Eine FAIRe Anwendungssoftware für textbasierte Forschungsdaten: Das UV2 Annotationstool

Der Beitrag stellt die FAIR-Prinzipien für Forschungssoftware nach Chue Hong et al. (2021) vor und diskutiert ihre Umsetzung am Beispiel des UV2-Annotationstools. Hierbei werden die umgesetzten Entwicklungsstrategien des Continuous Integration / Continuous Delivery und des test-driven development, die komponentenbasierte Architektur und die thematische Strukturierung des Quellcodes sowie die Art des ausführbaren Artefakts (Docker Container) vorgestellt und bezüglich der FAIR-Prinzipien bewertet.The article introduces the FAIR principles for research software, as proposed in Chue Hong et al. (2021), and discusses their realisation by means of the UV2 annotation tool. We examine the following aspects of the tool’s implementation: the component-based architecture, the structuring of the source code, the type of the executable artefact (docker container), and the way the development strategies Continuous Integration / Continuous Delivery and test-driven development are realized

Much Ado About Nothing? On the Categorial Status of et and ne in Medieval French

In this article, we reconsider the syntactical analysis as well as the categorial status of two Medieval French elements, et and ne. In this connection, we illustrate and compare various approaches which principally differ with regard to the assignment of a unique category or of various categories to these elements. In the context of this comparison, we address some of the questions pertaining to their motivations and the evidence which has been offered in their favor, showing that approaches which assign a unique category to et and ne, respectively, prove to be empirically more adequate.Beaucoup de bruit pour rien ? A propos du statut catégoriel de et ainsi que de ne en français médiéval Dans cet article nous proposons une réflexion sur l’analyse syntaxique et le statut de deux éléments du français médiéval : et et ne. A cette fin, nous envisageons et illustrons différentes approches qui se distinguent principalement en ce qui concerne l’attribution d’un statut catégoriel unique ou multiple à ces éléments. En comparant ces approches, nous abordons les questions qui président à leurs motivations et nous débattons les arguments proposés en leur faveur, à la lumière des faits observés. Il s’ensuit que l’approche qui attribue un statut catégoriel cohérent à chacun des deux éléments en question s’avère la plus pertinente

Much Ado About Nothing? On the Categorial Status of et and ne in Medieval French

In this article, we reconsider the syntactical analysis as well as the categorial status of two Medieval French elements, et and ne. In this connection, we illustrate and compare various approaches which principally differ with regard to the assignment of a unique category or of various categories to these elements. In the context of this comparison, we address some of the questions pertaining to their motivations and the evidence which has been offered in their favor, showing that approaches which assign a unique category to et and ne, respectively, prove to be empirically more adequate.Beaucoup de bruit pour rien ? A propos du statut catégoriel de et ainsi que de ne en français médiéval Dans cet article nous proposons une réflexion sur l’analyse syntaxique et le statut de deux éléments du français médiéval : et et ne. A cette fin, nous envisageons et illustrons différentes approches qui se distinguent principalement en ce qui concerne l’attribution d’un statut catégoriel unique ou multiple à ces éléments. En comparant ces approches, nous abordons les questions qui président à leurs motivations et nous débattons les arguments proposés en leur faveur, à la lumière des faits observés. Il s’ensuit que l’approche qui attribue un statut catégoriel cohérent à chacun des deux éléments en question s’avère la plus pertinente

Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland

Turbic Cryosols (permafrost soils characterized by cryoturbation, i.e., by mixing of soil layers due to freezing and thawing) are widespread across the Arctic, and contain large amounts of poorly decomposed organic material buried in the subsoil. This cryoturbated organic matter exhibits retarded decomposition compared to organic material in the topsoil. Since soil organic matter (SOM) decomposition is known to be tightly linked to N availability, we investigated N transformation rates in different soil horizons of three tundra sites in north-eastern Siberia and Greenland. We measured gross rates of protein depolymerization, N mineralization (ammonification) and nitrification, as well as microbial uptake of amino acids and NH4+ using an array of 15N pool dilution approaches. We found that all sites and horizons were characterized by low N availability, as indicated by low N mineralization compared to protein depolymerization rates (with gross N mineralization accounting on average for 14% of gross protein depolymerization). The proportion of organic N mineralized was significantly higher at the Greenland than at the Siberian sites, suggesting differences in N limitation. The proportion of organic N mineralized, however, did not differ significantly between soil horizons, pointing to a similar N demand of the microbial community of each horizon. In contrast, absolute N transformation rates were significantly lower in cryoturbated than in organic horizons, with cryoturbated horizons reaching not more than 32% of the transformation rates in organic horizons. Our results thus indicate a deceleration of the entire N cycle in cryoturbated soil horizons, especially strongly reduced rates of protein depolymerization (16% of organic horizons) which is considered the rate-limiting step in soil N cycling.publishedVersio

Development of a high density 600K SNP genotyping array for chicken

Background: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.Results: We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10-15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.Conclusions: This Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

The functions of soils are intimately linked to their three-dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi-isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting-edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates

HACE1 deficiency causes an autosomal recessive neurodevelopmental syndrome

Background: The genetic etiology of neurodevelopmental defects is extremely diverse, and the lack of distinctive phenotypic features means that genetic criteria are often required for accurate diagnostic classification. We aimed to identify the causative genetic lesions in two families in which eight affected individuals displayed variable learning disability, spasticity and abnormal gait. Methods: Autosomal recessive inheritance was suggested by consanguinity in one family and by sibling recurrences with normal parents in the second. Autozygosity mapping and exome sequencing, respectively, were used to identify the causative gene. Results: In both families, biallelic loss-of-function mutations in HACE1 were identified. HACE1 is an E3 ubiquitin ligase that regulates the activity of cellular GTPases, including Rac1 and members of the Rab family. In the consanguineous family, a homozygous mutation p.R219* predicted a truncated protein entirely lacking its catalytic domain. In the other family, compound heterozygosity for nonsense mutation p.R748* and a 20-nt insertion interrupting the catalytic HECT domain was present; Western analysis of patient cells revealed an absence of detectable HACE1 protein. Conclusion: HACE1 mutations underlie a new autosomal recessive neurodevelopmental disorder. Previous studies have implicated HACE1 as a tumour suppressor gene; however, since cancer predisposition was not observed either in homozygous or heterozygous mutation carriers, this concept may require re-evaluation

The stigma of obesity in the general public and its implications for public health - a systematic review

<p>Abstract</p> <p>Background</p> <p>Up to this date, prevalence rates of obesity are still rising. Aside from co-morbid diseases, perceived discrimination and stigmatization leads to worsen outcomes in obese individuals. Higher stigmatizing attitudes towards obese individuals may also result in less support of preventive and interventive measures. In light of the immense burden of obesity on health care systems and also on the individuals' quality of life, accepted and subsidized preventive measures are needed. Policy support might be determined by views of the lay public on causes of obesity and resulting weight stigma. This study seeks to answer how representative samples of the lay public perceive people with obesity or overweight status (stigmatizing attitudes); what these samples attribute obesity to (causal attribution) and what types of interventions are supported by the lay public and which factors determine that support (prevention support).</p> <p>Methods</p> <p>A systematic literature search was conducted. All studies of representative samples reporting results on (a) stigmatizing attitudes towards overweight and obese individuals, (b) causal beliefs and (c) prevention support were included.</p> <p>Results</p> <p>Only 7 articles were found. One study reported prevalence rates of stigmatizing attitudes. About a quarter of the population in Germany displayed definite stigmatizing attitudes. Other studies reported causal attributions. While external influences on weight are considered as well, it seems that internal factors are rated to be of higher importance. Across the studies found, regulative prevention is supported by about half of the population, while childhood prevention has highest approval rates. Results on sociodemographic determinants differ substantially.</p> <p>Conclusions</p> <p>Further research on public attitudes toward and perception of overweight and obesity is urgently needed to depict the prevailing degree of stigmatization. Introducing a multidimensional concept of the etiology of obesity to the lay public might be a starting point in stigma reduction.</p