Global Regulatory Pathways and Cross-talk Control Pseudomonas aeruginosa Environmental Lifestyle and Virulence Phenotype

Pseudomonas aeruginosa is a metabolically versatile environmental bacterium and an opportunistic human pathogen that relies on numerous signaling pathways to sense, respond, and adapt to fluctuating environmental cues. Although the environmental signals sensed by these pathways are poorly understood, they are largely responsible for determining whether P. aeruginosa adopts a planktonic or sessile lifestyle. These environmental lifestyle extremes parallel the acute and chronic infection phenotypes observed in human disease. In this review, we focus on four major pathways (cAMP/Vfr and c-di-GMP signaling, quorum sensing, and the Gac/Rsm pathway) responsible for sensing and integrating external stimuli into coherent regulatory control at the transcriptional, translational, and post-translational level. A common theme among these pathways is the inverse control of factors involved in promoting motility and acute infection and those associated with biofilm formation and chronic infection. In many instances these regulatory pathways influence one another, forming a complex network allowing P. aeruginosa to assimilate numerous external signals into an integrated regulatory circuit that controls a lifestyle continuum

The Use of Remote Sensing Techniques for Monitoring and Characterization of Slope Instability

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Understanding changes in slope geometry and knowledge of underlying engineering properties of the rock mass are essential for the safe design of man-made slopes and to reduce the significant risks associated with slope failure. Recent advances in the geomatics industry have provided the capability to obtain accurate, fully geo-referenced three-dimensional datasets that can be subsequently interrogated to provide engineering-based solutions for monitoring of deformation processes, rock mass characterization and additional insight into any underlying failure mechanisms. Importantly, data can also be used to spatially locate and map geological features and provide displacement or deformation rate information relating to movement of critical sections or regions of a slope. This paper explores the benefits that can be obtained by incorporating different remote sensing techniques and conventional measurement devices to provide a comprehensive database required for development of an effective slope monitoring and risk management program. The integration of different techniques, such as high accuracy discrete point measurement at critical locations, which can be used to complement larger scale less dense three-dimensional survey will be explored. Case studies using a combination of aerial and terrestrial laser scanning, unmanned aerial vehicle and hand-held scanning devices will demonstrate their ability to provide spatial data for informing decision making processes and ensuring compliance with Regulations

Investigation and modeling of direct toppling using a three-dimensional distinct element approach with incorporation of point cloud geometry

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordBlock toppling instability can be a common problem in natural rock masses, especially in mining environments where excavation activity may trigger discontinuity-controlled instability by modifying the natural slope geometry. Traditional investigations of block toppling failure consider classic kinematic analyses and simplified two-dimensional limit equilibrium methods. This approach is still the most commonly adopted, but the simple two-dimensional conceptual model may often oversimplify the instability mechanisms, ignoring potential critical factors specifically related to the three-dimensional geometry. This paper uses a three-dimensional distinct element method approach applied to an example case study, identifying the critical parameters that influence direct toppling instability in an open pit environment. Terrestrial laser scanning was used to obtain detailed three-dimensional geometrical information of the slope face geometry for subsequent stability analyses. A series of sensitivity analyses on critical parameters such as friction angle, discontinuity shear and normal stiffness, discontinuity spacing, and orientation was performed, using simple conceptual three-dimensional numerical modeling. Results of the analyses revealed the importance of undertaking three-dimensional analyses for direct toppling investigations that allow identification of critical parameters. A three-dimensional distinct element analysis was then performed using a more realistic complex volumetric mesh model of the case study slope which confirmed the previous modeling results but also identified unstable blocks in high slope angle areas, providing useful information for life of mine design. The paper highlights the importance of slope geometry and fracture network orientation on potential slope instability mechanisms.European CommissionEuropean Commissio

Application of Remote Sensing Data for Evaluation of Rockfall Potential within a Quarry Slope

This is the final version. Available on open access from MDPI via the DOI in this recordIn recent years data acquisition from remote sensing has become readily available to the quarry sector. This study demonstrates how such data may be used to evaluate and back analyse rockfall potential of a legacy slope in a blocky rock mass. Use of data obtained from several aerial LiDAR (Light Detection and Ranging) and photogrammetric campaigns taken over a number of years (2011 to date) provides evidence for potential rockfall evolution from a slope within an active quarry operation in Cornwall, UK. Further investigation, through analysis of point cloud data obtained from terrestrial laser scanning, was undertaken to characterise the orientation of discontinuities present within the rock slope. Aerial and terrestrial LiDAR data were subsequently used for kinematic analysis, production of surface topography models and rockfall trajectory analyses using both 2D and 3D numerical simulations. The results of an Unmanned Aerial Vehicle (UAV)-based 3D photogrammetric analysis enabled the reconstruction of high resolution topography, allowing one to not only determine geometrical properties of the slope surface and geomechanical characterisation but provide data for validation of numerical simulations. The analysis undertaken shows the effectiveness of the existing rockfall barrier, while demonstrating how photogrammetric data can be used to inform back analyses of the underlying failure mechanism and investigate potential runout

