Swift: A modern highly-parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications

Numerical simulations have become one of the key tools used by theorists in all the fields of astrophysics and cosmology. The development of modern tools that target the largest existing computing systems and exploit state-of-the-art numerical methods and algorithms is thus crucial. In this paper, we introduce the fully open-source highly-parallel, versatile, and modular coupled hydrodynamics, gravity, cosmology, and galaxy-formation code Swift. The software package exploits hybrid shared- and distributed-memory task-based parallelism, asynchronous communications, and domain-decomposition algorithms based on balancing the workload, rather than the data, to efficiently exploit modern high-performance computing cluster architectures. Gravity is solved for using a fast-multipole-method, optionally coupled to a particle mesh solver in Fourier space to handle periodic volumes. For gas evolution, multiple modern flavours of Smoothed Particle Hydrodynamics are implemented. Swiftalso evolves neutrinos using a state-of-the-art particle-based method. Two complementary networks of sub-grid models for galaxy formation as well as extensions to simulate planetary physics are also released as part of the code. An extensive set of output options, including snapshots, light-cones, power spectra, and a coupling to structure finders are also included. We describe the overall code architecture, summarise the consistency and accuracy tests that were performed, and demonstrate the excellent weak-scaling performance of the code using a representative cosmological hydrodynamical problem with ≈300 billion particles. The code is released to the community alongside extensive documentation for both users and developers, a large selection of example test problems, and a suite of tools to aid in the analysis of large simulations run with Swift

Swift: A modern highly-parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications

Numerical simulations have become one of the key tools used by theorists in all the fields of astrophysics and cosmology. The development of modern tools that target the largest existing computing systems and exploit state-of-the-art numerical methods and algorithms is thus crucial. In this paper, we introduce the fully open-source highly-parallel, versatile, and modular coupled hydrodynamics, gravity, cosmology, and galaxy-formation code Swift. The software package exploits hybrid task-based parallelism, asynchronous communications, and domain-decomposition algorithms based on balancing the workload, rather than the data, to efficiently exploit modern high-performance computing cluster architectures. Gravity is solved for using a fast-multipole-method, optionally coupled to a particle mesh solver in Fourier space to handle periodic volumes. For gas evolution, multiple modern flavours of Smoothed Particle Hydrodynamics are implemented. Swift also evolves neutrinos using a state-of-the-art particle-based method. Two complementary networks of sub-grid models for galaxy formation as well as extensions to simulate planetary physics are also released as part of the code. An extensive set of output options, including snapshots, light-cones, power spectra, and a coupling to structure finders are also included. We describe the overall code architecture, summarize the consistency and accuracy tests that were performed, and demonstrate the excellent weak-scaling performance of the code using a representative cosmological hydrodynamical problem with $\approx$$300$ billion particles. The code is released to the community alongside extensive documentation for both users and developers, a large selection of example test problems, and a suite of tools to aid in the analysis of large simulations run with Swift.Comment: 39 pages, 18 figures, submitted to MNRAS. Code, documentation, and examples available at www.swiftsim.co

Opportunities for linking research to policy: lessons learned from implementation research in sexual and reproductive health within the ANSER network

Background: The uptake of findings from sexual and reproductive health and rights research into policy-making remains a complex and non-linear process. Different models of research utilisation and guidelines to maximise this in policy-making exist, however, challenges still remain for researchers to improve uptake of their research findings and for policy-makers to use research evidence in their work. Methods: A participatory workshop with researchers was organised in November 2017 by the Academic Network for Sexual and Reproductive Health and Rights Policy (ANSER) to address this gap. ANSER is a consortium of experienced researchers, some of whom have policy-making experience, working on sexual and reproductive health and rights issues across 16 countries and 5 continents. The experiential learning cycle was used to guide the workshop discussions based on case studies and to encourage participants to focus on key lessons learned. Workshop findings were thematically analysed using specific stages from Hanney et al.’s (Health Res Policy Syst 1:2, 2003) framework on the place of policy-making in the stages of assessment of research utilisation and outcomes. Results: The workshop identified key strategies for translating research into policy, including joint agenda-setting between researchers and policy-makers, as well as building trust and partnerships with different stakeholders. These were linked to stages within Hanney et al.’s framework as opportunities for engaging with policy-makers to ensure uptake of research findings. Conclusion: The engagement of stakeholders during the research development and implementation phases, especially at strategic moments, has a positive impact on uptake of research findings. The strategies and stages described in this paper can be applied to improve utilisation of research findings into policy development and implementation globally

