Land Cover Classification from Very High-Resolution UAS Data for Flood Risk Mapping.

Monitoring the world's areas that are more vulnerable to natural hazards has become crucial worldwide. In order to reduce disaster risk, effective tools and relevant land cover (LC) data are needed. This work aimed to generate a high-resolution LC map of flood-prone rural villages in southwest Niger using multispectral drone imagery. The LC was focused on highly thematically detailed classes. Two photogrammetric flights of fixed-wing unmanned aerial systems (UAS) using RGB and NIR optical sensors were realized. The LC input dataset was generated using structure from motion (SfM) standard workflow, resulting in two orthomosaics and a digital surface model (DSM). The LC system is composed of nine classes, which are relevant for estimating flood-induced potential damages, such as houses and production areas. The LC was generated through object-oriented supervised classification using a random forest (RF) classifier. Textural and elevation features were computed to overcome the mapping difficulties due to the high spectral homogeneity of cover types. The training-test dataset was manually defined. The segmentation resulted in an F1_score of 0.70 and a median Jaccard index of 0.88. The RF model performed with an overall accuracy of 0.94, with the grasslands and the rocky clustered areas classes the least performant.

Evaluation of Different LiDAR Technologies for the Documentation of Forgotten Cultural Heritage under Forest Environments.

In the present work, three LiDAR technologies (Faro Focus 3D X130-Terrestrial Laser Scanner, TLS-, Kaarta Stencil 2-16-Mobile mapping system, MMS-, and DJI Zenmuse L1-Airborne LiDAR sensor, ALS-) have been tested and compared in order to assess the performances in surveying built heritage in vegetated areas. Each of the mentioned devices has their limits of usability, and different methods to capture and generate 3D point clouds need to be applied. In addition, it has been necessary to apply a methodology to be able to position all the point clouds in the same reference system. While the TLS scans and the MMS data have been geo-referenced using a set of vertical markers and sphere measured by a GNSS receiver in RTK mode, the ALS model has been geo-referenced by the GNSS receiver integrated in the unmanned aerial system (UAS), which presents different characteristics and accuracies. The resulting point clouds have been analyzed and compared, focusing attention on the number of points acquired by the different systems, the density, and the nearest neighbor distance.

Towards a Combined Use of Geophysics and Remote Sensing Techniques for the Characterization of a Singular Building: "El Torreón" (the Tower) at Ulaca Oppidum (Solosancho, Ávila, Spain).

This research focuses on the study of the ruins of a large building known as "El Torreón" (the Tower), belonging to the Ulaca oppidum (Solosancho, Province of Ávila, Spain). Different remote sensing and geophysical approaches have been used to fulfil this objective, providing a better understanding of the building's functionality in this town, which belongs to the Late Iron Age (ca. 300-50 BCE). In this sense, the outer limits of the ruins have been identified using photogrammetry and convergent drone flights. An additional drone flight was conducted in the surrounding area to find additional data that could be used for more global interpretations. Magnetometry was used to analyze the underground bedrock structure and ground penetrating radar (GPR) was employed to evaluate the internal layout of the ruins. The combination of these digital methodologies (surface and underground) has provided a new perspective for the improved interpretation of "El Torreón" and its characteristics. Research of this type presents additional guidelines for better understanding of the role of this structure with regards to other buildings in the Ulaca oppidum. The results of these studies will additionally allow archaeologists to better plan future interventions while presenting new data that can be used for the interpretation of this archaeological complex on a larger scale.

Loosely Coupled GNSS and UWB with INS Integration for Indoor/Outdoor Pedestrian Navigation.

The growth of location-based services (LBS) has increased rapidly in last years, mainly due to the possibility to exploit low-cost sensors installed in portable devices, such as smartphones and tablets. This work aims to show a low-cost multi-sensor platform developed by the authors in which an ultra-wideband (UWB) indoor positioning system is added to a classical global navigation satellite systems-inertial navigation system (GNSS-INS) integration, in order to acquire different synchronized data for further data fusion analysis in order to exploit seamless positioning. The data fusion is based on an extended Kalman filter (EKF) and on a geo-fencing approach which allows the navigation solution to be provided continuously. In particular, the proposed algorithm aims to solve a navigation task of a pedestrian user moving from an outdoor space to an indoor environment. The methodology and the system setup is presented with more details in the paper. The data acquired and the real-time positioning estimation are analysed in depth and compared with ground truth measurements. Particular attention is given to the UWB positioning system and its behaviour with respect to the environment. The proposed data fusion algorithm provides an overall horizontal and 3D accuracy of 35 cm and 45 cm, respectively, obtained considering 5 different measurement campaigns.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

BACKGROUND: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. FINDINGS: PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. CONCLUSIONS: PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.

Interferon regulatory factor 5 is a potential target of autoimmune response triggered by Epstein-barr virus and Mycobacterium avium subsp. paratuberculosis in rheumatoid arthritis: investigating a mechanism of molecular mimicry.

