Niemcza diorites and moznodiorites (Sudetes, SW Poland): a record of changing geotectonic setting at ca. 340 Ma

Granites sensu lato in the Sudetes intruded in several episodes during the Variscan orogeny recording different stages of crust and mantle evolution. Correlating precise ages with geochemistry of the Variscan granites provides information on the evolution of these sources within the Variscan orogen. The Variscan intrusive rocks from the Niemcza Zone (Bohemian Massif, Sudetes, SW Poland) include undeformed dioritic to syenitic rocks and magmatically foliated granodiorites. In this study we analysed low SiO2 (48–53 wt.%) monzodioritic rocks from Przedborowa and Koźmice. The monzodiorites contain late-magmatic zircons with ages of 341.8 ± 1.9 Ma for Przedborowa and 335.6 ± 2.3 Ma for Koźmice, interpreted as emplacement ages of the dioritic magmas. Older Przedborowa rocks are lower in K, Mg, Rb and Ni than the Koźmice rocks and similar compositional trend is also observed in the Central Bohemian Plutonic Complex. The implication is that the mantle underlying the Niemcza Zone became more enriched from ca. 342 to ca. 336 Ma, probably following the collision of the Saxothuringian and Moldanubian/Lugian domains. The magmatism related to the collision occurred ca. 12 Ma later than that in the Central Bohemian Plutonic Complex, but was accompanied by a similar change in magma chemistry from high-K (Przedborowa) to shoshonitic (Koźmice, Kośmin enclaves) and probably to ultrapotassic (Wilków Wielki)

Semantic interoperability: ontological unpacking of a viral conceptual model

Background. Genomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers. Results. In this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the “ontological unpacking” method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it. Conclusions. We propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the “I” in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research

An Initial Empirical Assessment of an Ontological Model of the Human Genome

Conceptual modeling is used to model application domains for which an information system is needed. One of the most complex domains to which conceptual modeling has been applied is that of the human genome. Due to its complexity, its understanding is often left to domain experts. Conceptual models represent genomics-related concepts, with various purposes, including domain clarification or data structures design for facilitating data integration. However, traditional conceptual models, which might be expressed, for example, with UML, may not be appropriate for properly explaining such a complex domain, thus requiring an additional layer to ground the model on well-accepted ontological foundations. To achieve this result, an “ontological unpacking” method has been proposed that uses OntoUML as a visual formalism. In this research, we carry out an empirical study to compare the two mentioned representations. The study involved a small group of participants, who responded to a set of questions by reading either a UML model or its related OntoUML unpacked version; the results enabled us to assess their understanding of the domain. We aim to initiate a practical evaluation framework to assess the effectiveness, efficiency and user beliefs of models derived by ontologically unpacking traditional conceptual models. The results of the analysis provide the basis for a broader assessment

Ontological Representation of FAIR Principles: A Blueprint for FAIRer Data Sources

Guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of datasets, known as FAIR principles, were introduced in 2016 to enable machines to perform automatic actions on a variety of digital objects, including datasets. Since then, the principles have been widely adopted by data creators and users worldwide with the ‘FAIR’ acronym becoming a common part of the vocabulary of data scientists. However, there is still some controversy on how datasets should be interpreted since not all datasets that are claimed to be FAIR, necessarily follow the principles. In this research, we propose the OntoUML FAIR Principles Schema, as an ontological representation of FAIR principles for data practitioners. The work is based on OntoUML, an ontologically well-founded language for Ontology-driven Conceptual Modeling. OntoUML is a proxy for ontological analysis that has proven effective in supporting the explanation of complex domains. Our schema aims to disentangle the intricacies of the FAIR principles’ definition, by resolving aspects that are ambiguous, under-specified, recursively-specified, or implicit. The schema can be considered as a blueprint, or a template to follow when the FAIR classification strategy of a dataset must be designed. To demonstrate the usefulness of the schema, we present a practical example based on genomic data and discuss how the results provided by the OntoUML FAIR Principles Schema contribute to existing data guidelines

Multiple polar and non‐polar nematic phases.

