Publication of Atmospheric Model Data using the ATMODAT Standard

Scientific data should be published in a way so that other scientists can benefit from these data, enabling further research. The FAIR Data Principles are defining the basic prerequisite for a good data publication: data should be Findable, Accessible, Interoperable, and Reusable. Increasingly, research communities are developing discipline-specific data publication standards under consideration of the FAIR Data Principles. A very comprehensive yet strict data standard has been developed for the climate model output within the Climate Model Intercomparison Project (CMIP), which largely builds upon the Climate and Forecast Metadata Conventions (CF conventions). There are, however, many areas of atmospheric modelling where data cannot be standardised according to the CMIP data standard because, e.g., the data contain specific variables which are not covered by the CMIP standard. Furthermore, fulfilling the strict CMIP data standard for smaller Model Intercomparison Projects (MIPs) requires much effort (in time and manpower) and hence the outcome of these MIPs often remains non-standardised. For innovative model diagnostics, preexisting standards are also not flexible enough. For that reason, the ATMODAT standard, a quality guideline for atmospheric model data, was created. The ATMODAT standard defines a set of requirements that aim at ensuring the high reusability of atmospheric model data publications. The requirements include the use of the netCDF file format, the application of the CF conventions, rich and standardised file metadata, and the publication of the data with a DataCite DOI. Additionally, a tool for checking the conformity of data and metadata to this standard, the atmodat data checker, was developed and is available on GitHub under an open licence. By using the more flexible ATMODAT standard, the publication of standardised datasets is simplified for smaller MIPs. This standardisation process is presented as an example using the data of an aerosol-climate model from the AeroCOM MIP. Furthermore, the landing pages of ATMODAT-compliant data publications can be highlighted with the EASYDAB logo. EASYDAB (Earth System Data Branding) is a newly developed quality label for carefully curated and highly standardised data publications. The ATMODAT data standardisation can easily be transferred to data from other disciplines and contribute to their improved reusability

Upgrade of the ultracold neutron source at the pulsed reactor TRIGA Mainz

The performance of the upgraded solid deuterium ultracold neutron source at the pulsed reactor TRIGA Mainz is described. The current configuration stage comprises the installation of a He liquefier to run UCN experiments over long-term periods, the use of stainless steel neutron guides with improved transmission as well as sputter-coated non-magnetic $^{58}$NiMo alloy at the inside walls of the thermal bridge and the converter cup. The UCN yield was measured in a `standard' UCN storage bottle (stainless steel) with a volume of 32 litres outside the biological shield at the experimental area yielding UCN densities of 8.5 /cm$^3$; an increase by a factor of 3.5 compared to the former setup. The measured UCN storage curve is in good agreement with the predictions from a Monte Carlo simulation developed to model the source. The growth and formation of the solid deuterium converter during freeze-out are affected by the ortho/para ratio of the H$_2$ premoderator.Comment: 12 pages, 7 figure

Restriction of HIV-1 Genotypes in Breast Milk Does Not Account for the Population Transmission Genetic Bottleneck That Occurs following Transmission

BACKGROUND. Breast milk transmission of HIV-1 remains a major route of pediatric infection. Defining the characteristics of viral variants to which breastfeeding infants are exposed is important for understanding the genetic bottleneck that occurs in the majority of mother-to-child transmissions. The blood-milk epithelial barrier markedly restricts the quantity of HIV-1 in breast milk, even in the absence of antiretroviral drugs. The basis of this restriction and the genetic relationship between breast milk and blood variants are not well established. METHODOLOGY/PRINCIPAL FINDINGS. We compared 356 HIV-1 subtype C gp160 envelope (env) gene sequences from the plasma and breast milk of 13 breastfeeding women. A trend towards lower viral population diversity and divergence in breast milk was observed, potentially indicative of clonal expansion within the breast. No differences in potential N-linked glycosylation site numbers or in gp160 variable loop amino acid lengths were identified. Genetic compartmentalization was evident in only one out of six subjects in whom contemporaneously obtained samples were studied. However, in samples that were collected 10 or more days apart, six of seven subjects were classified as having compartmentalized viral populations, highlighting the necessity of contemporaneous sampling for genetic compartmentalization studies. We found evidence of CXCR4 co-receptor using viruses in breast milk and blood in nine out of the thirteen subjects, but no evidence of preferential localization of these variants in either tissue. CONCLUSIONS/SIGNIFICANCE. Despite marked restriction of HIV-1 quantities in milk, our data indicate intermixing of virus between blood and breast milk. Thus, we found no evidence that a restriction in viral genotype diversity in breast milk accounts for the genetic bottleneck observed following transmission. In addition, our results highlight the rapidity of HIV-1 env evolution and the importance of sample timing in analyses of gene flow.National Institute of Child Health and Human Development; National Institutes of Health (R01 HD 39611, R01 HD 40777); International Maternal Pediatric Adolescent AIDS Clinical Trials Group (U01 AI068632-01); National Institutes of Health Cellular, Biochemical; Molecular Sciences Training Program Grant (T 32 067587

