Using density surface models to estimate spatio-temporal changes in population densities and trend

Funding – Centre for Research into Ecological and Environmental Modelling, University of St Andrews and U.S. Geological Survey provided funding for this analysis through a studentship to RJC.Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from standard design‐based methods. Spatio–temporal models allow us to target priority areas where, and at times when, a population may most benefit. Generalised additive models were fitted to a 31‐year time series of point‐transect surveys of an endangered Hawaiian forest bird, the Hawai'i ‘ākepa Loxops coccineus. This allowed us to estimate bird densities over space and time. We used two methods to quantify uncertainty in density estimates from the spatio–temporal model: the delta method (which assumes independence between detection and distribution parameters) and a variance propagation method. With the delta method we observed a 52% decrease in the width of the design‐based 95% confidence interval (CI), while we observed a 37% decrease in CI width when propagating the variance. We mapped bird densities as they changed across space and time, allowing managers to evaluate management actions. Integrating detection function modelling with spatio–temporal modelling exploits survey data more efficiently by producing finer‐grained abundance estimates than are possible with design‐based methods as well as producing more precise abundance estimates. Model‐based approaches require switching from making assumptions about the survey design to assumptions about bird distribution. Such a switch warrants carefully considered. In this case the model‐based approach benefits conservation planning through improved management efficiency and reduced costs by taking into account both spatial shifts and temporal changes in population abundance and distribution.Publisher PDFPeer reviewe

Incorporating animal movement into distance sampling

R. Glennie gratefully acknowledges the Carnegie Trust for funding his work on this research project.Distance sampling is a popular statistical method to estimate the density of wild animal populations. Conventional distance sampling represents animals as fixed points in space that are detected with an unknown probability that depends on the distance between the observer and the animal. Animal movement can cause substantial bias in density estimation. Methods to correct for responsive animal movement exist, but none account for nonresponsive movement independent of the observer. Here, an explicit animal movement model is incorporated into distance sampling, combining distance sampling survey data with animal telemetry data. Detection probability depends on the entire unobserved path the animal travels. The intractable integration over all possible animal paths is approximated by a hidden Markov model. A simulation study shows the method to be negligibly biased (<5%) in scenarios where conventional distance sampling overestimates abundance by up to 100%. The method is applied to line transect surveys (1999–2006) of spotted dolphins (Stenella attenuata) in the eastern tropical Pacific where abundance is shown to be positively biased by 21% on average, which can have substantial impact on the population dynamics estimated from these abundance estimates and on the choice of statistical methodology applied to future surveysPreprintPostprintPeer reviewe

Optoacoustic solitons in Bragg gratings

Optical gap solitons, which exist due to a balance of nonlinearity and dispersion due to a Bragg grating, can couple to acoustic waves through electrostriction. This gives rise to a new species of ``gap-acoustic'' solitons (GASs), for which we find exact analytic solutions. The GAS consists of an optical pulse similar to the optical gap soliton, dressed by an accompanying phonon pulse. Close to the speed of sound, the phonon component is large. In subsonic (supersonic) solitons, the phonon pulse is a positive (negative) density variation. Coupling to the acoustic field damps the solitons' oscillatory instability, and gives rise to a distinct instability for supersonic solitons, which may make the GAS decelerate and change direction, ultimately making the soliton subsonic.Comment: 5 pages, 3 figure

