Lessons Learnt from Monitoring the Etna Volcano Using an IoT Sensor Network through a Period of Intense Eruptive Activity.

This paper describes the successes and failures after 4 years of continuous operation of a network of sensors, communicating nodes, and gateways deployed on the Etna Volcano in Sicily since 2019, including a period of Etna intense volcanic activity that occurred in 2021 and resulted in over 60 paroxysms. It documents how the installation of gateways at medium altitude allowed for data collection from sensors up to the summit craters. Most of the sensors left on the volcanic edifice during winters and during this period of intense volcanic activity were destroyed, but the whole gateway infrastructure remained fully operational, allowing for a very fruitful new field campaign two years later, in August 2023. Our experience has shown that the best strategy for IoT deployment on very active and/or high-altitude volcanoes like Etna is to permanently install gateways in areas where they are protected both from meteorological and volcanic hazards, that is mainly at the foot of the volcanic edifice, and to deploy temporary sensors and communicating nodes in the more exposed areas during field trips or in the summer season.

Growth Response of Cuttings to Drought and Intermittent Flooding for Three Salix Species and Implications for Riverbank Soil Bioengineering.

Willows are used as cuttings or in fascines for riverbank soil bioengineering, to control erosion with their high resprouting ability and rapid growth. However, water availability is highly variable along riverbanks both in time and space and constitutes a major stress limiting willow establishment. A species-specific understanding of willow cutting response to water stress is critical to design successful riverbank soil bioengineering projects given exclusive use of local species is often recommended. In a three-month greenhouse experiment, we investigated the effects of three soil moisture treatments (drought-soil saturation-intermittent flooding) on survival, biomass production and root growth of cuttings of three willow species used for soil bioengineering along NE American streams (Salix discolor-S. eriocephala-S. interior). Cutting survival was high for all species and treatments (>89%). Biomass production and root volume only differed between species. S. eriocephala produced the highest biomass and root volume, and S. discolor invested more in belowground than aboveground biomass. Root length responded to soil moisture differently between species. Under intermittent flooding, S. eriocephala produced shorter roots, while S. interior produced longer roots. For riverbank soil bioengineering, S. eriocephala should be favored at medium elevation and S. interior at lower elevation.

From Sensor to Cloud: An IoT Network of Radon Outdoor Probes to Monitor Active Volcanoes.

While radon in soil gases has been identified for decades as a potential precursor of volcanic eruptions, there has been a recent interest for monitoring radon in air on active volcanoes. We present here the first network of outdoor air radon sensors that was installed successfully on Mt. Etna volcano, Sicily, Italy in September 2019. Small radon sensors designed for workers and home dosimetry were tropicalized in order to be operated continuously in harsh volcanic conditions with an autonomy of several months. Two stations have been installed on the south flank of the volcano at ~3000 m of elevation. A private network has been deployed in order to transfer the measurements from the stations directly to a server located in France, using a low-power wide-area transmission technology from Internet of Things (IoT) called LoRaWAN. Data finally feed a data lake, allowing flexibility in data management and sharing. A first analysis of the radon datasets confirms previous observations, while adding temporal information never accessed before. The observed performances confirm IoT solutions are very adapted to active volcano monitoring in terms of range, autonomy, and data loss.

Fast-growing willows significantly reduce invasive knotweed spread.

Competitive interactions seem to play a major role in invasive plant success. However, they have mostly been addressed through the invader impacts on other species of the plant community and rarely through the way plant communities can contain alien species. Understanding such mechanisms would help in designing restoration projects using plant community competitive properties to control invasive populations. In this study, we looked at the role of competitive interactions in the success of Fallopia japonica (Houtt.) Ronse Decraene using a native willow frequently used in bioengineering techniques: Salix viminalis L. S. viminalis has a high growth rate and is, as such, a potential candidate to compete with F. japonica in restoration projects of invaded areas. Both species were grown in semi-controlled conditions in mesocosms (truck dumpsters), alone or in competition. Morphological traits (plant height, specific leaf area) as well as biomass (aboveground and underground) were measured on each species during two growing seasons. We also quantified spatial expansion of F. japonica. Even under a dense canopy of S. viminalis, F. japonica was able to survive and grow. However, its performance was significantly reduced compared to monocultures and its spatial colonization was less extended. Although S. viminalis biomass was affected by F. japonica, F. japonica expressed competitive stress through a modification of ramet density and height. There was no significant effect of F. japonica on S. viminalis height, enabling this species to dominate. Synthesis and applications: We conclude that S. viminalis succeeded in reducing F. japonica growth by developing a competitive canopy. Bioengineering techniques aiming at restoring a competitive neighborhood can control F. japonica. However, F. japonica's broad underground extension should be taken into account in any management strategy in order to successfully limit its development and spatial spread.

