1. Nut digraphsNino Bašić, Patrick W. Fowler, Maxine M. McCarthy, Primož Potočnik, 2026, original scientific article Abstract: A nut graph is a simple graph whose kernel is spanned by a single full vector (i.e., the adjacency matrix has a single zero eigenvalue and all non-zero kernel eigenvectors have no zero entry). We classify generalisations of nut graphs to nut digraphs: a digraph whose kernel (resp. co-kernel) is spanned by a full vector is dextro-nut (resp. laevo-nut); a bi-nut digraph is both laevo- and dextro-nut; an ambi-nut digraph is a bi-nut digraph where kernel and co-kernel are spanned by the same vector; a digraph is inter-nut if the intersection of the kernel and co-kernel is spanned by a full vector. It is known that a nut graph is connected, leafless and non-bipartite. It is shown here that an ambi-nut digraph is strongly connected, non-bipartite (i.e., has a non-bipartite underlying graph) and has minimum in-degree and minimum out-degree of at least 2. Refined notions of core and core-forbidden vertices apply to singular digraphs. Infinite families of nut digraphs and systematic coalescence, crossover and multiplier constructions are introduced. Relevance of nut digraphs to topological physics is discussed.
Keywords: nut graph, core graph, nullity, directed graph, nut digraph, dextro-nut, laevo-nut, bi-nut, ambi-nut, inter-nut, dextro-core vertex, laevo-core vertex, graph spectra
Published in DiRROS: 09.03.2026; Views: 319; Downloads: 213
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2. Inter-laboratory assessment of different digital PCR platforms for quantification of human cytomegalovirus DNAJernej Pavšič, Alison S. Devonshire, Andrej Blejec, Carole A. Foy, Fran Van Heuverswyn, Gerwyn M. Jones, Heinz Schimmel, Jana Žel, Jim F. Huggett, Nicholas Redshaw, Maria Karczmarczyk, Erkan Mozioglu, Sema Akyürek, Müslüm Akgöz, Mojca Milavec, 2017, original scientific article Abstract: Quantitative PCR (qPCR) is an important tool in pathogen detection. However, the use of different qPCR components, calibration materials and DNA extraction methods reduces comparability between laboratories, which can result in false diagnosis and discrepancies in patient care. The wider establishment of a metrological framework for nucleic acid tests could improve the degree of standardisation of pathogen detection and the quantification methods applied in the clinical context. To achieve this, accurate methods need to be developed and implemented as reference measurement procedures, and to facilitate characterisation of suitable certified reference materials. Digital PCR (dPCR) has already been used for pathogen quantification by analysing nucleic acids. Although dPCR has the potential to provide robust and accurate quantification of nucleic acids, further assessment of its actual performance characteristics is needed before it can be implemented in a metrological framework, and to allow adequate estimation of measurement uncertainties. Here, four laboratories demonstrated reproducibility (expanded measurement uncertainties below 15%) of dPCR for quantification of DNA from human cytomegalovirus, with no calibration to a common reference material. Using whole-virus material and extracted DNA, an intermediate precision (coefficients of variation below 25%) between three consecutive experiments was noted. Furthermore, discrepancies in estimated mean DNA copy number concentrations between laboratories were less than twofold, with DNA extraction as the main source of variability. These data demonstrate that dPCR offers a repeatable and reproducible method for quantification of viral DNA, and due to its satisfactory performance should be considered as candidate for reference methods for implementation in a metrological framework.
Keywords: digital PCR, DNA quantification, inter-laboratory assessment, human cytomegalovirus, virus reference materials
Published in DiRROS: 24.07.2024; Views: 1492; Downloads: 858
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3. Inter-comparison of marine microbiome sampling protocolsFrancisco Pascoal, Maria Paola Tomasino, Roberta Piredda, Grazia Marina Quero, Luís Torgo, Julie Poulain, Tinkara Tinta, Timotej Turk Dermastia, 2023, original scientific article Abstract: Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
Keywords: marine microbiome, standardized sampling, inter-comparison, amplicon sequencing, microbial diversity, seawater sampling
Published in DiRROS: 12.07.2024; Views: 1542; Downloads: 1110
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