Kate E. Jones
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View article: acoupi: An open‐source Python framework for deploying bioacoustic <scp>AI</scp> models on edge devices
acoupi: An open‐source Python framework for deploying bioacoustic <span>AI</span> models on edge devices Open
Passive acoustic monitoring (PAM) coupled with artificial intelligence (AI) is becoming an essential tool for biodiversity monitoring. Traditional PAM systems require manual data offloading and impose substantial demands on data storage an…
View article: Land use gradients drive spatial variation in Lassa fever host communities in the Eastern Province of Sierra Leone
Land use gradients drive spatial variation in Lassa fever host communities in the Eastern Province of Sierra Leone Open
The natal multimammate mouse ( Mastomys natalensis ) is the primary reservoir host of Mammarenavirus lassaense (LASV), a zoonotic pathogen causing Lassa fever and endemic to West Africa. The occurrence and abundance of this species is regu…
View article: Climate-driven rodent infection dynamics align with Lassa fever seasonality in humans
Climate-driven rodent infection dynamics align with Lassa fever seasonality in humans Open
Lassa fever (LF), caused by Lassa mammarenavirus (LASV), imposes a major public health burden in West Africa. The Natal multimammate mouse ( Mastomys natalensis , MN) is the principal reservoir, yet the extent to which host dynamics shape …
View article: Sustainable cattle management by communities supports African wildlife
Sustainable cattle management by communities supports African wildlife Open
Community-based conservation (CBC) initiatives aim to reconcile biodiversity protection with local livelihoods, yet their effectiveness in protecting wildlife remains uncertain, often hinging on local management 1,2 . We evaluated a global…
View article: Evidence of ecosystem process recovery across a large-scale coral reef restoration programme using AI accelerated soundscape analysis
Evidence of ecosystem process recovery across a large-scale coral reef restoration programme using AI accelerated soundscape analysis Open
Coral reef restoration efforts are on the increase globally. However, reporting on the ecological outcomes of these efforts is rare and typically focuses on coral related metrics. As a result, understanding of whether restoration can recov…
View article: Scaling Lassa Virus Dynamics within Anthropogenic Ecosystems (SCAPES) study: a mixed-methods observational cohort study of humans, rodents, and landscapes in Nigeria
Scaling Lassa Virus Dynamics within Anthropogenic Ecosystems (SCAPES) study: a mixed-methods observational cohort study of humans, rodents, and landscapes in Nigeria Open
Introduction Zoonotic spillover driven by human activity remains a critical challenge. Research focusing on disease ecology or human–animal interactions provide detailed but often siloed local insights disconnected from global processes an…
View article: Contact networks of small mammals highlight potential transmission foci of Lassa mammarenavirus
Contact networks of small mammals highlight potential transmission foci of Lassa mammarenavirus Open
Introduction Lassa fever, caused by Mammarenavirus lassaense (LASV), is an endemic zoonosis in several West African countries. Human infections primarily arise from rodent-to-human transmission, with Mastomys natalensis, a synanthropic spe…
View article: Using tropical reef, bird and unrelated sounds for superior transfer learning in marine bioacoustics
Using tropical reef, bird and unrelated sounds for superior transfer learning in marine bioacoustics Open
Machine learning has the potential to revolutionize passive acoustic monitoring (PAM) for ecological assessments. However, high annotation and computing costs limit the field’s adoption. Generalizable pretrained networks can overcome these…
View article: Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out
Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out Open
Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in con…
View article: A scalable transfer learning workflow for extracting biological and behavioural insights from forest elephant vocalizations
A scalable transfer learning workflow for extracting biological and behavioural insights from forest elephant vocalizations Open
Animal vocalizations encode rich biological information—such as age, sex, behavioural context and emotional state—making bioacoustic analysis a promising non‐invasive method for assessing welfare and population demography. However, traditi…
View article: Contact networks of small mammals highlight potential transmission foci of Mammarenavirus lassaense
Contact networks of small mammals highlight potential transmission foci of Mammarenavirus lassaense Open
Lassa fever (Mammarenavirus lassaense; LASV), is an endemic zoonosis in West Africa. Human infections arise from rodent-to-human transmission, mainly from the synanthropic reservoir Mastomys natalensis. In Sierra Leone, small-mammal commun…
View article: Land use gradients drive spatial variation in Lassa fever host communities in the Eastern Province of Sierra Leone.