Investigation of landslide failure mechanisms adjacent to lignite mining operations in North Bohemia (Czech Republic) through a limit equilibrium/finite element modelling approach

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Understanding the impact of data uncertainty is a fundamental part of ensuring safe design of manmade excavations. Although good levels of knowledge are achievable from field investigations and experience, a natural geological environment is subject to intrinsic variability that may compromise the correct prediction of the system response to the perturbations caused by mining, with direct consequences for the stability and safety of the operations. Different types of geoscientific evidence, including geological, geomorphic, geotechnical, geomatics, and geophysical data have been used to develop and perform two-dimensional Limit Equilibrium and Finite Element Method stability analyses of a lignite open-pit mine in North Bohemia (Czech Republic) affected by recent landslides. A deterministic-probabilistic approach was adopted to investigate the effect of uncertainty of the input parameters on model response. The key factors affecting the system response were identified by specific Limit Equilibrium sensitivity analyses and studied in further detail by Finite Element probabilistic analyses and the results were compared. The work highlights that complementary use of both approaches can be recommended for routine checks of model response and interpretation of the associated results. Such an approach allows a reduction of system uncertainty and provides an improved understanding of the landslides under study. Importantly, two separate failure mechanisms have been identified from the analyses performed and verified through comparisons with inclinometer data and field observations. The results confirm that the water table level and material input parameters have the greatest influence on the stability of the slope.This work was supported by the Research Fund for Coal and Steel of the European Union [grant number 752504]

Ultrasonic inspection of flooded mineshafts for stability monitoring

This is the author accepted manuscript.The final version is available from Maney via the DOI in this record.Inspecting abandoned mine shafts is critical in ensuring their safety through early identification of signs of deterioration. Since the common inspection methods of CCTV and LiDAR are not very effective underwater, two modules have been designed for inspecting the linings of flooded, abandoned mine shafts. Using sonar technology, they allow the early stages of degradation to the lining to be detected which – since this could be indicative of imminent collapse – provides protection against the consequential risk to property and human life. Detailed measurements of several shafts’ cross-sections have been recorded using profiling and imaging sonar technology. Although imaging sonar provides very different results in the confined and reverberant environment of a mine shaft, compared to its more common environment of a seabed, it was shown that when combined with the profiling sonar, it allows shafts to be surveyed in a shorter period of time and improves the reliability of the profiling function.European Commissio

Evaluation of the Use of UAV Photogrammetry for Rock Discontinuity Roughness Characterization

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this recordThis paper describes the results of a field investigation with the objective of evaluating the possibility to produce drone-derived 3D digital point clouds sufficiently dense and accurate to determine discontinuity surface roughness characteristics. A discontinuous rock mass in Italy was chosen as the investigation site and Structure from Motion and Multi-View Stereo techniques adopted for producing three-dimensional point clouds from the two-dimensional image sequences. Since the roughness of discontinuities depends on direction, scale and resolution of the sampling, data were always collected along the maximum slope gradient. The scale effect was evaluated by analysing discontinuity profiles of different lengths (10 cm, 30 cm, 60 cm and 100 cm), with measurements taken from drone flights flown at different distances from the rocky slopes (10 m, 20 m and 30 m). The accuracy of the derived joint roughness coefficients was evaluated by direct comparison with discontinuity profiles measured during fieldwork using conventional techniques and from contemporaneous terrestrial laser scanning. Results from this research show that 3D digital point clouds, derived from the processing of drone-flight images, were successfully used for reliable representation of discontinuity roughness for profiles longer than 60 cm, whereas less reliable results were achieved for shorter profile lengths. This, even if strictly related to this case study since several factors can affect the minimum profile length, represents a significant contribution to improve the knowledge on the use of remotely captured data for characterising the discontinuities in natural or man-made rock outcrops, particularly where access difficulties do not allow conventional engineering-geological surveys to be undertaken

A Sentinel-2 based multispectral convolutional neural network for detecting artisanal small-scale mining in Ghana: Applying deep learning to shallow mining

