SARS-CoV-2 genomic monitoring in the São Paulo State unveils new sublineages of the AY.43 strain

Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in S&atildeo Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies

The recent stress state of Germany – results of a geomechanical–numerical 3D model

A decisive criterion for the selection and the long-term safety of a deep geological repository for high radioactive waste is the crustal stress state and its future changes. The basis of any prognosis is the recent crustal stress state, but the state of knowledge in Germany is quite low in this respect. There are stress orientation data provided by the World Stress Map (WSM, Heidbach et al., 2018) and stress magnitude data from a database (Morawietz et al., 2020) for Germany, both providing selective information on the recent stress field. However, these data are often incomplete, of low quality and spatially unevenly distributed. Therefore, a 3D continuous description is not possible with these data so far, at most for the orientation of the maximum horizontal stress (SHmax), but not for the most important magnitudes of the minimum (Shmin) and SHmax. In the course of the SpannEnD project, a geomechanical–numerical 3D model of Germany is created, with which a continuous description of the complete tensor of the recent stress field in Germany is possible. The model covers an area of 1250×1000 km2 from Poland in the east, to France in the west, from Italy in the south to Scandinavia in the north. The depth extent is 100 km. Even though the focus is primarily on Germany, the model area was chosen to be so wide to minimize boundary effects and for a simplified definition of the displacement boundary conditions, which are ideally oriented perpendicular or parallel to the orientation of SHmax. The model contains a total of 21 units: The upper part of the lithospheric mantle, the lower crust, four laterally overlapping units of the upper crust, and 14 stratigraphic units of the sedimentary cover. The stratigraphic subdivision of the sedimentary cover is only done in the core area of the model; because this area is the focus of our study, our calibration data are mainly from this region and well-resolved geometry data are available. Outside of the core area, the sediments are grouped into an undifferentiated unit. The units are parameterized with density and elastic material parameters (Poisson's ratio and Young's modulus). The model has a lateral resolution of 2.5×2.5 km2 and a vertical resolution of a maximum of 240 m; in total it includes 11.1 million hexahedral elements. The equilibrium of forces between body and surface forces is solved by finite element method. The model is calibrated with Shmin and SHmax magnitudes from the WSM and data from the stress magnitude database. First, an initial stress state is generated and in a second step displacement boundary conditions are defined at the model edges, which are adjusted until a best-fit to the calibration data is found. The results show good agreement with both the SHmax orientation data from the WSM and the magnitudes of the two principal horizontal stresses (Shmin and SHmax) from the magnitude database.

The dynamics of changes within grammatical gender of dialectal nouns – selected issues

Due to problems with obtaining the materials and the description thereof, dialectal inflection is an element of language which does not attract lots of dialectologists’ attention. On the other hand, the inflection of Wielkopolska dialects poses more problems in the description because there is no starting point in the form of previous characteristics of inflection that would create a need for a continuous description that shows the changes in the evolution of a dialect. The language spoken in rural areas in the late 20th and the early 21st centuries has entered a stage of dynamic changes on all its levels. This fact cannot be disregarded in selecting the appropriate research tools. Dialectal inflection cannot be unambiguously categorised, it is full of inconsistencies and deviations from (what seems to be) the adopted paradigm. As a result, it is much more interesting to show it as a flexible creation of oral language i.e. in a dynamic way, resulting from statistical analyses. The dynamics of inflection forms within grammatical gender is a part of a larger monograph dedicated to the gender-related variability of nouns and the change of gender in the course of inflection and the well-recognised opposition of masculine gender and non-masculine gender. My intention was not only to describe phenomena of grammatical gender of the nouns recorded in contemporary Wielkopolska as well as to show the changes against the material from the 1950s–1980s. The gender category defies attempts at restoring some normative order in it. Oral language is particularly susceptible to gender-related variations where the rules of correction are suspended. Oral language tends to be dynamic and this active nature determines the intensity of the specific features of the spoken variety of the Polish language – the right form is created when an act of speech appears (conformity with the general Polish norm does not count – communication prevails). Despite its specificity, the spoken variety stays within the more or less flexible language norm. An analysis of the materials intended to illustrate the dynamics of changes within grammatical gender leads to drawing general conclusions. Dialects are a variety of the national language to which we would like to attribute many distinctive historical and even pre-historical features. However, this is a variety of language which evolves as do the other varieties of the national language. Speakers will always choose forms which suffice for an efficient act of communication. Dialects are at a stage of their development where researchers try to determine elements typical of a dialect and forget to examine their latest structure which results from the latest communication needs of speakers in rural areas.