Specific Targeting of Plant and Apicomplexa Parasite Tubulin through Differential Screening Using In Silico and Assay-Based Approaches.

Dinitroanilines are chemical compounds with high selectivity for plant cell α-tubulin in which they promote microtubule depolymerization. They target α-tubulin regions that have diverged over evolution and show no effect on non-photosynthetic eukaryotes. Hence, they have been used as herbicides over decades. Interestingly, dinitroanilines proved active on microtubules of eukaryotes deriving from photosynthetic ancestors such as Toxoplasma gondii and Plasmodium falciparum, which are responsible for toxoplasmosis and malaria, respectively. By combining differential in silico screening of virtual chemical libraries on Arabidopsis thaliana and mammal tubulin structural models together with cell-based screening of chemical libraries, we have identified dinitroaniline related and non-related compounds. They inhibit plant, but not mammalian tubulin assembly in vitro, and accordingly arrest A. thaliana development. In addition, these compounds exhibit a moderate cytotoxic activity towards T. gondii and P. falciparum. These results highlight the potential of novel herbicidal scaffolds in the design of urgently needed anti-parasitic drugs.

Functional and taxonomic plant diversity for riverbank protection works: bioengineering techniques close to natural banks and beyond hard engineering.

Erosion control is a major issue in the Prealps region since piedmont is subject to both intense flood hazards and anthropic pressure. Riverbank protections may have major impacts on local ecosystem functioning and ecological corridor continuity. This study aimed to estimate the effects of the types of riverbank protection technique (from pure riprap to pure bioengineering) on the taxonomic and ecological composition of plant communities in comparison with unmanaged riverbanks as the referential system. Thirty-eight embankments were sampled in the foothills of the French and Swiss Alps. Four distinct riverbank techniques were analyzed and natural young willow stands were chosen as the referential system. At each site, vegetation was sampled along three transects from the waterline to the top of the riverbank. Plant communities were characterized using biological group composition (growth forms and life history, life strategies and distribution in space and time) and functional diversity indices (MFAD, FDc and wFDc). We identified 177 distinct plant species on 38 sites. Higher species richness levels were observed on bioengineered banks (from an average of 12 species recorded on ripraps to 27 species recorded on bioengineered banks) strongly dominated by Salicaceae species, especially for fascine and cribwall banks. Functional analyses of plant communities highlighted significant differences among bank types (p-value: 0.001) for all selected biological groups. Competitive - ruderal strategy, rooting shoots, stems or leaves that lie down or break off, and unisexual - dioecious, as well as pioneer plants and low shrubs (<4 m tall) distinguished bioengineered bank types. Functional diversity indices confirmed these differences among bank types (MFAD: p-value: 0.002; FDc: p-value: 0.003; wFDc: p-value: 0.005). Riprap always showed the lowest levels on functional diversity indices, fascine and cribwall banks were at the medium level and finally mixed and natural banks the highest level. These results confirm the low ecological potential of purely hard engineering techniques and highlight the similarity of bioengineered techniques and unmanaged riverbanks.

Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities.

Little is still known about the low dose effects of radiation on the microbial communities in the environment. Mineral springs are ecosystems than can be affected by natural radioactivity. These extreme environments are, therefore, observatories for studying the influence of chronic radioactivity on the natural biota. In these ecosystems we find diatoms, unicellular microalgae, playing an essential role in the food chain. The present study aimed to investigate, using DNA metabarcoding, the effect of natural radioactivity in two environmental compartments (i.e. spring sediments and water) on the genetic richness, diversity and structure of diatom communities in 16 mineral springs in the Massif Central, France. Diatom biofilms were collected during October 2019, and a 312 bp region of the chloroplast gene rbcL (coding for the Ribulose Bisphosphate Carboxylase) used as a barcode for taxonomic assignation. A total of 565 amplicon sequence variants (ASV) were found. The dominant ASV were associated with Navicula sanctamargaritae, Gedaniella sp., Planothidium frequentissimum, Navicula veneta, Diploneis vacillans, Amphora copulata, Pinnularia brebissonii, Halamphora coffeaeformis, Gomphonema saprophilum, and Nitzschia vitrea, but some of the ASVs could not be assigned at the species level. Pearson correlation failed to show a correlation between ASV' richness and radioactivity parameters. Non-parametric MANOVA analysis based on ASVs occurrence or abundances revealed that geographical location was the main factor influencing ASVs distribution. Interestingly, 238U was the second factor that explained diatom ASV structure. Among the ASVs in the mineral springs monitored, ASV associated with one of the genetic variants of Planothidium frequentissimum was well represented in the springs and with higher levels of 238U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium.