Malawi District Energy Officer Blueprint : Recommendations Paper

This recommendations paper outlines the proposed role of District Energy Officers (DEOs) in Malawi as a conduit for the Government of Malawi to facilitate the decentralisation of a sustainable energy policy to district level. If developed sensitively and effectively and resourced appropriately, the implementation of DEOs in Malawi could help to strengthen levels of community ownership and empowerment; achieved through energy initiatives, improved communication and networking around energy issues at district level, electricity access development at district level and enhanced electricity literacy through roles in sensitisation and dissemination of knowledge of decentralised energy technologies and processes This paper confirms the Government of Malawi’s proposal that the introduction of an effective DEO programme will assist the Government in decentralisation of its national renewable energy strategy while aligning renewable electricity development with key national energy use targets ; 20% of national energy generation from renewable energy sources and a reduction of 22% in biomass usage by 2025. A decentralised DEO role, working within a centralised management and financial structure is supported by this recommendations paper as an effective methodology for energy decentralisation in Malawi. The support structure and accountability structure outlined in this recommendations paper can be used by the Government of Malawi to empower rural communities in Malawi in taking ownership of their energy sources and their energy use, primarily through design and support of community based development. DEOs act to improve community livelihoods through an increase in local earning potential and co-constructively act to improve national energy security and poverty alleviation across all districts of Malawi

Decentralization : the key to accelerating access to distributed energy services in sub-Saharan Africa?

The decentralization of governance is increasingly considered crucial for delivering development and is being widely adopted in sub-Saharan countries. At the same time, distributed (decentralized) energy systems are increasingly recognized for their role in achieving universal access to energy and are being promoted in sub-Saharan countries. However, little attention has been paid by governments and energy practitioners to the dynamic interrelationships between national and local government and the role of governance decentralization in transitioning to distributed energy systems. This paper traces the complex relationships between accelerated delivery of distributed energy and decentralized local governance systems. The argument is grounded in an exploration of two different approaches to decentralized energy systems governance in Kenya and Malawi. For Kenya, analysis focuses on the energy sector since the adoption of the new decentralized constitution in 2010. In Malawi, it focuses on the involvement of the authors in piloting Local Authority Energy Officers in districts under the decentralization of Malawian energy policy. Our analysis shows that accelerating the speed and scale of implementation for distributed energy systems and enhancing their sustainability and socio-economic impacts is directly linked to the quality of local and national governance structures and their interrelationships. The paper extends existing work in energy and evidence literacy for policy actors by developing an analytical framework, to enable more effective local governance within energy access initiatives in the Global South

Protecting the Visual Fidelity of Machine Learning Datasets Using QR Codes

Machine learning is becoming increasingly popular in a variety of modern technology. However, research has demonstrated that machine learning models are vulnerable to adversarial examples in their inputs. Potential attacks include poisoning datasets by perturbing input samples to mislead a machine learning model into producing undesirable results. Such perturbations are often subtle and imperceptible from a human\u27s perspective. This paper investigates two methods of verifying the visual fidelity of image based datasets by detecting perturbations made to the data using QR codes. In the first method, a verification string is stored for each image in a dataset. These verification strings can be used to determine whether an image in the dataset has been perturbed. In the second method, only a single verification string stored and is used to verify whether an entire dataset is intact

New density estimates of a threatened sifaka species (Propithecus coquereli) in Ankarafantsika National Park

Propithecus coquereli is one of the last sifaka species for which no reliable and extensive density estimates are yet available. Despite its endangered conservation status [IUCN, 2012] and recognition as a flagship species of the northwestern dry forests of Madagascar, its population in its last main refugium, the Ankarafantsika National Park (ANP), is still poorly known. Using line transect distance sampling surveys we estimated population density and abundance in the ANP. Furthermore, we investigated the effects of road, forest edge, river proximity and group size on sighting frequencies, and density estimates. We provide here the first population density estimates throughout the ANP. We found that density varied greatly among surveyed sites (from 5 to ∼100 ind/km2) which could result from significant (negative) effects of road, and forest edge, and/or a (positive) effect of river proximity. Our results also suggest that the population size may be ∼47,000 individuals in the ANP, hinting that the population likely underwent a strong decline in some parts of the Park in recent decades, possibly caused by habitat loss from fires and charcoal production and by poaching. We suggest community-based conservation actions for the largest remaining population of Coquerel's sifaka which will (i) maintain forest connectivity; (ii) implement alternatives to deforestation through charcoal production, logging, and grass fires; (iii) reduce poaching; and (iv) enable long-term monitoring of the population in collaboration with local authorities and researchers.Optimus!Alive- IGC fellowship, FCT fellowship: (SFRH/BD/64875/2009), University of Mahajanga, Groupement de Recherche International (GDRI), "Laboratoire d'Excellence" (LABEX) entitled TULIP (ANR-10-LABX-41), the Rufford Small Grant Foundation grant: (10941-1)

