Woody plant encroachment drives population declines in 20% of common open ecosystem bird species.

Grassy ecosystems cover more than 40% of the world's terrestrial surface, supporting crucial ecosystem services and unique biodiversity. These ecosystems have experienced major losses from conversion to agriculture with the remaining fragments threatened by global change. Woody plant encroachment, the increase in woody cover threatening grassy ecosystems, is a major global change symptom, shifting the composition, structure, and function of plant communities with concomitant effects on all biodiversity. To identify generalisable impacts of encroachment on biodiversity, we urgently need broad-scale studies on how species respond to woody cover change. Here, we make use of bird atlas, woody cover change data (between 2007 and 2016) and species traits, to assess: (1) population trends and woody cover responses using dynamic occupancy models; (2) how outcomes relate to habitat, diet and nesting traits; and (3) predictions of future occupancy trends, for 191 abundant, southern African bird species. We found that: (1) 63% (121) of species showed a decline in occupancy, with 18% (34) of species' declines correlated with increasing woody cover (i.e. losers). Only 2% (4) of species showed increasing population trends linked with increased woody cover (i.e. winners); (2) Open habitat specialist, invertivorous, ground nesting birds were the most frequent losers, however, we found no definitive evidence that the selected traits could predict outcomes; and (3) We predict open habitat loser species will take on average 52 years to experience 50% population declines with current rates of encroachment. Our results bring attention to concerning region-wide declining bird population trends and highlight woody plant encroachment as an important driver of bird population dynamics. Importantly, these findings should encourage improved management and restoration of our remaining grassy ecosystems. Furthermore, our findings show the importance of lands beyond protected areas for biodiversity, and the urgent need to mitigate the impacts of woody plant encroachment on bird biodiversity.

Identification of Bridge Key Performance Indicators Using Survival Analysis for Future Network-Wide Structural Health Monitoring.

Machine learning and statistical approaches have transformed the management of infrastructure systems such as water, energy and modern transport networks. Artificial Intelligence-based solutions allow asset owners to predict future performance and optimize maintenance routines through the use of historic performance and real-time sensor data. The industrial adoption of such methods has been limited in the management of bridges within aging transport networks. Predictive maintenance at bridge network level is particularly complex due to the considerable level of heterogeneity encompassed across various bridge types and functions. This paper reviews some of the main approaches in bridge predictive maintenance modeling and outlines the challenges in their adaptation to the future network-wide management of bridges. Survival analysis techniques have been successfully applied to predict outcomes from a homogenous data set, such as bridge deck condition. This paper considers the complexities of European road networks in terms of bridge type, function and age to present a novel application of survival analysis based on sparse data obtained from visual inspections. This research is focused on analyzing existing inspection information to establish data foundations, which will pave the way for big data utilization, and inform on key performance indicators for future network-wide structural health monitoring.

Human impacts in African savannas are mediated by plant functional traits.

Tropical savannas have a ground cover dominated by C4 grasses, with fire and herbivory constraining woody cover below a rainfall-based potential. The savanna biome covers 50% of the African continent, encompassing diverse ecosystems that include densely wooded Miombo woodlands and Serengeti grasslands with scattered trees. African savannas provide water, grazing and browsing, food and fuel for tens of millions of people, and have a unique biodiversity that supports wildlife tourism. However, human impacts are causing widespread and accelerating degradation of savannas. The primary threats are land cover-change and transformation, landscape fragmentation that disrupts herbivore communities and fire regimes, climate change and rising atmospheric CO2 . The interactions among these threats are poorly understood, with unknown consequences for ecosystem health and human livelihoods. We argue that the unique combinations of plant functional traits characterizing the major floristic assemblages of African savannas make them differentially susceptible and resilient to anthropogenic drivers of ecosystem change. Research must address how this functional diversity among African savannas differentially influences their vulnerability to global change and elucidate the mechanisms responsible. This knowledge will permit appropriate management strategies to be developed to maintain ecosystem integrity, biodiversity and livelihoods.