Assessing radiation dosimetry for microorganisms in naturally radioactive mineral springs using GATE and Geant4-DNA Monte Carlo simulations.

Mineral springs in Massif Central, France can be characterized by higher levels of natural radioactivity in comparison to the background. The biota in these waters is constantly under radiation exposure mainly from the α-emitters of the natural decay chains, with 226Ra in sediments ranging from 21 Bq/g to 43 Bq/g and 222Rn activity concentrations in water up to 4600 Bq/L. This study couples for the first time micro- and nanodosimetric approaches to radioecology by combining GATE and Geant4-DNA to assess the dose rates and DNA damages to microorganisms living in these naturally radioactive ecosystems. It focuses on unicellular eukaryotic microalgae (diatoms) which display an exceptional abundance of teratological forms in the most radioactive mineral springs in Auvergne. Using spherical geometries for the microorganisms and based on γ-spectrometric analyses, we evaluate the impact of the external exposure to 1000 Bq/L 222Rn dissolved in the water and 30 Bq/g 226Ra in the sediments. Our results show that the external dose rates for diatoms are significant (9.7 µGy/h) and comparable to the threshold (10 µGy/h) for the protection of the ecosystems suggested by the literature. In a first attempt of simulating the radiation induced DNA damage on this species, the rate of DNA Double Strand Breaks per day is estimated to 1.11E-04. Our study confirms the significant mutational pressure from natural radioactivity to which microbial biodiversity has been exposed since Earth origin in hydrothermal springs.

The EMBRACE web service collection.

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

Virtual screening identification of novel severe acute respiratory syndrome 3C-like protease inhibitors and in vitro confirmation.

The 3C-like protease (3CL(pro)) of severe acute respiratory syndrome associated coronavirus (SARS-CoV) is vital for SARS-CoV replication and is a promising drug target. Structure based virtual screening of 308307 chemical compounds was performed using the computation tool Autodock 3.0.5 on a WISDOM Production Environment. The top 1468 ranked compounds with free binding energy ranging from -14.0 to -17.09 kcal mol(-1) were selected to check the hydrogen bond interaction with amino acid residues in the active site of 3CL(pro). Fifty-three compounds from 35 main groups were tested in an in vitro assay for inhibition of 3CL(pro) expressed by Escherichia coli. Seven of the 53 compounds were selected; their IC(50) ranged from 38.57±2.41 to 101.38±3.27 µM. Two strong 3CL(pro) inhibitors were further identified as competitive inhibitors of 3CL(pro) with K(i) values of 9.11±1.6 and 9.93±0.44 µM. Hydrophobic and hydrogen bond interactions of compound with amino acid residues in the active site of 3CL(pro) were also identified.

Discovery of novel inhibitors for human intestinal maltase: virtual screening in a WISDOM environment and in vitro evaluation.

Human intestinal maltase (HMA) is an α-glucosidase that hydrolyses α-1,4-linkages from the non-reducing end of malto-oligosaccharides. HMA is an important target to discover of new drugs for the treatment of type 2 diabetes. In this study, 308,307 compounds were virtually screened with HMA using Autodock 3.0.5 in a WISDOM production environment to discover novel inhibitors. The 42 top-scoring free binding energy compounds, representing 17 groups containing potential hydrogen bonding with key residues in the active site pocket of HMA, were tested in vitro for their inhibitory activities against recombinant HMA expressed from Pichia pastoris. Compounds 17 and 18 were competitive inhibitors exclusively for HMA without any in vitro inhibition for human pancreatic α-amylase. The K(i) values were 20 µM for both compound 17 and 18.

Highlighting the impact of social relationships on the propagation of respiratory viruses using percolation theory.

We develop a site-bond percolation model, called PERCOVID, in order to describe the time evolution of all epidemics propagating through respiratory tract or by skin contacts in human populations. This model is based on a network of social relationships representing interconnected households experiencing governmental non-pharmaceutical interventions. As a very first testing ground, we apply our model to the understanding of the dynamics of the COVID-19 pandemic in France from December 2019 up to December 2021. Our model shows the impact of lockdowns and curfews, as well as the influence of the progressive vaccination campaign in order to keep COVID-19 pandemic under the percolation threshold. We illustrate the role played by social interactions by comparing two typical scenarios with low or high strengths of social relationships as compared to France during the first wave in March 2020. We investigate finally the role played by the α and δ variants in the evolution of the epidemic in France till autumn 2021, paying particular attention to the essential role played by the vaccination. Our model predicts that the rise of the epidemic observed in July and August 2021 would not result in a new major epidemic wave in France.