Preventing kidney transplant failure by screening for antibodies against human leucocyte antigens followed by optimised immunosuppression: OuTSMART RCT

Design: Investigator-led, prospective, open-labelled marker-based strategy (hybrid) randomised trial. Background: Allografts in 3% of kidney transplant patients fail annually. Development of antibodies against human leucocyte antigens is a validated predictive biomarker of allograft failure. Under immunosuppression is recognised to contribute, but whether increasing immunosuppression can prevent allograft failure in human leucocyte antigen Ab+ patients is unclear. Participants: Renal transplant recipients &gt; 1 year post-transplantation attending 13 United Kingdom transplant clinics, without specific exclusion criteria. Interventions: Regular screening for human leucocyte antigen antibodies followed, in positive patients by interview and tailored optimisation of immunosuppression to tacrolimus, mycophenolate mofetil and prednisolone. Objective: To determine if optimisation of immunosuppression in human leucocyte antigen Ab+ patients can cost-effectively prevent kidney allograft failure. Outcome: Time to graft failure after 43 months follow-up in patients receiving the intervention, compared to controls, managed by standard of care. Costs and quality-adjusted life-years were used in the cost-effectiveness analysis. Randomisation and blinding: Random allocation (1 : 1) to unblinded biomarker-led care or double-blinded standard of care stratified by human leucocyte antigen antibodies status (positive/negative) and in positives, presence of donor-specific antibodies (human leucocyte antigen antibodies against donor human leucocyte antigen) or not (human leucocyte antigen antibodies against non-donor human leucocyte antigen), baseline immunosuppression and transplant centre. Biomaker-led care human leucocyte antigen Ab+ patients received intervention. Human leucocyte antigen Ab-negative patients were screened every 8 months. Recruitment Began September 2013 and for 37 months. The primary endpoint, scheduled for June 2020, was moved to March 2020 because of COVID-19. Numbers randomised: From 5519 screened, 2037 were randomised (1028 biomaker-led care, 1009 to standard of care) including 198 with human leucocyte antigen antibodies against donor human leucocyte antigen (106 biomaker-led care, 92 standard of care) and 818 with human leucocyte antigens antibodies against non-donor human leucocyte antigen (427 biomaker-led care, 391 standard of care). Numbers analysed: Two patients were randomised in error so 2035 were included in the intention-to-treat analysis. Outcome: The trial had 80% power to detect a hazard ratio of 0.49 in biomarker-led care DSA+ group, &gt; 90% power to detect hazard ratio of 0.35 in biomarker-led care non-DSA+ group (with 5% type 1 error). Actual hazard ratios for graft failure in these biomarker-led care groups were 1.54 (95% CI: 0.72 to 3.30) and 0.97 (0.54 to 1.74), respectively. There was 90% power to demonstrate non-inferiority of overall biomarker-led care group with assumed hazard ratio of 1.4: This was not demonstrated as the upper confidence limit for graft failure exceeded 1.4: (1.02, 95% CI 0.72 to 1.44). The hazard ratio for biopsy-proven rejection in the overall biomarker-led care group was 0.5 [95% CI: 0.27 to 0.94: p = 0.03]. The screening approach was not cost-effective in terms of cost per quality-adjusted life-year. Harms: No significant differences in other secondary endpoints or adverse events. Limitations: Tailored interventions meant optimisation was not possible in some patients. We did not study pathology on protocol transplant biopsies in DSA+ patients. Conclusions: No evidence that optimised immunosuppression in human leucocyte antigen Ab+ patients delays renal transplant failure. Informing patients of their human leucocyte antigen antibodies status appears to reduce graft rejection. Future work: We need a better understanding of the pathophysiology of transplant failure to allow rational development of effective therapies. Trial registration: This trial is registered as EudraCT (2012-004308-36) and ISRCTN (46157828). Funding: This project was funded by the National Institute for Health and Care Research (NIHR) Efficacy and Mechanism Evaluation programme (11/100/34) and will be published in full in Efficacy and Mechanism Evaluation; Vol. 10, No. 5. See the NIHR Journals Library website for further project information