Savanna woody encroachment is widespread across three continents.

Tropical savannas are a globally extensive biome prone to rapid vegetation change in response to changing environmental conditions. Via a meta-analysis, we quantified savanna woody vegetation change spanning the last century. We found a global trend of woody encroachment that was established prior the 1980s. However, there is critical regional variation in the magnitude of encroachment. Woody cover is increasing most rapidly in the remaining uncleared savannas of South America, most likely due to fire suppression and land fragmentation. In contrast, Australia has experienced low rates of encroachment. When accounting for land use, African savannas have a mean rate annual woody cover increase two and a half times that of Australian savannas. In Africa, encroachment occurs across multiple land uses and is accelerating over time. In Africa and Australia, rising atmospheric CO2 , changing land management and rainfall are likely causes. We argue that the functional traits of each woody flora, specifically the N-fixing ability and architecture of woody plants, are critical to predicting encroachment over the next century and that African savannas are at high risk of widespread vegetation change.

INNOVATE: A prospective cohort study combining serum and urinary biomarkers with novel diffusion-weighted magnetic resonance imaging for the prediction and characterization of prostate cancer.

BACKGROUND: Whilst multi-parametric magnetic resonance imaging (mp-MRI) has been a significant advance in the diagnosis of prostate cancer, scanning all patients with elevated prostate specific antigen (PSA) levels is considered too costly for widespread National Health Service (NHS) use, as the predictive value of PSA levels for significant disease is poor. Despite the fact that novel blood and urine tests are available which may predict aggressive disease better than PSA, they are not routinely employed due to a lack of clinical validity studies. Furthermore approximately 40 % of mp-MRI studies are reported as indeterminate, which can lead to repeat examinations or unnecessary biopsy with associated patient anxiety, discomfort, risk and additional costs. METHODS/DESIGN: We aim to clinically validate a panel of minimally invasive promising blood and urine biomarkers, to better select patients that will benefit from a multiparametric prostate MRI. We will then test whether the performance of the mp-MRI can be improved by the addition of an advanced diffusion-weighted MRI technique, which uses a biophysical model to characterise tissue microstructure called VERDICT; Vascular and Extracellular Restricted Diffusion for Cytometry in Tumours. INNOVATE is a prospective single centre cohort study in 365 patients. mp-MRI will act as the reference standard for the biomarker panel. A clinical outcome based reference standard based on biopsy, mp-MRI and follow-up will be used for VERDICT MRI. DISCUSSION: We expect the combined effect of biomarkers and VERDICT MRI will improve care by better detecting aggressive prostate cancer early and make mp-MRI before biopsy economically viable for universal NHS adoption. TRIAL REGISTRATION: INNOVATE is registered on ClinicalTrials.gov, with reference NCT02689271 .

Initial validation of equilibrium contrast imaging for extracellular volume quantification using a three-dimensional engineered tissue model.

BACKGROUND: To test the principles underpinning equilibrium contrast imaging estimation of tissue extracellular volume (ECV) fraction, using a three-dimensional (3D) engineered tissue model with known cellular and extracellular volumes. METHODS: Six 3D tissue models (tumoroids) consisting of cell cultures within a collagen containing hydrogel were constructed after culture centrifugation and direct measurement of the cell component volume. Measured tumoroid ECV ranged from 0.89 to 1. ECV was calculated after measuring the T1 relaxation time at 3 Tesla using inversion recovery relaxometry (TI 100-1500 ms) within the tumoroids and surrounding medium before and 375 min after spiking the medium with Gadolinium (to achieve a concentration of 1.4 mM/L). Linear regression model prediction of directly measured ECV (ECVm ) by EQ-MRI measured ECV (ECVeq ); and Bland-Altman agreement between measures was assessed. RESULTS: The fractional cellular volume measured by EQ-MRI (ECVeq ) within the tumoroids ranged from 0.821 to 0.963. ECVeq was a good predictor of ECVm (R2 = 0.77, P = 0.02). The regression line Y-axis intercept (when X = 0) was 0.045 ± 0.019 with a slope of 1.28 ± 0.35. Bland-Altman comparison demonstrated 95% limits of agreement between -0.002 and 0.114 with a bias (SD) of 0.056 (0.03). CONCLUSION: This study supports the principles of ECV estimation using equilibrium contrast MRI, but future development of this model may allow validation over a wider, more physiological ECV range and a greater understanding of the effect of tissue extracellular protein burden on ECV.