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordArtisanal Small-scale Mining (ASM) is a critical source of livelihoods for large areas of the Global South but it can bring with it many problems, including deforestation, water pollution and low worker safety. Timely and comprehensive management of ASM is crucial to ensure that it can take place safely and cleanly, supporting sustainable development. The informal nature of the sector presents challenges related to documenting the locations of ASM. Remote sensing methods have been used to detect ASM, although difficulties with accuracy, resolution and persistent cloud cover have been encountered. This paper proposes a method of ASM detection using a deep convolutional neural network model applied to open source Sentinel-2 multispectral satellite imagery. Firstly, the model is evaluated against both existing ASM detection methods and visual inspection of randomly sampled points. Secondly, the model is used to map mining and urban land use changes over a dataset spanning four years and 6 million hectares of southern Ghana, demonstrating the ability of this method to process very large areas. The omission and commission errors of less than 8% from the sampled points indicate that this model has achieved unprecedented levels of accuracy for the task of detecting ASM from satellite imagery. When applied to the case study area, the data on ASM trends over time demonstrate a correlation between the Ghanaian government's 2017 clampdown and ASM activities. The ASM land use category decreased by 6000 ha in 2017, despite a net increase of 15000 ha over the period 2015–2019. Additionally, the model was applied to quantify the extent of illegal mining related deforestation within Ghana's protected forests, measured at over 3500 ha, with 2400 of these lost since 2015. The results demonstrate that this methodology can detect ASM in Ghana with a high degree of accuracy at a minimal cost in terms of financial and human resources. The model shows strong generalisation abilities, offering exciting potential for using this methodology to further monitor and analyse ASM related land use changes worldwide

A Hierarchical Cascade of Second Messengers Regulates Pseudomonas aeruginosa Surface Behaviors

Biofilms are surface-attached multicellular communities. Using single-cell tracking microscopy, we showed that apilY1 mutant of Pseudomonas aeruginosa is defective in early biofilm formation. We leveraged the observation that PilY1 pro- tein levels increase on a surface to perform a genetic screen to identify mutants altered in surface-grown expression of this pro- tein. Based on our genetic studies, we found that soon after initiating surface growth, cyclic AMP (cAMP) levels increase, depen- dent on PilJ, a chemoreceptor-like protein of the Pil-Chp complex, and the type IV pilus (TFP). cAMP and its receptor protein Vfr, together with the FimS-AlgR two-component system (TCS), upregulate the expression of PilY1 upon surface growth. FimS and PilJ interact, suggesting a mechanism by which Pil-Chp can regulate FimS function. The subsequent secretion of PilY1 is dependent on the TFP assembly system; thus, PilY1 is not deployed until the pilus is assembled, allowing an ordered signaling cascade. Cell surface-associated PilY1 in turn signals through the TFP alignment complex PilMNOP and the diguanylate cyclase SadC to activate downstream cyclic di-GMP (c-di-GMP) production, thereby repressing swarming motility. Overall, our data support a model whereby P. aeruginosa senses the surface through the Pil-Chp chemotaxis-like complex, TFP, and PilY1 to reg- ulate cAMP and c-di-GMP production, thereby employing a hierarchical regulatory cascade of second messengers to coordinate its program of surface behaviors

Contribution of high-resolution virtual outcrop models for the definition of rockfall activity and associated hazard modelling

This is the final version. Available from MDPI via the DOI in this record. Data Availability Statement: The data are contained within the article.The increased accessibility of drone technology and structure from motion 3D scene reconstruction have transformed the approach for mapping inaccessible slopes undergoing active rockfalls and generating virtual outcrop models (VOM). The Poggio Baldi landslide (Central Italy) and its natural laboratory offers the possibility to monitor and characterise the slope to define a workflow for rockfall hazard analysis. In this study, the analysis of multitemporal VOM (2016–2019) informed a rockfall trajectory analysis that was carried out with a physical-characteristic-based GIS model. The rockfall scenarios were reconstructed and then tested based on the remote sensing observations of the rock mass characteristics of both the main scarp and the rockfall fragment inventory deposited on the slope. The highest concentration of trajectory endpoints occurred at the very top of the debris talus, which was constrained by a narrow channel, while longer horizontal travel distances were allowed on the lower portion of the slope. To further improve the understanding of the Poggio Baldi landslide, a time-independent rockfall hazard analysis aiming to define the potential runout associated with several rock block volumetric classes is a critical component to any subsequent risk analysis in similar mountainous settings featuring marly–arenaceous multilayer sedimentary successions and reactivated main landslide scarps.Sapienza University of RomeNHAZCA SrlParco Nazionale delle Foreste Casentinesi, Monte Falterona e CampignaDepartment of Earth Sciences of the University of Rome “Sapienza