A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast.

Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application "molecularDNA", an example for users of Geant4-DNA, will soon be distributed through Geant4.

Sentinel e-health network on grid: developments and challenges.

Grid technologies have proven their capabilities to settle challenging problems of medical data access. The grid ability to access distributed databases in a secure and reliable way while preserving data ownership opened new perspectives in medical data sharing and disease surveillance. This paper focuses on the implementation challenges of grid-powered sentinel networks within the e-sentinelle project. This initiative aims to create a lightweight grid dedicated to cancer data exchange and enable automatic disease surveillance according to definition of epidemiological alarms. Particularly, issues related to security, patient identification, databases integration, data representation and medical record linkage are discussed.

Grid-based International Network for Flu observation (g-INFO).

The 2009 H1N1 outbreak has demonstrated that continuing vigilance, planning, and strong public health research capability are essential defenses against emerging health threats. Molecular epidemiology of influenza virus strains provides scientists with clues about the temporal and geographic evolution of the virus. In the present paper, researchers from France and Vietnam are proposing a global surveillance network based on grid technology: the goal is to federate influenza data servers and deploy automatically molecular epidemiology studies. A first prototype based on AMGA and the WISDOM Production Environment extracts daily from NCBI influenza H1N1 sequence data which are processed through a phylogenetic analysis pipeline deployed on EGEE and AuverGrid e-infrastructures. The analysis results are displayed on a web portal (http://g-info.healthgrid.org) for epidemiologists to monitor H1N1 pandemics.

Hospital and Population-Based Evidence for COVID-19 Early Circulation in the East of France.

BACKGROUND: Understanding SARS-CoV-2 dynamics and transmission is a serious issue. Its propagation needs to be modeled and controlled. The Alsace region in the East of France has been among the first French COVID-19 clusters in 2020. METHODS: We confront evidence from three independent and retrospective sources: a population-based survey through internet, an analysis of the medical records from hospital emergency care services, and a review of medical biology laboratory data. We also check the role played in virus propagation by a large religious meeting that gathered over 2000 participants from all over France mid-February in Mulhouse. RESULTS: Our results suggest that SARS-CoV-2 was circulating several weeks before the first officially recognized case in Alsace on 26 February 2020 and the sanitary alert on 3 March 2020. The religious gathering seems to have played a role for secondary dissemination of the epidemic in France, but not in creating the local outbreak. CONCLUSIONS: Our results illustrate how the integration of data coming from multiple sources could help trigger an early alarm in the context of an emerging disease. Good information data systems, able to produce earlier alerts, could have avoided a general lockdown in France.

Bedrock radioactivity influences the rate and spectrum of mutation.

All organisms on Earth are exposed to low doses of natural radioactivity but some habitats are more radioactive than others. Yet, documenting the influence of natural radioactivity on the evolution of biodiversity is challenging. Here, we addressed whether organisms living in naturally more radioactive habitats accumulate more mutations across generations using 14 species of waterlice living in subterranean habitats with contrasted levels of radioactivity. We found that the mitochondrial and nuclear mutation rates across a waterlouse species' genome increased on average by 60% and 30%, respectively, when radioactivity increased by a factor of three. We also found a positive correlation between the level of radioactivity and the probability of G to T (and complementary C to A) mutations, a hallmark of oxidative stress. We conclude that even low doses of natural bedrock radioactivity influence the mutation rate possibly through the accumulation of oxidative damage, in particular in the mitochondrial genome.

WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures.

BACKGROUND: Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. MOTIVATION: Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase. METHODS: In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures. RESULTS: On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed. CONCLUSION: The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.

Grid-enabled sentinel network for cancer surveillance.

Recent developments of grid services for secured distributed data management open new perspectives for disease surveillance. In this paper, we report on our initiative to develop a surveillance network for breast cancer in the Auvergne region. The network gathers cytopathology laboratories, structures in charge of cancer screening and institutes in charge of cancer epidemiology. Data stored in cytopathology laboratories are queried through the grid for the purpose of second diagnosis and to produce statistical indicators. The paper describes the network goal and design and discusses specific issues related to patient identification and security.

Centralised versus decentralised management of patients' medical records.

For more than 20 years, many countries have been trying to set up a standardised medical record at the regional or at the national level. Most of them have not reached this goal, essentially due to two main difficulties related to patient identification and medical records standardisation. Moreover, the issues raised by the centralisation of all gathered medical data have to be tackled particularly in terms of security and privacy. We discuss here the interest of a non-centralised management of medical records which would require a specific procedure that gives to the patient access to his/her distributed medical data, wherever he/she is located.