First Measurement of the 96^{96}Ru(p,γ\gamma)97^{97}Rh Cross Section for the p-Process with a Storage Ring

This work presents a direct measurement of the $^{96}$Ru($p, \gamma$)$^{97}$Rh cross section via a novel technique using a storage ring, which opens opportunities for reaction measurements on unstable nuclei. A proof-of-principle experiment was performed at the storage ring ESR at GSI in Darmstadt, where circulating $^{96}$Ru ions interacted repeatedly with a hydrogen target. The $^{96}$Ru($p, \gamma$)$^{97}$Rh cross section between 9 and 11 MeV has been determined using two independent normalization methods. As key ingredients in Hauser-Feshbach calculations, the $\gamma$-ray strength function as well as the level density model can be pinned down with the measured ($p, \gamma$) cross section. Furthermore, the proton optical potential can be optimized after the uncertainties from the $\gamma$-ray strength function and the level density have been removed. As a result, a constrained $^{96}$Ru($p, \gamma$)$^{97}$Rh reaction rate over a wide temperature range is recommended for $p$-process network calculations.Comment: 10 pages, 7 figs, Accepted for publication at PR

Modeling Structural Colors from Disordered One-Component Colloidal Nanoparticle-based Supraballs using Combined Experimental and Simulation Techniques

Bright, saturated structural colors in birds have inspired synthesis of self-assembled, disordered arrays of assembled nanoparticles with varied particle spacings and refractive indices. However, predicting colors of assembled nanoparticles, and thereby guiding their synthesis, remains challenging due to the effects of multiple scattering and strong absorption. Here, we use a computational approach to first reconstruct the nanoparticles' assembled structures from small-angle scattering measurements and then input the reconstructed structures to a finite-difference time-domain method to predict their color and reflectance. This computational approach is successfully validated by comparing its predictions against experimentally measured reflectance and provides a pathway for reverse engineering colloidal assemblies with desired optical and photothermal properties.Comment: 14 pages, 3 figures, 1 ToC figur

Effect of Sarcopenia on the Increase in Liver Volume and Function After Portal Vein Embolization

Purpose: Sarcopenia is associated with a decreased kinetic growth rate (KGR) of the future liver remnant (FLR) after portal vein embolization (PVE). However, little is known on the increase in FLR function (FLRF) after PVE. This study evaluated the effect of sarcopenia on the functional growth rate (FGR) after PVE measured with hepatobiliary scintigraphy (HBS). Methods: All patients who underwent PVE at the Amsterdam UMC between January 2005 and August 2017 were analyzed. Functional imaging by HBS was used to determine FGR. Liver volumetry was performed using multiphase contrast computed tomography (CT). Muscle area measurement to determine sarcopenia was taken at the third lumbar level (L3). Results: Out of the 95 included patients, 9 were excluded due to unavailable data. 70/86 (81%) patients were sarcopenic. In the multivariate logistic regression analysis, sarcopenia (p = 0.009) and FLR volume (FRLV) before PVE (p = 0.021) were the only factors correlated with KGR, while no correlation was found with FGR. 90-day mortality was similar across the sarcopenic and non-sarcopenic group (4/53 [8%] versus 1/11 [9%]; p = 1.000). The resection rates were also comparable (53/70 [75%] versus 11/16 [69%]; p = 0.542). Conclusion: FGR after PVE as measured by HBS appears to be preserved in sarcopenic patients. This is in contrast to KGR after PVE as measured by liver volumetry which is decreased in sarcopenic patients. Level of Evidence: Level 3b, cohort and case control studies.</p

