A new space of generalised vector-valued functions of Bounded Variation

In [15], the authors introduced the space $GBV_\star(\Omega)$ to minimise a class of functionals whose study is motivated by fracture mechanics. In this paper, we extend the definition of $GBV_\star(\Omega)$ to the vectorial case, introducing the space $GBV_\star(\Omega,\mathbb{R}^k)$. We study the main properties of $GBV_\star(\Omega,\mathbb{R}^k)$ and prove a lower semicontinuity result useful for minimisation purposes. With the Direct Method in mind, we adapt the arguments of [15] to show that minimising sequences in $GBV_\star(\Omega,\mathbb{R}^k)$ can be modified to obtain a minimising sequence converging $\mathcal{L}^d$-a.e in $\Omega$

Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

2openInternationalMetagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.openAlbanese, Davide; Donati, ClaudioAlbanese, D.; Donati, C

Gamma-convergence of quadratic functionals perturbed by bounded linear functionals

Given a bounded open set $\Omega\subset \mathbb{R}^n$, we study sequences of quadratic functionals on the Sobolev space $H^1_0(\Omega)$, perturbed by sequences of bounded linear functionals. We prove that their $\Gamma$-limits, in the weak topology of $H^1_0(\Omega)$, can always be written as the sum of a quadratic functional, a linear functional, and a non-positive constant. The classical theory of $G$- and $H$-convergence completely characterises the quadratic and linear parts of the $\Gamma$-limit and shows that their coefficients do not depend on $\Omega$. The constant, which instead depends on $\Omega$ and will be denoted by $-\nu(\Omega)$, plays an important role in the study of the limit behaviour of the energies of the solutions. The main result of this paper is that, passing to a subsequence, we can prove that $\nu$ coincides with a non-negative Radon measure on a sufficiently large collection of bounded open sets $\Omega$. Moreover, we exhibit an example that shows that the previous result cannot be obtained for every bounded open set. The specific form of this example shows that the compactness theorem for the localisation method in $\Gamma$-convergence cannot be easily improved

The Importance of Rock Mass Damage in the Kinematics of Landslides

The stability and kinematics of rock slopes are widely considered to be functions of lithological, structural, and environmental features. Conversely, slope damage features are often overlooked and considered as byproducts of slope deformation. This paper analyzes and discusses the potential role of slope damage, its time-dependent nature, and its control on both the stability of rock slopes and their kinematics. The analysis of several major landslides and unstable slopes, combined with a literature survey, shows that slope damage can play an important role in controlling short- and long-term slope stability. Seasonal and continuously active events cause permanent deformation within the slope due to the accumulation of slope damage features, including rock mass dilation and intact rock fracturing. Rock mass quality, lithology, and scale control the characteristics and complexity of slope damage, as well as the failure mechanism. The authors propose that the role of slope damage in slope kinematics should always be considered in slope stability analysis, and that an integrated characterization–monitoring–numerical modelling approach can enhance our understanding of slope damage, its evolution, and the controlling factors. Finally, it is emphasized that there is currently a lack of guidelines or frameworks for the quantitative assessment and classification of slope damage, which requires a multidisciplinary approach combining rock mechanics, geomorphology, engineering geology, remote sensing, and geophysics

Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.

Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes

Low-grade fibromyxoid sarcoma of the extremities: A clinicopathologic study of 24cases and review of the literature

Low-grade fibromyxoid sarcoma (LGFMS) and hybrid sclerosing epithelioid fibrosarcoma (SEF)/LGFMS have a low potential for recurrence (10%) and metastasis (5%) but they are notorious for late occurring metastases. The aim of this study was to evaluate the outcome of LGFMS and review similar cases reported in the literature. We retrospectively evaluated 24 LGFMS operated at a single Institution. All cases were histologically revised. Mean age was 34 years (range, 8 to 74). Two cases presented areas of SEF (hybrid tumours). Three patients presented with metastasis at diagnosis. A strong cytoplasmic staining for MUC4 antibody was found in the majority of neoplastic cells. RT-PCR was feasible in 6 cases and it detected the presence of FUS-CREB3L2 fusion gene chimeric transcript. Mean follow-up was 44 months (range, 6 to 217). Two patients developed lung metastasis after 9 and 26 months respectively. Low-grade fibromyxoid sarcoma has a various histopathologic spectrum with few cases of LGFMS that share histopathologic resemblance with SEF, thereby reinforcing a possibility of a link within these two. It is of paramount importance an accurate and extensive sampling and examination of the whole specimen, in order to identify higher risk patients