Multi-species population indices for sets of species including rare, disappearing or newly occurring species

NI is funded by Natural Environment Research Council award NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.Multi-species indices (MSI) are widely used as ecological indicators and as instruments to inform environmental policies. Many of these indices combine species-specific estimates of relative population sizes using the geometric mean. Because the geometric mean is not defined when values of zero occur, usually only commoner species are included in MSIs and zero values are replaced by a small non-zero value. The latter can exhibit an arbitrary influence on the geometric mean MSI. Here, we show how the compound Poisson and the negative binomial model can be used in such cases to obtain an MSI that has similar features to the geometric mean, including weighting halving and doubling of a species’ population equally. In contrast to the geometric mean, these two statistical models can handle zero values in population sizes and thus accommodate newly occurring and temporarily or permanently disappearing species in the MSI. We compare the MSIs obtained by the two statistical models with the geometric mean MSI and measure sensitivity to changes in evenness and to population trends in rare and abundant species. Additionally, we outline sources of uncertainty and discuss how to measure them. We found that, in contrast to the geometric mean and the negative binomial MSI, the compound Poisson MSI is less sensitive to changes in evenness when total abundance is constant. Further, we found that the compound Poisson model can be influenced more than the other two methods by trends of species showing a low interannual variance. The negative binomial MSI is less sensitive to trends in rare species compared with the other two methods, and similarly sensitive to trends in abundant species as the geometric mean. While the two new MSIs have the advantage that they are not arbitrarily influenced by rare, newly appearing and disappearing species, both do not weight all species equally. We recommend replacing the geometric mean MSI with either compound Poisson or negative binomial when there are species with a population size of zero in some years having a strong influence on the geometric mean MSI. Further, we recommend providing additional information alongside the MSIs. For example, it is particularly important to give an evenness index in addition to the compound Poisson MSI and to indicate the number of disappearing and newly occurring species alongside the negative binomial MSI.Publisher PDFPeer reviewe

British Lung Foundation/United Kingdom primary immunodeficiency network consensus statement on the definition, diagnosis, and management of granulomatous-lymphocytic interstitial lung disease in common variable immunodeficiency disorders

A proportion of people living with common variable immunodeficiency disorders develop granulomatous-lymphocytic interstitial lung disease (GLILD). We aimed to develop a consensus statement on the definition, diagnosis, and management of GLILD. All UK specialist centers were contacted and relevant physicians were invited to take part in a 3-round online Delphi process. Responses were graded as Strongly Agree, Tend to Agree, Neither Agree nor Disagree, Tend to Disagree, and Strongly Disagree, scored +1, +0.5, 0, −0.5, and −1, respectively. Agreement was defined as greater than or equal to 80% consensus. Scores are reported as mean ± SD. There was 100% agreement (score, 0.92 ± 0.19) for the following definition: “GLILD is a distinct clinico-radio-pathological ILD occurring in patients with [common variable immunodeficiency disorders], associated with a lymphocytic infiltrate and/or granuloma in the lung, and in whom other conditions have been considered and where possible excluded.” There was consensus that the workup of suspected GLILD requires chest computed tomography (CT) (0.98 ± 0.01), lung function tests (eg, gas transfer, 0.94 ± 0.17), bronchoscopy to exclude infection (0.63 ± 0.50), and lung biopsy (0.58 ± 0.40). There was no consensus on whether expectant management following optimization of immunoglobulin therapy was acceptable: 67% agreed, 25% disagreed, score 0.38 ± 0.59; 90% agreed that when treatment was required, first-line treatment should be with corticosteroids alone (score, 0.55 ± 0.51)