Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of lightning and radar reflectivity factor data assimilation on the very short-term rainfall forecasts of RAMS@ISAC: application to two case studies in Italy

Abstract. In this paper, we study the impact of lightning and radar reflectivity factor data assimilation on the precipitation VSF (very short-term forecast, 3 h in this study) for two severe weather events that occurred in Italy. The first case refers to a moderate and localized rainfall over central Italy that occurred on 16 September 2017. The second case occurred on 9 and 10 September 2017 and was very intense and caused damages in several geographical areas, especially in Livorno (Tuscany) where nine people died. The first case study was missed by several operational forecasts, including that performed by the model used in this paper, while the Livorno case was partially predicted by operational models. We use the RAMS@ISAC model (Regional Atmospheric Modelling System at Institute for Atmospheric Sciences and Climate of the Italian National Research Council), whose 3D-Var extension to the assimilation of radar reflectivity factor is shown in this paper for the first time. Results for the two cases show that the assimilation of lightning and radar reflectivity factor, especially when used together, have a significant and positive impact on the precipitation forecast. For specific time intervals, the data assimilation is of practical importance for civil protection purposes because it changes a missed forecast of intense precipitation (≥40 mm in 3 h) to a correct one. While there is an improvement of the rainfall VSF thanks to the lightning and radar reflectivity factor data assimilation, its usefulness is partially reduced by the increase in false alarms, especially when both datasets are assimilated.
Evaluation of molecular typing for national surveillance of invasive clinical Haemophilus influenzae isolates from Denmark

Haemophilus influenzae is a gram-negative coccobacillus known to cause respiratory and invasive infections. It can possess a polysaccharide capsule that can be categorized into six different serotypes (i.e., Hia, Hib, Hic, Hid, Hie, and Hif) and non-encapsulated strains that are defined as non-typeable. Furthermore, H. influenzae can be characterized into eight biotypes (I–VIII). Traditionally, isolates have been serotyped and biotyped using phenotypic methods; however, these methods are not always reliable. In this study, we evaluate the use of whole-genome sequencing (WGS) for national surveillance and characterization of clinical Danish H. influenzae isolates. In Denmark, all clinical invasive isolates between 2014 and 2021 have been serotyped using a traditional phenotypic latex agglutination test as well as in silico serotyped using the in silico programs “hinfluenzae_capsule_characterization” and “hicap” to compare the subsequent serotypes. Moreover, isolates were also biotyped using a phenotypic enzyme test and the genomic data for the detection of the genes encoding ornithine, tryptophan, and urease. The results showed a 99–100% concordance between the two genotypic approaches and the phenotypic serotyping, respectively. The biotyping showed a 95% concordance between genotyping and phenotyping. In conclusion, our results show that in a clinical surveillance setting, in silico serotyping and WGS-based biotyping are a robust and reliable approach for typing clinical H. influenzae isolates.
Continuous-interval shear wave velocity profiling by auto-source and seismic piezocone tests

A new exploratory procedure for collecting continuous shear wave velocity measurements via cone penetration testing using a special autoseis source is presented whereby wavelets can be generated and recorded every 1 to 10 s. The continuous-interval seismic piezocone test (CiSCPTu) offers a fast, productive, and reliable means to expedite the collection of downhole shear wave velocity profiles, as well as additional readings on cone tip resistance, sleeve friction, and penetration porewater pressures with depth. A site in Windsor, Virginia, is utilized for illustrating the collection of data, calibration, and post-processing issues arising from large numbers of wavelets that require filtering, windowing, and selection in both time and frequency domain analyses. At the test site, the geology consists of shallow Holocene deposits of clays and sands to 8 m that are underlain by much stiffer calcareous sandy marine clay soils of Miocene age, which extend beyond the termination depths of the soundings at 30 m.
Rapid concurrent measurement of the soil water characteristics curve and the hydraulic conductivity function utilizing the continuous pressurization method

Natural disasters including earthquakes, typhoons and heavy rainfalls induce various risks such as slope failures. The conventional unsaturated soils hydrological properties mainly the Soil Water Characteristics Curve (SWCC) and the Hydraulic Conductivity Function (HCF) determination techniques are limited due to the complexity and prolonged time required. Thus a simple method that considers short time and high accuracy under the drying and the wetting phases considering remolded and undisturbed samples is lacking. Through this paper, a novel systematic testing setup utilizing the Continuous Pressurization Method (CPM) that allows rapid, concurrent, continuous, direct determination of the SWCC and the HCF considering both remolded and undisturbed samples was developed. It was found that the air pressurizing rate influence on the obtained SWCC using the developed system can be neglected. It was confirmed that remolded samples do not properly represent the in-situ conditions with significant error that should be carefully considered. It must be noted that applying low air pressurizing rate induces almost linear suction profile, however, it changes into higher order non-linear profile when applying high air pressurizing rates or achieving low degrees of saturation. A correction function based on Van Genuchten (VG) model was proposed which has finally led to obtaining accurate reliable HCFs. Finally, it was concluded that the developed system is rapid, direct, reliable, continuous with accurate repeatability that allows concurrent determination of both the SWCC and the HCF under the drying and wetting phases. Where the system allows concurrent determination of the SWCC and HCF in less than 7% of the testing time required using the conventional methods and considers testing both remolded and undisturbed soil samples.
Evidence for microbial iron reduction in the methanic sediments of the oligotrophic southeastern Mediterranean continental shelf