Increasing temperatures can improve seedling establishment in arid-adapted savanna trees.

Plant species are shifting their ranges in response to global climate change, thus intensifying the need to predict such changes accurately. As the environmental requirements controlling plant distribution act differently at each developmental stage, there is a need to acquire a demographic-specific understanding of the factors which determine these distributions. Here we investigated the germination niche of two common savanna species Acacia nigrescens and Colophospermum mopane, with the aims to disentangle the direct and indirect effects of temperature on seed germination and establishment and to explore the impact of higher temperatures on the establishment success of savanna trees. Under laboratory conditions, we used thermal gradient plates to determine the thermal germination niche of both species, and a water stress experiment was conducted on C. mopane to account for water-temperature interactions. Using these data we parameterised a soil-moisture model to determine germination and establishment success under field conditions at current and future temperatures (+4 °C). Based on this model, higher future temperatures will not limit germination directly, but they will reduce the number of germination events by reducing the time window of suitable available soil water. Conversely, warmer conditions will accelerate the rate of radicle extension and increase the frequency of seedling establishment events. An additional advantage of higher temperatures is that fewer seeds will germinate, resulting in slower seed bank depletion when successful seedling establishment events do occur.

A trillion trees: carbon capture or fuelling fires?

Afforesting grassy systems for carbon gain using flammable plantation trees could shift the fire regime from lower intensity grass-fuelled fires to high-intensity crown fires. Future changes in climate will worsen this. We highlight the fire risk of trees planted for carbon and costs of fire protection using African examples.

Conflation of reforestation with restoration is widespread.

Across Africa, vast areas of nonforest are threatened by inappropriate restoration in the form of tree planting.

The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

Valuing the functionality of tropical ecosystems beyond carbon.

Land-based carbon sequestration projects, such as tree planting, are a prominent strategy to offset carbon emissions. However, we risk reducing natural ecosystems to one metric - carbon. Emphasis on restoring ecosystems to balance ecosystem services, biodiversity conservation, and carbon sequestration is a more appropriate strategy to protect their functioning.

Steal the rain: Interception loses and rainfall partitioning by a broad-leaf and a fine-leaf woody encroaching species in a southern African semi-arid savanna.

Woody plant encroachment (WPE) has been found to alter ecosystem functioning and services in savannas. In rain-limited savannas, increasing woody cover can reduce streamflow and groundwater by altering evapotranspiration rates and rainfall partitioning, but the ecological relevance of this impact is not well known. This study quantified the altered partitioning of rainfall by two woody plant structural types (fine- and broad-leaved trees) across a gradient of encroachment in a semi-arid savanna in South Africa. Averaged across both plant functional types, loss of rainfall through canopy interception and subsequent evaporation roughly doubled (from 20.5% to 43.6% of total rainfall) with a roughly 13-fold increase in woody cover (from 2.4 to 31.4 m2/ha tree basal cover). Spatial partitioning changes comprised fourfold increases in stemflow (from 0.8% to 3.9% of total rainfall) and a decline in throughfall proportion of about two-fifths (from 80.2% to 47.3% of total rainfall). Changes in partitioning were dependent on plant functional type; rainfall interception by the fine-leaved multi-stemmed shrub Dichrostachys cinerea was almost double that of the broad-leaved tree Terminalia sericea at the highest levels of woody encroachment (i.e., 49.7% vs. 29.1% of total rainfall intercepted at tree basal area of 31.4 m2/ha). Partitioning was also dependent on rainfall characteristics, with the proportion of rainfall intercepted inversely related to rainfall event size and intensity. Therefore, increasing tree cover in African grassy ecosystems reduces the amount of canopy throughfall, especially beneath canopies of fine-leaved species in smaller rainfall events. Rainfall interception traits may thus confer a selective advantage, especially for fine-leaved woody plant species in semi-arid savannas.

