Two decades of digital photogrammetry: Revisiting Chandler’s 1999 paper on “Effective application of automated digital photogrammetry for geomorphological research” – a synthesis

This is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this record.Digital photogrammetry has experienced rapid development regarding the technology involved and its ease of use over the past two decades. We revisit the work of Jim Chandler who in 1999 published a technical communication seeking to familiarise novice users of photogrammetric methods with important theoretical concepts and practical considerations. In doing so, we assess considerations such as camera calibration and the need for photo-control and check points, as they apply to modern software and workflows, in particular for Structure-from-Motion (SfM) photogrammetry. We also highlight the implications of lightweight drones being the new platform of choice for many photogrammetry-based studies in the geosciences. Finally, we present three examples based on our own work, showing the opportunities that SfM photogrammetry offers at different scales and systems: at the micro-scale for monitoring geomorphological change, and at the meso-scale for hydrological modelling and the reconstruction of vegetation canopies. Our examples showcase developments and applications of photogrammetry which go beyond what was considered feasible 20 years ago and indicate future directions that applications may take. Nevertheless, we demonstrate that, in-line with Chandler’s recommendations, the pre-calibration of consumer-grade cameras, instead of relying entirely on self-calibration by software, can yield palpable benefits in micro-scale applications and that measurements of sufficient control points are still central to generating reproducible, high-accuracy products. With the unprecedented ease of use and wide areas of application, scientists applying photogrammetric methods would do well to remember basic considerations and seek methods for the validation of generated products.European Union’s Horizon 2020 researchMarie Skłodowska-CurieUK Department for Environment, Food and Rural Affair

Drain blocking has limited short-term effects on greenhouse gas fluxes in a Molinia caerulea dominated shallow peatland (article)

This is the final version. Available on open access from Elsevier via the DOI in this recordThe dataset associated with this article is available in ORE at https://doi.org/10.24378/exe.2723Drained peatlands dominated by purple moor grass (Molinia caerulea) are widespread in the UK and Western Europe. Although substantial carbon stores may be present in these peatlands, in this degraded state they are not currently acting as carbon sinks. Therefore, M.caerulea dominated peatlands have been identified as potential sites for ecohydrological restoration to tackle the current climate emergency. However, at present little is known about whether ditch blocking can raise water tables and promote the recovery of bog plant species, and the subsequent effects on carbon sequestration in these peatlands. To investigate the potential for restoration, we measured changes in water table depth, vegetation composition, photosynthesis at 1000 μmol Photons m−2 s−1 (PG1000), ecosystem respiration (REco) and partitioned below-ground respiration in two M.caerulea dominated peatlands in which drainage ditches had been blocked located in Exmoor National Park, southwest England. Measurements were made in two headwater catchments at ⅛, ¼ and ½ of the distance between adjacent drainage ditches at four control-restored paired sites, during the growing seasons pre- (2012) and post- (2014, 2016 & 2018) restoration. Restoration had a small but significant (p = 0.009) effect on water table depths however, this did not result in a significant change in vegetation composition (p > 0.350). Ecosystem respiration increased in both the control and restored locations following restoration however, this increase was significantly smaller (p = 0.010) at the restored locations, possibly due to a similarly reduced increase in photosynthesis, although this change was not significant (p = 0.116). Below-ground respiration showed no significant changes following restoration. This research illustrates how degraded these shallow peatlands are, and raises concerns that ditch blocking alone may not bring about the high and stable water tables required to perturb the existing Molinia caerulea-dominated ecosystem and substantially alter the carbon balance. Additional restoration measures may be required.South West Water (SWW)University of ExeterTechnology Strategy Board CouncilNatural Environment Research Council (NERC

Assessing the impact of peat erosion on growing season CO2 fluxes by comparing erosional peat pans and surrounding vegetated haggs (article)