Abstract. Dissimilatory iron reduction is probably one of the oldest types of metabolisms that still participates in important biogeochemical cycles, such as those of carbon and sulfur. It is one of the more energetically favorable anaerobic microbial respiration processes and is usually coupled to the oxidation of organic matter. Traditionally this process is thought to be limited to the shallow part of the sedimentary column in most aquatic systems. However, iron reduction has also been observed in the methanic zone of many marine and freshwater sediments, well below its expected zone and occasionally accompanied by decreases in methane, suggesting a link between the iron and the methane cycles. Nevertheless, the mechanistic nature of this link (competition, redox or other) has yet to be established and has not been studied in oligotrophic shallow marine sediments. In this study we present combined geochemical and molecular evidences for microbial iron reduction in the methanic zone of the oligotrophic southeastern (SE) Mediterranean continental shelf. Geochemical porewater profiles indicate iron reduction in two zones, the uppermost part of the sediment, and the deeper zone, in the layer of high methane concentration. Results from a slurry incubation experiment indicate that the deep methanic iron reduction is microbially mediated. The sedimentary profiles of microbial abundance and quantitative PCR (qPCR) of the mcrA gene, together with Spearman correlation between the microbial data and Fe(II) concentrations in the porewater, suggest types of potential microorganisms that may be involved in the iron reduction via several potential pathways: H2 or organic matter oxidation, an active sulfur cycle, or iron-driven anaerobic oxidation of methane. We suggest that significant upward migration of methane in the sedimentary column and its oxidation by sulfate may fuel the microbial activity in the sulfate methane transition zone (SMTZ). The biomass created by this microbial activity can be used by the iron reducers below, in the methanic zone of the sediments of the SE Mediterranean.
Pluto's Interaction With Energetic Heliospheric Ions

Pluto energies of a few kiloelectron volts and suprathermal ions with tens of kiloelectron volts and above. We measure this population using the Pluto Energetic Particle Spectrometer Science Investigation (PEPSSI) instrument on board the New Horizons spacecraft that flew by Pluto in 2015. Even though the measured ions have gyroradii larger than the size of Pluto and the cross section of its magnetosphere, we find that the boundary of the magnetosphere is depleting the energetic ion intensities by about an order of magnitude close to Pluto. The intensity is increasing exponentially with distance to Pluto and reaches nominal levels of the interplanetary medium at about 190RP distance. Inside the wake of Pluto, we observe oscillations of the ion intensities with a periodicity of about 0.2 hr. We show that these can be quantitatively explained by the electric field of an ultralow‐frequency wave and discuss possible physical drivers for such a field. We find no evidence for the presence of plutogenic ions in the considered energy range.
Flood vulnerability assessment using a GIS‐based multi‐criteria approach—The case of Attica region

The identification of flood‐prone areas is a fundamental component of rational urban planning and proper natural disaster management policy. The aim of the present study is to introduce a framework for the identification of flood‐prone areas using geographical information systems techniques and decision‐making, based on a comparative evaluation for various scenarios. As a case study, the Attica region in Greece is selected, which is occasionally affected by heavy rainfall, the main cause of flooding in the region, coupled with the fact that human activities and urbanization of recent years play a significant role in flood occurrence. In this context, the development and application of a GIS‐based multi‐criteria analysis method for the determination of areas susceptible to flood events is initially presented. The entire spatial analysis is performed using SAGA 6.3. 0 and ArcMap 10.2 Desktop, by applying a number of alternative modifications and, finally, by evaluating different scenarios regarding methods for the criteria standardization, criteria hierarchy and factors' weighting estimation. The proposed framework has an advantage among other approaches, since it takes into account mainly static data that are linked to flooding, such as the topography and land cover distribution and it can be easily customized in ungauged catchments.
Une approche de résumé automatique basée sur les collocations (A Collocation-Driven Approach to Text Summarization)