Clinical validity of plasma and urinary desmosine as biomarkers for chronic obstructive pulmonary disease.

BACKGROUND: Although an increased concentration of degraded elastin products in patients with chronic obstructive pulmonary disease (COPD) has been reported for many years, its clinical validity and utility remain uncertain due to technical difficulties, small study groups and the unknown relationship between exacerbation and elastin degradation. The objectives of this study were to determine the validity of urinary and blood total desmosine/isodesmosine in patients with COPD and asthma and to evaluate their relationship to exacerbation status and lung function. METHODS: Urinary and blood desmosine levels were measured using validated isotopic dilution liquid chromatography-tandem mass spectrometry methods. RESULTS: 390 study participants were recruited from the following groups: healthy volunteers, stable asthma, stable and 'during an exacerbation' COPD. Compared with healthy non-smokers, we found increased urinary or blood desmosine levels in patients with COPD, but no differences in patients with asthma or healthy smokers. The elevation of urinary desmosine levels was associated with the exacerbation status in patients with COPD. Approximately 40% of patients with stable and 'during an exacerbation' COPD showed elevated blood desmosine levels. Blood desmosine levels were strongly associated with age and were negatively correlated with lung diffusing capacity for carbon monoxide. CONCLUSION: The results suggest that urinary desmosine levels are raised by exacerbations of COPD whereas blood desmosine levels are elevated in a subgroup of patients with stable COPD and reduced lung diffusing capacity. The authors speculate that a raised blood desmosine level may identify patients with increased elastin degradation suitable for targeted therapy. Future prospective studies are required to investigate this hypothesis.

The role of large wild animals in climate change mitigation and adaptation.

Two major environmental challenges of our time are responding to climate change and reversing biodiversity decline. Interventions that simultaneously tackle both challenges are highly desirable. To date, most studies aiming to find synergistic interventions for these two challenges have focused on protecting or restoring vegetation and soils but overlooked how conservation or restoration of large wild animals might influence the climate mitigation and adaptation potential of ecosystems. However, interactions between large animal conservation and climate change goals may not always be positive. Here, we review wildlife conservation and climate change mitigation in terrestrial and marine ecosystems. We elucidate general principles about the biome types where, and mechanisms by which, positive synergies and negative trade-offs between wildlife conservation and climate change mitigation are likely. We find that large animals have the greatest potential to facilitate climate change mitigation at a global scale via three mechanisms: changes in fire regime, especially in previously low-flammability biomes with a new or intensifying fire regime, such as mesic grasslands or warm temperate woodlands; changes in terrestrial albedo, particularly where there is potential to shift from closed canopy to open canopy systems at higher latitudes; and increases in vegetation and soil carbon stocks, especially through a shift towards below-ground carbon pools in temperate, tropical and sub-tropical grassland ecosystems. Large animals also contribute to ecosystem adaptation to climate change by promoting complexity of trophic webs, increasing habitat heterogeneity, enhancing plant dispersal, increasing resistance to abrupt ecosystem change and through microclimate modification.

What shapes the range edge of a dominant African savanna tree, Colophospermum mopane? A demographic approach.