An open-access stress magnitude database for Germany and adjacent regions

Knowledge of the crustal stress state is important for the assessment of subsurface stability. In particular, stress magnitudes are essential for the calibration of geomechanical models that estimate a continuous description of the 3-D stress field from pointwise and incomplete stress data. Well established is the World Stress Map Project, a global and publicly available database for stress orientations, but for stress magnitude data only local data collections are available. Herein, we present the first comprehensive and open-access stress magnitude database for Germany and adjacent regions, consisting of 568 data records. In addition, we introduce a quality ranking scheme for stress magnitude data for the first time.

Deep Learning of (Periodic) Minimal Coordinates for Multibody Simulations

Mechanical systems are typically described through multi-body models with redundant coordinates, related by imposed constraints, where the dynamics is expressed with Differential Algebraic Equations. Alternatively, for rigid models, it may be preferable to employ minimal coordinates that do not require additional constraints, thus leading to Ordinary Differential Equations. However, to reduce a general multibody model to minimal coordinates and perform the simulation in the reduced space, the mapping between the minimal coordinates and the full coordinates is required. In this work, it is proposed to approximate such mapping using a neural network. In order to avoid overfitting and guarantee a continuous description of the solution manifold, the multibody dynamics information are included in the neural network training. The particular case where periodic minimal coordinates are required is treated and validated. In general, the methodology can be used when the mapping is unknown such as for spatial mechanisms with closed loops.

Collective migration and patterning during early development of zebrafish posterior lateral line

The morphogenesis of zebrafish posterior lateral line (PLL) is a good predictive model largely used in biology to study cell coordinated reorganization and collective migration regulating pathologies and human embryonic processes. PLL development involves the formation of a placode formed by epithelial cells with mesenchymal characteristics which migrates within the animal myoseptum while cyclically assembling and depositing rosette-like clusters (progenitors of neuromast structures). The overall process mainly relies on the activity of specific diffusive chemicals, which trigger collective directional migration and patterning. Cell proliferation and cascade of phenotypic transitions play a fundamental role as well. The investigation on the mechanisms regulating such a complex morphogenesis has become a research topic, in the last decades, also for the mathematical community. In this respect, we present a multiscale hybrid model integrating a discrete approach for the cellular level and a continuous description for the molecular scale. The resulting numerical simulations are then able to reproduce both the evolution of wild-type (i.e. normal) embryos and the pathological behaviour resulting form experimental manipulations involving laser ablation. A qualitative analysis of the dependence of these model outcomes from cell-cell mutual interactions, cell chemical sensitivity and internalization rates is included. The aim is first to validate the model, as well as the estimated parameter values, and then to predict what happens in situations not tested yet experimentally. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems'.

World Stress Map Beyond Orientations - The First Quality Ranking Scheme for Stress Magnitude Data

<p>The World Stress Map (WSM) compiles orientations of the maximum horizontal stress S<sub>Hmax</sub> and provides the only public global database of this kind. To make the S<sub>Hmax</sub> orientation data from a wide range of stress indicators comparable, a quality ranking scheme has been developed. However, for the assessment of subsurface stability, not only the orientations but also data of the principal stress magnitudes are essential to calibrate 3D geomechanical-numerical models that deliver a continuous description of the complete 3D stress tensor. Thus, a comprehensive extension of the WSM database with quality-ranked stress magnitude data is needed. In a pilot study, we compiled an open-access stress magnitude database for Germany and adjacent regions, consisting of 568 data records. Indicators of stress magnitudes are diverse and include e.g. hydraulic fracturing and overcoring. To make data from different sources comparable, we developed a quality ranking scheme for stress magnitude data for the first time. In contrast to the established WSM quality ranking for S<sub>Hmax</sub> orientation data records, estimates of stress magnitudes cannot be averaged over large rock volumes or depth ranges. Instead, each point-wise information has to be considered separately. Thus, we developed a new approach for the quality ranking scheme of S<sub>hmin</sub> magnitude data records which considers both the type of stress magnitude indicator and the degree of information availability. We present the results of our work including the data quality ranking scheme, which will serve as a template for a global stress compilation within the framework of the WSM project. The next countries and regions that we will explore are Australia, Scandinavia and India. We invite you to contribute to this project in your area or country of interest and to join the WSM team as an official collaborator.</p>