Dans cet article, nous décrivons une nouvelle approche pour la création de résumés extractifs – tâche qui consiste à créer automatiquement un résumé pour un document en sélectionnant un sous-ensemble de ses phrases – qui exploite des informations collocationnelles spécifiques à un domaine, acquises préalablement à partir d’un corpus de développement. Un extracteur de collocations fondé sur l’analyse syntaxique est utilisé afin d’inférer un modèle de contenu qui est ensuite appliqué au document à résumer. Cette approche a été utilisée pour la création des versions simples pour les articles de Wikipedia en anglais, dans le cadre d’un projet visant la création automatique d’articles simplifiées, similaires aux articles recensées dans Simple English Wikipedia. Une évaluation du système développé reste encore à faire. Toutefois, les résultats préalables obtenus pour les articles sur des villes montrent le potentiel de cette approche guidée par collocations pour la sélection des phrases pertinentes.
An Ensemble Square Root Filter for the joint assimilation of surface soil moiture and leaf area index within LDAS-Monde: application over the Euro-Mediterranean region

Abstract. This paper introduces an Ensemble Square Root Filter (EnSRF), a deterministic Ensemble Kalman Filter, to the context of assimilating jointly observations of surface soil moisture (SSM) and leaf area index (LAI) in the Land Data Assimilation System LDAS-Monde. By ingesting those satellite-derived products, LDAS-Monde constrains the Interaction between Soil, Biosphere and Atmosphere (ISBA) land surface model (LSM), coupled with the CNRM (Centre National de Recherches Météorologiques) version of the Total Runoff Integrating Pathways (CTRIP), to improve the reanalysis of land surface variables (LSVs). To evaluate its ability to produce improved LSVs reanalyses, the EnSRF is compared with the Simplified Extended Kalman, which has been routinely operated in LDAS-Monde, in a real case over the well-studied Euro-Mediterranean region at a 0.25° spatial resolution between 2008 and 2017. Both data assimilation approaches provide a positive impact on SSM and LAI estimates with respect to the model alone, putting them closer to assimilated observations. SEKF and EnSRF have a similar behaviour for LAI showing performances that are influenced by the vegetation type. For SSM, EnSRF estimates tend to be closer to observations than SEKF. The impact of assimilating SSM and LAI is also assessed on unobserved soil moisture in the other layers of soil. Unobserved control variables are updated in the EnSRF through covariances and correlations sampled from the ensemble linking them to observed control variables. In our context, a strong correlation between SSM and soil moisture in deeper soil layers is exhibited, as expected, showing seasonal patterns that vary geographically. Moderate correlation and anti-correlations are also noticed between LAI and soil moisture in spring, summer and autumn, their absolute value tending to be larger for soil moisture in root-zone areas, showing that assimilating LAI can have an influence on soil moisture. Finally an independent evaluation of both assimilation approaches is conducted using satellite estimates of evapotranspiration and gross primary production (GPP) as well as measures of river discharges from gauging stations. The EnSRF shows a systematic albeit moderate improvement for evapotranspiration and GPP and a highly positive impact on river discharges, while the SEKF exhibits a more contrasting performance.
Modeled and Observed Volcanic Aerosol Control on Stratospheric NOy and Cly

Decreases in stratospheric NOx associated with enhanced aerosol have been observed after large volcanic eruptions, for example, after the eruption of Mount Pinatubo in 1991. While the 1991 Mount Pinatubo eruption was the last large explosive eruption, recent studies have shed light on the impacts of moderate‐sized eruptions since the year 2000 on the global stratospheric aerosol budget. We use an ensemble of simulations from a coupled climate‐chemistry model to quantify and analyze changes in NO and NO2 (NOx), N2O5, HNO3, ClO, and ClONO2 during periods of increased stratospheric volcanic aerosol concentrations since 2000. By using an ensemble approach, we are able to distinguish forced responses from internal variability. We also compare the model ensemble results to satellite measurements of these changes in atmospheric composition, including measurements from the Optical Spectrograph and Infrared Imaging Spectrometer on the Odin satellite and the Aura Microwave Limb Sounder. We find decreases in stratospheric NOx concentrations up to 20 hPa, consistent with increases in stratospheric HNO3 concentrations. The HNO3 perturbations also extend higher, up to 5 hPa, associated with periods of increased volcanic aerosol concentrations in both model simulations and observations, though correlations with volcanic aerosol are considerably higher in the model simulations. The model simulates increases in ClO at altitudes and magnitudes similar to the NOx reductions, but this response is below the detectable limit in the available observations (100 pptv). We also demonstrate the value of accounting for transport‐related anomalies of atmospheric trace gases by regression onto N2O anomalies.
Improving the reproducibility of geospatial scientific workflows: the use of geosocial media in facilitating disaster response