Blockchainlab: expertisecentrum voor wérkende blockchaintoepassingen

Publicatie ter gelegenheid van het op 17 oktober 2018 in Cursus- en Vergadercentrum Domstad plaatsgevonden Utrecht Blockchain Congres. Aanleiding was het feit dat het Blockchainlab van Hogeschool Utrecht recentelijk is erkend als regionaal én nationaal expertisecentrum op het gebied van blockchains. Afgaande op de positieve reacties en de hoge opkomst kunnen we terugkijken op een geslaagd event

A systematic evaluation of Flow Field Flow Fractionation and single-particle ICP-MS to obtain the size distribution of organo-mineral iron oxyhydroxide colloids

Colloidal iron(III)oxyhydroxides (FeOx)are important reactive adsorbents in nature. This study was set up to determine the size of environmentally relevant FeOx colloids with new methods, i.e. Flow Field Flow Fractionation (FlFFF-UV-ICP-MS)and single-particle ICP-MS/MS (sp-ICP-MS)and to compare these with standard approaches, i.e. dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), microscopy (TEM), membrane filtration, centrifugation and dialysis. Seven synthetic nano- and submicron FeOx with different mineralogy and coating were prepared and two soil solutions were included. The FlFFF was optimized for Fe recovery, yielding 70–90%. The FlFFF determines particle size with high resolution in a 1 mM NH 4 HCO 3 (pH 8.3)background and can detect Fe-NOM complexes 4 HCO 3 )and it has acceptable element recoveries. </p

Development and Validation of a Method for the Detection of Titanium Dioxide Particles in Human Tissue with Single Particle ICP-MS

Human biomonitoring studies to determine total titanium (total-Ti) and titanium dioxide (TiO2) particles require very sensitive inductively coupled plasma high resolution mass spectrometry (ICP-HRMS) methods. The result of such studies can only be reliably when used in a risk assessment if the analytical methods are fully validated, as reported here for human liver and spleen. For total-Ti an acidic HNO3/HF digestion was applied, followed by ICP-HRMS analysis of the acidic digests. For TiO2 particles a two-step digestion procedure was developed. In the first step the formaldehyde-fixed tissue was depolymerized and in the second step an enzymatic digestion was performed. Sample digests were analyzed with ICP-HRMS operated in single particle mode to detect TiO2 particles. Both methods were validated according to NEN 7777 using a scheme of duplicate analysis over an eight day period. Detection limits for total-Ti and TiO2 particles were 0.01 and 0.005 mg Ti/kg with a particle size quantification limit of 85 nm for TiO2 particles. Repeatability and reproducibility were 24% and 31% for the total titanium concentration, 22% and 39% for the particle titanium concentration, and 29% and 24% for the titanium dioxide particle size. In total 30 human tissue samples were analyzed with the developed and validated method. The results show a total-Ti content in the range of 0.02-0.09 mg Ti/kg in liver and 0.02-0.4 mg Ti/kg in spleen. The concentrations of particle TiO2 ranged from 0.01-0.08 mg Ti/kg in liver and from 0.01-0.1 mg Ti/kg in spleen. On the average, particle TiO2 explained up to 67% of the total-Ti concentrations. The detected TiO2 particles had a particle size range of 85 to 720 nm

Relation between disease phenotype and HLA-DQ genotype in diabetic patients diagnosed in early adulthood

We investigated inaugural disease phenotype in relation to the presence or absence of diabetes-associated autoantibodies and human leukocyte antigen (HLA) DQ risk genotypes in adult-onset diabetic patients. Blood samples and questionnaires were obtained from 1584 recent-onset Belgian Caucasian patients (age 15-39 yr at diagnosis of primary diabetes) who were recruited by the Belgian Diabetes Registry over an 11-yr period. At clinical diagnosis, antibody-positive patients (n = 1198) were on average younger and had more symptoms, a more acute disease onset, lower body mass index, and random C-peptide levels, but higher insulin needs, glycemia, and prevalence of ketonuria, HLA-DQ, and 5' insulin gene susceptibility genotypes (P < 0.001 vs. antibody-negative patients; n = 386). In antibody-positive patients, these characteristics did not differ according to HLA-DQ genotype. However, in antibody-negative subjects, we found that patients were younger (P = 0.001); had a lower body mass index (P < 0.001), higher insulin needs (P = 0.014), and amylasemia (P = 0.001); and tended to have a higher glycemia and lower C-peptide in the presence of susceptible HLA-DQ genotypes. Differences according to HLA-DQ genotype subsisted after careful age-matching. In conclusion, we found no relation between initial disease phenotype and HLA-DQ genotype in antibody-positive diabetic young adults. In contrast, antibody-negative patients displayed more type I-like features when carrying susceptible HLA-DQ genotypes known to promote the development of antibody-positive diabetes. The overrepresentation of these susceptibility genotypes in antibody-negative patients suggests the existence of an immune-mediated disease process with as yet unidentified immune markers in a subgroup of seronegative patients