Land use gradients drive spatial variation in Lassa fever host communities in the Eastern Province of Sierra Leone. Open
1. The natal multimammate mouse (Mastomys natalensis) is the primary reservoir host of Lassa mammarenavirus (LASV), a zoonotic pathogen causing Lassa fever that is endemic to West Africa. The occurrence and abundance of this species is reg…
View article: acoupi: An Open-Source Python Framework for Deploying Bioacoustic AI Models on Edge Devices
acoupi: An Open-Source Python Framework for Deploying Bioacoustic AI Models on Edge Devices Open
1. Passive acoustic monitoring (PAM) coupled with artificial intelligence (AI) is becoming an essential tool for biodiversity monitoring. Traditional PAM systems require manual data offloading and impose substantial demands on storage and …
View article: Towards a ‘people and nature’ paradigm for biodiversity and infectious disease
Towards a ‘people and nature’ paradigm for biodiversity and infectious disease Open
Zoonotic and vector-borne infectious diseases are among the most direct human health consequences of biodiversity change. The COVID-19 pandemic increased health policymakers’ attention on the links between ecological degradation and diseas…
View article: Regional Biomes outperform broader spatial units in capturing biodiversity responses to land‐use change
Regional Biomes outperform broader spatial units in capturing biodiversity responses to land‐use change Open
Biogeographic context, such as biome type, has a critical influence on ecological resilience, as climatic and environmental conditions impact how communities respond to anthropogenic threats. For example, land‐use change causes a greater l…
View article: Whombat: An open‐source audio annotation tool for machine learning assisted bioacoustics
Whombat: An open‐source audio annotation tool for machine learning assisted bioacoustics Open
Automated analysis of bioacoustic recordings using machine learning (ML) methods has the potential to greatly scale biodiversity monitoring efforts. The use of ML for high‐stakes applications, such as conservation and scientific research, …
View article: INQUIRE: A Natural World Text-to-Image Retrieval Benchmark
INQUIRE: A Natural World Text-to-Image Retrieval Benchmark Open
We introduce INQUIRE, a text-to-image retrieval benchmark designed to challenge multimodal vision-language models on expert-level queries. INQUIRE includes iNaturalist 2024 (iNat24), a new dataset of five million natural world images, alon…
View article: Health and economic impacts of Lassa vaccination campaigns in West Africa
Health and economic impacts of Lassa vaccination campaigns in West Africa Open
Lassa fever is a zoonotic disease identified by the World Health Organization (WHO) as having pandemic potential. This study estimates the health-economic burden of Lassa fever throughout West Africa and projects impacts of a series of vac…
View article: Deep learning-based ecological analysis of camera trap images is impacted by training data quality and quantity
Deep learning-based ecological analysis of camera trap images is impacted by training data quality and quantity Open
Large image collections generated from camera traps offer valuable insights into species richness, occupancy, and activity patterns, significantly aiding biodiversity monitoring. However, the manual processing of these datasets is time-con…
View article: The anthropogenic fingerprint on emerging infectious diseases
The anthropogenic fingerprint on emerging infectious diseases Open
Emerging infectious diseases are increasingly understood as a hallmark of the Anthropocene 1–3 . Most experts agree that anthropogenic ecosystem change and high-risk contact among people, livestock, and wildlife have contributed to the rec…
View article: Biodiversity shows unique responses to land-use change across regional biomes
Biodiversity shows unique responses to land-use change across regional biomes Open
Biogeography has a critical influence on how ecological communities respond to threats and how effective conservation interventions are designed. For example, the resilience of ecological communities is linked to environmental and climatic…
View article: Leveraging tropical reef, bird and unrelated sounds for superior transfer learning in marine bioacoustics
Leveraging tropical reef, bird and unrelated sounds for superior transfer learning in marine bioacoustics Open
Machine learning has the potential to revolutionize passive acoustic monitoring (PAM) for ecological assessments. However, high annotation and compute costs limit the field's efficacy. Generalizable pretrained networks can overcome these c…
View article: Valuing the economic benefits of species recovery programmes
Valuing the economic benefits of species recovery programmes Open
Accounting for the values placed on nature by the public is key to successful policies in reversing ongoing biodiversity declines. However, biodiversity values are rarely included in policy decisions, resulting in poorer outcomes for peopl…
View article: Health and economic impacts of Lassa vaccination campaigns in West Africa
Health and economic impacts of Lassa vaccination campaigns in West Africa Open
Lassa fever is a zoonotic disease identified by the World Health Organization (WHO) as having pandemic potential. This study estimates the health-economic burden of Lassa fever throughout West Africa and projects impacts of a series of vac…
View article: Ecological impacts of climate change will transform public health priorities for zoonotic and vector-borne disease
Ecological impacts of climate change will transform public health priorities for zoonotic and vector-borne disease Open
Climate change impacts on zoonotic/vector-borne diseases pose significant threats to humanity 1 but these links are, in general, poorly understood 2 . Here, we project present and future geographical risk patterns for 141 infectious agents…
View article: Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out
Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out Open
Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in con…
View article: A dataset of small-mammal detections in West Africa and their associated micro-organisms
A dataset of small-mammal detections in West Africa and their associated micro-organisms Open
Rodents, a globally distributed and ecologically important mammalian order, serve as hosts for various zoonotic pathogens. However, sampling of rodents and their pathogens suffers from taxonomic and spatial biases. This affects consolidate…
View article: The Role of International Human Rights Law in Shaping National Immigration Policies
The Role of International Human Rights Law in Shaping National Immigration Policies Open
Purpose: The main objective of this study was to explore the role of international human rights in shaping national immigration policies.
Methodology: The study adopted a desktop research methodology. Desk research refers to secondary dat…
View article: A Dataset of Small-Mammal Detections in West Africa and Their Associated Micro-Organisms
A Dataset of Small-Mammal Detections in West Africa and Their Associated Micro-Organisms Open
Rodents, a globally distributed and ecologically important mammalian order, serve as hosts for various zoonotic pathogens. However, sampling of rodents and their pathogens suffers from taxonomic and spatial biases. This affects consolidate…