GRASS in the Desert? Developing FOSS tools for monitoring desertification

The use of Change Vector Analysis (CVA) combined with the Tasselled Cap tranform (TCT) is a powerful remote sensing tool to monitor forests and vegetated areas, but its application to arid and semiarid environment is not straightforward. This question is tackled through the calculation of a new set of TCT coefficients using R and GRASS-GIS for SPOT and Landsat satellites, then applied and tested in change detection analysis on a short (seasonal) and a long (decades) temporal scale. Results show that the combined procedure is an effective method to detect changes in desert environment. Furthermore, the new TCT allows the use of this combined procedure for studies in arid and semi-arid regions, eliminating the doubts on its compatibility with the area of study. Further development is the creation of a new GRASS-GIS module to performe CVA, thus enabling the simple usage of this technique, until now not available in most common software

A combined change detection procedure to study desertification using opensource tools

Abstract Background and Methods The paper presents a combination of two unsupervised techniques for change detection studies in arid and semi-arid areas. Among Remote Sensing change detection techniques, unsupervised approaches have the advantage of promptly producing a map of the change between two dates, but often the interpretation of the results is not straightforward, and requires further processing of the image. The aim of the research is to propose a new time effective and semi-automated reproducible technique in order to reduce the weakness of the unsupervised approach in change detection. Two techniques, Change Vector Analysis (CVA) and Maximum Autocorrelation Factor transform of Multivariate Alteration Detector components (MAD/MAF) are chosen to serve the purpose. Results and Conclusions The results of the research, applied to two case studies in the Middle East region, indicate that the chosen techniques complement each other, since MAD/MAF gives a detailed spatial extent while CVA gives the semantic interpretation of the output. The research brings further understanding to the use of both unsupervised procedures and the methodology can be used as a fast semi-automatic preliminary step for more accurate change detection studies. A further output is a new add-on implementing CVA for the GFOSS (Geospatial Free and Open Source Software) project Grass GIS

Remote Sensing Techniques for Change Detection Analysis in Arid and Semi-arid areas

Desertification constitutes a natural hazard for human livelihood, wildlife and vegetation worldwide. Arid and semi-arid areas are the most likely to undergo processes of desertification, and it is a concern of the international community to control, monitor and prevent such a phenomenon. As a mainly arid region, the Middle East is particularly vulnerable to climate-induced impacts on water resources, challenged by high growth population rates and a water-stressed situation. Aim of the reasearch is to investigate Remote Sensing (RS) techniques for desertication studies, with a special focus on the Middle East region. RS is an efficient tool for environmental studies on wide areas of the Earth surface, allowing fast and reproducible analysis on regional and continental scales . For this research two RS methods of change detection analysis have been investigated and further implemented: Change Vector Analysis (CVA), applied to the Tasselled Cap Transform (TCT) outputs, and the Maximum Autocorrelation Factor (MAF) transformation of the Multivariate Alteration Detector (MAD) components (MAD/MAF). The research introduces improvements in the use of both techniques adapting them to desertification studies and proposes a new RS methodology, which has been proven effective in detecting the surface change in arid and semi-arid areas. An added value of the research is the availability of the source code, implemented for this study, to other users, through GFOSS software

Impact of monotherapy on HIV-1 reservoir, immune activation, and co-infection with Epstein-Barr virus

Abstract Objectives Although monotherapy (mART) effectiveness in maintaining viral suppression and CD4 cell count has been extensively examined in HIV-1-infected patients, its impact on HIV-1 reservoir, immune activation, microbial translocation and co-infection with Epstein-Barr Virus (EBV) is unclear. Methods This retrospective study involved 32 patients who switched to mART; patients were studied at baseline, 48 and 96 weeks after mART initiation. Thirty-two patients who continued combined antiretroviral therapy (cART) over the same period of time were included in the study. Markers of HIV-1 reservoir (HIV-1 DNA and intracellular HIV-1 RNA) were quantified by real-time PCR. Markers of T-(CD3(+)CD8(+)CD38(+)) and B-(CD19(+)CD80/86(+) and CD19(+)CD10-CD21(low)CD27(+)) cell activation were evaluated by flow cytometry. Plasma levels of microbial translocation markers were quantified by real-time PCR (16S ribosomal DNA and mitochondrial [mt] DNA) or by ELISA (LPS and sCD14). EBV was typed and quantified by multiplex real-time PCR. Results At baseline, no differences were found between mART and cART groups. Three (10%) mART-treated patients had a virological failure vs none in the cART group. Levels of HIV-1 DNA, intracellular HIV-1 RNA and EBV-DNA remained stable in the mART group, while decreased significantly in the cART group. Percentages of T-and B-activated cells significantly increased in the mART-treated patients, while remained at low levels in the cART-treated ones (p = 0.014 and p<0.001, respectively). Notably, levels of mtDNA remained stable in the cART group, but significantly rose in the mART one (p<0.001). Conclusions Long-term mART is associated with higher levels of T-and B-cell activation and, conversely to cART, does not reduce the size of HIV-1 reservoir and EBV co-infection

Synthetic Population Catalyst : a micro-simulated population of England with circadian activities

