Afterlive: A performant code for Vlasov-Hybrid simulations

A parallelized implementation of the Vlasov-Hybrid method [Nunn, 1993] is presented. This method is a hybrid between a gridded Eulerian description and Lagrangian meta-particles. Unlike the Particle-in-Cell method [Dawson, 1983] which simply adds up the contribution of meta-particles, this method does a reconstruction of the distribution function $f$ in every time step for each species. This interpolation method combines meta-particles with different weights in such a way that particles with large weight do not drown out particles that represent small contributions to the phase space density. These core properties allow the use of a much larger range of macro factors and can thus represent a much larger dynamic range in phase space density. The reconstructed phase space density $f$ is used to calculate momenta of the distribution function such as the charge density $\rho$. The charge density $\rho$ is also used as input into a spectral solver that calculates the self-consistent electrostatic field which is used to update the particles for the next time-step. Afterlive (A Fourier-based Tool in the Electrostatic limit for the Rapid Low-noise Integration of the Vlasov Equation) is fully parallelized using MPI and writes output using parallel HDF5. The input to the simulation is read from a JSON description that sets the initial particle distributions as well as domain size and discretization constraints. The implementation presented here is intentionally limited to one spatial dimension and resolves one or three dimensions in velocity space. Additional spatial dimensions can be added in a straight forward way, but make runs computationally even more costly.Comment: Accepted for publication in Computer Physics Communication

PICPANTHER: A simple, concise implementation of the relativistic moment implicit Particle-in-Cell method

A three-dimensional, parallelized implementation of the electromagnetic relativistic moment implicit particle-in-cell method in Cartesian geometry (Noguchi et. al., 2007) is presented. Particular care was taken to keep the C++11 codebase simple, concise, and approachable. GMRES is used as a field solver and during the Newton-Krylov iteration of the particle pusher. Drifting Maxwellian problem setups are available while more complex simulations can be implemented easily. Several test runs are described and the code's numerical and computational performance is examined. Weak scaling on the SuperMUC system is discussed and found suitable for large-scale production runs.Comment: 29 pages, 8 figure

Glucocorticoid Receptor Gene Variants and Neonatal Outcome in Very-Low-Birth-Weight Preterm Infants

Background: Induction of lung maturation by prenatal steroid treatment has become the standard of care for pregnant women at risk for preterm birth. In addition to the beneficial effects on lung maturation, prenatal steroids have been shown to reduce the incidence of neonatal death, necrotizing enterocolitis, sepsis, and intraventricular hemorrhage. However, little is known about the role of interindividual differences in corticoid sensitivity arising from polymorphisms in the glucocorticoid receptor (GR) gene. Objectives: To assess the impact of GR polymorphisms N363S (rs56149945), R23K (rs6190), and BclI (rs41423247) on neonatal outcome. Methods: The GR polymorphisms N363S, R23K, and BclI were examined in 10,490 very-low-birth-weight (VLBW) preterm infants from 49 German tertiary level neonatal units (German Neonatal Network, GNN) with respect to neonatal outcome. Results: Infants carrying the BclI genotype were at higher risk to develop bronchopulmonary dysplasia (BPD) (OR 1.12 per BclI allele, 95% CI: 1.02-1.23, p = 0.013) in a logistic regression model adjusted for gestational age, mechanical ventilation, and small for gestational age status. A similar relative risk was seen in the children (89.4%) who received antenatal betamethasone treatment (OR 1.16, 95% CI: 1.05-1.27, p = 0.003), whereas no such effect was detectable in infants without antenatal steroids. N363S and R23K did not show any stable association with neonatal outcome parameters. Conclusion: Except for a slightly higher risk of BPD in carriers of the GRBclI variant, the GR gene polymorphisms BclI, N363S, and R23K did not affect neonatal outcome parameters in this large multicenter cohort of VLBW preterm infants