OBJECTIVES: Rheumatoid arthritis (RA) is a chronic disease characterised by a pro-inflammatory cytokines linked erosive joint damage and by humoral and cellular response against a broad range of self-peptides. Molecular mimicry between Epstein-Barr virus (EBV), Mycobacterium avium subsp. paratuberculosis (MAP) and host peptides has long been regarded as an RA pathogenetic mechanism. Using bioinformatic analysis we identified high sequence homology among interferon regulatory factor 5 (IRF5), EBV antigen BOLF1 and MAP antigen MAP_4027. Our objective was to evaluate the presence in sera of RA patients of antibodies (Abs) directed against human homologous IRF5 cross-reacting with BOLF1 and MAP_4027. METHODS: Frequency of reactivity against IRF5424-434, BOLF1305-320 and MAP_402718-32 was tested by indirect ELISA in sera from 71 RA patients and 60 healthy controls (HCs). RESULTS: RA sera show a remarkable high frequency of reactivity against IRF5424-434 in comparison to HCs (69% vs. 8%; p<0.0001). Similarly, seroreactivity against BOLF1305-320 was more frequently detected in RA sera than in HCs counterpart (58% vs. 8%; p<0.0001). Frequency of Abs against MAP_402718-32 was 17% in RA sera vs. 5% in HCs with a p-value at the threshold level (p<0.051). Prevalence of Abs against at least one of the assessed epitopes reached 72% in RA patients and 15% among HCs. Levels of Abs in RA patients were significantly related to systemic inflammation. CONCLUSIONS: IRF5 is a potential autoimmune target of RA. Our results support the hypothesis that EBV and MAP infections may be involved in the pathogenesis of RA, igniting a secondary immune response that cross-reacts against RA self-peptides.

Rheumatoid arthritis patient antibodies highly recognize IL-2 in the immune response pathway involving IRF5 and EBV antigens.

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by a progressive joint damage due to largely unknown environmental factors acting in concert with risk alleles conferring genetic susceptibility. A major role has been attributed to viral infections that include past contacts with Epstein-Barr virus (EBV) and, more recently, to non-protein coding sequences of human endogenous retrovirus K (HERV-K) integrated in the human genome. Molecular mimicry between viral and self proteins is supposed to cause the loss of immune tolerance in predisposed hosts. There are evidences that anti-IL-2 antibodies (Abs) are present in subjects affected by autoimmune diseases and may be responsible for alterations in regulatory T cell responses. In this study, we evaluated the levels of Abs against IL-2, viral epitopes and interferon regulatory factor 5 (IRF5) in 140 RA patients and 137 healthy controls (HCs). Ab reactivity reached the highest levels for IRF5, EBV and IL-2 (56%, 44% and 39%, respectively) in RA with significantly lower values among HCs (7-9%, p < 0.0001), which suggests a possible cross-reaction between IRF5/EBV homologous antigens and shifts in T cell balance disrupted by anti-IL-2 Abs.

wft4galaxy: a workflow testing tool for galaxy.

MOTIVATION: Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way to automatically test Galaxy workflows and ensure their correctness has appeared in the literature. RESULTS: With wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container-the latter reducing installation effort to a minimum. AVAILABILITY AND IMPLEMENTATION: Available at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0. CONTACT: marcoenrico.piras@crs4.it.

Asymmetric dimethylarginine and arterial stiffness in patients with rheumatoid arthritis: A case-control study.

OBJECTIVE: To investigate whether levels of asymmetric dimethylarginine (ADMA), as a measure of endothelial dysfunction, are higher in patients with rheumatoid arthritis compared with healthy control subjects. The relationships between ADMA and surrogate measures of arterial stiffness were evaluated. METHODS: Patients with rheumatoid arthritis and healthy control subjects were recruited. ADMA was quantified via enzyme-linked immunosorbent assay. Arterial stiffness was evaluated using pulse wave analysis. RESULTS: There was no significant difference in plasma ADMA concentration between patients with rheumatoid arthritis (n = 30) and healthy controls (n = 30). Aortic augmentation pressure was significantly higher in patients than in controls. C-reactive protein and Health Assessment Questionnaire score were independent predictors of arterial stiffness in patients. There was no relationship between ADMA concentration and aortic augmentation pressure in the study population as a whole. CONCLUSIONS: Arterial stiffness appears to be increased in rheumatoid arthritis and independently associated with systemic inflammation and physical disability. ADMA concentration was not increased in this small group of patients with rheumatoid arthritis compared with healthy controls; nor was it associated with arterial stiffness.

Global microRNA profiling of peripheral blood mononuclear cells in patients with Behçet's disease.