ABSTRACT Reproducibility is widely regarded as crucial for scientific studies, yet there is still a lack of reproducibility in geospatial research. New sources of crowdsourced geoinformation provide new opportunities, but also complicate the reproducibility situation. Consequently, there is untapped potential in the domain of disaster response to reuse scientific methodology. Shared, executable scientific workflows can help in improving reproducibility. In this paper, we created reproducible scientific workflows for disaster response from three published studies using geosocial media sources. They have been adapted to a scientific workflow management system to investigate and evaluate their suitability for the creation of geospatial footprints of wildfire events from Twitter data. We investigated how scientific workflows adapt to various analytical processes and compared their performance using MODIS active fires data as ground truth. A systematic qualitative and quantitative evaluation demonstrated that scientific workflows can help increase the reproducibility of geospatial analytics.
Fishery and population dynamics of Epinephelus malabaricus (Bloch & Schneider, 1801) off Tuticorin, southeast coast of India

Fishery, population characteristics and stock estimates of grouper with special reference to Epinephelus malabaricus from Tuticorin were carried out during 2015-2017. Among the groupers, E. malabaricus was the dominant resource contributing 42.2%, with an annual average production of 420t along this region. The asymptotic length (L∞), growth coefficient (K) and arbitrary origin of growth (t0) were estimated at 99.75 cm, 0.53 y-1 and 0.18 respectively. The mortality parameters, the instantaneous total mortality rate (Z), fishing mortality (F) and natural mortality rates (M) were estimated at 1.14 y-1, 0.62 y-1 and 0.52 y-1 respectively. The recruitment season was during April to August. The length structured virtual population (VPA) analysis revealed a heavy fishing pressure on length group between 40 and 55cm and there is no sign of recruitment over-fishing in this region. The estimated maximum sustainable yield (MSY) and annual catch were 384 t and 420 t respectively. E. malabaricus was optimally exploited as the exploitation ratio (E) was 0.54 but the study infers that further increase in effort may have a detrimental effect on the stock of this species. The results of this study will serve as baseline information for formulating future management measures for the resource along the coast.
Mediterranean Specific Climate Classification and Future Evolution
Under RCP Scenarios

Abstract. The Mediterranean is one of the most sensitive regions to anthropogenic and climatic changes mostly affecting its water resources and related practices. With multiple studies raising serious concerns of climate shifts and aridity expansion in the region, this one aims to establish a new high resolution classification for hydrology purposes based on Mediterranean specific climate indices. This classification is useful in following up hydrological (water resources management, floods, droughts, etc.), and ecohydrological applications such as Mediterranean agriculture like olive cultivation and other environmental practices. The proposed approach includes the use of classic climatic indices and the definition of new climatic indices mainly precipitation seasonality index Is or evapotranspiration threshold SPET both in line with river flow regimes, a Principal Component Analysis to reduce the number of indices, K-Means classification to distribute them into classes and finally the construction of a decision tree based on the distances to classes kernels to reproduce the classification without having to repeat the whole process. The classification was set and validated by WorldClim-2 at 1-km high resolution gridded data for the 1970–2000 baseline period and 144 stations data over 30 to 120 years, both at monthly time steps. Climatic classes coincided with a geographical distribution in the Mediterranean ranging from the most seasonal and dry class in the south to the least seasonal and most humid class in the North, showing up the climatic continuity from one place to another and enhancing the visibility of change trends. The MED-CORDEX ALADIN historical and projected data at 12-km resolution simulated under RCP 4.5 and 8.5 scenarios for the 2070–2100 period served to assess the climate change impact on this classification by superimposing the projected changes on the baseline high resolution classification. Both RCP scenarios showed a 7 % to 9 % increase of the average seasonality index Is and 3 % to 20 % increase of the average aridity index IArid for the least seasonal classes. These classes located to the north are slowly evolving towards moderate coastal classes which might affect hydrologic regimes due to shorter humid seasons and earlier snowmelts. This kind of classification might be reproduced at the global scale, using same or other climatic indices specific for each region highlighting their physiographic characteristics and hydrological response.
Unsaturated behavior of an earthfill dam during coupled initial impoundment and a prolonged rainfall

Newly constructed earth-fill dams in a residual soil rich area have a high probability of failure occurrence in the first five years of operation. Monitoring a rate of the first impoundment of the dams is critical for monitoring the effectiveness and designed function of the dam over its service life. However, stability of the dams is uncertain under influential factors such as variability of soil properties of support foundations, simultaneous increases of water level in the upstream and infiltration in downstream dam surface from prolonged heavy rainfall event. In this study, failure mechanism for an earth-fill dam due to concurrent rises in water level upstream and rainfall infiltration was investigated using saturated-unsaturated soil principles. Seepage was analyzed using Finite Element Method and slope stability was analyzed using Limit Equilibrium Method. Results of the failure mechanism were compared and discussed with respect to varying stiffness of residual soil support foundation, coupled rising water reservoir and applied prolonged rainfall.