This is the author accepted manuscript. The final version is available from International Mire Conservation Group and International Peat Society via the DOI in this record.The research data supporting this publication are openly available from the University of Exeter's institutional repository at: https://doi.org/10.24378/exe.1143.Peatlands are recognised as an important but vulnerable ecological resource. Understanding the effects of existing damage, in this case erosion, enables more informed land management decisions to be made. Over the growing seasons of 2013 and 2014 photosynthesis and ecosystem respiration were measured using closed chamber techniques within vegetated haggs and erosional peat pans in Dartmoor National Park, southwest England. Below-ground total and heterotrophic respiration were measured and autotrophic respiration estimated from the vegetated haggs. The mean water table was significantly higher in the peat pans than in the vegetated haggs; because of this, and the switching from submerged to dry peat, there were differences in vegetation composition, photosynthesis and ecosystem respiration. In the peat pans photosynthetic CO2 uptake and ecosystem respiration were greater than in the vegetated haggs and strongly dependent on the depth to water table (r2>0.78, p<0.001). Whilst in the vegetated haggs, photosynthesis and ecosystem respiration had the strongest relationships with normalised difference vegetation index (NDVI) (r2=0.82, p<0.001) and soil temperature at 15 cm depth (r2=0.77, p=0.001). Autotrophic and total below-ground respiration in the vegetated haggs varied with soil temperature; heterotrophic respiration increased as water tables fell. An empirically derived net ecosystem model estimated that over the two growing seasons both the vegetated haggs (29 and 20 gC m 2; 95 % confidence intervals of -570 to 762 and -873 to 1105 gC m-2) and the peat pans (7 and 8 gC m 2; 95 % confidence intervals of -147 to 465 and -136 to 436 gC m 2) were most likely net CO2 sources. This study suggests that not only the visibly degraded bare peat pans but also the surrounding vegetated haggs are losing carbon to the atmosphere, particularly during warmer and drier conditions, highlighting a need for ecohydrological restoration.MomentaSouth West Water (SWW)Dartmoor National Park Authorit

Diversity of Matriptase Expression Level and Function in Breast Cancer

Overexpression of matriptase has been reported in a variety of human cancers and is sufficient to trigger tumor formation in mice, but the importance of matriptase in breast cancer remains unclear. We analysed matriptase expression in 16 human breast cancer cell lines and in 107 primary breast tumors. The data revealed considerable diversity in the expression level of this protein indicating that the significance of matriptase may vary from case to case. Matriptase protein expression was correlated with HER2 expression and highest expression was seen in HER2-positive cell lines, indicating a potential role in this subgroup. Stable overexpression of matriptase in two breast cancer cell lines had different consequences. In MDA-MB-231 human breast carcinoma cells the only noted consequence of matriptase overexpression was modestly impaired growth in vivo. In contrast, overexpression of matriptase in 4T1 mouse breast carcinoma cells resulted in visible changes in morphology, actin staining and cell to cell contacts. This correlated with downregulation of the cell-cell adhesion molecule E-cadherin. These results suggest that the functions of matriptase in breast cancer are likely to be variable and cell context dependent

Plasminogen binding and activation at the breast cancer cell surface: the integral role of urokinase activity

INTRODUCTION: The regulation of extracellular proteolytic activity via the plasminogen activation system is complex, involving numerous activators, inhibitors, and receptors. Previous studies on monocytic and colon cell lines suggest that plasmin pre-treatment can increase plasminogen binding, allowing the active enzyme to generate binding sites for its precursor. Other studies have shown the importance of pre-formed receptors such as annexin II heterotetramer. However, few studies have used techniques that exclusively characterise cell-surface events and these mechanisms have not been investigated at the breast cancer cell surface. METHODS: We have studied plasminogen binding to MCF-7 in which urokinase plasminogen activator receptor (uPAR) levels were upregulated by PMA (12-O-tetradecanoylphorbol-13-acetate) stimulation, allowing flexible and transient modulation of cell-surface uPA. Similar experiments were also performed using MDA-MB-231 cells, which overexpress uPAR/uPA endogenously. Using techniques that preserve cell integrity, we characterise the role of uPA as both a plasminogen receptor and activator and quantify the relative contribution of pre-formed and cryptic plasminogen receptors to plasminogen binding. RESULTS: Cell-surface plasminogen binding was significantly enhanced in the presence of elevated levels of uPA in an activity-dependent manner and was greatly attenuated in the presence of the plasmin inhibitor aprotinin. Pre-formed receptors were also found to contribute to increased plasminogen binding after PMA stimulation and to co-localise with uPA/uPAR and plasminogen. Nevertheless, a relatively modest increase in plasminogen-binding capacity coupled with an increase in uPA led to a dramatic increase in the proteolytic capacity of these cells. CONCLUSION: We show that the majority of lysine-dependent plasminogen binding to breast cancer cells is ultimately regulated by plasmin activity and is dependent on the presence of significant levels of active uPA. The existence of a proteolytic positive feedback loop in plasminogen activation has profound implications for the ability of breast cancer cells expressing high amounts of uPA to accumulate a large proteolytic capacity at the cell surface, thereby conferring invasive potential