Development and Validation of a Method for the Detection of Titanium Dioxide Particles in Human Tissue with Single Particle ICP-MS

Human biomonitoring studies to determine total titanium (total-Ti) and titanium dioxide (TiO2) particles require very sensitive inductively coupled plasma high resolution mass spectrometry (ICP-HRMS) methods. The result of such studies can only be reliably when used in a risk assessment if the analytical methods are fully validated, as reported here for human liver and spleen. For total-Ti an acidic HNO3/HF digestion was applied, followed by ICP-HRMS analysis of the acidic digests. For TiO2 particles a two-step digestion procedure was developed. In the first step the formaldehyde-fixed tissue was depolymerized and in the second step an enzymatic digestion was performed. Sample digests were analyzed with ICP-HRMS operated in single particle mode to detect TiO2 particles. Both methods were validated according to NEN 7777 using a scheme of duplicate analysis over an eight day period. Detection limits for total-Ti and TiO2 particles were 0.01 and 0.005 mg Ti/kg with a particle size quantification limit of 85 nm for TiO2 particles. Repeatability and reproducibility were 24% and 31% for the total titanium concentration, 22% and 39% for the particle titanium concentration, and 29% and 24% for the titanium dioxide particle size. In total 30 human tissue samples were analyzed with the developed and validated method. The results show a total-Ti content in the range of 0.02-0.09 mg Ti/kg in liver and 0.02-0.4 mg Ti/kg in spleen. The concentrations of particle TiO2 ranged from 0.01-0.08 mg Ti/kg in liver and from 0.01-0.1 mg Ti/kg in spleen. On the average, particle TiO2 explained up to 67% of the total-Ti concentrations. The detected TiO2 particles had a particle size range of 85 to 720 nm

Eco-, geno- and human toxicology of bio-active nanoparticles for biomedical applications

Gene delivery has become an increasingly important strategy for treating a variety of human diseases, including infections, genetic disorders and tumours. To avoid the difficulties of using viral carriers, more and more non-viral gene delivery nanoparticles are developed. Among these new approaches polyethylene imine (PEI) is currently considered as one of the most effective polymer based method solution and considered as the gold standard. The toxicity of nanoparticles is a major concern when used for medical application. In this study we chose two nanoparticles for an in depth toxicological and ecotoxicological evaluation, one well characterized, PEI, and another novel polymer, poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA). In the present study we have assessed the toxicity of these cation nanoparticles as such and of the polyplexes - nanoparticles covered with DNA. As these nanoparticles are also frequently used in high volumes in various industries and as such may enter in the environment, we also made an initial assessment of ecotoxicological effects assessment. The following nanoparticles related aspects have been studied during the project: development and characterization, ecotoxicity, general toxicity and specific toxicity. To this end a battery of different tests was used. The conclusion of these tests is that toxicity is varying between different nanoparticles and between different DNA covering ratios. In general, in the different systems tested, the PEI polymer is more toxic than the PDMAEMA polymer. The same difference is seen for the polyplexes and the higher the charge ratio, the more toxic are the polyplexes. Our study also clearly shows the need for a broad spectrum of toxicity assays for a comprehensive risk assessment. Our study has performed such a comprehensive analysis of two biomedical nanoparticles.status: publishe

Eco-, geno- and human toxicology of bio-active nanoparticles for biomedical applications

Gene delivery has become an increasingly important strategy for treating a variety of human diseases, including infections, genetic disorders and tumours. To avoid the difficulties of using viral carriers, more and more non-viral gene delivery nanoparticles are developed. Among these new approaches polyethylene imine (PEI) is currently considered as one of the most effective polymer based method solution and considered as the gold standard. The toxicity of nanoparticles is a major concern when used for medical application. In this study we chose two nanoparticles for an in depth toxicological and ecotoxicological evaluation, one well characterized, PEI, and another novel polymer, poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA). In the present study we have assessed the toxicity of these cation nanoparticles as such and of the polyplexes - nanoparticles covered with DNA. As these nanoparticles are also frequently used in high volumes in various industries and as such may enter in the environment, we also made an initial assessment of ecotoxicological effects assessment. The following nanoparticles related aspects have been studied during the project: development and characterization, ecotoxicity, general toxicity and specific toxicity. To this end a battery of different tests was used. The conclusion of these tests is that toxicity is varying between different nanoparticles and between different DNA covering ratios. In general, in the different systems tested, the PEI polymer is more toxic than the PDMAEMA polymer. The same difference is seen for the polyplexes and the higher the charge ratio, the more toxic are the polyplexes. Our study also clearly shows the need for a broad spectrum of toxicity assays for a comprehensive risk assessment. Our study has performed such a comprehensive analysis of two biomedical nanoparticles. (C) 2009 Elsevier Ireland Ltd. All rights reserved