Funding: This work was supported by Wave 1 of The UKRI Strategic Priorities Fund under the EPSRC Grant EP/W006022/1, particularly the “Ecosystem of Digital Twin” and “Shocks and Resilience” themes within that grant & The Alan Turing Institute.The Synthetic Population Catalyst (SPC) is an open-source tool for the simulation of populations. Building on previous efforts, synthetic populations can be created for any area in England, from a small geographical unit to the entire country, and linked to geolocalised daily activities. In contrast to most transport models, the output is focussed on the population itself and the way people socially interact together, rather than on a precise modelling of the volume of transport trips from one area to another. SPC is therefore particularly well suited, for example, to study the spread of a pandemic within a population. Other applications include identifying segregation patterns and potential causes of inequality of opportunity amongst individuals. It is fast, thanks to its Rust codebase. The outputs for each lieutenancy area in England are directly available without having to run the code.PostprintPeer reviewe

Speleothems uncover Late Holocene environmental changes across the Nuragic period in Sardinia (Italy): A possible human influence on land use during bronze to post-Iron Age cultural shifts

During the Bronze and Iron Age, Sardinia was home of one of the most technologically advanced Mediterranean societies (the Nuragic culture). Given its key geographical location, the island was also the fulcrum of deep cultural exchanges. Toward the end of the Iron Age, Phoenicians, and especially Carthaginians and Romans, massively frequented Sardinia for different purposes. This marks an important cultural transition for the region, as the ancient Nuragic-related society terminated. At the same time, this impacted the subsistence and land use practices. Together with middle to late Holocene climate changes, the novel anthropic activities had a pivotal role in shaping the landscape around the island. However, high resolution climate and environmental records for these culturally important phases are still lacking in Sardinia. Thus, this paper explores palaeoenvironmental changes from the Bronze Age to post Iron Ages times by using carbonate speleothems from Suttaterra de Sarpis Cave (Urzulei, central east Sardinia), strategically located nearby the Or Murales Nuragic Village. U–Th ages (n = 20) indicate that five stalagmites comprehensively span the last ~7000 years. Peculiarly, they all show an evident stratigraphic discontinuity. Age models attest that hiatuses can be at times associated with the discontinuities, spanning periods of ~1200 to ~200 years. Importantly, the discontinuities occurred from the Late Iron Age to the Roman period. Based on fabric observations, trace elements and δ13C- δ18O analyses, the discontinuities are primarily attributed to a progressive change of land use above the cave. We suppose that deforestation aimed to clearance for agriculture and livestock practices probably was the most impacting factor for infiltration dynamics and soil state, thus affecting the studied speleothems, although archaeological and historical data are absent for the specific study area. Instead, this is in line with the cultural transition occurring in Sardinia toward the end of the Iron Age, with novel agricultural practices imported by the overseas populations. The anthropic disturbance to the millennial-long karst equilibrium possibly overprinted the response of speleothem proxies to climate oscillations, although future higher resolution analyses are necessary to better investigate the evolution of climate during the Holocene as well as its role in the development of ancient civilizations. Indeed, this is the first speleothem-based Holocene palaeoenvironmental reconstruction accomplished in Sardinia. Considering the paucity of natural lakes in this key location, speleothems here demonstrate their potential in exploring humandriven palaeoenvironmental changes during times of cultural transitions within the Mediterranean context

Role of R5 phenotypic variation in mother-to-child transmission of HIV-1

chronic viral infections transmitted to infants: from mechanisms to prevention and care Meetin

Global Issues – Local Alternatives

After realising their theses’ topics were all related to environmental and human sustainability, a group of young researchers from the Erasmus Mundus International Masters in Global Markets, Local Creativities decided they could take action by sharing their research findings in an easily-understandable, non-academic language, impacting communities outside the academic bubble by making knowledge accessible.This book is the result of the ambition of this group of researchers to critically discuss the main issues of our times: environmental emergency and social inequality. Through a collection of thought-provoking case studies, the reader is invited to reflect upon global issues, from the perspective of local initiatives, considering three main aspects of globalisation: space, global dynamics and social scene, and the role of institutions

A self-repair history: compensatory effect of a de novo variant on the FANCA c.2778+83C>G splicing mutation

Introduction: Fanconi anemia (FA) is a genome instability condition that drives somatic mosaicism in up to 25% of all patients, a phenomenon now acknowledged as a good prognostic factor. Herein, we describe the case of P1, a FA proband carrying a splicing variant, molecularly compensated by a de novo insertion. Methods and Results: Targeted next-generation sequencing on P1's peripheral blood DNA detected the known FANCA c.2778 + 83C &gt; G intronic mutation and suggested the presence of a large deletion on the other allele, which was then assessed by MLPA and RT-PCR. To determine the c.2778 + 83C &gt; G splicing effect, we performed a RT-PCR on P1's lymphoblastoid cell line (LCL) and on the LCL of another patient (P2) carrying the same variant. Although we confirmed the expected alternative spliced form with a partial intronic retention in P2, we detected no aberrant products in P1's sample. Sequencing of P1's LCL DNA allowed identification of the de novo c.2778 + 86insT variant, predicted to compensate 2778 + 83C &gt; G impact. Albeit not found in P1's bone marrow (BM) DNA, c.2778 + 86insT was detected in a second P1's LCL established afterward, suggesting its occurrence at a low level in vivo. Minigene assay recapitulated the c.2778 + 83C &gt; G effect on splicing and the compensatory role of c.2778 + 86insT in re-establishing the physiological mechanism. Accordingly, P1's LCL under mitomycin C selection preserved the FA pathway activity in terms of FANCD2 monoubiquitination and cell survival. Discussion: Our findings prove the role of c.2778 + 86insT as a second-site variant capable of rescuing c.2778 + 83C &gt; G pathogenicity in vitro, which might contribute to a slow hematopoietic deterioration and a mild hematologic evolution