Inflammation and breast cancer. Metalloproteinases as common effectors of inflammation and extracellular matrix breakdown in breast cancer

Two rapidly evolving fields are converging to impact breast cancer: one has identified novel substrates of metalloproteinases that alter immune cell function, and the other has revealed a role for inflammation in human cancers. Evidence now shows that the mechanisms underlying these two fields interact in the context of breast cancer, providing new opportunities to understand this disease and uncover novel therapeutic strategies. The metalloproteinase class of enzymes is well studied in mammary gland development and physiology, but mostly in the context of extracellular matrix modification. Aberrant metalloproteinase expression has also been implicated in breast cancer progression, where these genes act as tumor modifiers. Here, we review how the metalloproteinase axis impacts mammary physiology and tumorigenesis and is associated with inflammatory cell influx in human breast cancer, and evaluate its potential as a regulator of inflammation in the mammary gland

Project planning practices based on ERP projects in SMEs

Journal ArticleResearch Support, Non-U.S. Gov't© 2014 Published by Elsevier B.V.This is the author's version of a work accepted for publication by Elsevier. A definitive version was published in Science of The Total Environment Volume 493, 15 September 2014, Pages 961–973. doi:10.1016/j.scitotenv.2014.06.091Losses of dissolved organic carbon (DOC) from drained peatlands are of concern, due to the effects this has on the delivery of ecosystem services, and especially on the long-term store of carbon and the provision of drinking water. Most studies have looked at the effect of drainage in deep peat; comparatively, little is known about the behaviour of shallow, climatically marginal peatlands. This study examines water quality (DOC, Abs(400), pH, E4/E6 and C/C) during rainfall events from such environments in the south west UK, in order to both quantify DOC losses, and understand their potential for restoration. Water samples were taken over a 19 month period from a range of drains within two different experimental catchments in Exmoor National Park; data were analysed on an event basis. DOC concentrations ranging between 4 and 21 mg L(-1) are substantially lower than measurements in deep peat, but remain problematic for the water treatment process. Dryness plays a critical role in controlling DOC concentrations and water quality, as observed through spatial and seasonal differences. Long-term changes in depth to water table (30 days before the event) are likely to impact on DOC production, whereas discharge becomes the main control over DOC transport at the time scale of the rainfall/runoff event. The role of temperature during events is attributed to an increase in the diffusion of DOC, and therefore its transport. Humification ratios (E4/E6) consistently below 5 indicate a predominance of complex humic acids, but increased decomposition during warmer summer months leads to a comparatively higher losses of fulvic acids. This work represents a significant contribution to the scientific understanding of the behaviour and functioning of shallow damaged peatlands in climatically marginal locations. The findings also provide a sound baseline knowledge to support research into the effects of landscape restoration in the future

Assessing the impact of peat erosion on growing season CO2 fluxes by comparing erosional peat pans and surrounding vegetated haggs (dataset)

Net ecosystem exchange measurements collected using closed chamber technique with shade cloths from both vegetated haggs and peat pans. Outputs (ecosystem respiration and photosynthesis) from hyperbolic light response curves. Below ground heterotrophic and total below ground respiration measurements from vegetated haggs using closed chamber tequniques. Seasonal NEE models. All in Microsoft Excel.The article associated with this dataset is located in ORE at: http://hdl.handle.net/10871/36793This is the dataset used for the Gatis et al. (2019) article "Assessing the impact of peat erosion on growing season CO2 fluxes by comparing erosional peat pans and surrounding vegetated haggs" published in Wetlands Ecology and Management.MomentaSouth West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW)South West Water (SWW

Peatland restoration increases water storage and attenuates downstream stormflow but does not guarantee an immediate reversal of long-term ecohydrological degradation (dataset and analysis code)

Before and after peatland restoration data - Water table depths, stage, discharge, water quality (DOC, absorption at 254nm, 400nm, 465nm, pH), CO2 fluxes, CH4 fluxes, soil temperature. All data saved as csv files. Code used for data analysis provided in R.South West WaterSouth West Water (SWW)South West Water (SWW)South West Water (SWW)MomentaSouth West Water (SWW