was to validate and compare the performance of 4 organ dose reconstruction approaches for historical radiation treatment planning based on 2-dimensional radiographs.Methods and... Show morePurpose: Our purpose was to validate and compare the performance of 4 organ dose reconstruction approaches for historical radiation treatment planning based on 2-dimensional radiographs.Methods and materials: We considered 10 patients with Wilms tumor with planning computed tomography images for whom we developed typical historic Wilms tumor radiation treatment plans, using anteroposterior and posteroanterior parallel-opposed 6 MV flank fields, normalized to 14.4 Gy. Two plans were created for each patient, with and without corner blocking. Regions of interest (lungs, heart, nipples, liver, spleen, contralateral kidney, and spinal cord) were delineated, and dose-volume metrics including organ mean and minimum dose (Dmean and Dmin) were computed as the reference baseline for comparison. Dosimetry for the 20 plans was then independently reconstructed using 4 different approaches. Three approaches involved surrogate anatomy, among which 2 used demographic-matching criteria for phantom selection/building, and 1 used machine learning. The fourth approach was also machine learning-based, but used no surrogate anatomies. Absolute differences in organ dose-volume metrics between the reconstructed and the reference values were calculated.Results: For Dmean and Dmin (average and minimum point dose) all 4 dose reconstruction approaches performed within 10% of the prescribed dose (≤1.4 Gy). The machine learning-based approaches showed a slight advantage for several of the considered regions of interest. For Dmax (maximum point dose), the absolute differences were much higher, that is, exceeding 14% (2 Gy), with the poorest agreement observed for near-beam and out-of-beam organs for all approaches.Conclusions: The studied approaches give comparable dose reconstruction results, and the choice of approach for cohort dosimetry for late effects studies should still be largely driven by the available resources (data, time, expertise, and funding). Show less
Virgolin, M.; Wang, Z.Y.; Alderliesten, T.; Bosman, P.A.N. 2020
Purpose: Current phantoms used for the dose reconstruction of long-term childhood cancer survivors lack individualization. We design a method to predict highly individualized abdominal three... Show morePurpose: Current phantoms used for the dose reconstruction of long-term childhood cancer survivors lack individualization. We design a method to predict highly individualized abdominal three-dimensional (3-D) phantoms automatically.Approach: We train machine learning (ML) models to map (2-D) patient features to 3-D organat-risk (OAR) metrics upon a database of 60 pediatric abdominal computed tomographies with liver and spleen segmentations. Next, we use the models in an automatic pipeline that outputs a personalized phantom given the patient's features, by assembling 3-D imaging from the database. A step to improve phantom realism (i.e., avoid OAR overlap) is included. We compare five ML algorithms, in terms of predicting OAR left-right (LR), anterior-posterior (AP), inferior-superior (IS) positions, and surface Dice-Sorensen coefficient (sDSC). Furthermore, two existing human-designed phantom construction criteria and two additional control methods are investigated for comparison.Results: Different ML algorithms result in similar test mean absolute errors: similar to 8 mm for liver LR, IS, and spleen AP, IS; similar to 5 mm for liver AP and spleen LR; similar to 80% for abdomen sDSC; and similar to 60% to 65% for liver and spleen sDSC. One ML algorithm (GP-GOMEA) significantly performs the best for 6/9 metrics. The control methods and the human-designed criteria in particular perform generally worse, sometimes substantially (+5-mm error for spleen IS, -10% sDSC for liver). The automatic step to improve realism generally results in limited metric accuracy loss, but fails in one case (out of 60).Conclusion: Our ML-based pipeline leads to phantoms that are significantly and substantially more individualized than currently used human-designed criteria. (C) 2020 Society of Photo Optical Instrumentation Engineers (SPIE) Show less
Wang, Z.Y.; Virgolin, M.; Bosman, P.A.N.; Crama, K.F.; Balgobind, B.V.; Bel, A.; Alderliesten, T. 2020
Performing large-scale three-dimensional radiation dose reconstruction for patients requires a large amount of manual work. We present an image processing-based pipeline to automatically... Show morePerforming large-scale three-dimensional radiation dose reconstruction for patients requires a large amount of manual work. We present an image processing-based pipeline to automatically reconstruct radiation dose. The pipeline was designed for childhood cancer survivors that received abdominal radiotherapy with anterior-to-posterior and posterior-to-anterior field set-up. First, anatomical landmarks are automatically identified on two-dimensional radiographs. Second, these landmarks are used to derive parameters to emulate the geometry of the plan on a surrogate computed tomography. Finally, the plan is emulated and used as input for dose calculation. For qualitative evaluation, 100 cases of automatic and manual plan emulations were assessed by two experienced radiation dosimetrists in a blinded comparison. The two radiation dosimetrists approved 100%/100% and 92%/91% of the automatic/manual plan emulations, respectively. Similar approval rates of 100% and 94% hold when the automatic pipeline is applied on another 50 cases. Further, quantitative comparisons resulted in on average <5 mm difference in plan isocenter/borders, and <0.9 Gy in organ mean dose (prescribed dose: 14.4 Gy) calculated from the automatic and manual plan emulations. No statistically significant difference in terms of dose reconstruction accuracy was found for most organs at risk. Ultimately, our automatic pipeline results are of sufficient quality to enable effortless scaling of dose reconstruction data generation. (C) 2020 Society of Photo-Optical Instrumentation Engineers (SPIE) Show less
Umetsu, M.; Hollander, J.G.; Matysik, J.; Wang, Z.Y.; Adschiri, T.; Nozawa, T.; Groot, H.J.M. de 2004
(3(1)R)-bacteriochlorophyll (BChl) c solid aggregates with an absorbance around 740 nm were formed from BChl c dimers, and 2-D homonuclear C-13-C-13 radio frequency-driven dipolar recoupling as... Show more(3(1)R)-bacteriochlorophyll (BChl) c solid aggregates with an absorbance around 740 nm were formed from BChl c dimers, and 2-D homonuclear C-13-C-13 radio frequency-driven dipolar recoupling as well as proton-driven spin diffusion dipolar correlation NMR spectra have been collected in ultrahigh magnetic field. Doubling of signals is observed for most carbons in the BChl c macrocycle, leading to two correlation networks. In this way, two major fractions denoted types A and B are identified. Some of the ring carbons show multiple resonances, revealing additional slight differences in microstructural environment. 2-D heteronuclear H-1-C-13 correlation data have been recorded using the frequency- and phase-switched Lee-Goldburg technique to assign the H-1 response. N-15 chemical shifts are assigned from 2-D heteronuclear N-15-C-13 correlation experiments using spectrally induced filtering in combination with cross polarization. Also the nitrogen atoms in the pyrrole rings I, II, and IV (N-I, N-II, and N-IV, respectively) show two sets of resonances, each of which is connected to a single C-13 correlation network A or B. The C-13 chemical shifts are compared with the signals from antiparallel dimers in solution and with the response from chlorosomes previously reported. The data clearly show that the stacking in CH2Cl2-treated aggregates is different from the stacking in the chlorosomes and hexane-treated aggregates. Some degree of similarity with the antiparallel dimer form in solution transpires, in particular for the type A species. It is proposed that the CH2Cl2 precipitate represents a structural intermediate between the antiparallel dimer and the parallel stack as found in the chlorosome. Show less