Effect of Sarcopenia on the Increase in Liver Volume and Function After Portal Vein Embolization

Purpose: Sarcopenia is associated with a decreased kinetic growth rate (KGR) of the future liver remnant (FLR) after portal vein embolization (PVE). However, little is known on the increase in FLR function (FLRF) after PVE. This study evaluated the effect of sarcopenia on the functional growth rate (FGR) after PVE measured with hepatobiliary scintigraphy (HBS). Methods: All patients who underwent PVE at the Amsterdam UMC between January 2005 and August 2017 were analyzed. Functional imaging by HBS was used to determine FGR. Liver volumetry was performed using multiphase contrast computed tomography (CT). Muscle area measurement to determine sarcopenia was taken at the third lumbar level (L3). Results: Out of the 95 included patients, 9 were excluded due to unavailable data. 70/86 (81%) patients were sarcopenic. In the multivariate logistic regression analysis, sarcopenia (p = 0.009) and FLR volume (FRLV) before PVE (p = 0.021) were the only factors correlated with KGR, while no correlation was found with FGR. 90-day mortality was similar across the sarcopenic and non-sarcopenic group (4/53 [8%] versus 1/11 [9%]; p = 1.000). The resection rates were also comparable (53/70 [75%] versus 11/16 [69%]; p = 0.542). Conclusion: FGR after PVE as measured by HBS appears to be preserved in sarcopenic patients. This is in contrast to KGR after PVE as measured by liver volumetry which is decreased in sarcopenic patients. Level of Evidence: Level 3b, cohort and case control studies.</p

ESA Nanosatellites for D3S (Distributed Space Weather Sensor System)

In early 2021, SSTL was selected to be the prime contractor for an ongoing 18 month ESA-funded Phase 0/A study titled “SSA P3-SWE-LIII Nanosatellites for D3S”. The objective of the study is to assess the feasibility of using nanosatellites for future operational space weather monitoring missions as part of ESA's Distributed Space Weather Sensor System (D3S). The Phase 0 study initially involved an analysis of science measurement requirements and space weather instruments as well as an analysis of recent relevant nanosatellite missions and nanosatellite technologies which could be used on future ESA D3S Nanosatellites. This was followed by an initial trade-off of a range of high-level mission architecture concepts, eventually converging down to two mission architecture concepts proposed for further analysis during the remainder of the Phase 0 study. The aim of the first mission architecture concept is to provide near-real time measurements of radiation, thermal plasma and Ionospheric neutrals/plasma, via a constellation of 20x SSTL-21 satellites. The objective of the second mission architecture concept is to provide near-real time measurements of radiation, the Ionosphere and the Thermosphere, via a constellation of 6x 16U SSTL-Cube satellites. ESA selected the second mission architecture concept to take through into the Phase A study. This paper will mainly describe the details of the Phase 0 study, as well as touching on the current status of the Phase A study

Comparing methods of measuring sea-ice density in the East Antarctic

Remotely sensed derivation of sea-ice thickness requires sea·ice density. Sea-ice density was estimated with three techniques during the second Sea Ice Physics and Ecosystem eXperiment (SIPEX-II, September-November 2012, East Antarctica). The sea ice was first-year highly deformed, mean thickness 1.2 m with layers, consistent with rafting, and 6-7/10 columnar ice and 3/10 granular ice. Ice density was found to be lower than values (900-920 kg m⁻³ used previously to derive ice thickness, with columnar ice mean density of 870 kg m⁻³. At two different ice stations the mean density of the ice was 870 and 800 kg m⁻³, the lower density reflecting a high percentage of porous granular ice at the second station. Error estimates for mass/volume and liquid/solid water methods are presented. With 0.1 m long, 0.1 m core samples, the error on individual density estimates is 28 kg m⁻³. Errors are larger for smaller machined blocks. Errors increase to 46 kg m⁻³ if the liquid/solid volume method is used. The mass/volume method has a low bias due to brine drainage of at least 5%. Bulk densities estimated from ice and snow measurements along 100 m transects were high, and likely unrealistic as the assumption of isostatic balance is not suitable over these length scales in deformed ice