Liquid-crystal materials exhibiting up to three nematic phases are reported. Dielectric response measurements show that while the lower temperature nematic phase has ferroelectric order and the highest temperature nematic phase is apolar, the intermediate phase has local antiferroelectric order. The modification of the molecular structure by increasing the number of lateral fluorine substituents leads to one of the materials showing a direct isotropic-ferronematic phase transition

The role of ATP in the differential ability of Sr2+ to trigger Ca2+ oscillations in mouse and human eggs

At fertilization in mice and humans, the activation of the egg is caused by a series of repetitive Ca2+ oscillations which are initiated by phospholipase-C(zeta)ζ that generates inositol-1-4-5-trisphophate (InsP3). Ca2+ oscillations and egg activation can be triggered in mature mouse eggs by incubation in Sr2+ containing medium, but this does not appear to be effective in human eggs. Here we have investigated the reason for this apparent difference using mouse eggs, and human eggs that failed to fertilize after IVF or ICSI. Mouse eggs incubated in Ca2+-free, Sr2+-containing medium immediately underwent Ca2+ oscillations but human eggs consistently failed to undergo Ca2+ oscillations in the same Sr2+ medium. We tested the InsP3-receptor (IP3R) sensitivity directly by photo-release of caged InsP3 and found that mouse eggs were about 10 times more sensitive to InsP3 than human eggs. There were no major differences in the Ca2+ store content between mouse and human eggs. However, we found that the ATP concentration was consistently higher in mouse compared to human eggs. When ATP levels were lowered in mouse eggs by incubation in pyruvate-free medium, Sr2+ failed to cause Ca2+ oscillations. When pyruvate was added back to these eggs, the ATP levels increased and Ca2+ oscillations were induced. This suggests that ATP modulates the ability of Sr2+ to stimulate IP3R-induced Ca2+ release in eggs. We suggest that human eggs may be unresponsive to Sr2+ medium because they have a lower level of cytosolic ATP

Gattini 2010: Cutting Edge Science at the Bottom of the World

The high altitude Antarctic sites of Dome A and the South Pole offer intriguing locations for future large scale optical astronomical Observatories. The Gattini project was created to measure the optical sky brightness, large area cloud cover and aurora of the winter-time sky above such high altitude Antarctic sites. The Gattini-DomeA camera was installed on the PLATO instrument module as part of the Chinese-led traverse to the highest point on the Antarctic plateau in January 2008. This single automated wide field camera contains a suite of Bessel photometric filters (B, V, R) and a long-pass red filter for the detection and monitoring of OH emission. We have in hand one complete winter-time dataset (2009) from the camera that was recently returned in April 2010. The Gattini-South Pole UV camera is a wide-field optical camera that in 2011 will measure for the first time the UV properties of the winter-time sky above the South Pole dark sector. This unique dataset will consist of frequent images taken in both broadband U and B filters in addition to high resolution (R similar to 5000) long slit spectroscopy over a narrow bandwidth of the central field. The camera is a proof of concept for the 2m-class Antarctic Cosmic Web Imager telescope, a dedicated experiment to directly detect and map the redshifted lyman alpha fluorescence or Cosmic Web emission we believe possible due to the unique geographical qualities of the site. We present the current status of both projects

An adaptive information-theoretic experimental design procedure for high-to-low fidelity calibration of prostate cancer models

The use of mathematical models to make predictions about tumor growth and response to treatment has become increasingly prevalent in the clinical setting. The level of complexity within these models ranges broadly, and the calibration of more complex models requires detailed clinical data. This raises questions about the type and quantity of data that should be collected and when, in order to maximize the information gain about the model behavior while still minimizing the total amount of data used and the time until a model can be calibrated accurately. To address these questions, we propose a Bayesian information-theoretic procedure, using an adaptive score function to determine the optimal data collection times and measurement types. The novel score function introduced in this work eliminates the need for a penalization parameter used in a previous study, while yielding model predictions that are superior to those obtained using two potential pre-determined data collection protocols for two different prostate cancer model scenarios: one in which we fit a simple ODE system to synthetic data generated from a cellular automaton model using radiotherapy as the imposed treatment, and a second scenario in which a more complex ODE system is fit to clinical patient data for patients undergoing intermittent androgen suppression therapy. We also conduct a robust analysis of the calibration results, using both error and uncertainty metrics in combination to determine when additional data acquisition may be terminated

Intrinsically chiral ferronematic liquid crystals : An inversion of the helical twist sense at the chiral nematic – Chiral ferronematic phase transition

Funding Information: The research was supported by the National Science Centre (Poland) under the grant no. 2016/22/A/ST5/00319. C.T.I. and J.M.D.S. acknowledge the financial support of the Engineering and Physical Sciences Research Council [EP/V048775/1].Peer reviewedPostprin