High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

Individual reports suggest that the central nervous system (CNS) contains multiple immune cell types with diverse roles in tissue homeostasis, immune defense, and neurological diseases. It has been challenging to map leukocytes across the entire brain, and in particular in pathology, where phenotypic changes and influx of blood-derived cells prevent a clear distinction between reactive leukocyte populations. Here, we applied high-dimensional single-cell mass and fluorescence cytometry, in parallel with genetic fate mapping systems, to identify, locate, and characterize multiple distinct immune populations within the mammalian CNS. Using this approach, we revealed that microglia, several subsets of border-associated macrophages and dendritic cells coexist in the CNS at steady state and exhibit disease-specific transformations in the immune microenvironment during aging and in models of Alzheimer's disease and multiple sclerosis. Together, these data and the described framework provide a resource for the study of disease mechanisms, potential biomarkers, and therapeutic targets in CNS disease

Diabetes and gender incongruence: frequent mental health issues but comparable metabolic control – a DPV registry study

ContextThe condition when a person’s gender identity does not match the sex assigned at birth is called gender incongruence (GI). Numbers of GI people seeking medical care increased tremendously over the last decade. Diabetes mellitus is a severe and lifelong disease. GI combined with diabetes may potentiate into a burdensome package for affected people.ObjectiveThe study aimed to characterize people with GI and diabetes from an extensive standardized registry, the Prospective Diabetes Follow-up Registry (DPV), and to identify potential metabolic and psychological burdens.MethodsWe compared demographic and clinical registry data of persons with type 1 or type 2 diabetes and GI to those without GI and used propensity score matching (1:4) with age, diabetes duration and treatment year as covariates.Results75 persons with GI, 49 with type 1 and 26 with type 2 diabetes were identified. HbA1c values were similar in matched persons with type 1 or 2 diabetes and GI compared to those without GI. Lipid profiles showed no difference, neither in type 1 nor in type 2 diabetes. Diastolic blood pressure was higher in the type 1 and GI group than in those without, whereas systolic blood pressure showed comparable results in all groups. Depression and anxiety were significantly higher in GI people (type 1 and 2). Non-suicidal self-injurious behaviour was more common in type 1 and GI, as was suicidality in type 2 with GI.ConclusionMental health issues are frequent in people with diabetes and GI and need to be specially addressed in this population

Clinical and molecular genetic findings in COLQ-mutant congenital myasthenic syndromes

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'Fat mass and obesity associated' gene (FTO): No significant association of variant rs9939609 with weight loss in a lifestyle intervention and lipid metabolism markers in German obese children and adolescents

<p>Abstract</p> <p>Background</p> <p>We have previously identified strong association of six single nucleotide polymorphisms (SNPs) in <it>FTO </it>(fat mass and obesity associated gene) to early onset extreme obesity within the first genome wide association study (GWA) for this phenotype. The aim of this study was to investigate whether the obesity risk allele of one of these SNPs (rs9939609) is associated with weight loss in a lifestyle intervention program. Additionally, we tested for association of rs9939609 alleles with fasting blood parameters indicative of glucose and lipid metabolism.</p> <p>Methods</p> <p>We initially analysed rs9939609 in a case-control study comprising 519 German overweight and obese children and adolescents and 178 normal weight adults. In 207 of the obese individuals who took part in the outpatient obesity intervention program 'Obeldicks' we further analysed whether carrier status of the obesity risk A-allele of rs9939609 has a differential influence on weight loss after the intervention program. Additionally, we investigated in 480 of the overweight and obese patients whether rs9939609 is associated with fasting blood levels of glucose, triglycerides and HDL and LDL-cholesterol. Genotyping was performed using allele specific polymerase chain reaction (ARMS-PCR). For the association study (case-control approach), the Cochran-Armitage trend test was applied. Blood parameters were analysed using commercially available test kits and the log10-transformed blood parameters and changes in BMI-standard deviation scores (BMI-SDS) were analysed by linear regression with sex and age as covariates under an additive mode of inheritance with the rs9939609 A-allele as risk allele.</p> <p>Results</p> <p>We confirmed the association of the risk A-allele of rs9939609 with overweight and early onset obesity (one sided p = 0.036). However, we observed no association of rs9939609 alleles with weight loss or fasting levels of blood glucose, triglycerides and cholesterol.</p> <p>Conclusion</p> <p>We confirmed the rs9939609 A-allele as a risk factor for early onset obesity whereas its impact on weight loss or on serum levels of glucose, triglycerides and cholesterol could not be detected in our samples.</p> <p>Trial Registration</p> <p><b>This study is registered </b>at clinicaltrials.gov (NCT00435734).</p