Remote Sensing and Geovisualization of Rock Slopes and Landslides

Over the past two decades, advances in remote sensing methods and technology have enabled larger and more sophisticated datasets to be collected. Due to these advances, the need to effectively and efficiently communicate and visualize data is becoming increasingly important. We demonstrate that the use of mixed- (MR) and virtual reality (VR) systems has provided very promising results, allowing the visualization of complex datasets with unprecedented levels of detail and user experience. However, as of today, such visualization techniques have been largely used for communication purposes, and limited applications have been developed to allow for data processing and collection, particularly within the engineering–geology field. In this paper, we demonstrate the potential use of MR and VR not only for the visualization of multi-sensor remote sensing data but also for the collection and analysis of geological data. In this paper, we present a conceptual workflow showing the approach used for the processing of remote sensing datasets and the subsequent visualization using MR and VR headsets. We demonstrate the use of computer applications built in-house to visualize datasets and numerical modelling results, and to perform rock core logging (XRCoreShack) and rock mass characterization (EasyMineXR). While important limitations still exist in terms of hardware capabilities, portability, and accessibility, the expected technological advances and cost reduction will ensure this technology forms a standard mapping and data analysis tool for future engineers and geoscientists

A Robust SAR Speckle Tracking Workflow for Measuring and Interpreting the 3D Surface Displacement of Landslides

We present a workflow for investigating large, slow-moving landslides which combines the synthetic aperture radar (SAR) technique, GIS post-processing, and airborne laser scanning (ALS), and apply it to Fels landslide in Alaska, US. First, we exploit a speckle tracking (ST) approach to derive the easting, northing, and vertical components of the displacement vectors across the rock slope for two five-year windows, 2010–2015 and 2015–2020. Then, we perform post-processing in a GIS environment to derive displacement magnitude, trend, and plunge maps of the landslide area. Finally, we compare the ST-derived displacement data with structural lineament maps and profiles extracted from the ALS dataset. Relying on remotely sensed data, we estimate that the thickness of the slide mass is more than 100 m and displacements occur through a combination of slumping at the toe and planar sliding in the central and upper slope. Our approach provides information and interpretations that can assist in optimizing and planning fieldwork activities and site investigations at landslides in remote locations

Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy

Erwinia amylovora is a Gram-negative bacterium that colonizes a wide variety of plant species causing recurrent local outbreaks of fire blight in crops of the Rosaceae family. Recent genomic surveys have documented the limited genomic diversity of this species, possibly related to a recent evolutionary bottleneck and a strong correlation between geography and phylogenetic structure of the species. Despite its economic importance, little is known about the genetic variability of co-circulating strains during local outbreaks. Here, we report the genome sequences of 82 isolates of E. amylovora, collected from different host plants in a period of 16 years in Trentino, a small region in the Northeastern Italian Alps that has been characterized by recurrent outbreaks of fire blight in apple orchards. While the genome isolated before 2018 are closely related to other strains already present in Europe, we found a novel subclade composed only by isolates that were sampled starting from 2018 and demonstrate that the endemic population of this pathogen can be composed by mixture of strain

Editorial: Developments of remote sensing and numerical modeling applications for landslide analysis

The Research Topic “Developments of Remote Sensing and Numerical Modeling Applications for Landslide Analysis” gathers high-quality original research articles on case studies covering a broad spectrum of subaerial landslide types from a wide range of places throughout the world