Climate is widely assumed to be the primary process that limits the distribution ranges of plants. Yet, savannas have vegetation not at equilibrium with climate, instead its structure and function are shaped by interactions between fire, herbivory, climate, and vegetation. I use the rich literature of a dominant African savanna woody plant, Colophospermum mopane, to demonstrate that climate and disturbance interact with each demographic stage to shape this species range limits. This synthesis highlights that climate-based predictions for the range of C. mopane inadequately represents the processes that shape its distribution. Instead, seed bank depletion and rainfall limitation create a demographic bottleneck at the early seedling stage. The legacy of top-kill from disturbance changes tree stand architecture causing a critical limitation in seed supply. Exposure to top-kill at all demographic stages causes a vigorous resprouting response and shifts tree architecture from that of 1-2 stemmed tall trees to that of a short multi-stemmed shrub. The shorter, multi-stemmed shrubs are below the height threshold (4 m) at which they can produce seeds, resulting in shrub-dominated landscapes that are effectively sterile. This effect is likely most pronounced at the range edge where top-kill-inducing disturbances increase in frequency. The proposed mechanistic, demographic-based understanding of C. mopane's range limits highlights the complexity of processes that interact to shape its range edges. This insight serves as a conceptual model for understanding the determinants of range limits of other dominant woody savannas species living in disturbance limited ecosystems.

Understanding the barriers to NET-ZERO transport for rural roads: a Northern Ireland case study.

INTRODUCTION: Climate-related disasters have cost the world over £450 billion over the last 3 years. In the race to mitigate these effects, the UK government has committed to net-zero emissions by 2050. Transport provides the largest single sector contribution to CO2 emissions, the road network accounts for up to 91%. As the only UK country without a formal climate change bill Northern Ireland could compromise the overall effort. CASE DESCRIPTION: In this research a survey of road asset owners, managers, academics, consultants, public transport providers was undertaken to seek to understand the current barriers to adapting a dispersed rural road network in Northern Ireland for net-zero transport. The survey data was collected though an online form with a combination of multiple choice and open ended questions. Thematic analysis was used to code and analyse the data collected which enabled a discussion around the key expert opinions gathered. DISCUSSION AND EVALUATION: The paper presents details of the current road network in Northern Ireland and highlights some of the issues faced by asset owners. The survey questions were developed though engagement with transport professionals in Northern Ireland and focus predominantly on road use rather than the impact of current land management practices or environmental conditions such as flood risk. The response highlights a clear enthusiasm for change in the operation of the public road network which is hindered by a lack of government strategy and limited public consultation. CONCLUSIONS: The high response rate (41%) for the survey highlights the interest of those in the transport sector to engage in activities which can support a better understanding of how road networks contribute to CO2 emissions. Within the survey data a requirement for behavioural change was highlighted as a key step to reduce transport related emissions, the enthusiasm for change demonstrates this is the optimum time to engage with the public and develop clear transport strategies. More accurate findings and empirical evidence could have been established had the study considered specific, transport planning, environmental and land use conditions for Northern Ireland. This will be the focus of further research in this area to enable clear translation of the research to other countries.

Evaluation of PSA and PSA Density in a Multiparametric Magnetic Resonance Imaging-Directed Diagnostic Pathway for Suspected Prostate Cancer: The INNOVATE Trial.