OBJECTIVES: To explore the post-transcriptional regulation of the peripheral blood mononuclear cells (PBMCs) transcriptome by microRNAs in Behçet's disease (BD). METHODS: Using TaqMan Low Density Array-based microRNAs expression profiling, the expression of 750 mature human microRNAs in PBMCs from 5 BD patients and 3 healthy controls (HC) was compared. The expression of deregulated microRNAs was then validated by quantitative real time-polymerase chain reaction (qRT-PCR), in 42 BD patients and 8 HC. RESULTS: In the initial screening, 13 microRNAs appeared deregulated in BD vs HC. Among them, the differential expression of miR-720 and miR-139-3p was confirmed by qRT-PCR, (p<0.05 and FDR<5%). Areas under the receiver operating characteristic curve for miR-139-3p, miR-720 and miR-139-3p+miR-720 in the validation cohort were 0.84, 0.87 and 0.92 respectively, indicating good discrimination between BD patients and HC. Post-hoc analysis showed that 9 out of 13 microRNAs from the discovery phase were significantly upregulated in active vs. quiescent BD, suggesting inflammation as a key regulator of microRNAs machinery in BD. In silico analysis revealed that several BD candidate susceptibility genes are predicted target of significantly deregulated microRNAs in active BD. A significant enrichment in microRNAs targeting elements of the Toll-like receptor (TLR) and T-cell receptor signalling pathways was also assumed. CONCLUSIONS: miR199-3p and miR720 deserve further confirmation as biomarkers of BD in larger studies. PBMCs from active BD displayed a unique signature of microRNAs which may be implicated in regulation of innate immunity activation and T-cell function.

Hallux metatarsophalangeal arthroscopy: indications and techniques.

With mounting attention focused on decreasing postsurgical pain and dysfunction, emphasis has been placed on approaching disorders using minimally invasive techniques. Surgical procedures of the hallux, such as hallux valgus correction, have earned the reputation for high postsurgical pain and prolonged recovery. Arthroscopic hallux procedures have the advantages of minimizing pain, swelling, and disability. Certain conditions, such as synovitis, loose bodies, and early-grade hallux rigidus, are better addressed arthroscopically. With the correct indications, hallux metatarsophalangeal arthroscopy can be a valuable tool for the foot and ankle surgeon.

Ultrasound in systemic sclerosis. A multi-target approach from joint to lung.

Ultrasound (US) is a cost-effective, noninvasive, accessible imaging modality that clinicians use at the point of care to assess disease activity and therapeutic efficacy in different rheumatic conditions. However, its utility has been prevalently demonstrated in the field of chronic arthritides. Only in the last few years there was an interest to explore the potential of US beyond the musculoskeletal area. In this way, preliminary US data about the assessment of the different targets involved in systemic sclerosis such as joints, tendons, skin, vessels, and lung have been provided. The main purpose of this US review is to provide an overview of the potential role of US in the multi-target assessment of SSc and to discuss the current evidence supporting its relevance and applications in daily clinical practice.

Antiphospholipid syndrome nephropathy (APSN) in patients with lupus nephritis: a retrospective clinical and renal pathology study.

Data about clinical-laboratory features and outcome of antiphospholipid syndrome nephropathy (APSN) in the course of lupus nephritis (LN) are scarce. To determine prevalence, clinical correlations and outcome of APSN in patients with LN, retrospective analysis of renal specimens and review of medical records from 48 LN patients were performed. APSN was found in 12/48 (25 %) of LN. Positivity for lupus anticoagulant (LAC) and double antiphospholipids positivity [LAC plus anticardiolipin (aCL)] were significantly more frequent in APSN-LN (p = 0.02 and p = 0.01, respectively) than in LN, while single aCL positivity was not. Overt antiphospholipid syndrome appeared more frequent in patients with APSN-LN (p = 0.05). There were no statistically significant differences between APSN-LN and LN in the proportion of each World Health Organization class of LN (with the exception of a trend toward fewer Class III LN in APS-LN) and in the systemic lupus erythematosus (SLE) disease duration and severity. At the time of renal biopsy, patients with APSN-LN had median serum creatinine levels significantly higher than patients with LN [1.45 (0.6-6.6) vs. 1.00 (0.7-3.0), p = 0.02]. Double antiphospholipid positivity was the only variable significantly associated with APSN-LN at multivariate regression analysis (OR 8, 95 % CI 1.7-37, p = 0,008). APSN-LN and LN did not differ significantly as regards the rate of complete (25 vs. 19.4 %, p = 0.72) and partial treatment response (25 vs. 29 %, p = 0.82) at 6 months and the progression to end-stage renal disease after a median follow-up of 8.1 ± 3.6 years (16.6 vs. 13.8 %, p = 0.82). APSN was demonstrated in a quart of LN, appeared to be independent from underlying LN class and SLE severity, and did not seem to confer a worse prognosis to LN. The findings of higher creatinine and more interstitial fibrosis in APSN should be confirmed in future prospective larger studies.