Objectives: To assess the clinical outcomes of mpMRI before biopsy and evaluate the space remaining for novel biomarkers. Methods: The INNOVATE study was set up to evaluate the validity of novel fluidic biomarkers in men with suspected prostate cancer who undergo pre-biopsy mpMRI. We report the characteristics of this clinical cohort, the distribution of clinical serum biomarkers, PSA and PSA density (PSAD), and compare the mpMRI Likert scoring system to the Prostate Imaging-Reporting and Data System v2.1 (PI-RADS) in men undergoing biopsy. Results: 340 men underwent mpMRI to evaluate suspected prostate cancer. 193/340 (57%) men had subsequent MRI-targeted prostate biopsy. Clinically significant prostate cancer (csigPCa), i.e., overall Gleason ≥ 3 + 4 of any length OR maximum cancer core length (MCCL) ≥4 mm of any grade including any 3 + 3, was found in 96/195 (49%) of biopsied patients. Median PSA (and PSAD) was 4.7 (0.20), 8.0 (0.17), and 9.7 (0.31) ng/mL (ng/mL/mL) in mpMRI scored Likert 3,4,5 respectively for men with csigPCa on biopsy. The space for novel biomarkers was shown to be within the group of men with mpMRI scored Likert3 (178/340) and 4 (70/350), in whom an additional of 40% (70/178) men with mpMRI-scored Likert3, and 37% (26/70) Likert4 could have been spared biopsy. PSAD is already considered clinically in this cohort to risk stratify patients for biopsy, despite this 67% (55/82) of men with mpMRI-scored Likert3, and 55% (36/65) Likert4, who underwent prostate biopsy had a PSAD below a clinical threshold of 0.15 (or 0.12 for men aged <50 years). Different thresholds of PSA and PSAD were assessed in mpMRI-scored Likert4 to predict csigPCa on biopsy, to achieve false negative levels of ≤5% the proportion of patients whom who test as above the threshold were unsuitably high at 86 and 92% of patients for PSAD and PSA respectively. When PSA was re tested in a sub cohort of men repeated PSAD showed its poor reproducibility with 43% (41/95) of patients being reclassified. After PI-RADS rescoring of the biopsied lesions, 66% (54/82) of the Likert3 lesions received a different PI-RADS score. Conclusions: The addition of simple biochemical and radiological markers (Likert and PSAD) facilitate the streamlining of the mpMRI-diagnostic pathway for suspected prostate cancer but there remains scope for improvement, in the introduction of novel biomarkers for risk assessment in Likert3 and 4 patients, future application of novel biomarkers tested in a Likert cohort would also require re-optimization around Likert3/PI-RADS2, as well as reproducibility testing.

Pediatric and adolescent lymphoma: comparison of whole-body STIR half-Fourier RARE MR imaging with an enhanced PET/CT reference for initial staging.

PURPOSE: To compare the diagnostic performance of rapid whole-body anatomic magnetic resonance (MR) staging of pediatric and adolescent lymphoma to an enhanced positron emission tomographic (PET)/computed tomographic (CT) reference standard. MATERIALS AND METHODS: Ethical permission was given by the University College London Hospital ethics committee, and informed written consent was obtained from all participants and/or parents or guardians. Thirty-one subjects (age range, 7.3-18.0 years; 18 male, 11 female) with histologically proved lymphoma were prospectively recruited. Pretreatment staging was performed with whole-body short inversion time inversion-recovery (STIR) half-Fourier rapid acquisition with relaxation enhancement (RARE) MR imaging, fluorine 18 fluorodeoxyglucose PET/CT, and contrast agent-enhanced chest CT. Twenty-six subjects had posttreatment PET/CT and compromised our final cohort. Eleven nodal and 11 extranodal sites per patient were assessed on MR imaging by two radiologists in consensus, with a nodal short-axis threshold of >1 cm and predefined extranodal positivity criteria. The same sites were independantly evaluated by two nuclear medicine physicians on PET/CT images. Disease positivity was defined as a maximum standardized uptake value >2.5 or nodal size >1 cm. An unblinded expert panel reevaluated the imaging findings, removing perceptual errors, and derived an enhanced PET/CT reference standard (taking into account chest CT and 3-month follow-up imaging) against which the reported and intrinsic performance of MR imaging was assessed by using the kappa statistic. RESULTS: There was very good agreement between MR imaging and the enhanced PET/CT reference standard for nodal and extranodal staging (kappa = 0.96 and 0.86, respectively) which improved following elimination of perceptual errors (kappa = 0.97 and 0.91, respectively). The sensitivity and specificity of MR imaging (following removal of perceptual error) were 98% and 99%, respectively, for nodal disease and 91% and 99%, respectively, for extranodal disease. CONCLUSION: Whole-body STIR half-Fourier RARE MR imaging of pediatric and adolescent lymphoma can accurately depict nodal and extranodal disease and may provide an alternative nonionizing imaging method for anatomic disease assessment at initial staging.

The Trouble with Trees: Afforestation Plans for Africa.

Extensive tree planting is widely promoted for reducing atmospheric CO2. In Africa, 1 million km2, mostly of grassy biomes, have been targeted for 'restoration' by 2030. The target is based on the erroneous assumption that these biomes are deforested and degraded. We discuss the pros and cons of exporting fossil fuel emission problems to Africa.